Index: /issm/trunk-jpl-damage/AUTHORS =================================================================== --- /issm/trunk-jpl-damage/AUTHORS (revision 11330) +++ /issm/trunk-jpl-damage/AUTHORS (revision 11330) @@ -0,0 +1,27 @@ +Ice Sheet System Model is a JPL/UCI collaboration to develop a massively-parallelized +multi-purpose finite element framework dedicated to ice sheet modeling + +Project Scientist: + Eric Rignot + +Project Manager: + Eric Larour + +Current core developers: + * Eric Larour + * Helene Seroussi + * Mathieu Morlighem + +Contributors: + We thank the following contributors for their help in making ISSM better! + + Robert Crippen, Jet Propulsion Laboratory. robbert.crippen@jpl.nasa.gov + HoleFiller routines to plug incomplete datasets. See HoleFiller module in src/m/matlab/utils + + Point Inclusion in Polygon Test (pnpoly.c used in Utils/Arguscontourtomesh/IsInPoly.c) + W. Randolph Franklin (WRF) + http://www.ecse.rpi.edu/Homepages/wrf/Research/Short_Notes/pnpoly.html + + DACE: A Matlab Kriging toolbox, Søren N.Lophaen, Hans Bruun Nielsen and Jacob + Søndergaard (Technical University of Denmark) + http://www2.imm.dtu.dk/~hbn/dace/ Index: /issm/trunk-jpl-damage/COPYING =================================================================== --- /issm/trunk-jpl-damage/COPYING (revision 11330) +++ /issm/trunk-jpl-damage/COPYING (revision 11330) @@ -0,0 +1,28 @@ +Copyright (c) 2002-2011, California Institute of Technology. +All rights reserved. Based on Government Sponsored Research under contracts +NAS7-1407 and/or NAS7-03001. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + 3. Neither the name of the California Institute of Technology (Caltech), + its operating division the Jet Propulsion Laboratory (JPL), the National + Aeronautics and Space Administration (NASA), nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE CALIFORNIA INSTITUTE OF TECHNOLOGY BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Index: /issm/trunk-jpl-damage/ChangeLog =================================================================== --- /issm/trunk-jpl-damage/ChangeLog (revision 11330) +++ /issm/trunk-jpl-damage/ChangeLog (revision 11330) @@ -0,0 +1,3 @@ +Go to + +https://issm.ess.uci.edu:80/trac/issm/timeline Index: /issm/trunk-jpl-damage/INSTALL =================================================================== --- /issm/trunk-jpl-damage/INSTALL (revision 11330) +++ /issm/trunk-jpl-damage/INSTALL (revision 11330) @@ -0,0 +1,2 @@ +For the installation process please go to the ISSM website +http://issm.jpl.nasa.gov/ Index: /issm/trunk-jpl-damage/LICENSE =================================================================== --- /issm/trunk-jpl-damage/LICENSE (revision 11330) +++ /issm/trunk-jpl-damage/LICENSE (revision 11330) @@ -0,0 +1,28 @@ +Copyright (c) 2002-2011, California Institute of Technology. +All rights reserved. Based on Government Sponsored Research under contracts +NAS7-1407 and/or NAS7-03001. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + 1. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + 3. Neither the name of the California Institute of Technology (Caltech), + its operating division the Jet Propulsion Laboratory (JPL), the National + Aeronautics and Space Administration (NASA), nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE CALIFORNIA INSTITUTE OF TECHNOLOGY BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Index: /issm/trunk-jpl-damage/Makefile.am =================================================================== --- /issm/trunk-jpl-damage/Makefile.am (revision 11330) +++ /issm/trunk-jpl-damage/Makefile.am (revision 11330) @@ -0,0 +1,2 @@ +EXTRA_DIST = reconf scripts test INSTALLICE LICENSE m4 examples cron etc doc packages ChangeLogCielo ChangeLogIce contributors.txt run READMEICE startup.m startup.m startup.m startup.m todo MakefileIce +SUBDIRS = src bin Index: /issm/trunk-jpl-damage/NEWS =================================================================== --- /issm/trunk-jpl-damage/NEWS (revision 11330) +++ /issm/trunk-jpl-damage/NEWS (revision 11330) @@ -0,0 +1,4 @@ + +please go to the ISSM website for the latest news: + +http://issm.jpl.nasa.gov/ Index: /issm/trunk-jpl-damage/README =================================================================== --- /issm/trunk-jpl-damage/README (revision 11330) +++ /issm/trunk-jpl-damage/README (revision 11330) @@ -0,0 +1,52 @@ +------------------------------------------------------------------------------ + +ISSM +Ice Sheet System Modeling: a framework for modeling ice flow on ice sheet/ice shelf +systems using Finite Elemenent Analysis, and parallel technologies. + +------------------------------------------------------------------------------ + +Jet Propulsion Laboratory + +Eric Eric Larour (Project Lead) +Mathieu Mathieu Morlighem (Anisotropic Meshing, Control Methods) +Helene Helene Seroussi (Coupling 2D-3D, Multi-model, full-Stokes) + +Email: issm@jpl.nasa.gov + +------------------------------------------------------------------------------ +License + +ISSM is California Institute of Technology Copyright. +------------------------------------------------------------------------------ +Overview + +More to come + +Refer to http://issm.jpl.nasa.gov/ for additional information. +------------------------------------------------------------------------------ +Distribution + +The directories contained in this distribution include: + +examples Example problems + +externalpackages Other libraries + +m4 m4 macros used for supporting autoconf. + +doc The Users, Reference, and Developers Manuals are + maintained here. Other references are available from + the ISSM Web site (http://issm.jpl.nasa.gov/) + +src The main source code repository for the ISSM system. + +test Files for regression and unit testing of the ISSM system. +------------------------------------------------------------------------------ +Installation + +The installation procedure uses a standard GNU installation based on autoconf. +The basic steps are to invoke 'configure' to generate Makefiles for your +particular system and then invoke 'make' to compile the sources. See the +INSTALL file for detailed instructions. +------------------------------------------------------------------------------ Index: /issm/trunk-jpl-damage/compile =================================================================== --- /issm/trunk-jpl-damage/compile (revision 11330) +++ /issm/trunk-jpl-damage/compile (revision 11330) @@ -0,0 +1,142 @@ +#! /bin/sh +# Wrapper for compilers which do not understand `-c -o'. + +scriptversion=2005-05-14.22 + +# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc. +# Written by Tom Tromey . +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2, or (at your option) +# any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that program. + +# This file is maintained in Automake, please report +# bugs to or send patches to +# . + +case $1 in + '') + echo "$0: No command. Try \`$0 --help' for more information." 1>&2 + exit 1; + ;; + -h | --h*) + cat <<\EOF +Usage: compile [--help] [--version] PROGRAM [ARGS] + +Wrapper for compilers which do not understand `-c -o'. +Remove `-o dest.o' from ARGS, run PROGRAM with the remaining +arguments, and rename the output as expected. + +If you are trying to build a whole package this is not the +right script to run: please start by reading the file `INSTALL'. + +Report bugs to . +EOF + exit $? + ;; + -v | --v*) + echo "compile $scriptversion" + exit $? + ;; +esac + +ofile= +cfile= +eat= + +for arg +do + if test -n "$eat"; then + eat= + else + case $1 in + -o) + # configure might choose to run compile as `compile cc -o foo foo.c'. + # So we strip `-o arg' only if arg is an object. + eat=1 + case $2 in + *.o | *.obj) + ofile=$2 + ;; + *) + set x "$@" -o "$2" + shift + ;; + esac + ;; + *.c) + cfile=$1 + set x "$@" "$1" + shift + ;; + *) + set x "$@" "$1" + shift + ;; + esac + fi + shift +done + +if test -z "$ofile" || test -z "$cfile"; then + # If no `-o' option was seen then we might have been invoked from a + # pattern rule where we don't need one. That is ok -- this is a + # normal compilation that the losing compiler can handle. If no + # `.c' file was seen then we are probably linking. That is also + # ok. + exec "$@" +fi + +# Name of file we expect compiler to create. +cofile=`echo "$cfile" | sed -e 's|^.*/||' -e 's/\.c$/.o/'` + +# Create the lock directory. +# Note: use `[/.-]' here to ensure that we don't use the same name +# that we are using for the .o file. Also, base the name on the expected +# object file name, since that is what matters with a parallel build. +lockdir=`echo "$cofile" | sed -e 's|[/.-]|_|g'`.d +while true; do + if mkdir "$lockdir" >/dev/null 2>&1; then + break + fi + sleep 1 +done +# FIXME: race condition here if user kills between mkdir and trap. +trap "rmdir '$lockdir'; exit 1" 1 2 15 + +# Run the compile. +"$@" +ret=$? + +if test -f "$cofile"; then + mv "$cofile" "$ofile" +elif test -f "${cofile}bj"; then + mv "${cofile}bj" "$ofile" +fi + +rmdir "$lockdir" +exit $ret + +# Local Variables: +# mode: shell-script +# sh-indentation: 2 +# eval: (add-hook 'write-file-hooks 'time-stamp) +# time-stamp-start: "scriptversion=" +# time-stamp-format: "%:y-%02m-%02d.%02H" +# time-stamp-end: "$" +# End: Index: /issm/trunk-jpl-damage/config.guess =================================================================== --- /issm/trunk-jpl-damage/config.guess (revision 11330) +++ /issm/trunk-jpl-damage/config.guess (revision 11330) @@ -0,0 +1,1542 @@ +#! /bin/sh +# Attempt to guess a canonical system name. +# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, +# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 +# Free Software Foundation, Inc. + +timestamp='2008-11-15' + +# This file is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA +# 02110-1301, USA. +# +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that program. + + +# Originally written by Per Bothner . +# Please send patches to . Submit a context +# diff and a properly formatted ChangeLog entry. +# +# This script attempts to guess a canonical system name similar to +# config.sub. If it succeeds, it prints the system name on stdout, and +# exits with 0. Otherwise, it exits with 1. +# +# The plan is that this can be called by configure scripts if you +# don't specify an explicit build system type. + +me=`echo "$0" | sed -e 's,.*/,,'` + +usage="\ +Usage: $0 [OPTION] + +Output the configuration name of the system \`$me' is run on. + +Operation modes: + -h, --help print this help, then exit + -t, --time-stamp print date of last modification, then exit + -v, --version print version number, then exit + +Report bugs and patches to ." + +version="\ +GNU config.guess ($timestamp) + +Originally written by Per Bothner. +Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, +2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. + +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." + +help=" +Try \`$me --help' for more information." + +# Parse command line +while test $# -gt 0 ; do + case $1 in + --time-stamp | --time* | -t ) + echo "$timestamp" ; exit ;; + --version | -v ) + echo "$version" ; exit ;; + --help | --h* | -h ) + echo "$usage"; exit ;; + -- ) # Stop option processing + shift; break ;; + - ) # Use stdin as input. + break ;; + -* ) + echo "$me: invalid option $1$help" >&2 + exit 1 ;; + * ) + break ;; + esac +done + +if test $# != 0; then + echo "$me: too many arguments$help" >&2 + exit 1 +fi + +trap 'exit 1' 1 2 15 + +# CC_FOR_BUILD -- compiler used by this script. Note that the use of a +# compiler to aid in system detection is discouraged as it requires +# temporary files to be created and, as you can see below, it is a +# headache to deal with in a portable fashion. + +# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still +# use `HOST_CC' if defined, but it is deprecated. + +# Portable tmp directory creation inspired by the Autoconf team. + +set_cc_for_build=' +trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ; +trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ; +: ${TMPDIR=/tmp} ; + { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } || + { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } || + { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } || + { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ; +dummy=$tmp/dummy ; +tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ; +case $CC_FOR_BUILD,$HOST_CC,$CC in + ,,) echo "int x;" > $dummy.c ; + for c in cc gcc c89 c99 ; do + if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then + CC_FOR_BUILD="$c"; break ; + fi ; + done ; + if test x"$CC_FOR_BUILD" = x ; then + CC_FOR_BUILD=no_compiler_found ; + fi + ;; + ,,*) CC_FOR_BUILD=$CC ;; + ,*,*) CC_FOR_BUILD=$HOST_CC ;; +esac ; set_cc_for_build= ;' + +# This is needed to find uname on a Pyramid OSx when run in the BSD universe. +# (ghazi@noc.rutgers.edu 1994-08-24) +if (test -f /.attbin/uname) >/dev/null 2>&1 ; then + PATH=$PATH:/.attbin ; export PATH +fi + +UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown +UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown +UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown +UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown + +# Note: order is significant - the case branches are not exclusive. + +case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in + *:NetBSD:*:*) + # NetBSD (nbsd) targets should (where applicable) match one or + # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*, + # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently + # switched to ELF, *-*-netbsd* would select the old + # object file format. This provides both forward + # compatibility and a consistent mechanism for selecting the + # object file format. + # + # Note: NetBSD doesn't particularly care about the vendor + # portion of the name. We always set it to "unknown". + sysctl="sysctl -n hw.machine_arch" + UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \ + /usr/sbin/$sysctl 2>/dev/null || echo unknown)` + case "${UNAME_MACHINE_ARCH}" in + armeb) machine=armeb-unknown ;; + arm*) machine=arm-unknown ;; + sh3el) machine=shl-unknown ;; + sh3eb) machine=sh-unknown ;; + sh5el) machine=sh5le-unknown ;; + *) machine=${UNAME_MACHINE_ARCH}-unknown ;; + esac + # The Operating System including object format, if it has switched + # to ELF recently, or will in the future. + case "${UNAME_MACHINE_ARCH}" in + arm*|i386|m68k|ns32k|sh3*|sparc|vax) + eval $set_cc_for_build + if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep __ELF__ >/dev/null + then + # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout). + # Return netbsd for either. FIX? + os=netbsd + else + os=netbsdelf + fi + ;; + *) + os=netbsd + ;; + esac + # The OS release + # Debian GNU/NetBSD machines have a different userland, and + # thus, need a distinct triplet. However, they do not need + # kernel version information, so it can be replaced with a + # suitable tag, in the style of linux-gnu. + case "${UNAME_VERSION}" in + Debian*) + release='-gnu' + ;; + *) + release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'` + ;; + esac + # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM: + # contains redundant information, the shorter form: + # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used. + echo "${machine}-${os}${release}" + exit ;; + *:OpenBSD:*:*) + UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'` + echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE} + exit ;; + *:ekkoBSD:*:*) + echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE} + exit ;; + *:SolidBSD:*:*) + echo ${UNAME_MACHINE}-unknown-solidbsd${UNAME_RELEASE} + exit ;; + macppc:MirBSD:*:*) + echo powerpc-unknown-mirbsd${UNAME_RELEASE} + exit ;; + *:MirBSD:*:*) + echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE} + exit ;; + alpha:OSF1:*:*) + case $UNAME_RELEASE in + *4.0) + UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'` + ;; + *5.*) + UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'` + ;; + esac + # According to Compaq, /usr/sbin/psrinfo has been available on + # OSF/1 and Tru64 systems produced since 1995. I hope that + # covers most systems running today. This code pipes the CPU + # types through head -n 1, so we only detect the type of CPU 0. + ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1` + case "$ALPHA_CPU_TYPE" in + "EV4 (21064)") + UNAME_MACHINE="alpha" ;; + "EV4.5 (21064)") + UNAME_MACHINE="alpha" ;; + "LCA4 (21066/21068)") + UNAME_MACHINE="alpha" ;; + "EV5 (21164)") + UNAME_MACHINE="alphaev5" ;; + "EV5.6 (21164A)") + UNAME_MACHINE="alphaev56" ;; + "EV5.6 (21164PC)") + UNAME_MACHINE="alphapca56" ;; + "EV5.7 (21164PC)") + UNAME_MACHINE="alphapca57" ;; + "EV6 (21264)") + UNAME_MACHINE="alphaev6" ;; + "EV6.7 (21264A)") + UNAME_MACHINE="alphaev67" ;; + "EV6.8CB (21264C)") + UNAME_MACHINE="alphaev68" ;; + "EV6.8AL (21264B)") + UNAME_MACHINE="alphaev68" ;; + "EV6.8CX (21264D)") + UNAME_MACHINE="alphaev68" ;; + "EV6.9A (21264/EV69A)") + UNAME_MACHINE="alphaev69" ;; + "EV7 (21364)") + UNAME_MACHINE="alphaev7" ;; + "EV7.9 (21364A)") + UNAME_MACHINE="alphaev79" ;; + esac + # A Pn.n version is a patched version. + # A Vn.n version is a released version. + # A Tn.n version is a released field test version. + # A Xn.n version is an unreleased experimental baselevel. + # 1.2 uses "1.2" for uname -r. + echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` + exit ;; + Alpha\ *:Windows_NT*:*) + # How do we know it's Interix rather than the generic POSIX subsystem? + # Should we change UNAME_MACHINE based on the output of uname instead + # of the specific Alpha model? + echo alpha-pc-interix + exit ;; + 21064:Windows_NT:50:3) + echo alpha-dec-winnt3.5 + exit ;; + Amiga*:UNIX_System_V:4.0:*) + echo m68k-unknown-sysv4 + exit ;; + *:[Aa]miga[Oo][Ss]:*:*) + echo ${UNAME_MACHINE}-unknown-amigaos + exit ;; + *:[Mm]orph[Oo][Ss]:*:*) + echo ${UNAME_MACHINE}-unknown-morphos + exit ;; + *:OS/390:*:*) + echo i370-ibm-openedition + exit ;; + *:z/VM:*:*) + echo s390-ibm-zvmoe + exit ;; + *:OS400:*:*) + echo powerpc-ibm-os400 + exit ;; + arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) + echo arm-acorn-riscix${UNAME_RELEASE} + exit ;; + arm:riscos:*:*|arm:RISCOS:*:*) + echo arm-unknown-riscos + exit ;; + SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) + echo hppa1.1-hitachi-hiuxmpp + exit ;; + Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*) + # akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE. + if test "`(/bin/universe) 2>/dev/null`" = att ; then + echo pyramid-pyramid-sysv3 + else + echo pyramid-pyramid-bsd + fi + exit ;; + NILE*:*:*:dcosx) + echo pyramid-pyramid-svr4 + exit ;; + DRS?6000:unix:4.0:6*) + echo sparc-icl-nx6 + exit ;; + DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*) + case `/usr/bin/uname -p` in + sparc) echo sparc-icl-nx7; exit ;; + esac ;; + sun4H:SunOS:5.*:*) + echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit ;; + sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) + echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit ;; + i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*) + eval $set_cc_for_build + SUN_ARCH="i386" + # If there is a compiler, see if it is configured for 64-bit objects. + # Note that the Sun cc does not turn __LP64__ into 1 like gcc does. + # This test works for both compilers. + if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then + if echo '\n#ifdef __amd64\nIS_64BIT_ARCH\n#endif' | \ + (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + SUN_ARCH="x86_64" + fi + fi + echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit ;; + sun4*:SunOS:6*:*) + # According to config.sub, this is the proper way to canonicalize + # SunOS6. Hard to guess exactly what SunOS6 will be like, but + # it's likely to be more like Solaris than SunOS4. + echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit ;; + sun4*:SunOS:*:*) + case "`/usr/bin/arch -k`" in + Series*|S4*) + UNAME_RELEASE=`uname -v` + ;; + esac + # Japanese Language versions have a version number like `4.1.3-JL'. + echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'` + exit ;; + sun3*:SunOS:*:*) + echo m68k-sun-sunos${UNAME_RELEASE} + exit ;; + sun*:*:4.2BSD:*) + UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null` + test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3 + case "`/bin/arch`" in + sun3) + echo m68k-sun-sunos${UNAME_RELEASE} + ;; + sun4) + echo sparc-sun-sunos${UNAME_RELEASE} + ;; + esac + exit ;; + aushp:SunOS:*:*) + echo sparc-auspex-sunos${UNAME_RELEASE} + exit ;; + # The situation for MiNT is a little confusing. The machine name + # can be virtually everything (everything which is not + # "atarist" or "atariste" at least should have a processor + # > m68000). The system name ranges from "MiNT" over "FreeMiNT" + # to the lowercase version "mint" (or "freemint"). Finally + # the system name "TOS" denotes a system which is actually not + # MiNT. But MiNT is downward compatible to TOS, so this should + # be no problem. + atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) + echo m68k-atari-mint${UNAME_RELEASE} + exit ;; + atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) + echo m68k-atari-mint${UNAME_RELEASE} + exit ;; + *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) + echo m68k-atari-mint${UNAME_RELEASE} + exit ;; + milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) + echo m68k-milan-mint${UNAME_RELEASE} + exit ;; + hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) + echo m68k-hades-mint${UNAME_RELEASE} + exit ;; + *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) + echo m68k-unknown-mint${UNAME_RELEASE} + exit ;; + m68k:machten:*:*) + echo m68k-apple-machten${UNAME_RELEASE} + exit ;; + powerpc:machten:*:*) + echo powerpc-apple-machten${UNAME_RELEASE} + exit ;; + RISC*:Mach:*:*) + echo mips-dec-mach_bsd4.3 + exit ;; + RISC*:ULTRIX:*:*) + echo mips-dec-ultrix${UNAME_RELEASE} + exit ;; + VAX*:ULTRIX*:*:*) + echo vax-dec-ultrix${UNAME_RELEASE} + exit ;; + 2020:CLIX:*:* | 2430:CLIX:*:*) + echo clipper-intergraph-clix${UNAME_RELEASE} + exit ;; + mips:*:*:UMIPS | mips:*:*:RISCos) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c +#ifdef __cplusplus +#include /* for printf() prototype */ + int main (int argc, char *argv[]) { +#else + int main (argc, argv) int argc; char *argv[]; { +#endif + #if defined (host_mips) && defined (MIPSEB) + #if defined (SYSTYPE_SYSV) + printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0); + #endif + #if defined (SYSTYPE_SVR4) + printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0); + #endif + #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) + printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0); + #endif + #endif + exit (-1); + } +EOF + $CC_FOR_BUILD -o $dummy $dummy.c && + dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` && + SYSTEM_NAME=`$dummy $dummyarg` && + { echo "$SYSTEM_NAME"; exit; } + echo mips-mips-riscos${UNAME_RELEASE} + exit ;; + Motorola:PowerMAX_OS:*:*) + echo powerpc-motorola-powermax + exit ;; + Motorola:*:4.3:PL8-*) + echo powerpc-harris-powermax + exit ;; + Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) + echo powerpc-harris-powermax + exit ;; + Night_Hawk:Power_UNIX:*:*) + echo powerpc-harris-powerunix + exit ;; + m88k:CX/UX:7*:*) + echo m88k-harris-cxux7 + exit ;; + m88k:*:4*:R4*) + echo m88k-motorola-sysv4 + exit ;; + m88k:*:3*:R3*) + echo m88k-motorola-sysv3 + exit ;; + AViiON:dgux:*:*) + # DG/UX returns AViiON for all architectures + UNAME_PROCESSOR=`/usr/bin/uname -p` + if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] + then + if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ + [ ${TARGET_BINARY_INTERFACE}x = x ] + then + echo m88k-dg-dgux${UNAME_RELEASE} + else + echo m88k-dg-dguxbcs${UNAME_RELEASE} + fi + else + echo i586-dg-dgux${UNAME_RELEASE} + fi + exit ;; + M88*:DolphinOS:*:*) # DolphinOS (SVR3) + echo m88k-dolphin-sysv3 + exit ;; + M88*:*:R3*:*) + # Delta 88k system running SVR3 + echo m88k-motorola-sysv3 + exit ;; + XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) + echo m88k-tektronix-sysv3 + exit ;; + Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) + echo m68k-tektronix-bsd + exit ;; + *:IRIX*:*:*) + echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` + exit ;; + ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. + echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id + exit ;; # Note that: echo "'`uname -s`'" gives 'AIX ' + i*86:AIX:*:*) + echo i386-ibm-aix + exit ;; + ia64:AIX:*:*) + if [ -x /usr/bin/oslevel ] ; then + IBM_REV=`/usr/bin/oslevel` + else + IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} + fi + echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} + exit ;; + *:AIX:2:3) + if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #include + + main() + { + if (!__power_pc()) + exit(1); + puts("powerpc-ibm-aix3.2.5"); + exit(0); + } +EOF + if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` + then + echo "$SYSTEM_NAME" + else + echo rs6000-ibm-aix3.2.5 + fi + elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then + echo rs6000-ibm-aix3.2.4 + else + echo rs6000-ibm-aix3.2 + fi + exit ;; + *:AIX:*:[456]) + IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'` + if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then + IBM_ARCH=rs6000 + else + IBM_ARCH=powerpc + fi + if [ -x /usr/bin/oslevel ] ; then + IBM_REV=`/usr/bin/oslevel` + else + IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} + fi + echo ${IBM_ARCH}-ibm-aix${IBM_REV} + exit ;; + *:AIX:*:*) + echo rs6000-ibm-aix + exit ;; + ibmrt:4.4BSD:*|romp-ibm:BSD:*) + echo romp-ibm-bsd4.4 + exit ;; + ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and + echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to + exit ;; # report: romp-ibm BSD 4.3 + *:BOSX:*:*) + echo rs6000-bull-bosx + exit ;; + DPX/2?00:B.O.S.:*:*) + echo m68k-bull-sysv3 + exit ;; + 9000/[34]??:4.3bsd:1.*:*) + echo m68k-hp-bsd + exit ;; + hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) + echo m68k-hp-bsd4.4 + exit ;; + 9000/[34678]??:HP-UX:*:*) + HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` + case "${UNAME_MACHINE}" in + 9000/31? ) HP_ARCH=m68000 ;; + 9000/[34]?? ) HP_ARCH=m68k ;; + 9000/[678][0-9][0-9]) + if [ -x /usr/bin/getconf ]; then + sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` + sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` + case "${sc_cpu_version}" in + 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 + 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 + 532) # CPU_PA_RISC2_0 + case "${sc_kernel_bits}" in + 32) HP_ARCH="hppa2.0n" ;; + 64) HP_ARCH="hppa2.0w" ;; + '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20 + esac ;; + esac + fi + if [ "${HP_ARCH}" = "" ]; then + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + + #define _HPUX_SOURCE + #include + #include + + int main () + { + #if defined(_SC_KERNEL_BITS) + long bits = sysconf(_SC_KERNEL_BITS); + #endif + long cpu = sysconf (_SC_CPU_VERSION); + + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1"); break; + case CPU_PA_RISC2_0: + #if defined(_SC_KERNEL_BITS) + switch (bits) + { + case 64: puts ("hppa2.0w"); break; + case 32: puts ("hppa2.0n"); break; + default: puts ("hppa2.0"); break; + } break; + #else /* !defined(_SC_KERNEL_BITS) */ + puts ("hppa2.0"); break; + #endif + default: puts ("hppa1.0"); break; + } + exit (0); + } +EOF + (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy` + test -z "$HP_ARCH" && HP_ARCH=hppa + fi ;; + esac + if [ ${HP_ARCH} = "hppa2.0w" ] + then + eval $set_cc_for_build + + # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating + # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler + # generating 64-bit code. GNU and HP use different nomenclature: + # + # $ CC_FOR_BUILD=cc ./config.guess + # => hppa2.0w-hp-hpux11.23 + # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess + # => hppa64-hp-hpux11.23 + + if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | + grep __LP64__ >/dev/null + then + HP_ARCH="hppa2.0w" + else + HP_ARCH="hppa64" + fi + fi + echo ${HP_ARCH}-hp-hpux${HPUX_REV} + exit ;; + ia64:HP-UX:*:*) + HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` + echo ia64-hp-hpux${HPUX_REV} + exit ;; + 3050*:HI-UX:*:*) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #include + int + main () + { + long cpu = sysconf (_SC_CPU_VERSION); + /* The order matters, because CPU_IS_HP_MC68K erroneously returns + true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct + results, however. */ + if (CPU_IS_PA_RISC (cpu)) + { + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; + case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; + default: puts ("hppa-hitachi-hiuxwe2"); break; + } + } + else if (CPU_IS_HP_MC68K (cpu)) + puts ("m68k-hitachi-hiuxwe2"); + else puts ("unknown-hitachi-hiuxwe2"); + exit (0); + } +EOF + $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` && + { echo "$SYSTEM_NAME"; exit; } + echo unknown-hitachi-hiuxwe2 + exit ;; + 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) + echo hppa1.1-hp-bsd + exit ;; + 9000/8??:4.3bsd:*:*) + echo hppa1.0-hp-bsd + exit ;; + *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) + echo hppa1.0-hp-mpeix + exit ;; + hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) + echo hppa1.1-hp-osf + exit ;; + hp8??:OSF1:*:*) + echo hppa1.0-hp-osf + exit ;; + i*86:OSF1:*:*) + if [ -x /usr/sbin/sysversion ] ; then + echo ${UNAME_MACHINE}-unknown-osf1mk + else + echo ${UNAME_MACHINE}-unknown-osf1 + fi + exit ;; + parisc*:Lites*:*:*) + echo hppa1.1-hp-lites + exit ;; + C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) + echo c1-convex-bsd + exit ;; + C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) + if getsysinfo -f scalar_acc + then echo c32-convex-bsd + else echo c2-convex-bsd + fi + exit ;; + C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) + echo c34-convex-bsd + exit ;; + C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) + echo c38-convex-bsd + exit ;; + C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) + echo c4-convex-bsd + exit ;; + CRAY*Y-MP:*:*:*) + echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*[A-Z]90:*:*:*) + echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \ + | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ + -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ + -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*TS:*:*:*) + echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*T3E:*:*:*) + echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit ;; + CRAY*SV1:*:*:*) + echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit ;; + *:UNICOS/mp:*:*) + echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' + exit ;; + F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) + FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` + FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` + FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` + echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + exit ;; + 5000:UNIX_System_V:4.*:*) + FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` + FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'` + echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + exit ;; + i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) + echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} + exit ;; + sparc*:BSD/OS:*:*) + echo sparc-unknown-bsdi${UNAME_RELEASE} + exit ;; + *:BSD/OS:*:*) + echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} + exit ;; + *:FreeBSD:*:*) + case ${UNAME_MACHINE} in + pc98) + echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; + amd64) + echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; + *) + echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; + esac + exit ;; + i*:CYGWIN*:*) + echo ${UNAME_MACHINE}-pc-cygwin + exit ;; + *:MINGW*:*) + echo ${UNAME_MACHINE}-pc-mingw32 + exit ;; + i*:windows32*:*) + # uname -m includes "-pc" on this system. + echo ${UNAME_MACHINE}-mingw32 + exit ;; + i*:PW*:*) + echo ${UNAME_MACHINE}-pc-pw32 + exit ;; + *:Interix*:[3456]*) + case ${UNAME_MACHINE} in + x86) + echo i586-pc-interix${UNAME_RELEASE} + exit ;; + EM64T | authenticamd | genuineintel) + echo x86_64-unknown-interix${UNAME_RELEASE} + exit ;; + IA64) + echo ia64-unknown-interix${UNAME_RELEASE} + exit ;; + esac ;; + [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) + echo i${UNAME_MACHINE}-pc-mks + exit ;; + i*:Windows_NT*:* | Pentium*:Windows_NT*:*) + # How do we know it's Interix rather than the generic POSIX subsystem? + # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we + # UNAME_MACHINE based on the output of uname instead of i386? + echo i586-pc-interix + exit ;; + i*:UWIN*:*) + echo ${UNAME_MACHINE}-pc-uwin + exit ;; + amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*) + echo x86_64-unknown-cygwin + exit ;; + p*:CYGWIN*:*) + echo powerpcle-unknown-cygwin + exit ;; + prep*:SunOS:5.*:*) + echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit ;; + *:GNU:*:*) + # the GNU system + echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` + exit ;; + *:GNU/*:*:*) + # other systems with GNU libc and userland + echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu + exit ;; + i*86:Minix:*:*) + echo ${UNAME_MACHINE}-pc-minix + exit ;; + arm*:Linux:*:*) + eval $set_cc_for_build + if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ARM_EABI__ + then + echo ${UNAME_MACHINE}-unknown-linux-gnu + else + echo ${UNAME_MACHINE}-unknown-linux-gnueabi + fi + exit ;; + avr32*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + cris:Linux:*:*) + echo cris-axis-linux-gnu + exit ;; + crisv32:Linux:*:*) + echo crisv32-axis-linux-gnu + exit ;; + frv:Linux:*:*) + echo frv-unknown-linux-gnu + exit ;; + ia64:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + m32r*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + m68*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + mips:Linux:*:*) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #undef CPU + #undef mips + #undef mipsel + #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) + CPU=mipsel + #else + #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) + CPU=mips + #else + CPU= + #endif + #endif +EOF + eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' + /^CPU/{ + s: ::g + p + }'`" + test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } + ;; + mips64:Linux:*:*) + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #undef CPU + #undef mips64 + #undef mips64el + #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) + CPU=mips64el + #else + #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) + CPU=mips64 + #else + CPU= + #endif + #endif +EOF + eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' + /^CPU/{ + s: ::g + p + }'`" + test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } + ;; + or32:Linux:*:*) + echo or32-unknown-linux-gnu + exit ;; + ppc:Linux:*:*) + echo powerpc-unknown-linux-gnu + exit ;; + ppc64:Linux:*:*) + echo powerpc64-unknown-linux-gnu + exit ;; + alpha:Linux:*:*) + case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in + EV5) UNAME_MACHINE=alphaev5 ;; + EV56) UNAME_MACHINE=alphaev56 ;; + PCA56) UNAME_MACHINE=alphapca56 ;; + PCA57) UNAME_MACHINE=alphapca56 ;; + EV6) UNAME_MACHINE=alphaev6 ;; + EV67) UNAME_MACHINE=alphaev67 ;; + EV68*) UNAME_MACHINE=alphaev68 ;; + esac + objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null + if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi + echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} + exit ;; + padre:Linux:*:*) + echo sparc-unknown-linux-gnu + exit ;; + parisc:Linux:*:* | hppa:Linux:*:*) + # Look for CPU level + case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in + PA7*) echo hppa1.1-unknown-linux-gnu ;; + PA8*) echo hppa2.0-unknown-linux-gnu ;; + *) echo hppa-unknown-linux-gnu ;; + esac + exit ;; + parisc64:Linux:*:* | hppa64:Linux:*:*) + echo hppa64-unknown-linux-gnu + exit ;; + s390:Linux:*:* | s390x:Linux:*:*) + echo ${UNAME_MACHINE}-ibm-linux + exit ;; + sh64*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + sh*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + sparc:Linux:*:* | sparc64:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + vax:Linux:*:*) + echo ${UNAME_MACHINE}-dec-linux-gnu + exit ;; + x86_64:Linux:*:*) + echo x86_64-unknown-linux-gnu + exit ;; + xtensa*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-gnu + exit ;; + i*86:Linux:*:*) + # The BFD linker knows what the default object file format is, so + # first see if it will tell us. cd to the root directory to prevent + # problems with other programs or directories called `ld' in the path. + # Set LC_ALL=C to ensure ld outputs messages in English. + ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \ + | sed -ne '/supported targets:/!d + s/[ ][ ]*/ /g + s/.*supported targets: *// + s/ .*// + p'` + case "$ld_supported_targets" in + elf32-i386) + TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu" + ;; + a.out-i386-linux) + echo "${UNAME_MACHINE}-pc-linux-gnuaout" + exit ;; + "") + # Either a pre-BFD a.out linker (linux-gnuoldld) or + # one that does not give us useful --help. + echo "${UNAME_MACHINE}-pc-linux-gnuoldld" + exit ;; + esac + # Determine whether the default compiler is a.out or elf + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #include + #ifdef __ELF__ + # ifdef __GLIBC__ + # if __GLIBC__ >= 2 + LIBC=gnu + # else + LIBC=gnulibc1 + # endif + # else + LIBC=gnulibc1 + # endif + #else + #if defined(__INTEL_COMPILER) || defined(__PGI) || defined(__SUNPRO_C) || defined(__SUNPRO_CC) + LIBC=gnu + #else + LIBC=gnuaout + #endif + #endif + #ifdef __dietlibc__ + LIBC=dietlibc + #endif +EOF + eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' + /^LIBC/{ + s: ::g + p + }'`" + test x"${LIBC}" != x && { + echo "${UNAME_MACHINE}-pc-linux-${LIBC}" + exit + } + test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; } + ;; + i*86:DYNIX/ptx:4*:*) + # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. + # earlier versions are messed up and put the nodename in both + # sysname and nodename. + echo i386-sequent-sysv4 + exit ;; + i*86:UNIX_SV:4.2MP:2.*) + # Unixware is an offshoot of SVR4, but it has its own version + # number series starting with 2... + # I am not positive that other SVR4 systems won't match this, + # I just have to hope. -- rms. + # Use sysv4.2uw... so that sysv4* matches it. + echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION} + exit ;; + i*86:OS/2:*:*) + # If we were able to find `uname', then EMX Unix compatibility + # is probably installed. + echo ${UNAME_MACHINE}-pc-os2-emx + exit ;; + i*86:XTS-300:*:STOP) + echo ${UNAME_MACHINE}-unknown-stop + exit ;; + i*86:atheos:*:*) + echo ${UNAME_MACHINE}-unknown-atheos + exit ;; + i*86:syllable:*:*) + echo ${UNAME_MACHINE}-pc-syllable + exit ;; + i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*) + echo i386-unknown-lynxos${UNAME_RELEASE} + exit ;; + i*86:*DOS:*:*) + echo ${UNAME_MACHINE}-pc-msdosdjgpp + exit ;; + i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*) + UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'` + if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then + echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL} + else + echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL} + fi + exit ;; + i*86:*:5:[678]*) + # UnixWare 7.x, OpenUNIX and OpenServer 6. + case `/bin/uname -X | grep "^Machine"` in + *486*) UNAME_MACHINE=i486 ;; + *Pentium) UNAME_MACHINE=i586 ;; + *Pent*|*Celeron) UNAME_MACHINE=i686 ;; + esac + echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} + exit ;; + i*86:*:3.2:*) + if test -f /usr/options/cb.name; then + UNAME_REL=`sed -n 's/.*Version //p' /dev/null >/dev/null ; then + UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')` + (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 + (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \ + && UNAME_MACHINE=i586 + (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \ + && UNAME_MACHINE=i686 + (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ + && UNAME_MACHINE=i686 + echo ${UNAME_MACHINE}-pc-sco$UNAME_REL + else + echo ${UNAME_MACHINE}-pc-sysv32 + fi + exit ;; + pc:*:*:*) + # Left here for compatibility: + # uname -m prints for DJGPP always 'pc', but it prints nothing about + # the processor, so we play safe by assuming i386. + echo i386-pc-msdosdjgpp + exit ;; + Intel:Mach:3*:*) + echo i386-pc-mach3 + exit ;; + paragon:*:*:*) + echo i860-intel-osf1 + exit ;; + i860:*:4.*:*) # i860-SVR4 + if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then + echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4 + else # Add other i860-SVR4 vendors below as they are discovered. + echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4 + fi + exit ;; + mini*:CTIX:SYS*5:*) + # "miniframe" + echo m68010-convergent-sysv + exit ;; + mc68k:UNIX:SYSTEM5:3.51m) + echo m68k-convergent-sysv + exit ;; + M680?0:D-NIX:5.3:*) + echo m68k-diab-dnix + exit ;; + M68*:*:R3V[5678]*:*) + test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;; + 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0) + OS_REL='' + test -r /etc/.relid \ + && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4.3${OS_REL}; exit; } + /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ + && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; + 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4; exit; } ;; + m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) + echo m68k-unknown-lynxos${UNAME_RELEASE} + exit ;; + mc68030:UNIX_System_V:4.*:*) + echo m68k-atari-sysv4 + exit ;; + TSUNAMI:LynxOS:2.*:*) + echo sparc-unknown-lynxos${UNAME_RELEASE} + exit ;; + rs6000:LynxOS:2.*:*) + echo rs6000-unknown-lynxos${UNAME_RELEASE} + exit ;; + PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*) + echo powerpc-unknown-lynxos${UNAME_RELEASE} + exit ;; + SM[BE]S:UNIX_SV:*:*) + echo mips-dde-sysv${UNAME_RELEASE} + exit ;; + RM*:ReliantUNIX-*:*:*) + echo mips-sni-sysv4 + exit ;; + RM*:SINIX-*:*:*) + echo mips-sni-sysv4 + exit ;; + *:SINIX-*:*:*) + if uname -p 2>/dev/null >/dev/null ; then + UNAME_MACHINE=`(uname -p) 2>/dev/null` + echo ${UNAME_MACHINE}-sni-sysv4 + else + echo ns32k-sni-sysv + fi + exit ;; + PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort + # says + echo i586-unisys-sysv4 + exit ;; + *:UNIX_System_V:4*:FTX*) + # From Gerald Hewes . + # How about differentiating between stratus architectures? -djm + echo hppa1.1-stratus-sysv4 + exit ;; + *:*:*:FTX*) + # From seanf@swdc.stratus.com. + echo i860-stratus-sysv4 + exit ;; + i*86:VOS:*:*) + # From Paul.Green@stratus.com. + echo ${UNAME_MACHINE}-stratus-vos + exit ;; + *:VOS:*:*) + # From Paul.Green@stratus.com. + echo hppa1.1-stratus-vos + exit ;; + mc68*:A/UX:*:*) + echo m68k-apple-aux${UNAME_RELEASE} + exit ;; + news*:NEWS-OS:6*:*) + echo mips-sony-newsos6 + exit ;; + R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) + if [ -d /usr/nec ]; then + echo mips-nec-sysv${UNAME_RELEASE} + else + echo mips-unknown-sysv${UNAME_RELEASE} + fi + exit ;; + BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. + echo powerpc-be-beos + exit ;; + BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. + echo powerpc-apple-beos + exit ;; + BePC:BeOS:*:*) # BeOS running on Intel PC compatible. + echo i586-pc-beos + exit ;; + BePC:Haiku:*:*) # Haiku running on Intel PC compatible. + echo i586-pc-haiku + exit ;; + SX-4:SUPER-UX:*:*) + echo sx4-nec-superux${UNAME_RELEASE} + exit ;; + SX-5:SUPER-UX:*:*) + echo sx5-nec-superux${UNAME_RELEASE} + exit ;; + SX-6:SUPER-UX:*:*) + echo sx6-nec-superux${UNAME_RELEASE} + exit ;; + SX-7:SUPER-UX:*:*) + echo sx7-nec-superux${UNAME_RELEASE} + exit ;; + SX-8:SUPER-UX:*:*) + echo sx8-nec-superux${UNAME_RELEASE} + exit ;; + SX-8R:SUPER-UX:*:*) + echo sx8r-nec-superux${UNAME_RELEASE} + exit ;; + Power*:Rhapsody:*:*) + echo powerpc-apple-rhapsody${UNAME_RELEASE} + exit ;; + *:Rhapsody:*:*) + echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE} + exit ;; + *:Darwin:*:*) + UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown + case $UNAME_PROCESSOR in + unknown) UNAME_PROCESSOR=powerpc ;; + esac + echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} + exit ;; + *:procnto*:*:* | *:QNX:[0123456789]*:*) + UNAME_PROCESSOR=`uname -p` + if test "$UNAME_PROCESSOR" = "x86"; then + UNAME_PROCESSOR=i386 + UNAME_MACHINE=pc + fi + echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE} + exit ;; + *:QNX:*:4*) + echo i386-pc-qnx + exit ;; + NSE-?:NONSTOP_KERNEL:*:*) + echo nse-tandem-nsk${UNAME_RELEASE} + exit ;; + NSR-?:NONSTOP_KERNEL:*:*) + echo nsr-tandem-nsk${UNAME_RELEASE} + exit ;; + *:NonStop-UX:*:*) + echo mips-compaq-nonstopux + exit ;; + BS2000:POSIX*:*:*) + echo bs2000-siemens-sysv + exit ;; + DS/*:UNIX_System_V:*:*) + echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE} + exit ;; + *:Plan9:*:*) + # "uname -m" is not consistent, so use $cputype instead. 386 + # is converted to i386 for consistency with other x86 + # operating systems. + if test "$cputype" = "386"; then + UNAME_MACHINE=i386 + else + UNAME_MACHINE="$cputype" + fi + echo ${UNAME_MACHINE}-unknown-plan9 + exit ;; + *:TOPS-10:*:*) + echo pdp10-unknown-tops10 + exit ;; + *:TENEX:*:*) + echo pdp10-unknown-tenex + exit ;; + KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) + echo pdp10-dec-tops20 + exit ;; + XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) + echo pdp10-xkl-tops20 + exit ;; + *:TOPS-20:*:*) + echo pdp10-unknown-tops20 + exit ;; + *:ITS:*:*) + echo pdp10-unknown-its + exit ;; + SEI:*:*:SEIUX) + echo mips-sei-seiux${UNAME_RELEASE} + exit ;; + *:DragonFly:*:*) + echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` + exit ;; + *:*VMS:*:*) + UNAME_MACHINE=`(uname -p) 2>/dev/null` + case "${UNAME_MACHINE}" in + A*) echo alpha-dec-vms ; exit ;; + I*) echo ia64-dec-vms ; exit ;; + V*) echo vax-dec-vms ; exit ;; + esac ;; + *:XENIX:*:SysV) + echo i386-pc-xenix + exit ;; + i*86:skyos:*:*) + echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//' + exit ;; + i*86:rdos:*:*) + echo ${UNAME_MACHINE}-pc-rdos + exit ;; +esac + +#echo '(No uname command or uname output not recognized.)' 1>&2 +#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2 + +eval $set_cc_for_build +cat >$dummy.c < +# include +#endif +main () +{ +#if defined (sony) +#if defined (MIPSEB) + /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, + I don't know.... */ + printf ("mips-sony-bsd\n"); exit (0); +#else +#include + printf ("m68k-sony-newsos%s\n", +#ifdef NEWSOS4 + "4" +#else + "" +#endif + ); exit (0); +#endif +#endif + +#if defined (__arm) && defined (__acorn) && defined (__unix) + printf ("arm-acorn-riscix\n"); exit (0); +#endif + +#if defined (hp300) && !defined (hpux) + printf ("m68k-hp-bsd\n"); exit (0); +#endif + +#if defined (NeXT) +#if !defined (__ARCHITECTURE__) +#define __ARCHITECTURE__ "m68k" +#endif + int version; + version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`; + if (version < 4) + printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); + else + printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); + exit (0); +#endif + +#if defined (MULTIMAX) || defined (n16) +#if defined (UMAXV) + printf ("ns32k-encore-sysv\n"); exit (0); +#else +#if defined (CMU) + printf ("ns32k-encore-mach\n"); exit (0); +#else + printf ("ns32k-encore-bsd\n"); exit (0); +#endif +#endif +#endif + +#if defined (__386BSD__) + printf ("i386-pc-bsd\n"); exit (0); +#endif + +#if defined (sequent) +#if defined (i386) + printf ("i386-sequent-dynix\n"); exit (0); +#endif +#if defined (ns32000) + printf ("ns32k-sequent-dynix\n"); exit (0); +#endif +#endif + +#if defined (_SEQUENT_) + struct utsname un; + + uname(&un); + + if (strncmp(un.version, "V2", 2) == 0) { + printf ("i386-sequent-ptx2\n"); exit (0); + } + if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ + printf ("i386-sequent-ptx1\n"); exit (0); + } + printf ("i386-sequent-ptx\n"); exit (0); + +#endif + +#if defined (vax) +# if !defined (ultrix) +# include +# if defined (BSD) +# if BSD == 43 + printf ("vax-dec-bsd4.3\n"); exit (0); +# else +# if BSD == 199006 + printf ("vax-dec-bsd4.3reno\n"); exit (0); +# else + printf ("vax-dec-bsd\n"); exit (0); +# endif +# endif +# else + printf ("vax-dec-bsd\n"); exit (0); +# endif +# else + printf ("vax-dec-ultrix\n"); exit (0); +# endif +#endif + +#if defined (alliant) && defined (i860) + printf ("i860-alliant-bsd\n"); exit (0); +#endif + + exit (1); +} +EOF + +$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` && + { echo "$SYSTEM_NAME"; exit; } + +# Apollos put the system type in the environment. + +test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; } + +# Convex versions that predate uname can use getsysinfo(1) + +if [ -x /usr/convex/getsysinfo ] +then + case `getsysinfo -f cpu_type` in + c1*) + echo c1-convex-bsd + exit ;; + c2*) + if getsysinfo -f scalar_acc + then echo c32-convex-bsd + else echo c2-convex-bsd + fi + exit ;; + c34*) + echo c34-convex-bsd + exit ;; + c38*) + echo c38-convex-bsd + exit ;; + c4*) + echo c4-convex-bsd + exit ;; + esac +fi + +cat >&2 < in order to provide the needed +information to handle your system. + +config.guess timestamp = $timestamp + +uname -m = `(uname -m) 2>/dev/null || echo unknown` +uname -r = `(uname -r) 2>/dev/null || echo unknown` +uname -s = `(uname -s) 2>/dev/null || echo unknown` +uname -v = `(uname -v) 2>/dev/null || echo unknown` + +/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null` +/bin/uname -X = `(/bin/uname -X) 2>/dev/null` + +hostinfo = `(hostinfo) 2>/dev/null` +/bin/universe = `(/bin/universe) 2>/dev/null` +/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null` +/bin/arch = `(/bin/arch) 2>/dev/null` +/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null` +/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null` + +UNAME_MACHINE = ${UNAME_MACHINE} +UNAME_RELEASE = ${UNAME_RELEASE} +UNAME_SYSTEM = ${UNAME_SYSTEM} +UNAME_VERSION = ${UNAME_VERSION} +EOF + +exit 1 + +# Local variables: +# eval: (add-hook 'write-file-hooks 'time-stamp) +# time-stamp-start: "timestamp='" +# time-stamp-format: "%:y-%02m-%02d" +# time-stamp-end: "'" +# End: Index: /issm/trunk-jpl-damage/config.sub =================================================================== --- /issm/trunk-jpl-damage/config.sub (revision 11330) +++ /issm/trunk-jpl-damage/config.sub (revision 11330) @@ -0,0 +1,1677 @@ +#! /bin/sh +# Configuration validation subroutine script. +# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, +# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 +# Free Software Foundation, Inc. + +timestamp='2008-09-08' + +# This file is (in principle) common to ALL GNU software. +# The presence of a machine in this file suggests that SOME GNU software +# can handle that machine. It does not imply ALL GNU software can. +# +# This file is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA +# 02110-1301, USA. +# +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that program. + + +# Please send patches to . Submit a context +# diff and a properly formatted ChangeLog entry. +# +# Configuration subroutine to validate and canonicalize a configuration type. +# Supply the specified configuration type as an argument. +# If it is invalid, we print an error message on stderr and exit with code 1. +# Otherwise, we print the canonical config type on stdout and succeed. + +# This file is supposed to be the same for all GNU packages +# and recognize all the CPU types, system types and aliases +# that are meaningful with *any* GNU software. +# Each package is responsible for reporting which valid configurations +# it does not support. The user should be able to distinguish +# a failure to support a valid configuration from a meaningless +# configuration. + +# The goal of this file is to map all the various variations of a given +# machine specification into a single specification in the form: +# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM +# or in some cases, the newer four-part form: +# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM +# It is wrong to echo any other type of specification. + +me=`echo "$0" | sed -e 's,.*/,,'` + +usage="\ +Usage: $0 [OPTION] CPU-MFR-OPSYS + $0 [OPTION] ALIAS + +Canonicalize a configuration name. + +Operation modes: + -h, --help print this help, then exit + -t, --time-stamp print date of last modification, then exit + -v, --version print version number, then exit + +Report bugs and patches to ." + +version="\ +GNU config.sub ($timestamp) + +Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, +2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. + +This is free software; see the source for copying conditions. There is NO +warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." + +help=" +Try \`$me --help' for more information." + +# Parse command line +while test $# -gt 0 ; do + case $1 in + --time-stamp | --time* | -t ) + echo "$timestamp" ; exit ;; + --version | -v ) + echo "$version" ; exit ;; + --help | --h* | -h ) + echo "$usage"; exit ;; + -- ) # Stop option processing + shift; break ;; + - ) # Use stdin as input. + break ;; + -* ) + echo "$me: invalid option $1$help" + exit 1 ;; + + *local*) + # First pass through any local machine types. + echo $1 + exit ;; + + * ) + break ;; + esac +done + +case $# in + 0) echo "$me: missing argument$help" >&2 + exit 1;; + 1) ;; + *) echo "$me: too many arguments$help" >&2 + exit 1;; +esac + +# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any). +# Here we must recognize all the valid KERNEL-OS combinations. +maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` +case $maybe_os in + nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \ + uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \ + storm-chaos* | os2-emx* | rtmk-nova*) + os=-$maybe_os + basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` + ;; + *) + basic_machine=`echo $1 | sed 's/-[^-]*$//'` + if [ $basic_machine != $1 ] + then os=`echo $1 | sed 's/.*-/-/'` + else os=; fi + ;; +esac + +### Let's recognize common machines as not being operating systems so +### that things like config.sub decstation-3100 work. We also +### recognize some manufacturers as not being operating systems, so we +### can provide default operating systems below. +case $os in + -sun*os*) + # Prevent following clause from handling this invalid input. + ;; + -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \ + -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \ + -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \ + -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\ + -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \ + -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \ + -apple | -axis | -knuth | -cray) + os= + basic_machine=$1 + ;; + -sim | -cisco | -oki | -wec | -winbond) + os= + basic_machine=$1 + ;; + -scout) + ;; + -wrs) + os=-vxworks + basic_machine=$1 + ;; + -chorusos*) + os=-chorusos + basic_machine=$1 + ;; + -chorusrdb) + os=-chorusrdb + basic_machine=$1 + ;; + -hiux*) + os=-hiuxwe2 + ;; + -sco6) + os=-sco5v6 + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco5) + os=-sco3.2v5 + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco4) + os=-sco3.2v4 + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco3.2.[4-9]*) + os=`echo $os | sed -e 's/sco3.2./sco3.2v/'` + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco3.2v[4-9]*) + # Don't forget version if it is 3.2v4 or newer. + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco5v6*) + # Don't forget version if it is 3.2v4 or newer. + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -sco*) + os=-sco3.2v2 + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -udk*) + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -isc) + os=-isc2.2 + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -clix*) + basic_machine=clipper-intergraph + ;; + -isc*) + basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` + ;; + -lynx*) + os=-lynxos + ;; + -ptx*) + basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'` + ;; + -windowsnt*) + os=`echo $os | sed -e 's/windowsnt/winnt/'` + ;; + -psos*) + os=-psos + ;; + -mint | -mint[0-9]*) + basic_machine=m68k-atari + os=-mint + ;; +esac + +# Decode aliases for certain CPU-COMPANY combinations. +case $basic_machine in + # Recognize the basic CPU types without company name. + # Some are omitted here because they have special meanings below. + 1750a | 580 \ + | a29k \ + | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ + | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \ + | am33_2.0 \ + | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \ + | bfin \ + | c4x | clipper \ + | d10v | d30v | dlx | dsp16xx \ + | fido | fr30 | frv \ + | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ + | i370 | i860 | i960 | ia64 \ + | ip2k | iq2000 \ + | m32c | m32r | m32rle | m68000 | m68k | m88k \ + | maxq | mb | microblaze | mcore | mep | metag \ + | mips | mipsbe | mipseb | mipsel | mipsle \ + | mips16 \ + | mips64 | mips64el \ + | mips64octeon | mips64octeonel \ + | mips64orion | mips64orionel \ + | mips64r5900 | mips64r5900el \ + | mips64vr | mips64vrel \ + | mips64vr4100 | mips64vr4100el \ + | mips64vr4300 | mips64vr4300el \ + | mips64vr5000 | mips64vr5000el \ + | mips64vr5900 | mips64vr5900el \ + | mipsisa32 | mipsisa32el \ + | mipsisa32r2 | mipsisa32r2el \ + | mipsisa64 | mipsisa64el \ + | mipsisa64r2 | mipsisa64r2el \ + | mipsisa64sb1 | mipsisa64sb1el \ + | mipsisa64sr71k | mipsisa64sr71kel \ + | mipstx39 | mipstx39el \ + | mn10200 | mn10300 \ + | mt \ + | msp430 \ + | nios | nios2 \ + | ns16k | ns32k \ + | or32 \ + | pdp10 | pdp11 | pj | pjl \ + | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ + | pyramid \ + | score \ + | sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ + | sh64 | sh64le \ + | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \ + | sparcv8 | sparcv9 | sparcv9b | sparcv9v \ + | spu | strongarm \ + | tahoe | thumb | tic4x | tic80 | tron \ + | v850 | v850e \ + | we32k \ + | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \ + | z8k | z80) + basic_machine=$basic_machine-unknown + ;; + m6811 | m68hc11 | m6812 | m68hc12) + # Motorola 68HC11/12. + basic_machine=$basic_machine-unknown + os=-none + ;; + m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k) + ;; + ms1) + basic_machine=mt-unknown + ;; + + # We use `pc' rather than `unknown' + # because (1) that's what they normally are, and + # (2) the word "unknown" tends to confuse beginning users. + i*86 | x86_64) + basic_machine=$basic_machine-pc + ;; + # Object if more than one company name word. + *-*-*) + echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 + exit 1 + ;; + # Recognize the basic CPU types with company name. + 580-* \ + | a29k-* \ + | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \ + | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \ + | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \ + | arm-* | armbe-* | armle-* | armeb-* | armv*-* \ + | avr-* | avr32-* \ + | bfin-* | bs2000-* \ + | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \ + | clipper-* | craynv-* | cydra-* \ + | d10v-* | d30v-* | dlx-* \ + | elxsi-* \ + | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \ + | h8300-* | h8500-* \ + | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ + | i*86-* | i860-* | i960-* | ia64-* \ + | ip2k-* | iq2000-* \ + | m32c-* | m32r-* | m32rle-* \ + | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ + | m88110-* | m88k-* | maxq-* | mcore-* | metag-* \ + | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ + | mips16-* \ + | mips64-* | mips64el-* \ + | mips64octeon-* | mips64octeonel-* \ + | mips64orion-* | mips64orionel-* \ + | mips64r5900-* | mips64r5900el-* \ + | mips64vr-* | mips64vrel-* \ + | mips64vr4100-* | mips64vr4100el-* \ + | mips64vr4300-* | mips64vr4300el-* \ + | mips64vr5000-* | mips64vr5000el-* \ + | mips64vr5900-* | mips64vr5900el-* \ + | mipsisa32-* | mipsisa32el-* \ + | mipsisa32r2-* | mipsisa32r2el-* \ + | mipsisa64-* | mipsisa64el-* \ + | mipsisa64r2-* | mipsisa64r2el-* \ + | mipsisa64sb1-* | mipsisa64sb1el-* \ + | mipsisa64sr71k-* | mipsisa64sr71kel-* \ + | mipstx39-* | mipstx39el-* \ + | mmix-* \ + | mt-* \ + | msp430-* \ + | nios-* | nios2-* \ + | none-* | np1-* | ns16k-* | ns32k-* \ + | orion-* \ + | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ + | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ + | pyramid-* \ + | romp-* | rs6000-* \ + | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ + | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ + | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \ + | sparclite-* \ + | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \ + | tahoe-* | thumb-* \ + | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* | tile-* \ + | tron-* \ + | v850-* | v850e-* | vax-* \ + | we32k-* \ + | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \ + | xstormy16-* | xtensa*-* \ + | ymp-* \ + | z8k-* | z80-*) + ;; + # Recognize the basic CPU types without company name, with glob match. + xtensa*) + basic_machine=$basic_machine-unknown + ;; + # Recognize the various machine names and aliases which stand + # for a CPU type and a company and sometimes even an OS. + 386bsd) + basic_machine=i386-unknown + os=-bsd + ;; + 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) + basic_machine=m68000-att + ;; + 3b*) + basic_machine=we32k-att + ;; + a29khif) + basic_machine=a29k-amd + os=-udi + ;; + abacus) + basic_machine=abacus-unknown + ;; + adobe68k) + basic_machine=m68010-adobe + os=-scout + ;; + alliant | fx80) + basic_machine=fx80-alliant + ;; + altos | altos3068) + basic_machine=m68k-altos + ;; + am29k) + basic_machine=a29k-none + os=-bsd + ;; + amd64) + basic_machine=x86_64-pc + ;; + amd64-*) + basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + amdahl) + basic_machine=580-amdahl + os=-sysv + ;; + amiga | amiga-*) + basic_machine=m68k-unknown + ;; + amigaos | amigados) + basic_machine=m68k-unknown + os=-amigaos + ;; + amigaunix | amix) + basic_machine=m68k-unknown + os=-sysv4 + ;; + apollo68) + basic_machine=m68k-apollo + os=-sysv + ;; + apollo68bsd) + basic_machine=m68k-apollo + os=-bsd + ;; + aux) + basic_machine=m68k-apple + os=-aux + ;; + balance) + basic_machine=ns32k-sequent + os=-dynix + ;; + blackfin) + basic_machine=bfin-unknown + os=-linux + ;; + blackfin-*) + basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'` + os=-linux + ;; + c90) + basic_machine=c90-cray + os=-unicos + ;; + cegcc) + basic_machine=arm-unknown + os=-cegcc + ;; + convex-c1) + basic_machine=c1-convex + os=-bsd + ;; + convex-c2) + basic_machine=c2-convex + os=-bsd + ;; + convex-c32) + basic_machine=c32-convex + os=-bsd + ;; + convex-c34) + basic_machine=c34-convex + os=-bsd + ;; + convex-c38) + basic_machine=c38-convex + os=-bsd + ;; + cray | j90) + basic_machine=j90-cray + os=-unicos + ;; + craynv) + basic_machine=craynv-cray + os=-unicosmp + ;; + cr16) + basic_machine=cr16-unknown + os=-elf + ;; + crds | unos) + basic_machine=m68k-crds + ;; + crisv32 | crisv32-* | etraxfs*) + basic_machine=crisv32-axis + ;; + cris | cris-* | etrax*) + basic_machine=cris-axis + ;; + crx) + basic_machine=crx-unknown + os=-elf + ;; + da30 | da30-*) + basic_machine=m68k-da30 + ;; + decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn) + basic_machine=mips-dec + ;; + decsystem10* | dec10*) + basic_machine=pdp10-dec + os=-tops10 + ;; + decsystem20* | dec20*) + basic_machine=pdp10-dec + os=-tops20 + ;; + delta | 3300 | motorola-3300 | motorola-delta \ + | 3300-motorola | delta-motorola) + basic_machine=m68k-motorola + ;; + delta88) + basic_machine=m88k-motorola + os=-sysv3 + ;; + dicos) + basic_machine=i686-pc + os=-dicos + ;; + djgpp) + basic_machine=i586-pc + os=-msdosdjgpp + ;; + dpx20 | dpx20-*) + basic_machine=rs6000-bull + os=-bosx + ;; + dpx2* | dpx2*-bull) + basic_machine=m68k-bull + os=-sysv3 + ;; + ebmon29k) + basic_machine=a29k-amd + os=-ebmon + ;; + elxsi) + basic_machine=elxsi-elxsi + os=-bsd + ;; + encore | umax | mmax) + basic_machine=ns32k-encore + ;; + es1800 | OSE68k | ose68k | ose | OSE) + basic_machine=m68k-ericsson + os=-ose + ;; + fx2800) + basic_machine=i860-alliant + ;; + genix) + basic_machine=ns32k-ns + ;; + gmicro) + basic_machine=tron-gmicro + os=-sysv + ;; + go32) + basic_machine=i386-pc + os=-go32 + ;; + h3050r* | hiux*) + basic_machine=hppa1.1-hitachi + os=-hiuxwe2 + ;; + h8300hms) + basic_machine=h8300-hitachi + os=-hms + ;; + h8300xray) + basic_machine=h8300-hitachi + os=-xray + ;; + h8500hms) + basic_machine=h8500-hitachi + os=-hms + ;; + harris) + basic_machine=m88k-harris + os=-sysv3 + ;; + hp300-*) + basic_machine=m68k-hp + ;; + hp300bsd) + basic_machine=m68k-hp + os=-bsd + ;; + hp300hpux) + basic_machine=m68k-hp + os=-hpux + ;; + hp3k9[0-9][0-9] | hp9[0-9][0-9]) + basic_machine=hppa1.0-hp + ;; + hp9k2[0-9][0-9] | hp9k31[0-9]) + basic_machine=m68000-hp + ;; + hp9k3[2-9][0-9]) + basic_machine=m68k-hp + ;; + hp9k6[0-9][0-9] | hp6[0-9][0-9]) + basic_machine=hppa1.0-hp + ;; + hp9k7[0-79][0-9] | hp7[0-79][0-9]) + basic_machine=hppa1.1-hp + ;; + hp9k78[0-9] | hp78[0-9]) + # FIXME: really hppa2.0-hp + basic_machine=hppa1.1-hp + ;; + hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) + # FIXME: really hppa2.0-hp + basic_machine=hppa1.1-hp + ;; + hp9k8[0-9][13679] | hp8[0-9][13679]) + basic_machine=hppa1.1-hp + ;; + hp9k8[0-9][0-9] | hp8[0-9][0-9]) + basic_machine=hppa1.0-hp + ;; + hppa-next) + os=-nextstep3 + ;; + hppaosf) + basic_machine=hppa1.1-hp + os=-osf + ;; + hppro) + basic_machine=hppa1.1-hp + os=-proelf + ;; + i370-ibm* | ibm*) + basic_machine=i370-ibm + ;; +# I'm not sure what "Sysv32" means. Should this be sysv3.2? + i*86v32) + basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` + os=-sysv32 + ;; + i*86v4*) + basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` + os=-sysv4 + ;; + i*86v) + basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` + os=-sysv + ;; + i*86sol2) + basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` + os=-solaris2 + ;; + i386mach) + basic_machine=i386-mach + os=-mach + ;; + i386-vsta | vsta) + basic_machine=i386-unknown + os=-vsta + ;; + iris | iris4d) + basic_machine=mips-sgi + case $os in + -irix*) + ;; + *) + os=-irix4 + ;; + esac + ;; + isi68 | isi) + basic_machine=m68k-isi + os=-sysv + ;; + m68knommu) + basic_machine=m68k-unknown + os=-linux + ;; + m68knommu-*) + basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'` + os=-linux + ;; + m88k-omron*) + basic_machine=m88k-omron + ;; + magnum | m3230) + basic_machine=mips-mips + os=-sysv + ;; + merlin) + basic_machine=ns32k-utek + os=-sysv + ;; + mingw32) + basic_machine=i386-pc + os=-mingw32 + ;; + mingw32ce) + basic_machine=arm-unknown + os=-mingw32ce + ;; + miniframe) + basic_machine=m68000-convergent + ;; + *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*) + basic_machine=m68k-atari + os=-mint + ;; + mips3*-*) + basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'` + ;; + mips3*) + basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown + ;; + monitor) + basic_machine=m68k-rom68k + os=-coff + ;; + morphos) + basic_machine=powerpc-unknown + os=-morphos + ;; + msdos) + basic_machine=i386-pc + os=-msdos + ;; + ms1-*) + basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'` + ;; + mvs) + basic_machine=i370-ibm + os=-mvs + ;; + ncr3000) + basic_machine=i486-ncr + os=-sysv4 + ;; + netbsd386) + basic_machine=i386-unknown + os=-netbsd + ;; + netwinder) + basic_machine=armv4l-rebel + os=-linux + ;; + news | news700 | news800 | news900) + basic_machine=m68k-sony + os=-newsos + ;; + news1000) + basic_machine=m68030-sony + os=-newsos + ;; + news-3600 | risc-news) + basic_machine=mips-sony + os=-newsos + ;; + necv70) + basic_machine=v70-nec + os=-sysv + ;; + next | m*-next ) + basic_machine=m68k-next + case $os in + -nextstep* ) + ;; + -ns2*) + os=-nextstep2 + ;; + *) + os=-nextstep3 + ;; + esac + ;; + nh3000) + basic_machine=m68k-harris + os=-cxux + ;; + nh[45]000) + basic_machine=m88k-harris + os=-cxux + ;; + nindy960) + basic_machine=i960-intel + os=-nindy + ;; + mon960) + basic_machine=i960-intel + os=-mon960 + ;; + nonstopux) + basic_machine=mips-compaq + os=-nonstopux + ;; + np1) + basic_machine=np1-gould + ;; + nsr-tandem) + basic_machine=nsr-tandem + ;; + op50n-* | op60c-*) + basic_machine=hppa1.1-oki + os=-proelf + ;; + openrisc | openrisc-*) + basic_machine=or32-unknown + ;; + os400) + basic_machine=powerpc-ibm + os=-os400 + ;; + OSE68000 | ose68000) + basic_machine=m68000-ericsson + os=-ose + ;; + os68k) + basic_machine=m68k-none + os=-os68k + ;; + pa-hitachi) + basic_machine=hppa1.1-hitachi + os=-hiuxwe2 + ;; + paragon) + basic_machine=i860-intel + os=-osf + ;; + parisc) + basic_machine=hppa-unknown + os=-linux + ;; + parisc-*) + basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'` + os=-linux + ;; + pbd) + basic_machine=sparc-tti + ;; + pbb) + basic_machine=m68k-tti + ;; + pc532 | pc532-*) + basic_machine=ns32k-pc532 + ;; + pc98) + basic_machine=i386-pc + ;; + pc98-*) + basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + pentium | p5 | k5 | k6 | nexgen | viac3) + basic_machine=i586-pc + ;; + pentiumpro | p6 | 6x86 | athlon | athlon_*) + basic_machine=i686-pc + ;; + pentiumii | pentium2 | pentiumiii | pentium3) + basic_machine=i686-pc + ;; + pentium4) + basic_machine=i786-pc + ;; + pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*) + basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + pentiumpro-* | p6-* | 6x86-* | athlon-*) + basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*) + basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + pentium4-*) + basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + pn) + basic_machine=pn-gould + ;; + power) basic_machine=power-ibm + ;; + ppc) basic_machine=powerpc-unknown + ;; + ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + ppcle | powerpclittle | ppc-le | powerpc-little) + basic_machine=powerpcle-unknown + ;; + ppcle-* | powerpclittle-*) + basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + ppc64) basic_machine=powerpc64-unknown + ;; + ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + ppc64le | powerpc64little | ppc64-le | powerpc64-little) + basic_machine=powerpc64le-unknown + ;; + ppc64le-* | powerpc64little-*) + basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + ps2) + basic_machine=i386-ibm + ;; + pw32) + basic_machine=i586-unknown + os=-pw32 + ;; + rdos) + basic_machine=i386-pc + os=-rdos + ;; + rom68k) + basic_machine=m68k-rom68k + os=-coff + ;; + rm[46]00) + basic_machine=mips-siemens + ;; + rtpc | rtpc-*) + basic_machine=romp-ibm + ;; + s390 | s390-*) + basic_machine=s390-ibm + ;; + s390x | s390x-*) + basic_machine=s390x-ibm + ;; + sa29200) + basic_machine=a29k-amd + os=-udi + ;; + sb1) + basic_machine=mipsisa64sb1-unknown + ;; + sb1el) + basic_machine=mipsisa64sb1el-unknown + ;; + sde) + basic_machine=mipsisa32-sde + os=-elf + ;; + sei) + basic_machine=mips-sei + os=-seiux + ;; + sequent) + basic_machine=i386-sequent + ;; + sh) + basic_machine=sh-hitachi + os=-hms + ;; + sh5el) + basic_machine=sh5le-unknown + ;; + sh64) + basic_machine=sh64-unknown + ;; + sparclite-wrs | simso-wrs) + basic_machine=sparclite-wrs + os=-vxworks + ;; + sps7) + basic_machine=m68k-bull + os=-sysv2 + ;; + spur) + basic_machine=spur-unknown + ;; + st2000) + basic_machine=m68k-tandem + ;; + stratus) + basic_machine=i860-stratus + os=-sysv4 + ;; + sun2) + basic_machine=m68000-sun + ;; + sun2os3) + basic_machine=m68000-sun + os=-sunos3 + ;; + sun2os4) + basic_machine=m68000-sun + os=-sunos4 + ;; + sun3os3) + basic_machine=m68k-sun + os=-sunos3 + ;; + sun3os4) + basic_machine=m68k-sun + os=-sunos4 + ;; + sun4os3) + basic_machine=sparc-sun + os=-sunos3 + ;; + sun4os4) + basic_machine=sparc-sun + os=-sunos4 + ;; + sun4sol2) + basic_machine=sparc-sun + os=-solaris2 + ;; + sun3 | sun3-*) + basic_machine=m68k-sun + ;; + sun4) + basic_machine=sparc-sun + ;; + sun386 | sun386i | roadrunner) + basic_machine=i386-sun + ;; + sv1) + basic_machine=sv1-cray + os=-unicos + ;; + symmetry) + basic_machine=i386-sequent + os=-dynix + ;; + t3e) + basic_machine=alphaev5-cray + os=-unicos + ;; + t90) + basic_machine=t90-cray + os=-unicos + ;; + tic54x | c54x*) + basic_machine=tic54x-unknown + os=-coff + ;; + tic55x | c55x*) + basic_machine=tic55x-unknown + os=-coff + ;; + tic6x | c6x*) + basic_machine=tic6x-unknown + os=-coff + ;; + tile*) + basic_machine=tile-unknown + os=-linux-gnu + ;; + tx39) + basic_machine=mipstx39-unknown + ;; + tx39el) + basic_machine=mipstx39el-unknown + ;; + toad1) + basic_machine=pdp10-xkl + os=-tops20 + ;; + tower | tower-32) + basic_machine=m68k-ncr + ;; + tpf) + basic_machine=s390x-ibm + os=-tpf + ;; + udi29k) + basic_machine=a29k-amd + os=-udi + ;; + ultra3) + basic_machine=a29k-nyu + os=-sym1 + ;; + v810 | necv810) + basic_machine=v810-nec + os=-none + ;; + vaxv) + basic_machine=vax-dec + os=-sysv + ;; + vms) + basic_machine=vax-dec + os=-vms + ;; + vpp*|vx|vx-*) + basic_machine=f301-fujitsu + ;; + vxworks960) + basic_machine=i960-wrs + os=-vxworks + ;; + vxworks68) + basic_machine=m68k-wrs + os=-vxworks + ;; + vxworks29k) + basic_machine=a29k-wrs + os=-vxworks + ;; + w65*) + basic_machine=w65-wdc + os=-none + ;; + w89k-*) + basic_machine=hppa1.1-winbond + os=-proelf + ;; + xbox) + basic_machine=i686-pc + os=-mingw32 + ;; + xps | xps100) + basic_machine=xps100-honeywell + ;; + ymp) + basic_machine=ymp-cray + os=-unicos + ;; + z8k-*-coff) + basic_machine=z8k-unknown + os=-sim + ;; + z80-*-coff) + basic_machine=z80-unknown + os=-sim + ;; + none) + basic_machine=none-none + os=-none + ;; + +# Here we handle the default manufacturer of certain CPU types. It is in +# some cases the only manufacturer, in others, it is the most popular. + w89k) + basic_machine=hppa1.1-winbond + ;; + op50n) + basic_machine=hppa1.1-oki + ;; + op60c) + basic_machine=hppa1.1-oki + ;; + romp) + basic_machine=romp-ibm + ;; + mmix) + basic_machine=mmix-knuth + ;; + rs6000) + basic_machine=rs6000-ibm + ;; + vax) + basic_machine=vax-dec + ;; + pdp10) + # there are many clones, so DEC is not a safe bet + basic_machine=pdp10-unknown + ;; + pdp11) + basic_machine=pdp11-dec + ;; + we32k) + basic_machine=we32k-att + ;; + sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele) + basic_machine=sh-unknown + ;; + sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v) + basic_machine=sparc-sun + ;; + cydra) + basic_machine=cydra-cydrome + ;; + orion) + basic_machine=orion-highlevel + ;; + orion105) + basic_machine=clipper-highlevel + ;; + mac | mpw | mac-mpw) + basic_machine=m68k-apple + ;; + pmac | pmac-mpw) + basic_machine=powerpc-apple + ;; + *-unknown) + # Make sure to match an already-canonicalized machine name. + ;; + *) + echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 + exit 1 + ;; +esac + +# Here we canonicalize certain aliases for manufacturers. +case $basic_machine in + *-digital*) + basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'` + ;; + *-commodore*) + basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'` + ;; + *) + ;; +esac + +# Decode manufacturer-specific aliases for certain operating systems. + +if [ x"$os" != x"" ] +then +case $os in + # First match some system type aliases + # that might get confused with valid system types. + # -solaris* is a basic system type, with this one exception. + -solaris1 | -solaris1.*) + os=`echo $os | sed -e 's|solaris1|sunos4|'` + ;; + -solaris) + os=-solaris2 + ;; + -svr4*) + os=-sysv4 + ;; + -unixware*) + os=-sysv4.2uw + ;; + -gnu/linux*) + os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'` + ;; + # First accept the basic system types. + # The portable systems comes first. + # Each alternative MUST END IN A *, to match a version number. + # -sysv* is not here because it comes later, after sysvr4. + -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \ + | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\ + | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \ + | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \ + | -aos* \ + | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \ + | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \ + | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \ + | -openbsd* | -solidbsd* \ + | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \ + | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \ + | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \ + | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \ + | -chorusos* | -chorusrdb* | -cegcc* \ + | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \ + | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \ + | -uxpv* | -beos* | -mpeix* | -udk* \ + | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \ + | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \ + | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \ + | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \ + | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \ + | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \ + | -skyos* | -haiku* | -rdos* | -toppers* | -drops*) + # Remember, each alternative MUST END IN *, to match a version number. + ;; + -qnx*) + case $basic_machine in + x86-* | i*86-*) + ;; + *) + os=-nto$os + ;; + esac + ;; + -nto-qnx*) + ;; + -nto*) + os=`echo $os | sed -e 's|nto|nto-qnx|'` + ;; + -sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \ + | -windows* | -osx | -abug | -netware* | -os9* | -beos* | -haiku* \ + | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*) + ;; + -mac*) + os=`echo $os | sed -e 's|mac|macos|'` + ;; + -linux-dietlibc) + os=-linux-dietlibc + ;; + -linux*) + os=`echo $os | sed -e 's|linux|linux-gnu|'` + ;; + -sunos5*) + os=`echo $os | sed -e 's|sunos5|solaris2|'` + ;; + -sunos6*) + os=`echo $os | sed -e 's|sunos6|solaris3|'` + ;; + -opened*) + os=-openedition + ;; + -os400*) + os=-os400 + ;; + -wince*) + os=-wince + ;; + -osfrose*) + os=-osfrose + ;; + -osf*) + os=-osf + ;; + -utek*) + os=-bsd + ;; + -dynix*) + os=-bsd + ;; + -acis*) + os=-aos + ;; + -atheos*) + os=-atheos + ;; + -syllable*) + os=-syllable + ;; + -386bsd) + os=-bsd + ;; + -ctix* | -uts*) + os=-sysv + ;; + -nova*) + os=-rtmk-nova + ;; + -ns2 ) + os=-nextstep2 + ;; + -nsk*) + os=-nsk + ;; + # Preserve the version number of sinix5. + -sinix5.*) + os=`echo $os | sed -e 's|sinix|sysv|'` + ;; + -sinix*) + os=-sysv4 + ;; + -tpf*) + os=-tpf + ;; + -triton*) + os=-sysv3 + ;; + -oss*) + os=-sysv3 + ;; + -svr4) + os=-sysv4 + ;; + -svr3) + os=-sysv3 + ;; + -sysvr4) + os=-sysv4 + ;; + # This must come after -sysvr4. + -sysv*) + ;; + -ose*) + os=-ose + ;; + -es1800*) + os=-ose + ;; + -xenix) + os=-xenix + ;; + -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*) + os=-mint + ;; + -aros*) + os=-aros + ;; + -kaos*) + os=-kaos + ;; + -zvmoe) + os=-zvmoe + ;; + -dicos*) + os=-dicos + ;; + -none) + ;; + *) + # Get rid of the `-' at the beginning of $os. + os=`echo $os | sed 's/[^-]*-//'` + echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2 + exit 1 + ;; +esac +else + +# Here we handle the default operating systems that come with various machines. +# The value should be what the vendor currently ships out the door with their +# machine or put another way, the most popular os provided with the machine. + +# Note that if you're going to try to match "-MANUFACTURER" here (say, +# "-sun"), then you have to tell the case statement up towards the top +# that MANUFACTURER isn't an operating system. Otherwise, code above +# will signal an error saying that MANUFACTURER isn't an operating +# system, and we'll never get to this point. + +case $basic_machine in + score-*) + os=-elf + ;; + spu-*) + os=-elf + ;; + *-acorn) + os=-riscix1.2 + ;; + arm*-rebel) + os=-linux + ;; + arm*-semi) + os=-aout + ;; + c4x-* | tic4x-*) + os=-coff + ;; + # This must come before the *-dec entry. + pdp10-*) + os=-tops20 + ;; + pdp11-*) + os=-none + ;; + *-dec | vax-*) + os=-ultrix4.2 + ;; + m68*-apollo) + os=-domain + ;; + i386-sun) + os=-sunos4.0.2 + ;; + m68000-sun) + os=-sunos3 + # This also exists in the configure program, but was not the + # default. + # os=-sunos4 + ;; + m68*-cisco) + os=-aout + ;; + mep-*) + os=-elf + ;; + mips*-cisco) + os=-elf + ;; + mips*-*) + os=-elf + ;; + or32-*) + os=-coff + ;; + *-tti) # must be before sparc entry or we get the wrong os. + os=-sysv3 + ;; + sparc-* | *-sun) + os=-sunos4.1.1 + ;; + *-be) + os=-beos + ;; + *-haiku) + os=-haiku + ;; + *-ibm) + os=-aix + ;; + *-knuth) + os=-mmixware + ;; + *-wec) + os=-proelf + ;; + *-winbond) + os=-proelf + ;; + *-oki) + os=-proelf + ;; + *-hp) + os=-hpux + ;; + *-hitachi) + os=-hiux + ;; + i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent) + os=-sysv + ;; + *-cbm) + os=-amigaos + ;; + *-dg) + os=-dgux + ;; + *-dolphin) + os=-sysv3 + ;; + m68k-ccur) + os=-rtu + ;; + m88k-omron*) + os=-luna + ;; + *-next ) + os=-nextstep + ;; + *-sequent) + os=-ptx + ;; + *-crds) + os=-unos + ;; + *-ns) + os=-genix + ;; + i370-*) + os=-mvs + ;; + *-next) + os=-nextstep3 + ;; + *-gould) + os=-sysv + ;; + *-highlevel) + os=-bsd + ;; + *-encore) + os=-bsd + ;; + *-sgi) + os=-irix + ;; + *-siemens) + os=-sysv4 + ;; + *-masscomp) + os=-rtu + ;; + f30[01]-fujitsu | f700-fujitsu) + os=-uxpv + ;; + *-rom68k) + os=-coff + ;; + *-*bug) + os=-coff + ;; + *-apple) + os=-macos + ;; + *-atari*) + os=-mint + ;; + *) + os=-none + ;; +esac +fi + +# Here we handle the case where we know the os, and the CPU type, but not the +# manufacturer. We pick the logical manufacturer. +vendor=unknown +case $basic_machine in + *-unknown) + case $os in + -riscix*) + vendor=acorn + ;; + -sunos*) + vendor=sun + ;; + -aix*) + vendor=ibm + ;; + -beos*) + vendor=be + ;; + -hpux*) + vendor=hp + ;; + -mpeix*) + vendor=hp + ;; + -hiux*) + vendor=hitachi + ;; + -unos*) + vendor=crds + ;; + -dgux*) + vendor=dg + ;; + -luna*) + vendor=omron + ;; + -genix*) + vendor=ns + ;; + -mvs* | -opened*) + vendor=ibm + ;; + -os400*) + vendor=ibm + ;; + -ptx*) + vendor=sequent + ;; + -tpf*) + vendor=ibm + ;; + -vxsim* | -vxworks* | -windiss*) + vendor=wrs + ;; + -aux*) + vendor=apple + ;; + -hms*) + vendor=hitachi + ;; + -mpw* | -macos*) + vendor=apple + ;; + -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*) + vendor=atari + ;; + -vos*) + vendor=stratus + ;; + esac + basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"` + ;; +esac + +echo $basic_machine$os +exit + +# Local variables: +# eval: (add-hook 'write-file-hooks 'time-stamp) +# time-stamp-start: "timestamp='" +# time-stamp-format: "%:y-%02m-%02d" +# time-stamp-end: "'" +# End: Index: /issm/trunk-jpl-damage/configs/config-altix64-castor.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-altix64-castor.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-altix64-castor.sh (revision 11330) @@ -0,0 +1,3 @@ +#!/bin/csh + +./configure --prefix=$ISSM_TIER --with-serial=no --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-mpi-include=/usr/include --with-mpi-lib="-L/usr/lib -lmpi" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install --with-mkl-dir=/opt/intel/mkl/9.1.023/lib/64 --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH --with-graphics-lib=/usr/X11R6/lib/libX11.so Index: /issm/trunk-jpl-damage/configs/config-cosmos.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-cosmos.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-cosmos.sh (revision 11330) @@ -0,0 +1,3 @@ +#!/bin/csh + +./configure --prefix=$ISSM_TIER --with-serial=no --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-mpi-include=/opt/mpich/gm/intel10.1/include --with-mpi-lib="-L/opt/mpich/gm/intel10.1/lib -lmpich -L/usr/local/gm/lib/ -lgm -lpthread -lrt" --with-petsc-arch=$ISSM_ARCH --with-mkl-dir=/opt/intel/mkl/10.0.5.025/lib/32/ --with-plapack-dir="-L$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH --with-vendor=intel-linux --with-graphics-lib=/usr/X11R6/lib/libX11.so Index: /issm/trunk-jpl-damage/configs/config-linux64-astrid-ad.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-linux64-astrid-ad.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-linux64-astrid-ad.sh (revision 11330) @@ -0,0 +1,36 @@ +#!/bin/sh + +./configure \ + --prefix=$ISSM_TIER \ + --with-serial=no\ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-march=opteron -O2" \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ + --with-rose-dir=$ISSM_TIER/externalpackages/rose/install/ \ + --with-adic2-dir=$ISSM_TIER/externalpackages/adic/install/ \ + --with-numthreads=24 \ + --without-thermal \ + --without-control \ + --without-hydrology \ + --without-diagnostic \ + --without-balanced \ + --without-responses \ + --without-slope \ + --without-rifts \ + --without-steadystate \ + --without-transient \ + --without-3d \ + --without-groundingline + +#--without-prognostic \ Index: /issm/trunk-jpl-damage/configs/config-linux64-astrid-mpich1.4.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-linux64-astrid-mpich1.4.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-linux64-astrid-mpich1.4.sh (revision 11330) @@ -0,0 +1,31 @@ +#!/bin/sh + +#External packages versions: +#petsc 3.1 or 3.2 +#mpich 1.4 + +./configure \ + --prefix=$ISSM_TIER \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_TIER/externalpackages/tao/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich -lmpl " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ + --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ + --with-shapelib-dir="$ISSM_TIER/externalpackages/shapelib/install" \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-march=opteron -O2" \ + --with-numthreads=32 \ + --enable-debugging Index: /issm/trunk-jpl-damage/configs/config-linux64-astrid-petsc2.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-linux64-astrid-petsc2.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-linux64-astrid-petsc2.sh (revision 11330) @@ -0,0 +1,7 @@ +#!/bin/sh + +#External packages versions: +#petsc 2.6 +#mpich 1.0.2 + +./configure --prefix=$ISSM_TIER --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3/$ISSM_ARCH --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" --with-graphics-lib=/usr/lib64/libX11.so --with-cxxoptflags="-march=opteron -O2" --with-numthreads=32 --with-scotch-dir=$ISSM_TIER/externalpackages/scotch/install --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install --enable-debugging --with-shapelib-dir=$ISSM_TIER/externalpackages/shapelib/install\ Index: /issm/trunk-jpl-damage/configs/config-linux64-astrid.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-linux64-astrid.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-linux64-astrid.sh (revision 11330) @@ -0,0 +1,31 @@ +#!/bin/sh + +#External packages versions: +#petsc 3.1 or 3.2 +#mpich 1.0.2 + +./configure \ + --prefix=$ISSM_TIER \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-tao-dir=$ISSM_TIER/externalpackages/tao/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ + --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ + --with-shapelib-dir="$ISSM_TIER/externalpackages/shapelib/install" \ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-march=opteron -O2" \ + --with-numthreads=32 \ + --enable-debugging Index: /issm/trunk-jpl-damage/configs/config-linux64-murdo-ad.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-linux64-murdo-ad.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-linux64-murdo-ad.sh (revision 11330) @@ -0,0 +1,37 @@ +#!/bin/sh + +./configure \ + --prefix=$ISSM_TIER \ + --with-serial=no\ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-hypre-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-ml-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ + --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -lg2c /usr/lib/gcc/x86_64-redhat-linux/4.1.1/libgfortran.a" \ + --with-adic2-dir=$ISSM_TIER/externalpackages/adic/install/ \ +--with-numthreads=24 \ + --without-thermal \ + --without-control \ + --without-hydrology \ + --without-diagnostic \ + --without-balanced \ + --without-responses \ + --without-slope \ + --without-rifts \ + --without-steadystate \ + --without-transient \ + --without-3d \ + --without-groundingline + +#--without-prognostic \ Index: /issm/trunk-jpl-damage/configs/config-linux64-murdo.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-linux64-murdo.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-linux64-murdo.sh (revision 11330) @@ -0,0 +1,28 @@ +#!/bin/sh + +./configure \ + --prefix=$ISSM_TIER \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ + --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ + --with-numthreads=18 \ + --with-ml-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-hypre-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --enable-debugging + + #--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + Index: /issm/trunk-jpl-damage/configs/config-macosx32-mathieu.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-macosx32-mathieu.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-macosx32-mathieu.sh (revision 11330) @@ -0,0 +1,31 @@ +#!/bin/sh + +#petsc 3.1 or 3.2 +#mpich 1.4 + +export FCFLAGS=" -m32" +export FFLAGS=" -m32" +export CFLAGS=" -arch i386" +export CXXFLAGS=" -arch i386" + +./configure \ + --prefix=$ISSM_TIER \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-fortran-lib="/usr/local/lib/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -DMATLAB_MEX_FILE -fno-common -no-cpp-precomp -fexceptions -arch i386 -DMX_COMPAT_32 -O3 -DNDEBUG -w " \ + --with-numthreads=8 Index: /issm/trunk-jpl-damage/configs/config-macosx32-ogive.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-macosx32-ogive.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-macosx32-ogive.sh (revision 11330) @@ -0,0 +1,26 @@ +#!/bin/sh + +#petsc 3.1 or 3.2 +#mpich 1.4 + +./configure \ + --prefix=$ISSM_TIER \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch i386 -g -O3 -DNDEBUG -DMX_COMPAT_32" \ + --with-numthreads=8 Index: /issm/trunk-jpl-damage/configs/config-macosx64-mathieu.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-macosx64-mathieu.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-macosx64-mathieu.sh (revision 11330) @@ -0,0 +1,26 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 + +./configure \ + --prefix=$ISSM_TIER \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-fortran-lib="/usr/local/lib/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-numthreads=8 Index: /issm/trunk-jpl-damage/configs/config-macosx64-ogive.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-macosx64-ogive.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-macosx64-ogive.sh (revision 11330) @@ -0,0 +1,31 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 +export FCFLAGS=" -m64" +export FFLAGS=" -m64" +export CFLAGS=" -arch x86_64" +export CXXFLAGS=" -arch x86_64" + +./configure \ + --prefix=$ISSM_TIER \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-fortran-lib="/usr/local/gfortran/lib/x86_64/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-numthreads=8 + #--with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ Index: /issm/trunk-jpl-damage/configs/config-macosx64-sophie.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-macosx64-sophie.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-macosx64-sophie.sh (revision 11330) @@ -0,0 +1,30 @@ +#!/bin/sh + +#petsc 3.2 +#mpich 1.4 +export FCFLAGS=" -m64" +export FFLAGS=" -m64" +export CFLAGS=" -arch x86_64" +export CXXFLAGS=" -arch x86_64" + +./configure \ + --prefix=$ISSM_TIER \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-fortran-lib="/sw/usr/local/lib/x86_64/libgfortran.a" \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -Wno-write-strings -no-cpp-precomp -fexceptions -arch x86_64 -O3 -DNDEBUG -w "\ + --with-numthreads=8 Index: /issm/trunk-jpl-damage/configs/config-pleiades-petsc2.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-pleiades-petsc2.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-pleiades-petsc2.sh (revision 11330) @@ -0,0 +1,21 @@ +#!/bin/csh + +./configure \ + --prefix=$ISSM_TIER \ + --with-serial=no \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=/nasa/sgi/mpt/1.25/include \ + --with-mpi-lib="-L/nasa/sgi/mpt/1.25/lib/ -lmpi -lpthread -lgfortran" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-mkl-dir=/nasa/intel/mkl/10.0.011/lib/64/ \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3 -xS" \ + --with-vendor=intel-pleiades Index: /issm/trunk-jpl-damage/configs/config-pleiades.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-pleiades.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-pleiades.sh (revision 11330) @@ -0,0 +1,21 @@ +#!/bin/csh + +./configure \ + --prefix=$ISSM_TIER \ + --with-serial=no \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ + --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=/nasa/sgi/mpt/1.25/include \ + --with-mpi-lib="-L/nasa/sgi/mpt/1.25/lib/ -lmpi -lpthread -lgfortran" \ + --with-petsc-arch=$ISSM_ARCH \ + --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-mkl-dir=/nasa/intel/mkl/10.0.011/lib/64/ \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-graphics-lib=/usr/lib64/libX11.so \ + --with-cxxoptflags="-O3 -xS" \ + --with-vendor=intel-pleiades Index: /issm/trunk-jpl-damage/configs/config-win32-eric.sh =================================================================== --- /issm/trunk-jpl-damage/configs/config-win32-eric.sh (revision 11330) +++ /issm/trunk-jpl-damage/configs/config-win32-eric.sh (revision 11330) @@ -0,0 +1,6 @@ +#!/bin/sh + + +#get configure.sh to pick up the intel compiler + +./configure --prefix=$ISSM_TIER --with-parallel=no --with-vendor=intel-win --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-petsc-arch=$ISSM_ARCH --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/f2cblaslapack/$ISSM_ARCH Index: /issm/trunk-jpl-damage/configure.ac =================================================================== --- /issm/trunk-jpl-damage/configure.ac (revision 11330) +++ /issm/trunk-jpl-damage/configure.ac (revision 11330) @@ -0,0 +1,23 @@ +AC_INIT(ISSM,4.0,issm@jpl.nasa.gov) +AM_CONFIG_HEADER(config.h) +#AC_PROG_LIBTOOL +#LT_INIT +AC_CANONICAL_TARGET +AM_INIT_AUTOMAKE +AC_PROG_RANLIB +AC_PROG_CC([gcc icl]) +AC_PROG_CPP +AC_PROG_CXX([g++ icl]) +AC_PROG_F77([ifort g77 gfortran]) +AC_F77_LIBRARY_LDFLAGS +AM_PROG_CC_C_O +AC_PATH_XTRA +ISSM_OPTIONS +AC_CONFIG_FILES([Makefile + src/Makefile + src/c/Makefile + src/ad/Makefile + src/mex/Makefile + bin/Makefile]) +AC_OUTPUT + Index: /issm/trunk-jpl-damage/cron/README =================================================================== --- /issm/trunk-jpl-damage/cron/README (revision 11330) +++ /issm/trunk-jpl-damage/cron/README (revision 11330) @@ -0,0 +1,16 @@ +The Cron directory holds scripts that can be used to run +jobs periodically on *nix systems. + +Just add an entry in the cron table to run the ice.sh script, +and all the scripts in this directory will be taken care of. + +For example, if you add: + +5 5 * * * cd $ISSM_TIER/cron && ./nightlyrun.sh + +This will run all the scripts in the Cron directory, every day, at 5:05 am. + + + +If users want to add their own scripts, just add the script to the cron directory and +add an entry in the issm.sh for this script. Index: /issm/trunk-jpl-damage/cron/configs/linux64_larour =================================================================== --- /issm/trunk-jpl-damage/cron/configs/linux64_larour (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/linux64_larour (revision 11330) @@ -0,0 +1,93 @@ +# +########### Configuration file for Eric Larour's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full paths) +ISSM_DIR="/u/astrid-r1b/larour/issm/" +ISSM_TIER="/u/astrid-r1b/larour/issm/trunk-jpl/cron/trunk-jpl" +#ISSM_TIER="/u/wilkes-r1b/morlighe/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="update" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/larour/issm/execution" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="none" +EXTERNALPACKAGESDIR="/u/astrid-r1b/larour/issm/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="no" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="eric.larour@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=8 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=8 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" Index: /issm/trunk-jpl-damage/cron/configs/linux64_morlighem_daily =================================================================== --- /issm/trunk-jpl-damage/cron/configs/linux64_morlighem_daily (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/linux64_morlighem_daily (revision 11330) @@ -0,0 +1,93 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full paths) +ISSM_DIR="/u/astrid-r1b/morlighe/svn/issm" +ISSM_TIER="/u/astrid-r1b/morlighe/svn/issm/trunk-jpl/cron/trunk-jpl" +#ISSM_TIER="/u/astrid-r1b/morlighe/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="update" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/morlighe/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="none" +EXTERNALPACKAGESDIR="/u/astrid-r1b/morlighe/issm/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="automake autoconf matlab mpich2 petsc metis triangle dakota chaco" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="mathieu.morlighem@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=8 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" Index: /issm/trunk-jpl-damage/cron/configs/linux64_morlighem_nightly =================================================================== --- /issm/trunk-jpl-damage/cron/configs/linux64_morlighem_nightly (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/linux64_morlighem_nightly (revision 11330) @@ -0,0 +1,93 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/u/astrid-r1b/morlighe/issm" +ISSM_TIER="/u/astrid-r1b/morlighe/issm/trunk-jpl/cron/trunk-jpl" +#ISSM_TIER="/u/astrid-r1b/morlighe/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="checkout" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/morlighe/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="install" +EXTERNALPACKAGESDIR="/u/astrid-r1b/morlighe/issm/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="mathieu.morlighem@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" Index: /issm/trunk-jpl-damage/cron/configs/linux64_morlighem_validation =================================================================== --- /issm/trunk-jpl-damage/cron/configs/linux64_morlighem_validation (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/linux64_morlighem_validation (revision 11330) @@ -0,0 +1,92 @@ +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/u/astrid-r1b/morlighe/issm" +ISSM_TIER="/u/astrid-r1b/morlighe/issm/trunk-jpl/cron/trunk-jpl" +#ISSM_TIER="/u/astrid-r1b/morlighe/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="checkout" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/morlighe/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="install" +EXTERNALPACKAGESDIR="/u/astrid-r1b/morlighe/issm/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco yams" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="mathieu.morlighem@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="'benchmark','all'" Index: /issm/trunk-jpl-damage/cron/configs/linux64_schlegel_daily =================================================================== --- /issm/trunk-jpl-damage/cron/configs/linux64_schlegel_daily (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/linux64_schlegel_daily (revision 11330) @@ -0,0 +1,93 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full paths) +ISSM_DIR="/u/astrid-r1b/schlegel/issmuci" +ISSM_TIER="/u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/trunk-jpl" +#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="update" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/schlegel/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="none" +EXTERNALPACKAGESDIR="/u/astrid-r1b/schlegel/issmuci/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="schlegel@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=8 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" Index: /issm/trunk-jpl-damage/cron/configs/linux64_schlegel_nightly =================================================================== --- /issm/trunk-jpl-damage/cron/configs/linux64_schlegel_nightly (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/linux64_schlegel_nightly (revision 11330) @@ -0,0 +1,93 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/u/astrid-r1b/schlegel/issmuci" +ISSM_TIER="/u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/trunk-jpl" +#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="checkout" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/schlegel/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="install" +EXTERNALPACKAGESDIR="/u/astrid-r1b/schlegel/issmuci/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="schlegel@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" Index: /issm/trunk-jpl-damage/cron/configs/linux64_schlegel_ucitrunk =================================================================== --- /issm/trunk-jpl-damage/cron/configs/linux64_schlegel_ucitrunk (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/linux64_schlegel_ucitrunk (revision 11330) @@ -0,0 +1,93 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/u/astrid-r1b/schlegel/issmuci" +ISSM_TIER="/u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/trunk" +#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="checkout" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/schlegel/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="install" +EXTERNALPACKAGESDIR="/u/astrid-r1b/schlegel/issmuci/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="schlegel@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" Index: /issm/trunk-jpl-damage/cron/configs/linux64_schlegel_validation =================================================================== --- /issm/trunk-jpl-damage/cron/configs/linux64_schlegel_validation (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/linux64_schlegel_validation (revision 11330) @@ -0,0 +1,92 @@ +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/u/astrid-r1b/schlegel/issmuci" +ISSM_TIER="/u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/trunk-jpl" +#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="checkout" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/schlegel/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="install" +EXTERNALPACKAGESDIR="/u/astrid-r1b/schlegel/issmuci/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco yams" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="schlegel@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="'benchmark','all'" Index: /issm/trunk-jpl-damage/cron/configs/linux64_seroussi =================================================================== --- /issm/trunk-jpl-damage/cron/configs/linux64_seroussi (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/linux64_seroussi (revision 11330) @@ -0,0 +1,92 @@ +# +########### Configuration file for Helene Seroussi's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/u/wilkes-r1b/seroussi/issm" +ISSM_TIER="/u/wilkes-r1b/seroussi/issm/trunk-jpl/cron/trunk-jpl" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="update" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/wilkes-r1b/seroussi/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="none" +EXTERNALPACKAGESDIR="/u/wilkes-r1b/seroussi/issm/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="helene.seroussi@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=8 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" Index: /issm/trunk-jpl-damage/cron/configs/linux64_seroussi_daily =================================================================== --- /issm/trunk-jpl-damage/cron/configs/linux64_seroussi_daily (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/linux64_seroussi_daily (revision 11330) @@ -0,0 +1,93 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full paths) +ISSM_DIR="/u/astrid-r1b/seroussi/issm" +ISSM_TIER="/u/astrid-r1b/seroussi/issm/trunk-jpl/cron/trunk-jpl" +#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="update" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/seroussi/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="none" +EXTERNALPACKAGESDIR="/u/astrid-r1b/seroussi/issm/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="helene.seroussi@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=8 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" Index: /issm/trunk-jpl-damage/cron/configs/linux64_seroussi_nightly =================================================================== --- /issm/trunk-jpl-damage/cron/configs/linux64_seroussi_nightly (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/linux64_seroussi_nightly (revision 11330) @@ -0,0 +1,93 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/u/astrid-r1b/seroussi/issm" +ISSM_TIER="/u/astrid-r1b/seroussi/issm/trunk-jpl/cron/trunk-jpl" +#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="checkout" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/seroussi/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="install" +EXTERNALPACKAGESDIR="/u/astrid-r1b/seroussi/issm/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="helene.seroussi@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" Index: /issm/trunk-jpl-damage/cron/configs/linux64_seroussi_ucitrunk =================================================================== --- /issm/trunk-jpl-damage/cron/configs/linux64_seroussi_ucitrunk (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/linux64_seroussi_ucitrunk (revision 11330) @@ -0,0 +1,93 @@ +# +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/u/astrid-r1b/seroussi/issm" +ISSM_TIER="/u/astrid-r1b/seroussi/issm/trunk-jpl/cron/trunk" +#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="checkout" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/seroussi/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="install" +EXTERNALPACKAGESDIR="/u/astrid-r1b/seroussi/issm/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="helene.seroussi@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" Index: /issm/trunk-jpl-damage/cron/configs/linux64_seroussi_validation =================================================================== --- /issm/trunk-jpl-damage/cron/configs/linux64_seroussi_validation (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/linux64_seroussi_validation (revision 11330) @@ -0,0 +1,92 @@ +########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/u/astrid-r1b/seroussi/issm" +ISSM_TIER="/u/astrid-r1b/seroussi/issm/trunk-jpl/cron/trunk-jpl" +#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" + +#ISSM Architecture +ISSM_ARCH="linux-gnu-amd64" + +#Machine configuration +MACHINE="astrid" + +#MATLAB path +MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="checkout" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/seroussi/ExecutionNightlyRun" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="install" +EXTERNALPACKAGESDIR="/u/astrid-r1b/seroussi/issm/trunk-jpl/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco yams" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="helene.seroussi@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=7 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="'benchmark','all'" Index: /issm/trunk-jpl-damage/cron/configs/macosx32_seroussi =================================================================== --- /issm/trunk-jpl-damage/cron/configs/macosx32_seroussi (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/macosx32_seroussi (revision 11330) @@ -0,0 +1,92 @@ +# +########### Configuration file for Helene Seroussi's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="/Users/seroussi/Desktop/issmuci" +ISSM_TIER="/Users/seroussi/Desktop/issmuci/trunk-jpl/cron/trunk-jpl" + +#ISSM Architecture +ISSM_ARCH="macosx-gnu" + +#Machine configuration +MACHINE="macmathieu" + +#MATLAB path +MATLAB_PATH="/Applications/MATLAB_R2009a.app/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="update" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="none" +EXTERNALPACKAGESDIR="" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="helene.seroussi@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=1 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" Index: /issm/trunk-jpl-damage/cron/configs/macosx64_larour =================================================================== --- /issm/trunk-jpl-damage/cron/configs/macosx64_larour (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/macosx64_larour (revision 11330) @@ -0,0 +1,91 @@ +# +########### Configuration file for Eric Larour's nightly run on Mac ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full pathto ISSM trunk) +ISSM_DIR="/Users/larour/issm/trunk" + +#ISSM Architecture +ISSM_ARCH="macosx-gnu" + +#Operating System +OS="macosx64" + +#MATLAB path +MATLAB_PATH="/Applications/MATLAB_R2008a/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="update" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="copy" +EXTERNALPACKAGESDIR="" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="yes" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_DIR/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="eric.larour@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=1 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" Index: /issm/trunk-jpl-damage/cron/configs/winxp32_larour =================================================================== --- /issm/trunk-jpl-damage/cron/configs/winxp32_larour (revision 11330) +++ /issm/trunk-jpl-damage/cron/configs/winxp32_larour (revision 11330) @@ -0,0 +1,92 @@ +# +########### Configuration file for Eric Larour's nightly run on Linux ############ + +#-------------------------------# +# 1: ISSM general configuration # +#-------------------------------# + +#ISSM main directory (full path) +ISSM_DIR="C:/home/issm/trunk-jpl" +ISSM_TIER="C:/home/issm/trunk-jpl/cron/trunk-jpl" + +#ISSM Architecture +ISSM_ARCH="cygwin-intel" + +#Machine configuration +MACHINE="wineric" + +#MATLAB path +MATLAB_PATH="C:/MATLAB/R2009a/" + +#----------------------# +# 2: ISSM Installation # +#----------------------# + +#ISSM_INSTALLATION can have 3 values: +# - "checkout" the existing version of the code will be erased and +# the latest version will be checked out +# - "update" the directory won't be erased but ISSM will be updated +# ->skip to section 3 +# - "none" leave ISSM as is in its directory +# ->skip to section 3 +ISSM_INSTALLATION="update" + +#SVN repository +REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + +#execution path used for parallel runs +EXECUTION_PATH="/u/astrid-r1b/larour/issm/execution" + +#-----------------------------------# +# 3: External packages installation # +#-----------------------------------# + +#ISSM_EXTERNALPACKAGES can have 3 values: +# - "install" install all external packages listed below +# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +# - "none" leave external packages as is +# ->skip to section 4 +ISSM_EXTERNALPACKAGES="none" +EXTERNALPACKAGESDIR="/cygdrive/c/home/externalpackages" + +#List of external pakages to be installed +EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + +#---------------------# +# 4: ISSM Compilation # +#---------------------# + +#ISSM_COMPILATION can have 2 values: +# - "yes" compile ISSM +# - "no" do not compile ISSM +ISSM_COMPILATION="no" + +#----------------------# +# 5: Mail notification # +#----------------------# + +#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +SKIPMAIL="no" + +#Sender email address +EMAIL_ADRESS="eric.larour@jpl.nasa.gov" + +#------------------------# +# 6: Nightly run options # +#------------------------# + +#number of cpus used in ISSM installation and compilation (one is usually +#safer as some packages are very sensitive to parallel compilation) +NUMCPUS_INSTALL=1 + +#number of cpus used in the nightly runs. +NUMCPUS_RUN=1 + +#Nightly run options. The matlab routine nightlyrun.m will be called +#as follows: nightlyrun($NROPTIONS). The options must be understandable +#by Matlab and nightlyrun.m +#ex: "'id',[101 102 103]" + +NROPTIONS="" Index: /issm/trunk-jpl-damage/cron/cronfiles/linux_cronfile =================================================================== --- /issm/trunk-jpl-damage/cron/cronfiles/linux_cronfile (revision 11330) +++ /issm/trunk-jpl-damage/cron/cronfiles/linux_cronfile (revision 11330) @@ -0,0 +1,14 @@ +#use /bin/bash to run commands, overriding the default set by cron +SHELL=/bin/bash + +#mail output to Mathieu +MAILTO=eric.larour@jpl.nasa.gov,mathieu.morlighem@jpl.nasa.gov,helene.seroussi@jpl.nasa.gov,Christopher.P.Borstad@jpl.nasa.gov,Nicole-Jeanne.Schlegel@jpl.nasa.gov,Feras.A.Habbal@jpl.nasa.gov + +#cronjob +00 09 * * 1-5 cd /u/astrid-r1b/seroussi/issm/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_seroussi_daily +30 12 * * 1-5 cd /u/astrid-r1b/seroussi/issm/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_seroussi_daily +00 15 * * 1-5 cd /u/astrid-r1b/seroussi/issm/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_seroussi_daily +00 18 * * 1-5 cd /u/astrid-r1b/seroussi/issm/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_seroussi_daily +00 23 * * 1-5 cd /u/astrid-r1b/seroussi/issm/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_seroussi_nightly +00 23 * * 6 cd /u/astrid-r1b/seroussi/issm/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_seroussi_validation +00 23 * * 7 cd /u/astrid-r1b/seroussi/issm/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_seroussi_ucitrunk Index: /issm/trunk-jpl-damage/cron/cronfiles/mac_cronfile =================================================================== --- /issm/trunk-jpl-damage/cron/cronfiles/mac_cronfile (revision 11330) +++ /issm/trunk-jpl-damage/cron/cronfiles/mac_cronfile (revision 11330) @@ -0,0 +1,8 @@ +#use /bin/bash to run commands, overriding the default set by cron +SHELL=/bin/bash + +#mail output to Helene +MAILTO=eric.larour@jpl.nasa.gov,mathieu.morlighem@jpl.nasa.gov,helene.seroussi@jpl.nasa.gov + +#cronjob: issm 9:00pm +50 9 * * * cd /Users/seroussi/Desktop/backup/svn/issm/trunk/cron/ && ./nightlyrun.sh configs/macosx32_seroussi Index: /issm/trunk-jpl-damage/cron/cronfiles/winxp32_cronfile =================================================================== --- /issm/trunk-jpl-damage/cron/cronfiles/winxp32_cronfile (revision 11330) +++ /issm/trunk-jpl-damage/cron/cronfiles/winxp32_cronfile (revision 11330) @@ -0,0 +1,8 @@ +#use /bin/bash to run commands, overriding the default set by cron +SHELL=/bin/bash + +#mail output to Eric +MAILTO=eric.larour@jpl.nasa.gov,mathieu.morlighem@jpl.nasa.gov,helene.seroussi@jpl.nasa.gov + +#cronjob: issm sunday-friday 9:00pm +0 21 * * 0-5 cd /cygdrive/c/home/issm/trunk/cron && ./nightlyrun.sh configs/winxp32_larour Index: /issm/trunk-jpl-damage/cron/mailinglist =================================================================== --- /issm/trunk-jpl-damage/cron/mailinglist (revision 11330) +++ /issm/trunk-jpl-damage/cron/mailinglist (revision 11330) @@ -0,0 +1,2 @@ +#Mailing list for nightly runs +MAILINGLIST="mathieu.morlighem@jpl.nasa.gov helene.seroussi@jpl.nasa.gov eric.larour@jpl.nasa.gov John.E.Schiermeier@jpl.nasa.gov Nicole-Jeanne.Schlegel@jpl.nasa.gov christopher.p.borstad@jpl.nasa.gov Feras.A.Habbal@jpl.nasa.gov Daria.J.Halkides@jpl.nasa.gov" Index: /issm/trunk-jpl-damage/cron/nightlyrun.sh =================================================================== --- /issm/trunk-jpl-damage/cron/nightlyrun.sh (revision 11330) +++ /issm/trunk-jpl-damage/cron/nightlyrun.sh (revision 11330) @@ -0,0 +1,317 @@ +#!/bin/bash +#This bash script calls the nightlyrun.m matlab file to run our nightly test decks. +#It then processes the results and sends an email to the Ice developpers. + +#some functions +function timer() #{{{1 +{ + if [[ $# -eq 0 ]]; then + echo $(date '+%s') + else + local stime=$1 + etime=$(date '+%s') + + if [[ -z "$stime" ]]; then stime=$etime; fi + + dt=$((etime - stime)) + ds=$((dt % 60)) + dm=$(((dt / 60) % 60)) + dh=$((dt / 3600)) + printf '%d:%02d:%02d' $dh $dm $ds + fi +} #}}} +function todaydate() #{{{1 +{ + suffix=`date | awk '{printf("%s-%s-%s %s",$2,$3,$6,$4);}'` + echo $suffix; +} #}}} +function host_name() #{{{1 +{ + #return host name depending on the OS + if [ "$1" = "wineric" ] + then + HOST_NAME=`hostname`; + else + HOST_NAME=`hostname -s`; + fi + echo $HOST_NAME; +} #}}} + +#Get configuration +#Source config file{{{1 +if [ $# -ne 1 ]; +then + #no config file specified: exit + echo "no config file specified. Exiting..." >&2 # Error message to stderr. + exit 1 +fi +if [ ! -f "$1" ] +then + echo "File $1 not found!" >&2 # Error message to stderr. + exit 1 +fi +source $1; +#}}} +#Export ISSM_* variables{{{1 +export ISSM_DIR +export ISSM_TIER +export ISSM_ARCH +#}}} +#Initialize variables {{{1 +TODAY=$(todaydate); +HOST_NAME=$(host_name $MACHINE); +START_TIME=$(timer); +ISSM_RELEASE=$(basename $(echo $REPOSITORY)); +USER=$(whoami); +INIT_PATH=$(pwd); +#}}} + +#Lauch installation +#Checkout/update/none ISSM if requested (ISSM_INSTALLATION){{{1 +if [ "$ISSM_INSTALLATION" == "checkout" ] +then + + #Erase previous code and Fetch the new one + rm -rf $ISSM_RELEASE + svn checkout $REPOSITORY + +elif [ "$ISSM_INSTALLATION" == "update" ] +then + + #only update ISSM + cd $ISSM_TIER + svn update + +elif [ "$ISSM_INSTALLATION" == "none" ] +then + + #do nothing + echo "Skipping ISSM installation" + +else + + #Error message + echo "ISSM_INSTALLATION supported values are: checkout, update and none. Exiting..." >&2 # Error message to stderr. + exit 1 + +fi +#}}} +#Create cluster's settings{{{1 +#create simpler cluster.rc file, with only the cluster we are interested in. +cd $ISSM_TIER/test/NightlyRun/ +cat << END > $HOST_NAME"_settings.m" +cluster.login='$USER'; +cluster.codepath='$ISSM_TIER/bin'; +cluster.executionpath='$EXECUTION_PATH'; +END +#}}} +#Source environment variables with new matlab path {{{1 +cd $ISSM_TIER/etc +source environment.sh MATLAB_DIR=$MATLAB_PATH +#}}} +#install/copy/none external packages (ISSM_EXTERNALPACKAGES){{{1 +if [ "$ISSM_EXTERNALPACKAGES" == "install" ] +then + cd $ISSM_TIER/externalpackages + for ep in $EXTERNALPACKAGES + do + cd $ep + case $ep in + "mpich2" ) ./install-1.0.2-linux64.sh ;; + "petsc" ) ./install-3.2-linux64.sh ;; + "metis" ) ./install-4.0-linux64.sh ;; + "triangle" ) ./install-linux64.sh ;; + "dakota" ) ./install-linux64-astrid.sh ;; + *) ./install.sh $NUMCPUS_INSTALL + esac + cd .. + done + +elif [ "$ISSM_EXTERNALPACKAGES" == "copy" ] +then + + #erase externapackages, and link with externalpackages_dir + cd $ISSM_TIER + rm -rf externalpackages + cp -Rf $EXTERNALPACKAGESDIR ./ + +elif [ "$ISSM_EXTERNALPACKAGES" == "none" ] +then + + #Do nothing + echo "Skipping external packages installation" + +else + + #Error message + echo "ISSM_EXTERNALPACKAGES supported values are: install, copy and none. Exiting..." >&2 # Error message to stderr. + exit 1 + +fi +#}}} +#ISSM compilation yes/no (ISSM_COMPILATION) {{{1 +if [ "$ISSM_COMPILATION" == "yes" ] +then + + cd $ISSM_TIER + make clean + make distclean + ./scripts/automakererun.sh + ./configs/config-linux64-astrid.sh + + #4: compile and install ISSM + if [ "$MACHINE" = "wineric" ] + then + cd $ISSM_TIER/src/c + ./intel-compile.sh + cd $ISSM_TIER/src/mex + make install + cd $ISSM_TIER + else + make -j $NUMCPUS_INSTALL + make -j $NUMCPUS_INSTALL install + fi + +elif [ "$ISSM_COMPILATION" == "no" ] +then + echo "Skipping ISSM compilation" +else + echo "ISSM_COMPILATION supported values are: yes and no. Exiting..." >&2 # Error message to stderr. + exit 1 +fi +#}}} + +#Prepare run +#create softlink to startup {{{1 +cd $ISSM_TIER/test/NightlyRun/ +ln -s $ISSM_TIER/startup.m . +#}}} +#Create nightlylog directory and info.log {{{1 +#put installation elapsed time in info.log +INSTALL_TIME=$(timer) +ELAPSED_INSTALL=$(timer $START_TIME) +rm -rf $ISSM_TIER/nightlylog +mkdir $ISSM_TIER/nightlylog +cat << END > $ISSM_TIER/nightlylog/info.log +today: $(echo $TODAY) +user: $(echo $USER) +host: $(echo $HOST_NAME) +OS: $(echo $MACHINE) +release: $(echo $ISSM_RELEASE) +init_path: $(echo $INIT_PATH) +elapsed_install: $(echo $ELAPSED_INSTALL) +END +#}}} +#check NUMCPUS_RUN options {{{1 +if [ "$NUMCPUS_RUN" = "" ] +then + echo "NUMCPUS_RUN option not found, defaulting to NUMCPUS_RUN = 1" + NUMCPUS_RUN=1 +fi +#}}} + +#Run tests +#Launch all tests on different cpus {{{1 +for (( i=1;i<=$NUMCPUS_RUN;i++ )) +do + #Launch matlab and the nightly run script + cat > $ISSM_TIER/nightlylog/matlab_run$i.m << EOF + warning off %necessary to avoid a info.log of several Go for parallel runs + try, + cd $ISSM_TIER/test/NightlyRun + startup; + $(if [ "$NROPTIONS" = "" ] + then + echo "runme('output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);" + else + echo "runme($NROPTIONS,'output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);" + fi + ) + catch me, + %An error occured, get report and exit + message=getReport(me) + directory=strsplit(pwd,'/'); + fid=fopen([ISSM_TIER '/nightlylog/matlaberror.log'], 'at'); + fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end}); + fprintf(fid,'%s',message); + fclose(fid); + end + disp('MATLABEXITEDCORRECTLY'); + exit +EOF + + #Start run from nightlylog directory + cd $ISSM_TIER/nightlylog/ + + #Start test + MATLAB_VERSION="7.6" #7.2,7.4,7.6 and 7.8 + /usr/local/pkgs/matlab-$MATLAB_VERSION/bin/matlab -nojvm -nosplash -r matlab_run$i -logfile matlab_log$i.log & +done + +#wait until matlab closes +wait +#}}} +#concatenate all reports {{{1 +cd $ISSM_TIER/nightlylog/ +mv matlab_log1.log matlab_log.log +for (( i=2;i<=$NUMCPUS_RUN;i++ )) +do + cat matlab_log.log matlab_log$i.log > matlab_log.log.bak + mv matlab_log.log.bak matlab_log.log +done +#}}} +#Complete info.log {{{1 +if [ $(cat matlab_log.log | grep "MATLABEXITEDCORRECTLY" | wc -l) -eq $NUMCPUS_RUN ] +then + MATLABCRASH=0 +else + MATLABCRASH=1 +fi +ELAPSED_RUN=$(timer $INSTALL_TIME) +ELAPSED_TOTAL=$(timer $START_TIME) +cat << END >> $ISSM_TIER/nightlylog/info.log +elapsed_run: $(echo $ELAPSED_RUN) +elapsed_total: $(echo $ELAPSED_TOTAL) +matlab_crash: $(echo $MATLABCRASH) +END +#}}} + +#Send Report +#Build html report {{{1 +cd $ISSM_TIER/nightlylog/ +sh ../scripts/report.sh +echo "html report located in $ISSM_TIER/nightlylog/report.html" +#}}} +#send mail if requested (SKIPMAIL) {{{1 +if [ "$SKIPMAIL" != "yes" ] +then + echo "sending report..." + source $ISSM_TIER/cron/mailinglist + for i in `echo $MAILINGLIST`; do + + if [ "$MACHINE" = "wineric" ] + then + email -html -f "ISSM Nightly run $EMAIL_ADRESS" -s "Nightly runs of $ISSM_RELEASE , configuration: $MACHINE, host: $HOST_NAME, user: $USER. " $i < $ISSM_TIER/test/Verification/NightlyRun/report.html + else + if [ "$MACHINE" = "astrid" ] + then +cat - $ISSM_TIER/nightlylog/report.html < +To: $i +Subject: Nightly runs of $ISSM_RELEASE, configuration: $MACHINE, host: $HOST_NAME, user: $USER. +Mime-Version: 1.0 +Content-Type: text/html +HERE + else +cat - $ISSM_TIER/nightlylog/report.html < +To: $i +Subject: Nightly runs of $ISSM_RELEASE, configuration: $MACHINE, host: $HOST_NAME, user: $USER. +Mime-Version: 1.0 +Content-Type: text/html +HERE + fi + fi + done +fi +#}}} Index: /issm/trunk-jpl-damage/depcomp =================================================================== --- /issm/trunk-jpl-damage/depcomp (revision 11330) +++ /issm/trunk-jpl-damage/depcomp (revision 11330) @@ -0,0 +1,589 @@ +#! /bin/sh +# depcomp - compile a program generating dependencies as side-effects + +scriptversion=2007-03-29.01 + +# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007 Free Software +# Foundation, Inc. + +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2, or (at your option) +# any later version. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA +# 02110-1301, USA. + +# As a special exception to the GNU General Public License, if you +# distribute this file as part of a program that contains a +# configuration script generated by Autoconf, you may include it under +# the same distribution terms that you use for the rest of that program. + +# Originally written by Alexandre Oliva . + +case $1 in + '') + echo "$0: No command. Try \`$0 --help' for more information." 1>&2 + exit 1; + ;; + -h | --h*) + cat <<\EOF +Usage: depcomp [--help] [--version] PROGRAM [ARGS] + +Run PROGRAMS ARGS to compile a file, generating dependencies +as side-effects. + +Environment variables: + depmode Dependency tracking mode. + source Source file read by `PROGRAMS ARGS'. + object Object file output by `PROGRAMS ARGS'. + DEPDIR directory where to store dependencies. + depfile Dependency file to output. + tmpdepfile Temporary file to use when outputing dependencies. + libtool Whether libtool is used (yes/no). + +Report bugs to . +EOF + exit $? + ;; + -v | --v*) + echo "depcomp $scriptversion" + exit $? + ;; +esac + +if test -z "$depmode" || test -z "$source" || test -z "$object"; then + echo "depcomp: Variables source, object and depmode must be set" 1>&2 + exit 1 +fi + +# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po. +depfile=${depfile-`echo "$object" | + sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`} +tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`} + +rm -f "$tmpdepfile" + +# Some modes work just like other modes, but use different flags. We +# parameterize here, but still list the modes in the big case below, +# to make depend.m4 easier to write. Note that we *cannot* use a case +# here, because this file can only contain one case statement. +if test "$depmode" = hp; then + # HP compiler uses -M and no extra arg. + gccflag=-M + depmode=gcc +fi + +if test "$depmode" = dashXmstdout; then + # This is just like dashmstdout with a different argument. + dashmflag=-xM + depmode=dashmstdout +fi + +case "$depmode" in +gcc3) +## gcc 3 implements dependency tracking that does exactly what +## we want. Yay! Note: for some reason libtool 1.4 doesn't like +## it if -MD -MP comes after the -MF stuff. Hmm. +## Unfortunately, FreeBSD c89 acceptance of flags depends upon +## the command line argument order; so add the flags where they +## appear in depend2.am. Note that the slowdown incurred here +## affects only configure: in makefiles, %FASTDEP% shortcuts this. + for arg + do + case $arg in + -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;; + *) set fnord "$@" "$arg" ;; + esac + shift # fnord + shift # $arg + done + "$@" + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile" + exit $stat + fi + mv "$tmpdepfile" "$depfile" + ;; + +gcc) +## There are various ways to get dependency output from gcc. Here's +## why we pick this rather obscure method: +## - Don't want to use -MD because we'd like the dependencies to end +## up in a subdir. Having to rename by hand is ugly. +## (We might end up doing this anyway to support other compilers.) +## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like +## -MM, not -M (despite what the docs say). +## - Using -M directly means running the compiler twice (even worse +## than renaming). + if test -z "$gccflag"; then + gccflag=-MD, + fi + "$@" -Wp,"$gccflag$tmpdepfile" + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile" + exit $stat + fi + rm -f "$depfile" + echo "$object : \\" > "$depfile" + alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz +## The second -e expression handles DOS-style file names with drive letters. + sed -e 's/^[^:]*: / /' \ + -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile" +## This next piece of magic avoids the `deleted header file' problem. +## The problem is that when a header file which appears in a .P file +## is deleted, the dependency causes make to die (because there is +## typically no way to rebuild the header). We avoid this by adding +## dummy dependencies for each header file. Too bad gcc doesn't do +## this for us directly. + tr ' ' ' +' < "$tmpdepfile" | +## Some versions of gcc put a space before the `:'. On the theory +## that the space means something, we add a space to the output as +## well. +## Some versions of the HPUX 10.20 sed can't process this invocation +## correctly. Breaking it into two sed invocations is a workaround. + sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +hp) + # This case exists only to let depend.m4 do its work. It works by + # looking at the text of this script. This case will never be run, + # since it is checked for above. + exit 1 + ;; + +sgi) + if test "$libtool" = yes; then + "$@" "-Wp,-MDupdate,$tmpdepfile" + else + "$@" -MDupdate "$tmpdepfile" + fi + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile" + exit $stat + fi + rm -f "$depfile" + + if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files + echo "$object : \\" > "$depfile" + + # Clip off the initial element (the dependent). Don't try to be + # clever and replace this with sed code, as IRIX sed won't handle + # lines with more than a fixed number of characters (4096 in + # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines; + # the IRIX cc adds comments like `#:fec' to the end of the + # dependency line. + tr ' ' ' +' < "$tmpdepfile" \ + | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \ + tr ' +' ' ' >> $depfile + echo >> $depfile + + # The second pass generates a dummy entry for each header file. + tr ' ' ' +' < "$tmpdepfile" \ + | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \ + >> $depfile + else + # The sourcefile does not contain any dependencies, so just + # store a dummy comment line, to avoid errors with the Makefile + # "include basename.Plo" scheme. + echo "#dummy" > "$depfile" + fi + rm -f "$tmpdepfile" + ;; + +aix) + # The C for AIX Compiler uses -M and outputs the dependencies + # in a .u file. In older versions, this file always lives in the + # current directory. Also, the AIX compiler puts `$object:' at the + # start of each line; $object doesn't have directory information. + # Version 6 uses the directory in both cases. + dir=`echo "$object" | sed -e 's|/[^/]*$|/|'` + test "x$dir" = "x$object" && dir= + base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'` + if test "$libtool" = yes; then + tmpdepfile1=$dir$base.u + tmpdepfile2=$base.u + tmpdepfile3=$dir.libs/$base.u + "$@" -Wc,-M + else + tmpdepfile1=$dir$base.u + tmpdepfile2=$dir$base.u + tmpdepfile3=$dir$base.u + "$@" -M + fi + stat=$? + + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" + exit $stat + fi + + for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" + do + test -f "$tmpdepfile" && break + done + if test -f "$tmpdepfile"; then + # Each line is of the form `foo.o: dependent.h'. + # Do two passes, one to just change these to + # `$object: dependent.h' and one to simply `dependent.h:'. + sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile" + # That's a tab and a space in the []. + sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile" + else + # The sourcefile does not contain any dependencies, so just + # store a dummy comment line, to avoid errors with the Makefile + # "include basename.Plo" scheme. + echo "#dummy" > "$depfile" + fi + rm -f "$tmpdepfile" + ;; + +icc) + # Intel's C compiler understands `-MD -MF file'. However on + # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c + # ICC 7.0 will fill foo.d with something like + # foo.o: sub/foo.c + # foo.o: sub/foo.h + # which is wrong. We want: + # sub/foo.o: sub/foo.c + # sub/foo.o: sub/foo.h + # sub/foo.c: + # sub/foo.h: + # ICC 7.1 will output + # foo.o: sub/foo.c sub/foo.h + # and will wrap long lines using \ : + # foo.o: sub/foo.c ... \ + # sub/foo.h ... \ + # ... + + "$@" -MD -MF "$tmpdepfile" + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile" + exit $stat + fi + rm -f "$depfile" + # Each line is of the form `foo.o: dependent.h', + # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'. + # Do two passes, one to just change these to + # `$object: dependent.h' and one to simply `dependent.h:'. + sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile" + # Some versions of the HPUX 10.20 sed can't process this invocation + # correctly. Breaking it into two sed invocations is a workaround. + sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" | + sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +hp2) + # The "hp" stanza above does not work with aCC (C++) and HP's ia64 + # compilers, which have integrated preprocessors. The correct option + # to use with these is +Maked; it writes dependencies to a file named + # 'foo.d', which lands next to the object file, wherever that + # happens to be. + # Much of this is similar to the tru64 case; see comments there. + dir=`echo "$object" | sed -e 's|/[^/]*$|/|'` + test "x$dir" = "x$object" && dir= + base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'` + if test "$libtool" = yes; then + tmpdepfile1=$dir$base.d + tmpdepfile2=$dir.libs/$base.d + "$@" -Wc,+Maked + else + tmpdepfile1=$dir$base.d + tmpdepfile2=$dir$base.d + "$@" +Maked + fi + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile1" "$tmpdepfile2" + exit $stat + fi + + for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" + do + test -f "$tmpdepfile" && break + done + if test -f "$tmpdepfile"; then + sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile" + # Add `dependent.h:' lines. + sed -ne '2,${; s/^ *//; s/ \\*$//; s/$/:/; p;}' "$tmpdepfile" >> "$depfile" + else + echo "#dummy" > "$depfile" + fi + rm -f "$tmpdepfile" "$tmpdepfile2" + ;; + +tru64) + # The Tru64 compiler uses -MD to generate dependencies as a side + # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'. + # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put + # dependencies in `foo.d' instead, so we check for that too. + # Subdirectories are respected. + dir=`echo "$object" | sed -e 's|/[^/]*$|/|'` + test "x$dir" = "x$object" && dir= + base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'` + + if test "$libtool" = yes; then + # With Tru64 cc, shared objects can also be used to make a + # static library. This mechanism is used in libtool 1.4 series to + # handle both shared and static libraries in a single compilation. + # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d. + # + # With libtool 1.5 this exception was removed, and libtool now + # generates 2 separate objects for the 2 libraries. These two + # compilations output dependencies in $dir.libs/$base.o.d and + # in $dir$base.o.d. We have to check for both files, because + # one of the two compilations can be disabled. We should prefer + # $dir$base.o.d over $dir.libs/$base.o.d because the latter is + # automatically cleaned when .libs/ is deleted, while ignoring + # the former would cause a distcleancheck panic. + tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4 + tmpdepfile2=$dir$base.o.d # libtool 1.5 + tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5 + tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504 + "$@" -Wc,-MD + else + tmpdepfile1=$dir$base.o.d + tmpdepfile2=$dir$base.d + tmpdepfile3=$dir$base.d + tmpdepfile4=$dir$base.d + "$@" -MD + fi + + stat=$? + if test $stat -eq 0; then : + else + rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4" + exit $stat + fi + + for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4" + do + test -f "$tmpdepfile" && break + done + if test -f "$tmpdepfile"; then + sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile" + # That's a tab and a space in the []. + sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile" + else + echo "#dummy" > "$depfile" + fi + rm -f "$tmpdepfile" + ;; + +#nosideeffect) + # This comment above is used by automake to tell side-effect + # dependency tracking mechanisms from slower ones. + +dashmstdout) + # Important note: in order to support this mode, a compiler *must* + # always write the preprocessed file to stdout, regardless of -o. + "$@" || exit $? + + # Remove the call to Libtool. + if test "$libtool" = yes; then + while test $1 != '--mode=compile'; do + shift + done + shift + fi + + # Remove `-o $object'. + IFS=" " + for arg + do + case $arg in + -o) + shift + ;; + $object) + shift + ;; + *) + set fnord "$@" "$arg" + shift # fnord + shift # $arg + ;; + esac + done + + test -z "$dashmflag" && dashmflag=-M + # Require at least two characters before searching for `:' + # in the target name. This is to cope with DOS-style filenames: + # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise. + "$@" $dashmflag | + sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile" + rm -f "$depfile" + cat < "$tmpdepfile" > "$depfile" + tr ' ' ' +' < "$tmpdepfile" | \ +## Some versions of the HPUX 10.20 sed can't process this invocation +## correctly. Breaking it into two sed invocations is a workaround. + sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +dashXmstdout) + # This case only exists to satisfy depend.m4. It is never actually + # run, as this mode is specially recognized in the preamble. + exit 1 + ;; + +makedepend) + "$@" || exit $? + # Remove any Libtool call + if test "$libtool" = yes; then + while test $1 != '--mode=compile'; do + shift + done + shift + fi + # X makedepend + shift + cleared=no + for arg in "$@"; do + case $cleared in + no) + set ""; shift + cleared=yes ;; + esac + case "$arg" in + -D*|-I*) + set fnord "$@" "$arg"; shift ;; + # Strip any option that makedepend may not understand. Remove + # the object too, otherwise makedepend will parse it as a source file. + -*|$object) + ;; + *) + set fnord "$@" "$arg"; shift ;; + esac + done + obj_suffix="`echo $object | sed 's/^.*\././'`" + touch "$tmpdepfile" + ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@" + rm -f "$depfile" + cat < "$tmpdepfile" > "$depfile" + sed '1,2d' "$tmpdepfile" | tr ' ' ' +' | \ +## Some versions of the HPUX 10.20 sed can't process this invocation +## correctly. Breaking it into two sed invocations is a workaround. + sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" "$tmpdepfile".bak + ;; + +cpp) + # Important note: in order to support this mode, a compiler *must* + # always write the preprocessed file to stdout. + "$@" || exit $? + + # Remove the call to Libtool. + if test "$libtool" = yes; then + while test $1 != '--mode=compile'; do + shift + done + shift + fi + + # Remove `-o $object'. + IFS=" " + for arg + do + case $arg in + -o) + shift + ;; + $object) + shift + ;; + *) + set fnord "$@" "$arg" + shift # fnord + shift # $arg + ;; + esac + done + + "$@" -E | + sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \ + -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' | + sed '$ s: \\$::' > "$tmpdepfile" + rm -f "$depfile" + echo "$object : \\" > "$depfile" + cat < "$tmpdepfile" >> "$depfile" + sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +msvisualcpp) + # Important note: in order to support this mode, a compiler *must* + # always write the preprocessed file to stdout, regardless of -o, + # because we must use -o when running libtool. + "$@" || exit $? + IFS=" " + for arg + do + case "$arg" in + "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI") + set fnord "$@" + shift + shift + ;; + *) + set fnord "$@" "$arg" + shift + shift + ;; + esac + done + "$@" -E | + sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile" + rm -f "$depfile" + echo "$object : \\" > "$depfile" + . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile" + echo " " >> "$depfile" + . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile" + rm -f "$tmpdepfile" + ;; + +none) + exec "$@" + ;; + +*) + echo "Unknown depmode $depmode" 1>&2 + exit 1 + ;; +esac + +exit 0 + +# Local Variables: +# mode: shell-script +# sh-indentation: 2 +# eval: (add-hook 'write-file-hooks 'time-stamp) +# time-stamp-start: "scriptversion=" +# time-stamp-format: "%:y-%02m-%02d.%02H" +# time-stamp-end: "$" +# End: Index: /issm/trunk-jpl-damage/doc/issmdoc.m =================================================================== --- /issm/trunk-jpl-damage/doc/issmdoc.m (revision 11330) +++ /issm/trunk-jpl-damage/doc/issmdoc.m (revision 11330) @@ -0,0 +1,15 @@ +%Quick documentation for ISSM + +%First get ISSM tier: +ISSM_TIER=issmtier; + +disp(sprintf('\n%s',' A comprehensive documentation is available on http://issm.jpl.nasa.gov')); +disp(sprintf('\n%s',' Example: how to create a square ice shelf')); +disp(sprintf('%s',' go to ',ISSM_TIER,'/examples/SquareIceshelf')); +disp(sprintf('%s',' md=model; %creates a new empty model structure')); +disp(sprintf('%s',' md=triangle(md,''DomainOutline.exp'',50000); %creates a mesh of the domain outline with a resolution of 50000m')); +disp(sprintf('%s',' md=geography(md,''all'',''''); %defines the glacier system as an ice shelf (no island)')); +disp(sprintf('%s',' md=parameterize(md,''Square.par''); %fills all the other fields of the model')); +disp(sprintf('%s',' md=setelementstype(md,''macayeal'',''all''); %defines all elements as MacAyeal''s')); +disp(sprintf('%s',' md=solve(md,DiagnosticSolutionEnum); %generate the velocity field')); +disp(sprintf('%s',' plotmodel(md,''data'',md.results.DiagnosticSolution.Vel); %displays the velocity (type plotdoc for plotmodel help)')); Index: /issm/trunk-jpl-damage/etc/environment.csh =================================================================== --- /issm/trunk-jpl-damage/etc/environment.csh (revision 11330) +++ /issm/trunk-jpl-damage/etc/environment.csh (revision 11330) @@ -0,0 +1,128 @@ +#ISSM_TIER and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...) +source $ISSM_TIER/etc/environment_variables.csh + +#Do we have any command line arguments? (such as MATLAB_DIR=otherdirthandefault), source them before exporting the variables +#to environment. + +#foreach i ($@) +#eval $i +#end + +#CRON utilities +setenv PATH {$PATH}:{$ISSM_TIER}/cron + +#SCRIPTS utilities +setenv PATH {$PATH}:{$ISSM_TIER}/scripts + +#MATLAB +setenv MATLAB_DIR {$MATLAB_DIR} +setenv PATH {$MATLAB_DIR}/bin:{$PATH} +setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$MATLAB_DIR/lib + +#MPI +setenv MPI_DIR {$MPI_DIR} +setenv PATH {$MPI_DIR}/bin:{$PATH} +setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$MPI_DIR/lib +setenv MANPATH {$MANPATH}:$MPI_DIR/man +setenv MPIRUN_NPROCS 8 + +#PETSC +setenv PETSC_DIR {$PETSC_DIR} +setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$PETSC_DIR/lib/{$ISSM_ARCH} + +#SLEPC +setenv SLEPC_DIR {$SLEPC_DIR} +setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$SLEPC_DIR/lib/{$ISSM_ARCH} + + +#Dakota +setenv DAKOTA_DIR {$DAKOTA_DIR} +setenv PATH {$PATH}:{$DAKOTA_DIR}/bin +setenv MANPATH {$MANPATH}:{$MPI_DIR}/man:{$DAKOTA_DIR}/docs/man:{$DAKOTA_DIR}/docs/man-ref + +#Qhull +setenv QHULL_DIR {$QHULL_DIR} +setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$QHULL_DIR}/lib + + +#Doxygen +setenv DOXYGEN_DIR {$DOXYGEN_DIR} +setenv MANPATH {$MANPATH}:{$DOXYGEN_DIR}/man +setenv PATH {$PATH}:{$DOXYGEN_DIR}/bin + +#MTOC +setenv MTOC_DIR {$MTOC_DIR} +setenv PATH {$PATH}:{$MTOC_DIR} + +#MATLAB +setenv MATLAB_DIR {$MATLAB_DIR} +setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$MATLAB_DIR}/bin/glnxa64 +setenv PATH {$PATH}:{$MATLAB_DIR}/bin + +#TRIANGLE +setenv TRIANGLE_DIR {$TRIANGLE_DIR} + +#METIS +setenv METIS_DIR {$METIS_DIR} + +#BLAS +setenv BLAS_DIR {$BLAS_DIR} + +#LAPACK +setenv LAPACK_DIR {$LAPACK_DIR} + +#SCALAPACK +setenv SCALAPACK_DIR {$SCALAPACK_DIR} + +#PLAPACK +setenv PLAPACK_DIR {$PLAPACK_DIR} + +#BLACS +setenv BLACS_DIR {$BLACS_DIR} + +#YAMS +setenv YAMS_DIR {$YAMS_DIR} +setenv PATH {$PATH}:{$YAMS_DIR} + +#TEX2IM +setenv TEX2IM_DIR {$TEX2IM_DIR} +setenv PATH {$PATH}:{$TEX2IM_DIR} + +#SOWING +setenv SOWING_DIR {$SOWING_DIR} +setenv PATH {$PATH}:{$SOWING_DIR}/bin +setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$SOWING_DIR}/lib +setenv MANPATH {$MANPATH}:{$SOWING_DIR}/man + +#Chaco +setenv CHACO_DIR {$CHACO_DIR} +setenv PATH {$PATH}:{$CHACO_DIR} + +#MeshPart +setenv MESHPART_DIR {$MESHPART_DIR} +setenv PATH {$PATH}:{$MESHPART_DIR} + +#SCOTCH +setenv SCOTCH_DIR {$SCOTCH_DIR} +setenv PATH {$PATH}:{$SCOTCH_DIR} +setenv MANPATH {$MANPATH}:{$SCOTCH_DIR}/man + +#AUTOCONF +setenv AUTOCONF_DIR {$AUTOCONF_DIR} +setenv PATH {$PATH}:{$AUTOCONF_DIR}/bin + +#AUTOMAKE +setenv AUTOMAKE_DIR {$AUTOMAKE_DIR} +setenv PATH {$PATH}:{$AUTOMAKE_DIR}/bin + +#BORLAND +setenv BORLAND_DIR {$BORLAND_DIR} +setenv PATH {$PATH}:{$BORLAND_DIR}/Bin + +#SSH +setenv SSH_DIR {$SSH_DIR} +setenv PATH {$PATH}:{$SSH_DIR} + +#VALGRIND +setenv VALGRIND_DIR {$VALGRIND_DIR} +setenv PATH {$PATH}:{$VALGRIND_DIR} Index: /issm/trunk-jpl-damage/etc/environment.sh =================================================================== --- /issm/trunk-jpl-damage/etc/environment.sh (revision 11330) +++ /issm/trunk-jpl-damage/etc/environment.sh (revision 11330) @@ -0,0 +1,225 @@ +#ISSM_TIER and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...) +source $ISSM_TIER/etc/environment_variables.sh + +#Do we have any command line arguments? (such as MATLAB_DIR=otherdirthandefault), source them before exporting the variables +#to environment. +for i in $@ +do + eval $i +done + +#CRON utilities +PATH="$PATH:$ISSM_TIER/cron" + +#scripts +PATH="$PATH:$ISSM_TIER/scripts" + +##MATLAB +export MATLAB_DIR +PATH="$MATLAB_DIR/bin:$PATH" #take precedence over /usr/local/bin/matlab +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$MATLAB_DIR/lib" +export LD_RUN_PATH="$LD_RUN_PATH:$MATLAB_DIR/lib" +#export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$MATLAB_DIR/bin/glnxa64" +#export LD_RUN_PATH="$LD_RUN_PATH:$MATLAB_DIR/bin/glnxa64" + +#MPI +export MPI_DIR +PATH="$MPI_DIR/bin:$PATH" +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$MPI_DIR/lib" +export LD_RUN_PATH="$LD_RUN_PATH:$MPI_DIR/lib" +export MANPATH="$MANPATH:$MPI_DIR/man" +export MPIRUN_NPROCS=24 + +#PETSC +export PETSC_DIR +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$PETSC_DIR/lib/$ISSM_ARCH" +export LD_RUN_PATH="$LD_RUN_PATH:$PETSC_DIR/lib/$ISSM_ARCH" + +#SLEPC +export SLEPC_DIR +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$SLEPC_DIR/lib/$ISSM_ARCH" +export LD_RUN_PATH="$LD_RUN_PATH:$SLEPC_DIR/lib/$ISSM_ARCH" + +#Dakota +export DAKOTA_DIR +PATH="$PATH:$DAKOTA_DIR/bin" +export MANPATH="$MANPATH:$MPI_DIR/man:$DAKOTA_DIR/docs/man:$DAKOTA_DIR/docs/man-ref" + +#Qhull +export QHULL_DIR +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$QHULL_DIR/lib" +export LD_RUN_PATH="$LD_RUN_PATH:$QHULL_DIR/lib" + +#Doxygen +export DOXYGEN_DIR +MANPATH="$MANPATH:$DOXYGEN_DIR/man" +PATH="$PATH:$DOXYGEN_DIR/bin" + +#MTOC +export MTOC_DIR +PATH="$PATH:$MTOC_DIR" + +#TRIANGLE +export TRIANGLE_DIR + +#METIS +export METIS_DIR + +#BLAS +export BLAS_DIR + +#LAPACK +export LAPACK_DIR + +#SCALAPACK +export SCALAPACK_DIR + +#PLAPACK +export PLAPACK_DIR + +#BLACS +export BLACS_DIR + +#YAMS +export YAMS_DIR +PATH="$PATH:$YAMS_DIR" + +#BAMG +export BAMG_DIR +PATH="$PATH:$BAMG_DIR" + +#TEX2IM +export TEX2IM_DIR +PATH="$PATH:$TEX2IM_DIR" + +#SOWING +export SOWING_DIR +PATH="$PATH:$SOWING_DIR/bin" +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$SOWING_DIR/lib" +export LD_RUN_PATH="$LD_RUN_PATH:$SOWING_DIR/lib" +export MANPATH="$MANPATH:$SOWING_DIR/man" + +#Chaco +export CHACO_DIR +PATH="$PATH:$CHACO_DIR" + +#MeshPart +export MESHPART_DIR +PATH="$PATH:$MESHPART_DIR" + +#SCOTCH +export SCOTCH_DIR +PATH="$PATH:$SCOTCH_DIR" +export MANPATH="$MANPATH:$SCOTCH_DIR/man" + +#AUTOCONF +export AUTOCONF_DIR +PATH="$AUTOCONF_DIR/bin:$PATH" + +#AUTOMAKE +export AUTOMAKE_DIR +PATH="$AUTOMAKE_DIR/bin:$PATH" + +export LIBTOOL_DIR +PATH="$LIBTOOL_DIR/bin:$PATH" + +#BORLAND +export BORLAND_DIR +PATH="$PATH:$BORLAND_DIR/Bin" + +#INTEL +#export INTEL_DIR +#PATH="$PATH:$INTEL_DIR" +#source $ISSM_TIER/externalpackages/intel/intel.sh + +#SDK +export SDK_DIR +PATH="$PATH:$SDK_DIR" + +#SSH +export SSH_DIR +PATH="$PATH:$SSH_DIR" + +#VALGRIND +export VALGRIND_DIR +PATH="$PATH:$VALGRIND_DIR" + +#GRAPHVIZ +export GRAPHVIZ_DIR +PATH="$PATH:$GRAPHVIZ_DIR" + +#CPPCHECK +export CPPCHECK_DIR +PATH="$PATH:$CPPCHECK_DIR" + +#GDAL +export GDAL_DIR +PATH="$GDAL_DIR/bin:$PATH" +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$GDAL_DIR/lib" + +#MERCURIAL +export PYTHONPATH="$PYTHONPATH:$MERCURIAL_DIR/mercurial/pure/" +export PATH="$PATH:$MERCURIAL_DIR/" + +#BOOST +export BOOSTROOT +export BOOST_DIR +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$BOOST_DIR/lib" +export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$BOOST_DIR/lib" + +#XERCES +export XERCESROOT +export XERCESCROOT + +#xaifBooster +export XAIFBOOSTERROOT +export XAIFBOOSTER_HOME +export XAIF_DIR +export PLATFORM + +#angel +export ANGELROOT + +#openanalysis +export OPENANALYSISROOT +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$OPENANALYSISROOT/lib" + +#JAVA +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$JVM_DIR" + +#BBFTP +export PATH="$PATH:$BBFTP_DIR/bin" + +#ADIC +export PATH="$PATH:$ADIC_DIR/bin" +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$ADIC_DIR/lib" +export LD_RUN_PATH="$LD_RUN_PATH:$ADIC_DIR/lib" + +#COLPACK +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$COLPACK_DIR/lib" +export LD_RUN_PATH="$LD_RUN_PATH:$COLPACK_DIR/lib" + +#ECLIPSE +export PATH="$PATH:$ECLIPSE_DIR" + +#FLAIM +export FLAIM_DIR + +#APPSCAN +export PATH="$PATH:$APPSCAN_DIR/install/bin" +export PATH="$PATH:$APPSCAN_DIR/bin"] + +#CPPCHECK +export PATH="$PATH:$CPPCHECK_DIR/bin" + +#RATS +export PATH="$PATH:$RATS_DIR/bin" + +#DYSON +export PATH="$PATH:$DYSON_DIR" + +#CMAKE +export PATH="$PATH:$CMAKE_DIR/bin" + +#SHAPELIB +export PATH="$PATH:$SHAPELIB_DIR/exec" Index: /issm/trunk-jpl-damage/etc/environment_variables.csh =================================================================== --- /issm/trunk-jpl-damage/etc/environment_variables.csh (revision 11330) +++ /issm/trunk-jpl-damage/etc/environment_variables.csh (revision 11330) @@ -0,0 +1,84 @@ +# +# +#This routine can only be run if the ISSM_TIER variable has been correctly set! +# +# + +#MATLAB +set MATLAB_DIR={$ISSM_TIER}/externalpackages/matlab/install + +#MPI +set MPI_DIR={$ISSM_TIER}/externalpackages/mpich2/install + +#PETSC +set PETSC_DIR={$ISSM_TIER}/externalpackages/petsc/install + +#SLEPC +set SLEPC_DIR={$ISSM_TIER}/externalpackages/slepc/install + +#Dakota +set DAKOTA_DIR={$ISSM_TIER}/externalpackages/dakota/install + +#Qhull +set QHULL_DIR={$ISSM_TIER}/externalpackages/qhull/install + +#Doxygen +set DOXYGEN_DIR={$ISSM_TIER}/externalpackages/doxygen/install + +#MTOC +set MTOC_DIR={$ISSM_TIER}/externalpackages/mtoc/install + +#Triangle +set TRIANGLE_DIR={$ISSM_TIER}/externalpackages/triangle/install + +#METIS +set METIS_DIR={$ISSM_TIER}/externalpackages/metis/install + +#BLAS +set BLAS_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/fblaslapack + +#LAPACK +set LAPACK_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/fblaslapack/$ISSM_ARCH + +#SCALAPACK +set SCALAPACK_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/SCALAPACK/$ISSM_ARCH + +#PLAPACK +set PLAPACK_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/PLAPACKR32 + +#BLACS +set BLACS_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/blacs-dev/$ISSM_ARCH + +#sowing +set SOWING_DIR={$ISSM_TIER}/externalpackages/sowing/install + +#YAMS +set YAMS_DIR={$ISSM_TIER}/externalpackages/yams/install + +#TEX2IM +set TEX2IM_DIR={$ISSM_TIER}/externalpackages/tex2im/install + +#Chaco +set CHACO_DIR={$ISSM_TIER}/externalpackages/chaco/install + +#MeshPart +set MESHPART_DIR={$ISSM_TIER}/externalpackages/meshpart/install + +#SCOTCH +set SCOTCH_DIR={$ISSM_TIER}/externalpackages/scotch/install + +#Development packages +#automake +set AUTOMAKE_DIR={$ISSM_TIER}/externalpackages/automake/install + +#autoconf +set AUTOCONF_DIR={$ISSM_TIER}/externalpackages/autoconf/install + +#borland +set BORLAND_DIR=/cygdrive/c/Borland + +#ssh +set SSH_DIR={$ISSM_TIER}/externalpackages/ssh + +#valgrind +set VALGRIND_DIR={$ISSM_TIER}/externalpackages/valgrind/install/bin Index: /issm/trunk-jpl-damage/etc/environment_variables.sh =================================================================== --- /issm/trunk-jpl-damage/etc/environment_variables.sh (revision 11330) +++ /issm/trunk-jpl-damage/etc/environment_variables.sh (revision 11330) @@ -0,0 +1,167 @@ +# +# +#This routine can only be run if the ISSM_TIER variable has been correctly set! +# +# + +#MATLAB +MATLAB_DIR="$ISSM_TIER/externalpackages/matlab/install" + +#MPI +MPI_DIR="$ISSM_TIER/externalpackages/mpich2/install" + +#PETSC +PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" + +#SLEPC +SLEPC_DIR="$ISSM_TIER/externalpackages/slepc/install" + +#Dakota +DAKOTA_DIR="$ISSM_TIER/externalpackages/dakota/install" + +#Qhull +QHULL_DIR="$ISSM_TIER/externalpackages/qhull/install" + +#Doxygen +DOXYGEN_DIR="$ISSM_TIER/externalpackages/doxygen/install" + +#MTOC +MTOC_DIR="$ISSM_TIER/externalpackages/mtoc/install" + +#Triangle +TRIANGLE_DIR="$ISSM_TIER/externalpackages/triangle/install" + +#METIS +METIS_DIR="$ISSM_TIER/externalpackages/metis/install" + +#BLAS +BLAS_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/fblaslapack" + +#LAPACK +LAPACK_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH" + +#SCALAPACK +SCALAPACK_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH" + +#PLAPACK +PLAPACK_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32" + +#BLACS +BLACS_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH" + +#sowing +SOWING_DIR="$ISSM_TIER/externalpackages/sowing/install" + +#BLACS +BLACS_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH" + +#YAMS +YAMS_DIR="$ISSM_TIER/externalpackages/yams/install" + +#BAMG +BAMG_DIR="$ISSM_TIER/externalpackages/bamg/install" + +#Chaco +CHACO_DIR="$ISSM_TIER/externalpackages/chaco/install" + +#MeshPart +MESHPART_DIR="$ISSM_TIER/externalpackages/meshpart/install" + +#SCOTCH +SCOTCH_DIR="$ISSM_TIER/externalpackages/scotch/install" + +#Development packages +#automake +AUTOMAKE_DIR="$ISSM_TIER/externalpackages/automake/install" + +#libtool +LIBTOOL_DIR="$ISSM_TIER/externalpackages/libtool/install" + +#autoconf +AUTOCONF_DIR="$ISSM_TIER/externalpackages/autoconf/install" + +#borland +#BORLAND_DIR="/cygdrive/c/Borland/" + +#intel +#INTEL_DIR="C:/IntelInstall/Compiler/11.1/038/bin/ia32/" + +#TEX2IM +TEX2IM_DIR="$ISSM_TIER/externalpackages/tex2im/install" + +#sdk +#SDK_DIR="C:/MicrosoftVisualStudio 9.0/Microsoft Visual C++ 2008 Express Edition with SP1 - ENU" + +#ssh +SSH_DIR="$ISSM_TIER/externalpackages/ssh" + +#valgrind +VALGRIND_DIR="$ISSM_TIER/externalpackages/valgrind/install/bin" + +#graphviz +GRAPHVIZ_DIR="$ISSM_TIER/externalpackages/graphviz/install/bin" + +#cppcheck +CPPCHECK_DIR="$ISSM_TIER/externalpackages/cppcheck/install" + +#gdal +GDAL_DIR="$ISSM_TIER/externalpackages/gdal/install" + +#mercurial +MERCURIAL_DIR="$ISSM_TIER/externalpackages/mercurial/install" + +#boost +BOOST_DIR="$ISSM_TIER/externalpackages/boost/install" +BOOSTROOT="$ISSM_TIER/externalpackages/boost/install" + +#OpenAnalysis +OPENANALYSISROOT="$ISSM_TIER/externalpackages/openanalysis/install" + +#xerces +XERCESROOT="$ISSM_TIER/externalpackages/xerces/install" +XERCESCROOT="$ISSM_TIER/externalpackages/xerces/src" + +#xaifBooster +XAIFBOOSTERROOT="$ISSM_TIER/externalpackages/xaifbooster/" +XAIF_DIR="$ISSM_TIER/externalpackages/xaifbooster/xaifBooster" +XAIFBOOSTER_HOME="$ISSM_TIER/externalpackages/xaifbooster/xaifBooster" +PLATFORM=x86-Linux + +#angel +ANGELROOT="$ISSM_TIER/externalpackages/angel/angel" + +#java +JVM_DIR=/usr/local/gcc/4.3.2/lib64/gcj-4.3.2-9/ + +#bbftp +BBFTP_DIR="$ISSM_TIER/externalpackages/bbftp/install" + +#adic2 +ADIC_DIR="$ISSM_TIER/externalpackages/adic/install" + +#colpack +COLPACK_DIR="$ISSM_TIER/externalpackages/colpack/install" + +#eclipse +ECLIPSE_DIR="$ISSM_TIER/externalpackages/eclipse/install" + +#flaim +FLAIM_DIR="$ISSM_TIER/externalpackages/flaim/install" + +#appscan +APPSCAN_DIR="$ISSM_TIER/externalpackages/appscan" + +#cppcheck +CPPCHECK_DIR="$ISSM_TIER/externalpackages/cppcheck/install" + +#rats +RATS_DIR="$ISSM_TIER/externalpackages/rats/install" + +#dyson +DYSON_DIR="$ISSM_TIER/externalpackages/dyson/" + +#cmake +CMAKE_DIR="$ISSM_TIER/externalpackages/cmake/install" + +#shapelib +SHAPELIB_DIR="$ISSM_TIER/externalpackages/shapelib/install" Index: /issm/trunk-jpl-damage/examples/SquareIceShelf/DomainOutline.exp =================================================================== --- /issm/trunk-jpl-damage/examples/SquareIceShelf/DomainOutline.exp (revision 11330) +++ /issm/trunk-jpl-damage/examples/SquareIceShelf/DomainOutline.exp (revision 11330) @@ -0,0 +1,10 @@ +## Name:DomainOutline +## Icon:0 +# Points Count Value +5 1.000000 +# X pos Y pos +0 0 +1000000 0 +1000000 1000000 +0 1000000 +0 0 Index: /issm/trunk-jpl-damage/examples/SquareIceShelf/Front.exp =================================================================== --- /issm/trunk-jpl-damage/examples/SquareIceShelf/Front.exp (revision 11330) +++ /issm/trunk-jpl-damage/examples/SquareIceShelf/Front.exp (revision 11330) @@ -0,0 +1,10 @@ +## Name:icefront +## Icon:0 +# Points Count Value +5 1. +# X pos Y pos +-1000 900000 +-1000 1100000 +1100000 1100000 +1100000 900000 +-1000 900000 Index: /issm/trunk-jpl-damage/examples/SquareIceShelf/README =================================================================== --- /issm/trunk-jpl-damage/examples/SquareIceShelf/README (revision 11330) +++ /issm/trunk-jpl-damage/examples/SquareIceShelf/README (revision 11330) @@ -0,0 +1,6 @@ +md=model; +md=mesh(md,'DomainOutline.exp',50000); +md=geography(md,'all',''); +md=parameterize(md,'Square.par'); +md=setelementstype(md,'macayeal','all'); +md=solve(md,DiagnosticSolutionEnum); Index: /issm/trunk-jpl-damage/examples/SquareIceShelf/Square.par =================================================================== --- /issm/trunk-jpl-damage/examples/SquareIceShelf/Square.par (revision 11330) +++ /issm/trunk-jpl-damage/examples/SquareIceShelf/Square.par (revision 11330) @@ -0,0 +1,30 @@ +%Start defining model parameters here + +disp(' creating thickness'); +hmin=300; +hmax=1000; +ymin=min(md.mesh.y); +ymax=max(md.mesh.y); +md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin); +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; + +disp(' creating drag'); +pos=find(md.mask.vertexonfloatingice); +md.friction.coefficient=200*ones(md.mesh.numberofvertices,1); +md.friction.coefficient(pos)=0; +md.friction.p=ones(md.mesh.numberofelements,1); +md.friction.q=ones(md.mesh.numberofelements,1); + +disp(' initial velocity'); +md.initialization.vx=zeros(md.mesh.numberofvertices,1); +md.initialization.vy=zeros(md.mesh.numberofvertices,1); +md.initialization.vz=zeros(md.mesh.numberofvertices,1); +md.initialization.vel=zeros(md.mesh.numberofvertices,1); + +disp(' creating flow law parameter'); +md.materials.rheology_B=paterson((273-20)*ones(md.mesh.numberofvertices,1)); +md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); + +disp(' creating boundary conditions'); +md=SetIceShelfBC(md,'Front.exp'); Index: /issm/trunk-jpl-damage/examples/SquareIceShelf/runme.m =================================================================== --- /issm/trunk-jpl-damage/examples/SquareIceShelf/runme.m (revision 11330) +++ /issm/trunk-jpl-damage/examples/SquareIceShelf/runme.m (revision 11330) @@ -0,0 +1,6 @@ +md=model; +md=triangle(md,'DomainOutline.exp',100000); +md=setmask(md,'all',''); +md=parameterize(md,'Square.par'); +md=setflowequation(md,'macayeal','all'); +md=solve(md,DiagnosticSolutionEnum); Index: /issm/trunk-jpl-damage/externalpackages/README =================================================================== --- /issm/trunk-jpl-damage/externalpackages/README (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/README (revision 11330) @@ -0,0 +1,22 @@ +To install all the ISSM libraries: + +1/ go into each library folder and type install.sh . + +2/ There is no guarantee the compilation will work on all systems. A lot of tweaking of the +install.sh files will probably be involved. Especially, the configuration part of the install. + +Update: +now install.sh can call configure.sh for the most complex libraries, ie Petsc and Dakota. For those +libraries, go in the configs/ directory, pick up the correct configuration file and copy it to the top +folder of the library compilation. Tweak if necessary. + +machine characteristics: + +-astrid: linux 64 bits +-castor: altix 64 bits +-cosmos: JPL cluster 32 bits +-macmathieu: iMac 24" 2009 32 bits +-macbookmathieu: MacBook Pro 13" 2010; OS X 10.6.7; 2.4GHz Intel Core 2 Duo 64 bits +-maceric: MacBook Pro 15" 2010 32 bits +-ogive: Mac Pro 2008 32 bits +-pleiades: AMES cluster Index: /issm/trunk-jpl-damage/externalpackages/adic/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/adic/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/adic/install.sh (revision 11330) @@ -0,0 +1,33 @@ +#!/bin/bash + +#Erase install +rm -rf source build install + +#Download code +hg clone http://mercurial.mcs.anl.gov/ad/ADIC -r 631 source + +#Then update to -r 631 +cd source +hg update -r 631 + +#Configure and Compile +cd source +./autogen.sh +./aclocal +cd .. +mkdir build +cd build +../source/configure \ + --with-rose=$ISSM_TIER/externalpackages/rose/install \ + --with-openanalysis=$ISSM_TIER/externalpackages/openanalysis/openanalysis/x86_64-Linux \ + --with-boost=$ISSM_TIER/externalpackages/boost/install \ + --with-xerces=$ISSM_TIER/externalpackages/xerces/src \ + --with-xaifbooster=$ISSM_TIER/externalpackages/xaifbooster/xaifBooster \ + --with-colpack=$ISSM_TIER/externalpackages/colpack/install\ + --prefix=$ISSM_TIER/externalpackages/adic/install +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk-jpl-damage/externalpackages/adic/tests/notes =================================================================== --- /issm/trunk-jpl-damage/externalpackages/adic/tests/notes (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/adic/tests/notes (revision 11330) @@ -0,0 +1,143 @@ +mini1.c is: +7:37 PM +#include + +void mini1(double *y, double *x) +{ + int i; + for (i = 0; i < 2; i=i+1) { + y[i] = x[i] + sin(x[i]*x[i]); + } + } + Eric Larour 7:37 PM + ok + Sri Hari Krishna Narayanan 7:37 PM + If you cat any of mini1_grad_length.ad.c mini1_dense_forward.ad.c mini1_sparse_forward.ad.c + 7:37 PM + You should be able to see the forward mode output + Eric Larour 7:38 PM + ok + Sri Hari Krishna Narayanan 7:38 PM + First the makefile compiles mini1_grad_length.ad.c with a runtime library to estimate the number of columns in the Jacobian. + Eric Larour 7:39 PM + ok, makes sense + Sri Hari Krishna Narayanan 7:39 PM + That generates the output : ADIC_GRADVEC_LENGTH 2 + Eric Larour 7:39 PM + where? + 7:39 PM + ok, sorry, got it + Sri Hari Krishna Narayanan 7:40 PM + The value is also written to : runtime_dense/adic_gradvec_length.h + Eric Larour 7:40 PM + where is the main for this? + 7:40 PM + oh, it creates a .h directly + Sri Hari Krishna Narayanan 7:40 PM + mini1_driver.c + 7:40 PM + yes. + 7:40 PM + The runtime library takes care of that + 7:40 PM + There is alot or #defined compilation going on + Eric Larour 7:41 PM + wraps around mini1_forward_array.exe ? + Sri Hari Krishna Narayanan 7:41 PM + /*intermediary: */ creates mini1_grad_length.exe + Eric Larour 7:41 PM + Isn't that the Makefile? what is the runtime library ? + 7:42 PM + ok, the Makefile launches the runtime library + Sri Hari Krishna Narayanan 7:42 PM + Makefile copies versions of the runtime library (bunch of macros in most cases) + Eric Larour 7:42 PM + what is the name of the runtime library? + Sri Hari Krishna Narayanan 7:43 PM + form $adicsrc/runtime/ + 7:43 PM + There are multiple versions + Eric Larour 7:44 PM + ah, I see the grad_length dir + 7:44 PM + is all that stuff compiled into adic2? + Sri Hari Krishna Narayanan 7:44 PM + The one used to estimate the grad_lengh is : $adicinstall/grad_length + 7:44 PM + yes + Eric Larour 7:44 PM + ok, makes sense + Sri Hari Krishna Narayanan 7:45 PM + For the next step though + 7:45 PM + the 'dense' case + 7:45 PM + the runtime library cannot be precompiled + 7:45 PM + the .h file has been created in the previous step + 7:46 PM + So we copy the runtime/dense to the local directory + Eric Larour 7:46 PM + because we can't guess the size of the gradient right? + Sri Hari Krishna Narayanan 7:46 PM + and copy the .h into it + 7:46 PM + correct + Eric Larour 7:46 PM + nice + Sri Hari Krishna Narayanan 7:46 PM + Then we compile it and create a .la file + 7:46 PM + which is then linked to create mini1_dense_forward.exe + 7:47 PM + When we run this, it also happens to run the analyticla derivates (the driver is built this way) + 7:47 PM + Also diveded differences + 7:47 PM + So you get the output: + 7:47 PM + Analytic result is: [1.968912] + Analytic result is: [1.968912] + DD result is: [1.968997] error {-8.45e-05} + DD result is: [1.968997] error {-8.45e-05} + AD result is: [1.968912] error {0.000000} + AD result is: [1.968912] error {0.000000} + 7:48 PM + The next step is to detect sparsity in the Jacobian and possibly compress it using Colpack (create a seed matrix). + 7:49 PM + The gradient computation takes place on the compressed matrix. + 7:49 PM + The output : ADIC_GRADVEC_LENGTH 1 + 7:49 PM + means that the seed matrix has one column. + 7:50 PM + After the calculation of the elements of the compressed matrix, it is then extracted to form the 'full Jacobian' (sorry if these tems are inexact). + 7:51 PM + The extracted output is then printed out: + 7:51 PM + AD result is: [1.968912] + AD result is: [1.968912] + 7:51 PM + And we are done! + Eric Larour 7:51 PM + This is a lot for me to take in at once I'm going to have to look through the makefile, + 7:51 PM + and your explanations, and figure it out + Sri Hari Krishna Narayanan 7:51 PM + Sure. + Eric Larour 7:52 PM + I'll get back to you as soon as I have injested all of this + Sri Hari Krishna Narayanan 7:52 PM + No problem. + Eric Larour 7:52 PM + I'll probably have a million questions + Sri Hari Krishna Narayanan 7:52 PM + This is an exhaustive test + 7:52 PM + FOr m ost purposes, we wil not need all of this + Eric Larour 7:52 PM + this is really nice, I'm pretty exited ! + Sri Hari Krishna Narayanan 7:52 PM + Jean belives for example the the grad_length version is pointless. I find it interesting though. + 7:53 PM + Okay. There are more interesting examples we can try Index: /issm/trunk-jpl-damage/externalpackages/adolc/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/adolc/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/adolc/install.sh (revision 11330) @@ -0,0 +1,28 @@ +#!/bin/bash + +#Some cleanup +rm -rf install ADOL-C-2.2.0 src + +#Create install directories +mkdir install src + +#Untar +tar -zxvf ADOL-C-2.2.0.tar.gz + +#Move ADOL-C into install directory +mv ADOL-C-2.2.0/* src +rm -rf ADOL-C-2.2.0 + +#Compile ADOL-C +cd src +./configure \ + --prefix=$ISSM_TIER/externalpackages/adolc/install \ + --enable-sparse \ + --enable-docexa \ + --enable-addexa +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk-jpl-damage/externalpackages/angel/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/angel/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/angel/install.sh (revision 11330) @@ -0,0 +1,11 @@ +#!/bin/bash + +#Some cleanup +rm -rf angel + +#download +svn co -r 82 https://angellib.svn.sourceforge.net/svnroot/angellib/trunk angel + +#Compile +cd angel +make Index: /issm/trunk-jpl-damage/externalpackages/appscan/bin/genouncemakePFile.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/appscan/bin/genouncemakePFile.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/appscan/bin/genouncemakePFile.sh (revision 11330) @@ -0,0 +1,593 @@ +#!/bin/bash + +#---------------------------------------------------------------------- +#VARIABLES containing information to generate OunceMake Properties file +#---------------------------------------------------------------------- +XMLHEADER="" +OUNCEHEADER="" +MAKEOPT="-f Makefile" + +COMPILER_TAG="Compiler" +COMPILER_MACRO="macro" + +C_COMPILER_MVALUE="\"CC\"" +CPP_COMPILER_MVALUE="\"CXX\"" + +MAKE_TAG="Make" +MAKE_MACRO="macro" +MAKE_MVALUE="\"MAKE\"" + + +LINKER_TAG="Linker" +LINKER_MACRO="macro" +LINKER_MVALUE="\"LD\"" + + +ARCHIVE_TAG="Executable" +ARCHIVE_MACRO="macro" +ARCHIVE_MVALUE="\"ARCHIVE\"" + +OUNCEOPT="" + +OUNCE_MAIN_TAG="OunceMakeProperties" +OUNCE_COMPILER_GPO_TAG="GlobalProjectOptions" +OUNCE_COMPILER_OPT="compiler_options" +OUNCE_COMPILER_OPT_gpp="\"-g++_linux_i386\"" +OUNCE_COMPILER_OPT_gcc="\"-gcc_linux_i386\"" + +OUNCE_INCLUDE_PATH="include_paths" +OUNCE_MACRO_PATH="macros" + +OUNCE_COMPILER_FO_TAG="FileOptions" +OUNCE_COMPILER_EXT="extensions" + +OUNCE_COMPILER_EXT_CPP="cpp;cxx" +OUNCE_COMPILER_EXT_C="c" + +#Did the search for a particular tool pass/fail +FAIL_FILE="failed.status" + +#--------------------------------- +#COMPILER data extraction function +#--------------------------------- + +function initialize { +#Create Directory for info + echo;echo + echo -e "Initialization....\t\t\t[\c " + echo -e "\E[33mSTARTED\c "; tput sgr0 + echo "]" + search_tool which + FILEPRE=${1} + + case "$1" in + "gcc"|"cc") + TESTFILE="testfoo.c" + ;; + "g++"|"CC") + TESTFILE="testfoo.cpp" + ;; + *) + echo "Error setting prefix" + ;; + esac + + DATAFOLDER="${FILEPRE}results" +#Declare files to generate and store results + RESULTFILE="${DATAFOLDER}/${FILEPRE}libinc.result" + SLIMFILE="${DATAFOLDER}/${FILEPRE}slim.inc" + SLIM2FILE="${DATAFOLDER}/${FILEPRE}slim2.inc" + +#Declare the Tags that enclose the information needed + START_TAG="#include <...> search starts here:" + END_TAG="End of search list." + +#Declare Variable to track Tags + MARK_FOUND=0 + +#For Macros + MACROSDUMPFILE="${DATAFOLDER}/${FILEPRE}macrosd.result" + INTFILE1="${DATAFOLDER}/${FILEPRE}interf1.result" + INTFILE2="${DATAFOLDER}/${FILEPRE}interf2.result" + + +#The file extensions for (both) options +CONFIG_FOLDER="config" +C_EXT="${CONFIG_FOLDER}/cext.data" +CPP_EXT="${CONFIG_FOLDER}/cppext.data" + +if [ -d ${CONFIG_FOLDER} ]; then + echo +else + mkdir ${CONFIG_FOLDER} + echo ${OUNCE_COMPILER_EXT_CPP} > ${C_EXT} + echo ${OUNCE_COMPILER_EXT_C} > ${CPP_EXT} +fi + + echo -e "Initialization....\t\t\t[\c " + echo -e "\E[33mDONE\c "; tput sgr0 + echo "]" +} + +function purgefiles { + echo -e "Purging files....\t\t\t[\c " + echo -e "\E[33mSTARTED\c "; tput sgr0 + echo "]" + if [ -e ${DATAFOLDER} ]; then + rm -R ${DATAFOLDER} + mkdir ${DATAFOLDER} + else + mkdir ${DATAFOLDER} + fi + echo -e "Purging files....\t\t\t[\c " + echo -e "\E[33mDONE\c "; tput sgr0 + echo "]" +} + + +function processGNUInclude { +echo +#Create the dummy file is does not exist +if [ -e ${TESTFILE} ]; then + echo "Will use an existing ${TESTFILE} file" +else + echo -e "int main(){\n return 0;\n}" &> ${TESTFILE} + if [ -e ${TESTFILE} ]; then + echo -e "Generating new test file\t\t[\c " + echo -e "\E[31m${TESTFILE}\c " ; tput sgr0 + echo "]" + else + echo -e "Error generating new test file\t\t[\c " + echo -e "\E[31m${TESTFILE}\c " ; tput sgr0 + echo "]" + #TO DO + #Will the user like to continue or exit? + fi +fi + + + echo + echo -e "Generating information for Compiler\t\t[\c " + echo -e "\E[31m${COMPILER}\c " ; tput sgr0 + echo "]" + +${COMPILER} -v ${TESTFILE} &> ${RESULTFILE} + + +cat ${RESULTFILE} | while read line +do + + if [ "${line}" = "${START_TAG}" ] + then + MARK_FOUND=1 + fi + + + if [ "${line}" = "${END_TAG}" ] + then + MARK_FOUND=0 + fi + + + if [ "${MARK_FOUND}" = 1 ] && [ "${line}" != "${START_TAG}" ] + then + let "inclib += 1" + echo ${line} 1>> ${SLIMFILE} + fi +done + +if [ -e ${SLIMFILE} ]; then + sed -e :a -e N -e 's/\n/; /' -e ta ${SLIMFILE} > ${RESULTFILE} + echo -e "Inc & Lib results are in file...\t\t[\c " + echo -e "\033[1m\E[31m${RESULTFILE}\033[0m\c " ; tput sgr0 + echo "]" +fi + +#String to contatenate the include path +concatpath="include_paths=\"" +#Merge file content +sed -e 's/\n/;/' ${SLIMFILE} > ${SLIM2FILE} + +} + + +function processGNUMacro { +#***************************** +#Generate macros for system +#***************************** + echo + echo -e "Generating Macro data for Compiler\t\t[\c " + echo -e "\E[31m${COMPILER} \c " ; tput sgr0 + echo "]" + + ${COMPILER} -dM -E ${TESTFILE} >> ${MACROSDUMPFILE} + sed 's/#define //' ${MACROSDUMPFILE} > ${INTFILE1} + if [ -e ${INTFILE1} ]; then + sed 's/ /=/' ${INTFILE1} > ${INTFILE2} + else + echo -e "\033[1m Sorry <${INTFILE1}> was not created.. \033[0m" + fi + + if [ -e ${INTFILE2} ]; then + #Remove the Macro's that have no values + sed '/^_.*=$/d' ${INTFILE2} > ${INTFILE1} + #Join the individual line and delimit with a (; ) + sed -e :a -e N -e 's/\n/; /' -e ta ${INTFILE1} > ${MACROSDUMPFILE} + #All done display the results file + echo -e "Macro results are in file...\t\t\t[\c " + echo -e "\033[1m\E[31m${MACROSDUMPFILE}\033[0m\c " ; tput sgr0 + echo "]" + else + echo -e "\033[1m Sorry <${MACROSDUMPFILE}> was not created.. \033[0m" + fi +} + +function processSUNMacro { +#******************************************* +#This function is for the SUN Compilers ONLY +#******************************************* + echo + echo -e "Generating Macro data for Compiler\t\t[\c " + echo -e "\E[31m${COMPILER} \c " ; tput sgr0 + echo "]" + + ${COMPILER} -xdumpmacros ${TESTFILE} &> ${MACROSDUMPFILE} + sed 's/#define //' ${MACROSDUMPFILE} > ${INTFILE1} + if [ -e ${INTFILE1} ]; then + sed 's/ /=/' ${INTFILE1} > ${INTFILE2} + else + echo -e "\033[1m Sorry <${INTFILE1}> was not created.. \033[0m" + fi + + if [ -e ${INTFILE2} ]; then + #Remove the Macro's that have no values + sed '/^_.*=$/d' ${INTFILE2} > ${INTFILE1} + #Join the individual line and delimit with a (; ) + sed -e :a -e N -e 's/\n/; /' -e ta ${INTFILE1} > ${MACROSDUMPFILE} + #All done display the results file + echo -e "Macro results are in file...\t\t\t[\c " + echo -e "\033[1m\E[31m${MACROSDUMPFILE}\033[0m\c " ; tput sgr0 + echo "]" + else + echo -e "\033[1m Sorry <${MACROSDUMPFILE}> was not created.. \033[0m" + fi +} + +#-------------------------- +#DATA Processing variables +#-------------------------- +PROPFILE="ouncemake_properties.xml" +PROBEFILE="probe.results" +ERRORLOG="error.log" + +#--------------------------------------- +#FUNCTION TO CREATE FILE +#-------------------------------------- + +function create_file { +#If a previous copy of file exist, delete it +if [ -e ${PROPFILE} ]; then + rm ${PROPFILE} +fi + +echo;echo +echo "CREATING THE PROPERTIES XML FILE" +#insert file headers +echo ${XMLHEADER} >> ${PROPFILE} +echo ${OUNCEHEADER} >> ${PROPFILE} +echo ${MAKEOPT} >> ${PROPFILE} +case "${1}" in + 'gcc') + search_tool gcc + ;; + 'g++') + search_tool g++ + ;; + 'bothGNU') + search_tool gcc + search_tool g++ + ;; + 'cc') + search_tool cc + ;; + 'CC') + search_tool CC + ;; + 'bothSUN') + search_tool gcc + search_tool g++ + ;; + '*') + ;; +esac +search_tool make +search_tool ld +search_tool ar +echo " ${OUNCEOPT}" >> ${PROPFILE} + +case "${1}" in + 'gcc') + singleGNUC gcc + ;; + 'g++') + singleGNUC g++ + ;; + 'bothGNU') + bothGNUC gcc + bothGNUC g++ + ;; + 'cc') + singleSUNC cc + ;; + 'CC') + singleSUNC CC + ;; + 'bothSUN') + bothSUNC cc + bothSUNC CC + ;; + '*') + ;; +esac + +echo "" >> ${PROPFILE} + +echo +echo -e "Successully created Properties file\t\t[\c " +echo -e "\033[1m\E[31m${PROPFILE}\033[0m\c " ; tput sgr0 +echo "]" +echo +} + +#when the system is unable to locate the tool +#the user is prompted to provide that information +function usersupplypath { + echo "Please provide the path to ${1}." + read TOOLPATH +} + + +function search_tool { +which $1 &> ${PROBEFILE} +#Why this approach? I had to be able to non-interactively +#know if the pattern was successfully found. + +sed -n -e "/.*no[ ]${1}[ ]in[ ].*/w $FAIL_FILE" ${PROBEFILE} + +#If the file is empty, the process PASSED +#else the Fail criteria was found. Process FAILED +if [ -e ${FAIL_FILE} ]; then + exec < ${FAIL_FILE} + read FAILPASS + if [${FAILPASS} = ""]; then + SEARCHTOOL="PASSED" + rm ${FAIL_FILE} + else + SEARCHTOOL="FAILED" + fi +fi + + +if [ ${SEARCHTOOL} == "FAILED" ] ; then + echo "Failed to find ${1} in PATH" >> ${ERRORLOG} + echo -e "check for $1 in ${TLOC}\t\t\t[$SEARCHTOOL]" +elif [ ${SEARCHTOOL} == "PASSED" ]; then + #Redirects stdin to a file so that + exec < ${PROBEFILE} + #I can read line by line + read TLOC + echo -e "check for $1 in ${TLOC}\t\t\t[\c " + echo -e "\E[33m${SEARCHTOOL}\c "; tput sgr0 + echo "]" +else + echo "Unable to process the request" + #exit +fi + +case "$1" in + 'gcc') + #set up the sub strings + TAG_L="<${COMPILER_TAG} ${COMPILER_MACRO}=${C_COMPILER_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + 'g++') + TAG_L="<${COMPILER_TAG} ${COMPILER_MACRO}=${CPP_COMPILER_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + 'make') + TAG_L="<${MAKE_TAG} ${MAKE_MACRO}=${MAKE_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + 'ld') + TAG_L="<${LINKER_TAG} ${LINKER_MACRO}=${LINKER_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + 'ar') + TAG_L="<${ARCHIVE_TAG} ${ARCHIVE_MACRO}=${ARCHIVE_MVALUE}>" + MVALUE="$TLOC" + TAG_R="" + ;; + '*') + ;; +esac + +#then concatenate +FULL_STRING="${TAG_L}${MVALUE}${TAG_R}" +#and store in file +echo " $FULL_STRING" >> ${PROPFILE} +} +function singleGNUC { + +echo " <${OUNCE_COMPILER_GPO_TAG}" >> ${PROPFILE} + +case "$1" in + 'gcc') + echo -e "\t ${OUNCE_COMPILER_OPT}=${OUNCE_COMPILER_OPT_gcc}" >> ${PROPFILE} + ;; + 'g++') + echo -e "\t ${OUNCE_COMPILER_OPT}=${OUNCE_COMPILER_OPT_gpp}" >> ${PROPFILE} + ;; + '*') + ;; +esac + +exec < ${RESULTFILE} +read INCLUDE_DATA +echo -e "\t ${OUNCE_INCLUDE_PATH}=\"${INCLUDE_DATA}\"" >> ${PROPFILE} +exec < ${MACROSDUMPFILE} +read MACRO_DATA +#Using single quotes to wrap double quotes in data +echo -e "\t ${OUNCE_MACRO_PATH}='${MACRO_DATA}' />" >> ${PROPFILE} + +} + + +function bothGNUC { + +echo -e "\t<${OUNCE_COMPILER_FO_TAG}" >> ${PROPFILE} + +case "$1" in + 'gcc') + FILEPRE="$1" + exec < ${C_EXT} + read CEXTENSIONS + if [ ${CEXTENSIONS} = "" ]; then + CEXTENSIONS=${OUNCE_COMPILER_EXT_C} + else + OUNCE_COMPILER_EXT_C=${CEXTENSIONS} + fi + echo -e "\t ${OUNCE_COMPILER_EXT}=\"${OUNCE_COMPILER_EXT_C}\"" >> ${PROPFILE} + ;; + 'g++') + FILEPRE="$1" + exec < ${CPP_EXT} + read CPPEXTENSIONS + if [ ${CPPEXTENSIONS} = "" ]; then + CPPEXTENSIONS=${OUNCE_COMPILER_EXT_CPP} + else + OUNCE_COMPILER_EXT_CPP=${CPPEXTENSIONS} + fi + echo -e "\t ${OUNCE_COMPILER_EXT}=\"${OUNCE_COMPILER_EXT_CPP}\"" >> ${PROPFILE} + ;; + '*') + ;; +esac + +#To make sure that the correct folder and file is read +DATAFOLDER="${FILEPRE}results" +#Declare files to generate and store results +RESULTFILE="${DATAFOLDER}/${FILEPRE}libinc.result" + +exec < ${RESULTFILE} +read INCLUDE_DATA +echo -e "\t ${OUNCE_INCLUDE_PATH}=\"${INCLUDE_DATA}\"" >> ${PROPFILE} +exec < ${MACROSDUMPFILE} +read MACRO_DATA +echo -e "\t ${OUNCE_MACRO_PATH}='${MACRO_DATA}'/>" >> ${PROPFILE} + +} + + +clear +echo +echo -e "\t \E[34m\033[1mOUNCEMAKE PROPERTIES FILE GENERATOR (1.0)b\033[0m";tput sgr0 + +#Start of the program +case "$1" in + '-t') + case "$2" in + "gcc") + COMPILER=${2} + initialize ${2} + purgefiles + processGNUInclude + processGNUMacro + create_file ${2} + ;; + "g++") + COMPILER=${2} + initialize ${2} + purgefiles + processGNUInclude + processGNUMacro + create_file ${2} + ;; + "bothGNU") + COMPILER="gcc" + initialize ${2} + purgefiles + processGNUInclude + processGNUMacro + COMPILER="g++" + initialize ${2} + purgefiles + processGNUInclude + processGNUMacro + create_file ${2} + ;; + "cc") + COMPILER=${2} + initialize ${2} + purgefiles + processSUNInclude + processSUNMacro + create_file ${2} + ;; + "CC") + COMPILER=${2} + initialize ${2} + purgefiles + # processSUNInclude + processSUNMacro + # create_file ${2} + ;; + "bothSUN") + COMPILER="cc" + initialize cc + purgefiles + processSUNInclude + processSUNMacro + COMPILER="CC" + initialize CC + purgefiles + processSUNInclude + processSUNMacro + create_file both + ;; + '*') + echo "Usage: -t [gcc|g++|bothGNU]" + exit $? + ;; + esac + ;; + '-h') + echo -e "Usage: -t [Options] -v " + echo -e "Options:" + echo -e "\t[gcc]\tC project only"; + echo -e "\t[g++]\tCPP project only" + echo -e "\t[bothGNU]\tMixed C and CPP project" + echo + echo -e "\t-v \tDisplay version information" + exit $? + ;; + '-v') + echo "Version 1.0 beta" + exit $? + ;; + *) + echo -e "Usage: -t [Options] -v " + echo -e "Options:" + echo -e "\t[gcc]\tC project only"; + echo -e "\t[g++]\tCPP project only" + echo -e "\t[both]\tMixed C and CPP project" + echo + echo -e "\t-v \tDisplay version information" + exit $? + ;; +esac +echo "[ P R O C E S S C O M P L E T E !!! ]" +echo Index: /issm/trunk-jpl-damage/externalpackages/appscan/hostname =================================================================== --- /issm/trunk-jpl-damage/externalpackages/appscan/hostname (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/appscan/hostname (revision 11330) @@ -0,0 +1,1 @@ +jplsec-codescan.jpl.nasa.gov Index: /issm/trunk-jpl-damage/externalpackages/appscan/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/appscan/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/appscan/install.sh (revision 11330) @@ -0,0 +1,9 @@ +#!/bin/bash + +#AppScan install directory. Just symlink to your existing AppScan software + +#Erase symlink +rm -rf install + +#Select or create a new simlink +ln -s /opt/IBM/AppScan_Source ./install Index: /issm/trunk-jpl-damage/externalpackages/autoconf/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/autoconf/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/autoconf/install.sh (revision 11330) @@ -0,0 +1,19 @@ +#!/bin/bash + +#Some cleanup +rm -rf install autoconf-2.63 src + +#Create install directories +mkdir install + +#Untar +tar -zxvf autoconf-2.63.tar.gz + +#Move autoconf into src directory +mv autoconf-2.63 src + +#Compile autoconf +cd src +./configure --prefix="$ISSM_TIER/externalpackages/autoconf/install" +make +make install Index: /issm/trunk-jpl-damage/externalpackages/automake/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/automake/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/automake/install.sh (revision 11330) @@ -0,0 +1,17 @@ +#!/bin/bash + +#Some cleanup +rm -rf install automake-1.10.2 src + +#Create install directories +mkdir install + +#Untar +tar -zxvf automake-1.10.2.tar.gz +mv automake-1.10.2 src + +#Compile automake +cd src +./configure --prefix="$ISSM_TIER/externalpackages/automake/install" +make +make install Index: /issm/trunk-jpl-damage/externalpackages/bbftp/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/bbftp/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/bbftp/install.sh (revision 11330) @@ -0,0 +1,23 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install bbftp-client-3.2.0 + +#Create install directories +mkdir install src + +#Untar +tar -zxvf bbftp-client-3.2.0.tar.gz + +#Move bbftp-client into install directory +mv bbftp-client-3.2.0/* src +rm -rf bbftp-client-3.2.0 + +#Apply patches +cd src + +#Configure and compile +cd bbftpc +./configure --prefix=$ISSM_TIER/externalpackages/bbftp/install +make +make install Index: /issm/trunk-jpl-damage/externalpackages/boost/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/boost/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/boost/install.sh (revision 11330) @@ -0,0 +1,24 @@ +#!/bin/bash + +#Some cleanup +rm -rf install boost_1_45_0 src +mkdir install src + +#Untar +tar -zxvf boost_1_45_0.tar.gz + +#Move boost into install directory +mv boost_1_45_0/* src +rm -rf boost_1_45_0 + +#Configure and compile +cd src +./bootstrap.sh --prefix=$ISSM_TIER/externalpackages/boost/install + +#Compile boost +if [ -z $1 ]; +then + ./bjam install +else + ./bjam -j $1 install +fi Index: /issm/trunk-jpl-damage/externalpackages/canos/InterX.m =================================================================== --- /issm/trunk-jpl-damage/externalpackages/canos/InterX.m (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/canos/InterX.m (revision 11330) @@ -0,0 +1,82 @@ +function P = InterX(L1,varargin) +%INTERX Intersection of curves +% P = INTERX(L1,L2) returns the intersection points of two curves L1 +% and L2. The curves L1,L2 can be either closed or open and are described +% by two-row-matrices, where each row contains its x- and y- coordinates. +% The intersection of groups of curves (e.g. contour lines, multiply +% connected regions etc) can also be computed by separating them with a +% column of NaNs as for example +% +% L = [x11 x12 x13 ... NaN x21 x22 x23 ...; +% y11 y12 y13 ... NaN y21 y22 y23 ...] +% +% P has the same structure as L1 and L2, and its rows correspond to the +% x- and y- coordinates of the intersection points of L1 and L2. If no +% intersections are found, the returned P is empty. +% +% P = INTERX(L1) returns the self-intersection points of L1. To keep +% the code simple, the points at which the curve is tangent to itself are +% not included. P = INTERX(L1,L1) returns all the points of the curve +% together with any self-intersection points. +% +% Example: +% t = linspace(0,2*pi); +% r1 = sin(4*t)+2; x1 = r1.*cos(t); y1 = r1.*sin(t); +% r2 = sin(8*t)+2; x2 = r2.*cos(t); y2 = r2.*sin(t); +% P = InterX([x1;y1],[x2;y2]); +% plot(x1,y1,x2,y2,P(1,:),P(2,:),'ro') + +% Author : NS +% Version: 3.0, 21 Sept. 2010 + +% Two words about the algorithm: Most of the code is self-explanatory. +% The only trick lies in the calculation of C1 and C2. To be brief, this +% is essentially the two-dimensional analog of the condition that needs +% to be satisfied by a function F(x) that has a zero in the interval +% [a,b], namely +% F(a)*F(b) <= 0 +% C1 and C2 exactly do this for each segment of curves 1 and 2 +% respectively. If this condition is satisfied simultaneously for two +% segments then we know that they will cross at some point. +% Each factor of the 'C' arrays is essentially a matrix containing +% the numerators of the signed distances between points of one curve +% and line segments of the other. + + %...Argument checks and assignment of L2 + error(nargchk(1,2,nargin)); + if nargin == 1, + L2 = L1; hF = @lt; %...Avoid the inclusion of common points + else + L2 = varargin{1}; hF = @le; + end + + %...Preliminary stuff + x1 = L1(1,:)'; x2 = L2(1,:); + y1 = L1(2,:)'; y2 = L2(2,:); + dx1 = diff(x1); dy1 = diff(y1); + dx2 = diff(x2); dy2 = diff(y2); + + %...Determine 'signed distances' + S1 = dx1.*y1(1:end-1) - dy1.*x1(1:end-1); + S2 = dx2.*y2(1:end-1) - dy2.*x2(1:end-1); + + C1 = feval(hF,D(bsxfun(@times,dx1,y2)-bsxfun(@times,dy1,x2),S1),0); + C2 = feval(hF,D((bsxfun(@times,y1,dx2)-bsxfun(@times,x1,dy2))',S2'),0)'; + + %...Obtain the segments where an intersection is expected + [i,j] = find(C1 & C2); + if isempty(i),P = zeros(2,0);return; end; + + %...Transpose and prepare for output + i=i'; dx2=dx2'; dy2=dy2'; S2 = S2'; + L = dy2(j).*dx1(i) - dy1(i).*dx2(j); + i = i(L~=0); j=j(L~=0); L=L(L~=0); %...Avoid divisions by 0 + + %...Solve system of eqs to get the common points + P = unique([dx2(j).*S1(i) - dx1(i).*S2(j), ... + dy2(j).*S1(i) - dy1(i).*S2(j)]./[L L],'rows')'; + + function u = D(x,y) + u = bsxfun(@minus,x(:,1:end-1),y).*bsxfun(@minus,x(:,2:end),y); + end +end Index: /issm/trunk-jpl-damage/externalpackages/canos/license.txt =================================================================== --- /issm/trunk-jpl-damage/externalpackages/canos/license.txt (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/canos/license.txt (revision 11330) @@ -0,0 +1,25 @@ +Copyright (c) 2006, Antoni J. Canós +Copyright (c) 2008, Douglas M. Schwarz +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. Index: /issm/trunk-jpl-damage/externalpackages/canos/licenseNS.txt =================================================================== --- /issm/trunk-jpl-damage/externalpackages/canos/licenseNS.txt (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/canos/licenseNS.txt (revision 11330) @@ -0,0 +1,24 @@ +Copyright (c) 2009, NS +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. Index: /issm/trunk-jpl-damage/externalpackages/canos/selfintersect.m =================================================================== --- /issm/trunk-jpl-damage/externalpackages/canos/selfintersect.m (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/canos/selfintersect.m (revision 11330) @@ -0,0 +1,174 @@ +function [x0,y0,segments]=selfintersect(x,y) + +%SELFINTERSECT Self-intersections of a curve. +% +% [X0,Y0,SEGMENTS] = SELFINTERSECT(X,Y) computes the locations where +% a curve self-intersects in a fast and robust way. +% The curve can be broken with NaNs or have vertical segments. +% Segments of the curve involved in each of the self-interesections are +% also provided. +% +% Vectors X and Y are equal-length vectors of at least four points defining +% the curve. +% X0 and Y0 are column vectors with the x- and y- coordinates, respectively +% of the N self-intersections. +% SEGMENTS is an N x 2 matrix containing the pairs of segments involved in +% each self-intersection. +% +% This program uses the theory of operation of the file "Fast and Robust Curve +% Intersections" submitted by Douglas M. Schwartz (intersections.m, F.Id: 11837). +% +% Example of use +% N=201; +% th=linspace(-3*pi,4*pi,N); +% R=1; +% x=R*cos(th)+linspace(0,6,N); +% y=R*sin(th)+linspace(0,1,N); +% t0=clock; +% [x0,y0,segments]=selfintersect(x,y) +% etime(clock,t0) +% plot(x,y,'b',x0,y0,'.r'); +% axis ('equal'); grid + +% +% See also INTERSECTIONS. +% +%Version: 1.0, December 11, 2006 +%Tested under MATLAB 6.5.0. R13. +% +% (c) Antoni J. Canos. +% ITACA. Techincal University of Valencia (Spain) +% Email: ancama2@dcom.upv.es + + +% Input checks. +error(nargchk(2,2,nargin)) +% x and y must be vectors with same number of points (at least 4 for self-intersection). +if sum(size(x) > 3) ~= 1 || sum(size(y) > 3) ~= 1 || ... + length(x) ~= length(y) + error('X and Y must be equal-length vectors of at least 4 points.') +end + +x0=[]; +y0=[]; +segments=[]; + +% Two similar curves are firstly created. +x1=x; x2=x; +y1=y; y2=y; + +x1 = x1(:); +y1 = y1(:); +x2 = x2(:); +y2 = y2(:); + +% Compute number of line segments in each curve and some differences we'll +% need later. +n1 = length(x1) - 1; +n2 = length(x2) - 1; + +dxy1 = diff([x1 y1]); +dxy2 = diff([x2 y2]); + +% Determine the combinations of i and j where the rectangle enclosing the +% i'th line segment of curve 1 overlaps with the rectangle enclosing the +% j'th line segment of curve 2. +[i,j] = find(repmat(min(x1(1:end-1),x1(2:end)),1,n2) <= ... + repmat(max(x2(1:end-1),x2(2:end)).',n1,1) & ... + repmat(max(x1(1:end-1),x1(2:end)),1,n2) >= ... + repmat(min(x2(1:end-1),x2(2:end)).',n1,1) & ... + repmat(min(y1(1:end-1),y1(2:end)),1,n2) <= ... + repmat(max(y2(1:end-1),y2(2:end)).',n1,1) & ... + repmat(max(y1(1:end-1),y1(2:end)),1,n2) >= ... + repmat(min(y2(1:end-1),y2(2:end)).',n1,1)); + +% Removing coincident and adjacent segments. +remove=find(abs(i-j)<2); +i(remove)=[]; +j(remove)=[]; + +% Removing duplicate combinations of segments. +remove=[]; +for ii=1:size(i,1) + ind=find((i(ii)==j(ii:end))&(j(ii)==i(ii:end))); + remove=[remove;ii-1+ind]; +end +i(remove)=[]; +j(remove)=[]; + +% Find segments pairs which have at least one vertex = NaN and remove them. +% This line is a fast way of finding such segment pairs. We take +% advantage of the fact that NaNs propagate through calculations, in +% particular subtraction (in the calculation of dxy1 and dxy2, which we +% need anyway) and addition. +remove = isnan(sum(dxy1(i,:) + dxy2(j,:),2)); +i(remove) = []; +j(remove) = []; + +% Find segments pairs which have at least one vertex = NaN and remove them. +% This line is a fast way of finding such segment pairs. We take +% advantage of the fact that NaNs propagate through calculations, in +% particular subtraction (in the calculation of dxy1 and dxy2, which we +% need anyway) and addition. +remove = isnan(sum(dxy1(i,:) + dxy2(j,:),2)); +i(remove) = []; +j(remove) = []; + +% Initialize matrices. We'll put the T's and B's in matrices and use them +% one column at a time. For some reason, the \ operation below is faster +% on my machine when A is sparse so we'll initialize a sparse matrix with +% the fixed values and then assign the changing values in the loop. +n = length(i); +T = zeros(4,n); +A = sparse([1 2 3 4],[3 3 4 4],-1,4,4,8); +B = -[x1(i) x2(j) y1(i) y2(j)].'; +index_dxy1 = [1 3]; % A(1) = A(1,1), A(3) = A(3,1) +index_dxy2 = [6 8]; % A(6) = A(2,2), A(8) = A(4,2) + +% Loop through possibilities. Set warning not to trigger for anomalous +% results (i.e., when A is singular). +warning_state = warning('off','MATLAB:singularMatrix'); +try + for k = 1:n + A(index_dxy1) = dxy1(i(k),:); + A(index_dxy2) = dxy2(j(k),:); + T(:,k) = A\B(:,k); + end + warning(warning_state) +catch + warning(warning_state) + rethrow(lasterror) +end + +% Find where t1 and t2 are between 0 and 1 and return the corresponding x0 +% and y0 values. Anomalous segment pairs can be segment pairs that are +% colinear (overlap) or the result of segments that are degenerate (end +% points the same). The algorithm will return an intersection point that +% is at the center of the overlapping region. Because of the finite +% precision of floating point arithmetic it is difficult to predict when +% two line segments will be considered to overlap exactly or even intersect +% at an end point. For this algorithm, an anomaly is detected when any +% element of the solution (a single column of T) is a NaN. + +in_range = T(1,:) >= 0 & T(2,:) >= 0 & T(1,:) < 1 & T(2,:) < 1; +anomalous = any(isnan(T)); +if any(anomalous) + ia = i(anomalous); + ja = j(anomalous); + % set x0 and y0 to middle of overlapping region. + T(3,anomalous) = (max(min(x1(ia),x1(ia+1)),min(x2(ja),x2(ja+1))) + ... + min(max(x1(ia),x1(ia+1)),max(x2(ja),x2(ja+1))))/2; + T(4,anomalous) = (max(min(y1(ia),y1(ia+1)),min(y2(ja),y2(ja+1))) + ... + min(max(y1(ia),y1(ia+1)),max(y2(ja),y2(ja+1))))/2; + x0 = T(3,in_range | anomalous).'; + y0 = T(4,in_range | anomalous).'; + i=i(in_range | anomalous); + j=j(in_range | anomalous); +else + x0 = T(3,in_range).'; + y0 = T(4,in_range).'; + i=i(in_range); + j=j(in_range); +end + +segments=sort([i,j],2); Index: /issm/trunk-jpl-damage/externalpackages/chaco/chaco.h =================================================================== --- /issm/trunk-jpl-damage/externalpackages/chaco/chaco.h (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/chaco/chaco.h (revision 11330) @@ -0,0 +1,39 @@ +/*!\file: chaco.h + * \brief prototypes for chaco library + */ + +#ifndef _CHACO_INCLUDES_H_ +#define _CHACO_INCLUDES_H_ + +#include "./defs.h" +#include "./params.h" + +extern "C" int interface( int nvtxs, /* number of vertices in full graph */ + int *start, /* start of edge list for each vertex */ + int *adjacency, /* edge list data */ + int *vwgts, /* weights for all vertices */ + float *ewgts, /* weights for all edges */ + float *x, + float *y, + float *z, /* coordinates for inertial method */ + char *outassignname, /* name of assignment output file */ + char *outfilename, /* output file name */ + short *assignment, /* set number of each vtx (length n) */ + int architecture, /* 0 => hypercube, d => d-dimensional mesh */ + int ndims_tot, /* total number of cube dimensions to divide */ + int mesh_dims[3], /* dimensions of mesh of processors */ + double *goal, /* desired set sizes for each set */ + int global_method, /* global partitioning algorithm */ + int local_method, /* local partitioning algorithm */ + int rqi_flag, /* should I use RQI/Symmlq eigensolver? */ + int vmax, /* how many vertices to coarsen down to? */ + int ndims, /* number of eigenvectors (2^d sets) */ + double eigtol, /* tolerance on eigenvectors */ + long seed); /* for random graph mutations */ + +extern "C" void read_params(FILE* pfile); /* file with new user parameters */ +extern "C" void smalloc_stats(void); +extern "C" double* smalloc(unsigned int n); /* number of bytes to be allocated */ + +#endif //ifndef _CHACO_INCLUDES_H_ + Index: /issm/trunk-jpl-damage/externalpackages/chaco/chaco.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/chaco/chaco.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/chaco/chaco.patch (revision 11330) @@ -0,0 +1,572 @@ +Only in src/code/assign: assign.o +diff -rc src/code/assign/assign_out.c old/code/assign/assign_out.c +*** src/code/assign/assign_out.c 2010-07-16 16:28:47.352242454 -0700 +--- old/code/assign/assign_out.c 1995-08-08 14:32:10.000000000 -0700 +*************** +*** 3,9 **** + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + + #include +- #include "defs.h" + + static void assign_out_normal(), assign_out_inv(); + +--- 3,8 ---- +Only in src/code/assign: assign_out.o +Only in src/code/assign: mapper.o +Only in src/code/assign: median.o +Only in src/code/assign: merge_assign.o +Only in src/code/assign: rec_median.o +Only in src/code/assign: rotate.o +Only in src/code/assign: y2x.o +Only in src/code/bpmatch: checkbp.o +Only in src/code/bpmatch: genvals2d.o +Only in src/code/bpmatch: genvals3d.o +Only in src/code/bpmatch: inits2d.o +Only in src/code/bpmatch: inits3d.o +Only in src/code/bpmatch: map2d.o +Only in src/code/bpmatch: map3d.o +Only in src/code/bpmatch: movevtxs.o +Only in src/code/bpmatch: sorts2d.o +Only in src/code/bpmatch: sorts3d.o +Only in src/code: chacominusblas.a +Only in src/code/coarsen: coarsen1.o +Only in src/code/coarsen: coarsen.o +Only in src/code/coarsen: interpolate.o +Only in src/code/coarsen: makeccoords.o +Only in src/code/coarsen: makefgraph.o +Only in src/code/coarsen: makev2cv.o +Only in src/code/coarsen: maxmatch1.o +Only in src/code/coarsen: maxmatch2.o +Only in src/code/coarsen: maxmatch3.o +Only in src/code/coarsen: maxmatch4.o +Only in src/code/coarsen: maxmatch5.o +Only in src/code/coarsen: maxmatch.o +Only in src/code/connect: add_edges.o +Only in src/code/connect: connected.o +Only in src/code/connect: find_edges.o +Only in src/code/eigen: bidir.o +Only in src/code/eigen: bisect.o +Only in src/code/eigen: checkeig_ext.o +Only in src/code/eigen: checkeig.o +Only in src/code/eigen: checkorth.o +Only in src/code/eigen: cksturmcnt.o +Only in src/code/eigen: eigensolve.o +diff -rc src/code/eigen/get_extval.c old/code/eigen/get_extval.c +*** src/code/eigen/get_extval.c 2010-07-16 16:28:47.353242463 -0700 +--- old/code/eigen/get_extval.c 1995-08-08 14:32:20.000000000 -0700 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + /* Finds first extended eigenpair of system corresponding to + tridiagonal T using using Rafael's bisection technique. */ +--- 4,9 ---- +Only in src/code/eigen: get_extval.o +Only in src/code/eigen: get_ritzvals.o +Only in src/code/eigen: lanc_seconds.o +Only in src/code/eigen: lanczos_ext_float.o +Only in src/code/eigen: lanczos_ext.o +Only in src/code/eigen: lanczos_FO.o +Only in src/code/eigen: lanczos_SO_float.o +Only in src/code/eigen: lanczos_SO.o +Only in src/code/eigen: lanpause.o +Only in src/code/eigen: makeorthlnk.o +Only in src/code/eigen: mkeigvecs.o +Only in src/code/eigen: mkscanlist.o +Only in src/code/eigen: orthog1.o +Only in src/code/eigen: orthogonalize.o +Only in src/code/eigen: orthogvec.o +Only in src/code/eigen: ql.o +Only in src/code/eigen: rqi_ext.o +Only in src/code/eigen: rqi.o +Only in src/code/eigen: scale_diag.o +Only in src/code/eigen: scanmax.o +Only in src/code/eigen: scanmin.o +Only in src/code/eigen: solistout.o +Only in src/code/eigen: sorthog.o +Only in src/code/eigen: splarax.o +Only in src/code/eigen: sturmcnt.o +Only in src/code/eigen: Tevec.o +Only in src/code/eigen: tri_solve.o +Only in src/code/eigen: warnings.o +Only in src/code/graph: check_graph.o +Only in src/code/graph: free_graph.o +Only in src/code/graph: graph_out.o +Only in src/code/graph: reformat.o +Only in src/code/graph: subgraph.o +Only in src/code/inertial: eigenvec2.o +Only in src/code/inertial: eigenvec3.o +Only in src/code/inertial: inertial1d.o +Only in src/code/inertial: inertial2d.o +Only in src/code/inertial: inertial3d.o +Only in src/code/inertial: inertial.o +Only in src/code/inertial: make_subgeom.o +Only in src/code/input: check_input.o +Only in src/code/input: input_assign.o +Only in src/code/input: input_geom.o +Only in src/code/input: input_graph.o +Only in src/code/input: input.o +Only in src/code/input: read_params.o +Only in src/code/input: read_val.o +Only in src/code/input: reflect_input.o +Only in src/code/internal: check_internal.o +Only in src/code/internal: force_internal.o +Only in src/code/internal: improve_internal.o +Only in src/code/klspiff: bilistops.o +Only in src/code/klspiff: buckets1.o +Only in src/code/klspiff: buckets_bi.o +Only in src/code/klspiff: buckets.o +Only in src/code/klspiff: coarsen_kl.o +Only in src/code/klspiff: compress_ewgts.o +Only in src/code/klspiff: count_weights.o +Only in src/code/klspiff: kl_init.o +Only in src/code/klspiff: kl_output.o +Only in src/code/klspiff: klspiff.o +Only in src/code/klspiff: make_bndy_list.o +Only in src/code/klspiff: make_kl_list.o +Only in src/code/klspiff: nway_kl.o +Only in src/code/klvspiff: bpm_improve.o +Only in src/code/klvspiff: bucketsv.o +Only in src/code/klvspiff: clear_dvals.o +Only in src/code/klvspiff: coarsen_klv.o +Only in src/code/klvspiff: countup_vtx_sep.o +Only in src/code/klvspiff: find_bndy.o +Only in src/code/klvspiff: flatten.o +Only in src/code/klvspiff: flow.o +Only in src/code/klvspiff: klv_init.o +Only in src/code/klvspiff: klvspiff.o +Only in src/code/klvspiff: make_bpgraph.o +Only in src/code/klvspiff: make_sep_list.o +diff -rc src/code/klvspiff/matching.c old/code/klvspiff/matching.c +*** src/code/klvspiff/matching.c 2010-07-16 16:28:47.356242493 -0700 +--- old/code/klvspiff/matching.c 1996-03-11 10:24:25.000000000 -0800 +*************** +*** 6,12 **** + code provided by Ed Rothberg at SGI. */ + + #include +- #include "defs.h" + + #define TRUE 1 + #define FALSE 0 +--- 6,11 ---- +Only in src/code/klvspiff: matching.o +Only in src/code/klvspiff: nway_klv.o +diff -rc src/code/main/defs.h old/code/main/defs.h +*** src/code/main/defs.h 2010-07-16 16:28:47.359242522 -0700 +--- old/code/main/defs.h 1995-08-08 14:32:41.000000000 -0700 +*************** +*** 1,39 **** +! #ifndef _CHACO_DEFS_H_ +! #define _CHACO_DEFS_H_ +! + #define TRUE 1 + #define FALSE 0 + +! #ifndef _HAVE_CHACO_ //protect ISSM compilation. This symbol is defined when we compile ISSM +! +! #define max(A, B) ((A) > (B) ? (A) : (B)) +! #define min(A, B) ((A) < (B) ? (A) : (B)) +! #define sign(A) ((A) < 0 ? -1 : 1) +! #define absval(A) ((A) < 0 ? -(A): (A)) +! +! /* Define constants that are needed in various places */ +! #define PI 3.141592653589793 +! #define TWOPI 6.283185307179586 +! #define HALFPI 1.570796326794896 +! +! #define check_graph chaco_check_graph +! +! +! #ifdef MATLAB +! #include "mat.h" +! #include "mex.h" +! #include "matrix.h" +! +! #define printf mexPrintf +! #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) +! #define malloc mxMalloc +! #define calloc mxCalloc +! #define realloc mxRealloc +! #define free mxFree +! #define exit(status) mexErrMsgTxt("exit=" #status) +! +! #endif +! +! #endif //#ifndef _HAVE_CHACO_ +! +! #endif //ifndef _CHACO_DEFS_H_ +--- 1,11 ---- +! #define max(A, B) ((A) > (B) ? (A) : (B)) +! #define min(A, B) ((A) < (B) ? (A) : (B)) +! #define sign(A) ((A) < 0 ? -1 : 1) +! #define absval(A) ((A) < 0 ? -(A): (A)) + #define TRUE 1 + #define FALSE 0 + +! /* Define constants that are needed in various places */ +! #define PI 3.141592653589793 +! #define TWOPI 6.283185307179586 +! #define HALFPI 1.570796326794896 +Only in src/code/main: interface.o +Only in src/code/main: main.o +diff -rc src/code/main/params.h old/code/main/params.h +*** src/code/main/params.h 2010-07-16 16:28:47.361242541 -0700 +--- old/code/main/params.h 1995-08-08 14:32:43.000000000 -0700 +*************** +*** 1,12 **** +- #ifndef _CHACO_PARAMS_H_ +- #define _CHACO_PARAMS_H_ +- +- + #define NAME_LENGTH 80 /* Maximum length of file name */ + #define LINE_LENGTH 200 /* Length of input files read at once */ + + #define MAXDIMS 3 /* Most cuts allowed at one time */ + #define MAXSETS 8 /* 2^MAXDIMS */ +- +- +- #endif //ifndef _CHACO_PARAMS_H_ +--- 1,5 ---- +Only in src/code/main: user_params.o +diff -rc src/code/Makefile old/code/Makefile +*** src/code/Makefile 2010-07-21 18:22:19.909939194 -0700 +--- old/code/Makefile 1997-10-02 10:23:22.000000000 -0700 +*************** +*** 2,18 **** + DEST= ${DEST_DIR}/chaco + CC = gcc + IFLAG = -Imain +! #IFLAG = -Imain -I/usr/local/pkgs/matlab-7.6/extern/include +! #CFLAGS = -O2 +! #OFLAGS = -O2 +! #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions +! CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g +! #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB +! OFLAGS = -O2 +! #AR = /usr/ccs/bin/ar rcv # for solaris 2 +! AR = /usr/bin/ar rcv +! #RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +! RANLIB = /usr/bin/ranlib + + FILES.c= main/user_params.c main/interface.c main/main.c \ + submain/balance.c submain/divide.c submain/submain.c \ +--- 2,9 ---- + DEST= ${DEST_DIR}/chaco + CC = gcc + IFLAG = -Imain +! CFLAGS = -O2 +! OFLAGS = -O2 + + FILES.c= main/user_params.c main/interface.c main/main.c \ + submain/balance.c submain/divide.c submain/submain.c \ +*************** +*** 96,196 **** + util/update.c util/vecout.c util/vecran.c \ + util/vecscale.c + +- +- FILESMINUSBLAS.c= main/user_params.c main/interface.c main/main.c \ +- submain/balance.c submain/divide.c submain/submain.c \ +- input/input_assign.c \ +- input/check_input.c input/input.c input/input_geom.c \ +- input/input_graph.c input/read_params.c input/reflect_input.c \ +- input/read_val.c \ +- graph/check_graph.c graph/free_graph.c \ +- graph/reformat.c graph/subgraph.c graph/graph_out.c \ +- inertial/eigenvec2.c inertial/eigenvec3.c inertial/inertial.c \ +- inertial/inertial1d.c inertial/inertial2d.c \ +- inertial/inertial3d.c inertial/make_subgeom.c \ +- klspiff/buckets.c klspiff/buckets_bi.c klspiff/buckets1.c \ +- klspiff/bilistops.c klspiff/coarsen_kl.c klspiff/count_weights.c \ +- klspiff/compress_ewgts.c klspiff/kl_init.c klspiff/kl_output.c \ +- klspiff/klspiff.c klspiff/make_bndy_list.c \ +- klspiff/make_kl_list.c klspiff/nway_kl.c \ +- klvspiff/bpm_improve.c klvspiff/bucketsv.c \ +- klvspiff/clear_dvals.c klvspiff/coarsen_klv.c \ +- klvspiff/countup_vtx_sep.c klvspiff/find_bndy.c klvspiff/flow.c \ +- klvspiff/klv_init.c klvspiff/klvspiff.c klvspiff/make_bpgraph.c \ +- klvspiff/make_sep_list.c klvspiff/matching.c klvspiff/nway_klv.c \ +- klvspiff/flatten.c \ +- coarsen/coarsen.c coarsen/interpolate.c coarsen/makefgraph.c \ +- coarsen/makeccoords.c \ +- coarsen/coarsen1.c coarsen/makev2cv.c \ +- coarsen/maxmatch.c coarsen/maxmatch1.c coarsen/maxmatch2.c \ +- coarsen/maxmatch3.c coarsen/maxmatch4.c coarsen/maxmatch5.c \ +- connect/add_edges.c connect/connected.c connect/find_edges.c \ +- eigen/bidir.c eigen/bisect.c eigen/checkeig.c \ +- eigen/checkeig_ext.c \ +- eigen/checkorth.c eigen/cksturmcnt.c eigen/mkeigvecs.c\ +- eigen/eigensolve.c eigen/get_extval.c eigen/get_ritzvals.c \ +- eigen/lanczos_FO.c eigen/lanczos_SO.c eigen/lanczos_SO_float.c \ +- eigen/lanczos_ext.c eigen/lanczos_ext_float.c eigen/lanc_seconds.c\ +- eigen/lanpause.c eigen/makeorthlnk.c eigen/mkscanlist.c \ +- eigen/orthog1.c eigen/orthogonalize.c eigen/orthogvec.c \ +- eigen/ql.c eigen/rqi.c eigen/rqi_ext.c eigen/scale_diag.c \ +- eigen/scanmax.c eigen/scanmin.c eigen/solistout.c \ +- eigen/sorthog.c eigen/splarax.c eigen/sturmcnt.c \ +- eigen/Tevec.c eigen/tri_solve.c eigen/warnings.c \ +- symmlq/aprod.c symmlq/msolve.c symmlq/pow_dd.c \ +- symmlq/symmlq.c \ +- tinvit/tinvit.c tinvit/pythag.c tinvit/epslon.c \ +- optimize/determinant.c optimize/func2d.c \ +- optimize/func3d.c optimize/opt2d.c optimize/opt3d.c \ +- assign/assign.c assign/assign_out.c assign/mapper.c \ +- assign/median.c assign/merge_assign.c \ +- assign/rec_median.c assign/rotate.c assign/y2x.c \ +- bpmatch/checkbp.c bpmatch/inits2d.c bpmatch/inits3d.c \ +- bpmatch/genvals2d.c bpmatch/genvals3d.c bpmatch/map2d.c \ +- bpmatch/map3d.c bpmatch/movevtxs.c \ +- bpmatch/sorts2d.c bpmatch/sorts3d.c \ +- refine_map/compute_cube_edata.c refine_map/compute_cube_vdata.c \ +- refine_map/refine_cube.c refine_map/update_cube_edata.c \ +- refine_map/update_cube_vdata.c refine_map/find_edge_cube.c \ +- refine_map/init_cube_edata.c refine_map/compute_mesh_edata.c \ +- refine_map/compute_mesh_vdata.c refine_map/find_edge_mesh.c \ +- refine_map/init_mesh_edata.c refine_map/refine_mesh.c \ +- refine_map/update_mesh_edata.c refine_map/update_mesh_vdata.c \ +- refine_map/refine_map.c refine_map/make_comm_graph.c \ +- refine_part/refine_part.c refine_part/kl_refine.c \ +- refine_part/make_maps_ref.c refine_part/make_terms_ref.c \ +- internal/force_internal.c internal/improve_internal.c \ +- internal/check_internal.c \ +- misc/define_subcubes.c misc/define_submeshes.c \ +- misc/divide_procs.c misc/merge_goals.c misc/make_term_props.c \ +- misc/count.c misc/countup.c misc/countup_cube.c \ +- misc/countup_mesh.c misc/make_subgoal.c \ +- misc/find_maxdeg.c misc/make_maps.c misc/make_setlists.c \ +- misc/sequence.c misc/perturb.c misc/simple_part.c \ +- misc/time_kernels.c misc/timing.c \ +- util/affirm.c util/array_alloc_2D.c util/bit_reverse.c \ +- util/checkpnt.c util/cpvec.c util/dot.c \ +- util/doubleout.c util/input_int.c util/gray.c \ +- util/machine_params.c util/makevwsqrt.c util/mkvec.c util/norm.c \ +- util/normalize.c util/mergesort.c \ +- util/randomize.c util/smalloc.c util/bail.c \ +- util/scadd.c util/seconds.c util/setvec.c util/shell_sort.c \ +- util/strout.c util/tri_prod.c util/true_or_false.c \ +- util/update.c util/vecout.c util/vecran.c \ +- util/vecscale.c +- + FILES.o= $(FILES.c:.c=.o) +- FILESMINUSBLAS.o= $(FILESMINUSBLAS.c:.c=.o) +- +- +- ${DEST}: ${FILES.c} chaco.a Makefile +- ${CC} ${OFLAGS} chaco.a -lm -o ${DEST} + +- chaco.a: ${FILES.o} +- ${AR} chaco.a ${FILES.o} ; ${RANLIB} chaco.a + +! chacominusblas.a: ${FILESMINUSBLAS.o} +! ${AR} chacominusblas.a ${FILESMINUSBLAS.o} ; ${RANLIB} chacominusblas.a + + lint: + lint ${IFLAG} ${FILES.c} -lm +--- 87,97 ---- + util/update.c util/vecout.c util/vecran.c \ + util/vecscale.c + + FILES.o= $(FILES.c:.c=.o) + + +! ${DEST}: ${FILES.o} Makefile +! ${CC} ${OFLAGS} ${FILES.o} -lm -o ${DEST} + + lint: + lint ${IFLAG} ${FILES.c} -lm +Only in src/code/misc: count.o +Only in src/code/misc: countup_cube.o +Only in src/code/misc: countup_mesh.o +Only in src/code/misc: countup.o +Only in src/code/misc: define_subcubes.o +Only in src/code/misc: define_submeshes.o +Only in src/code/misc: divide_procs.o +Only in src/code/misc: find_maxdeg.o +Only in src/code/misc: make_maps.o +Only in src/code/misc: make_setlists.o +Only in src/code/misc: make_subgoal.o +Only in src/code/misc: make_term_props.o +Only in src/code/misc: merge_goals.o +Only in src/code/misc: perturb.o +Only in src/code/misc: sequence.o +Only in src/code/misc: simple_part.o +Only in src/code/misc: time_kernels.o +diff -rc src/code/misc/timing.c old/code/misc/timing.c +*** src/code/misc/timing.c 2010-07-16 16:28:47.366242590 -0700 +--- old/code/misc/timing.c 1997-01-03 09:10:52.000000000 -0800 +*************** +*** 3,9 **** + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + + #include +- #include "defs.h" + + /* Timing parameters. */ + +--- 3,8 ---- +Only in src/code/misc: timing.o +Only in src/code/optimize: determinant.o +Only in src/code/optimize: func2d.o +Only in src/code/optimize: func3d.o +Only in src/code/optimize: opt2d.o +Only in src/code/optimize: opt3d.o +Only in src/code/refine_map: compute_cube_edata.o +Only in src/code/refine_map: compute_cube_vdata.o +Only in src/code/refine_map: compute_mesh_edata.o +Only in src/code/refine_map: compute_mesh_vdata.o +Only in src/code/refine_map: find_edge_cube.o +Only in src/code/refine_map: find_edge_mesh.o +Only in src/code/refine_map: init_cube_edata.o +Only in src/code/refine_map: init_mesh_edata.o +Only in src/code/refine_map: make_comm_graph.o +Only in src/code/refine_map: refine_cube.o +Only in src/code/refine_map: refine_map.o +Only in src/code/refine_map: refine_mesh.o +Only in src/code/refine_map: update_cube_edata.o +Only in src/code/refine_map: update_cube_vdata.o +Only in src/code/refine_map: update_mesh_edata.o +Only in src/code/refine_map: update_mesh_vdata.o +Only in src/code/refine_part: kl_refine.o +Only in src/code/refine_part: make_maps_ref.o +Only in src/code/refine_part: make_terms_ref.o +Only in src/code/refine_part: refine_part.o +Only in src/code/submain: balance.o +Only in src/code/submain: divide.o +Only in src/code/submain: submain.o +Only in src/code/symmlq: aprod.o +Only in src/code/symmlq: msolve.o +Only in src/code/symmlq: pow_dd.o +diff -rc src/code/symmlq/symmlqblas.f old/code/symmlq/symmlqblas.f +*** src/code/symmlq/symmlqblas.f 2010-07-21 18:09:10.370123273 -0700 +--- old/code/symmlq/symmlqblas.f 2010-07-21 14:02:09.633743650 -0700 +*************** +*** 16,22 **** + c uses unrolled loops for increments equal to one. + c jack dongarra, linpack, 3/11/78. + c +! double precision dx(1),dy(1),da + integer i,incx,incy,ix,iy,m,mp1,n + c + if(n.le.0)return +--- 16,22 ---- + c uses unrolled loops for increments equal to one. + c jack dongarra, linpack, 3/11/78. + c +! double precision dx(*),dy(*),da + integer i,incx,incy,ix,iy,m,mp1,n + c + if(n.le.0)return +Only in src/code/symmlq: symmlqblas.o +Only in src/code/symmlq: symmlq.o +Only in src/code/tinvit: epslon.o +Only in src/code/tinvit: pythag.o +Only in src/code/tinvit: tinvit.o +Only in src/code/util: affirm.o +Only in src/code/util: array_alloc_2D.o +diff -rc src/code/util/bail.c old/code/util/bail.c +*** src/code/util/bail.c 2010-07-16 16:28:47.368242609 -0700 +--- old/code/util/bail.c 1995-08-08 14:33:01.000000000 -0700 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + /* Wrapper for exit() - print message and exit with status code. Exit code + of 0 indicates normal termination. Exit code of 1 indicates early +--- 4,9 ---- +*************** +*** 15,20 **** +--- 14,20 ---- + int status; + { + extern FILE *Output_File; /* Output file or NULL */ ++ void exit(); + + if (msg != NULL && (int) strlen(msg) > 0) { + printf("%s\n", msg); +Only in src/code/util: bail.o +Only in src/code/util: bit_reverse.o +diff -rc src/code/util/checkpnt.c old/code/util/checkpnt.c +*** src/code/util/checkpnt.c 2010-07-16 16:28:47.370242629 -0700 +--- old/code/util/checkpnt.c 1995-08-08 14:33:01.000000000 -0700 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + /* Debug break point. */ + void checkpnt(tag) +--- 4,9 ---- +Only in src/code/util: checkpnt.o +Only in src/code/util: cpvec.o +Only in src/code/util: dot.o +diff -rc src/code/util/doubleout.c old/code/util/doubleout.c +*** src/code/util/doubleout.c 2010-07-16 16:28:47.372242648 -0700 +--- old/code/util/doubleout.c 1995-08-08 14:33:02.000000000 -0700 +*************** +*** 3,9 **** + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + + #include +- #include "defs.h" + + /* Print a double precision number with filtering format to screen. */ + void doubleout(number, mode) +--- 3,8 ---- +Only in src/code/util: doubleout.o +Only in src/code/util: gray.o +Only in src/code/util: input_int.o +Only in src/code/util: machine_params.o +Only in src/code/util: makevwsqrt.o +Only in src/code/util: mergesort.o +Only in src/code/util: mkvec.o +Only in src/code/util: normalize.o +Only in src/code/util: norm.o +Only in src/code/util: randomize.o +Only in src/code/util: scadd.o +Only in src/code/util: seconds.o +Only in src/code/util: setvec.o +Only in src/code/util: shell_sort.o +diff -rc src/code/util/smalloc.c old/code/util/smalloc.c +*** src/code/util/smalloc.c 2010-07-16 16:28:47.375242677 -0700 +--- old/code/util/smalloc.c 1996-03-11 10:44:07.000000000 -0800 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + static int nmalloc = 0; /* number of calls to malloc */ + static int nfree = 0; /* number of calls to free */ +--- 4,9 ---- +Only in src/code/util: smalloc.o +diff -rc src/code/util/strout.c old/code/util/strout.c +*** src/code/util/strout.c 2010-07-16 16:28:47.377242697 -0700 +--- old/code/util/strout.c 1995-08-08 14:33:05.000000000 -0700 +*************** +*** 4,10 **** + + #include + #include +- #include "defs.h" + + /* Wrapper for a printf statement with a string as only arg. + Prints to screen and to output file if there is one. */ +--- 4,9 ---- +Only in src/code/util: strout.o +Only in src/code/util: tri_prod.o +Only in src/code/util: true_or_false.o +Only in src/code/util: update.o +Only in src/code/util: vecout.o +Only in src/code/util: vecran.o +Only in src/code/util: vecscale.o Index: /issm/trunk-jpl-damage/externalpackages/chaco/chaco_README.txt =================================================================== --- /issm/trunk-jpl-damage/externalpackages/chaco/chaco_README.txt (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/chaco/chaco_README.txt (revision 11330) @@ -0,0 +1,55 @@ +Chaco-2.2.tar (5/03/00? -- 2.0 was 2/95) +http://www.sandia.gov/~bahendr/chaco.html + + +Note that meshpart pulls the object files from here, compiled with +the MATLAB flag for use in the mlchaco mex function, and assembles +them into a library in its own directory. This means that any +objects compiled for the mlchaco mex function and left here should +not be used for the stand-alone chaco executable, and vice versa. + + +[jschierm@astrid main]$ diff defs_old.h defs.h +11a12,27 [for running as a matlab mex function] +> +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> +> #define check_graph chaco_check_graph +> #endif +> + + +added #include "defs.h" to the following: +assign/assign_out.c +eigen/get_extval.c +klvspiff/matching.c +misc/timing.c +util/bail.c +util/checkpnt.c +util/doubleout.c +util/smalloc.c +util/strout.c + + +[jschierm@astrid code]$ diff Makefile_old Makefile +4,5c4,9 [fPIC required, CFLAGS and OFLAGS copied from Cielo gccopts_v75.sh for glnxa64] +< IFLAG = -Imain +< CFLAGS = -O2 +--- +> IFLAG = -Imain -I/usr/local/pkgs/matlab-7.6/extern/include +> #CFLAGS = -O2 +> #OFLAGS = -O2 +> #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions +> CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB +> #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions + Index: /issm/trunk-jpl-damage/externalpackages/chaco/chaco_jes_notes.txt =================================================================== --- /issm/trunk-jpl-damage/externalpackages/chaco/chaco_jes_notes.txt (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/chaco/chaco_jes_notes.txt (revision 11330) @@ -0,0 +1,86 @@ +7/13/09: + +[jschierm@astrid Chaco-2.2]$ diff ../chaco/code/Makefile code +5,6c5,8 [fPIC required, CFLAGS and OFLAGS copied from Cielo gccopts_v75.sh for glnxa64] +< CFLAGS = -O2 +< OFLAGS = -O2 +--- +> #CFLAGS = -O2 +> #OFLAGS = -O2 +> CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread -fexceptions +> OFLAGS = -O -DNDEBUG +34a37,38 [added for meshpart chaco.a library, specified by its makefile] +> coarsen/makecgraph.c \ +> coarsen/countcedges.c \ + +7/30/09: + +[jschierm@astrid main]$ diff defs_old.h defs.h +11a12,26 [for running as a matlab mex function] +> +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> +> #define check_graph chaco_check_graph +> #endif +> + +added #include "defs.h" to the following: +assign/assign_out.c +eigen/get_extval.c +klvspiff/matching.c +misc/timing.c +util/bail.c +util/checkpnt.c +util/doubleout.c +util/smalloc.c +util/strout.c + +[jschierm@astrid code]$ diff Makefile_old Makefile | more +4,5c4,9 +< IFLAG = -Imain +< CFLAGS = -O2 +--- +> IFLAG = -Imain -I/usr/local/pkgs/matlab-7.6/extern/include +> #CFLAGS = -O2 +> #OFLAGS = -O2 +> #CFLAGS = -fPIC -fno-omit-frame-pointer -D_GNU_SOURCE -pthread +> -fexceptions +> CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB +> #CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions + +8/25/09: + +added macro for fprintf to capture missing output: +[jschierm@astrid main]$ diff defs_old.h defs.h +11a12,27 +> +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> +> #define check_graph chaco_check_graph +> #endif +> + +6/15/10: + +- moved check_graph rename outside of MATLAB compiler directive. +- created library chaco.a (without MATLAB compiler directive) for Chaco x-layer to link and implemented it in chaco stand-alone link. + Index: /issm/trunk-jpl-damage/externalpackages/chaco/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/chaco/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/chaco/install.sh (revision 11330) @@ -0,0 +1,46 @@ +#!/bin/bash + +# Some cleanup +rm -rf Chaco-2.2 +rm -rf src +rm -rf install +mkdir src install + +# Untar +tar -xvzf Chaco-2.2.tar.gz + +# Move chaco to src directory +mv Chaco-2.2/* src +rm -rf Chaco-2.2 + +# Apply patches (all at once) +# (written by diff -rc src ~/Libs/Chaco-2.2 > chaco.patch) +patch -R -p0 < chaco.patch + +# Build chaco +cd src/code +if [ -z $1 ]; then + make +else + make -j $1 +fi +make chacominusblas.a + +# Clean up objects (but not library or executable) +make clean +cd ../.. + +# Populate install directory +cp -p src/exec/README install +cp -p src/exec/User_Params install +cp -p src/exec/*.coords install +cp -p src/exec/*.graph install +mkdir install/include +cp -p src/code/main/defs.h install/include/defs.h +cp -p src/code/main/params.h install/include/params.h +cp -p chaco.h install/include/chaco.h +mkdir install/lib +mv src/code/chaco.a install/lib/libchaco.a +mv src/code/chacominusblas.a install/lib/libchacominusblas.a +mkdir install/exec +mv src/exec/chaco install/exec Index: /issm/trunk-jpl-damage/externalpackages/chaco/mex/Chaco.c =================================================================== --- /issm/trunk-jpl-damage/externalpackages/chaco/mex/Chaco.c (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/chaco/mex/Chaco.c (revision 11330) @@ -0,0 +1,244 @@ + +#include +#include /* strcasecmp */ +#include /* clock,time,difftime */ +#include "mex.h" + + +#define THISFUNCTION "Chaco" + +/* Input Arguments */ + +#define A_IN prhs[0] +#define VWGTS_IN prhs[1] +#define EWGTS_IN prhs[2] +#define XYZ_IN prhs[3] +#define OPTNS_IN prhs[4] +#define NPARTS_IN prhs[5] +#define GOAL_IN prhs[6] + +/* Output Arguments */ + +#define ASSGN_OUT plhs[0] + + +void ChacoUsage( void ); + +int Chacox( + int nvtxs, /* number of vertices in graph */ + int *start, /* start of edge list for each vertex */ + int *adjacency, /* edge list data */ + int *vwgts, /* weights for all vertices */ + float *ewgts, /* weights for all edges */ + float *x, + float *y, + float *z, /* coordinates for inertial method */ + short *assignment, /* set number of each vtx (length nvtxs+1) */ + double options[10], /* architecture and partitioning options */ + int *nparts, /* number of parts options */ + double *goal /* desired set sizes */ +); + + +void mexFunction( + int nlhs, /* number of outputs */ + mxArray *plhs[], /* array of pointers to output arguments */ + int nrhs, /* number of inputs */ + const mxArray *prhs[] /* array of pointers to input arguments */ +) +{ + int nvtxs; /* number of vertices in graph */ + int *start; /* start of edge list for each vertex */ + int *adjacency; /* edge list data */ + int *vwgts=NULL; /* weights for all vertices */ + float *ewgts=NULL; /* weights for all edges */ + float *x=NULL; + float *y=NULL; + float *z=NULL; /* coordinates for inertial method */ + short *assignment=NULL; /* set number of each vtx (length nvtxs+1) */ + double options[10]={1,1,0,0,1,1,50,0,.001,7654321}; + /* architecture and partitioning options */ + int *nparts=NULL; /* number of parts options */ + double *goal=NULL; /* desired set sizes */ + + int i, nedges, nterms, ncols, ierr=0; + double *p; + mwIndex *mwstart, *mwadjacency; + + clock_t clock0,clock1; + time_t time0, time1; + + /* Check for proper number of arguments */ + + if (nrhs == 0 && nlhs == 0) { + ChacoUsage(); + return; + } + else if (nrhs < 1 || nlhs > 1) { + ChacoUsage(); + mexErrMsgTxt(" "); + } + + clock0=clock(); + time0 =time(NULL); + mexPrintf("\nChaco Module -- %s",ctime(&time0)); + + /* Assign pointers to the various parameters */ + /* and convert to the appropriate format for Chaco */ + + if (!mxIsEmpty(A_IN) && mxIsNumeric(A_IN) && mxIsSparse(A_IN)) { + nvtxs = mxGetN(A_IN); + mwstart = mxGetJc(A_IN); + start = mxMalloc((mxGetN(A_IN)+1)*sizeof(int)); + for (i=0; i<(mxGetN(A_IN)+1); i++) + start[i]= (int)mwstart[i]; + nedges = start[nvtxs]; + mwadjacency = mxGetIr(A_IN); + adjacency = mxMalloc(mxGetNzmax(A_IN)*sizeof(int)); + for (i=0; i= 2 && !mxIsEmpty(VWGTS_IN)) { + if (mxIsNumeric(VWGTS_IN) && !mxIsSparse(VWGTS_IN) && + (nterms=mxGetM(VWGTS_IN)*mxGetN(VWGTS_IN)) == nvtxs) { + vwgts = (int *) mxCalloc(nvtxs, sizeof(int)); + p = mxGetPr(VWGTS_IN); + for (i = 0; i < nvtxs; vwgts[i++] = (int) *p++); + } + else { + mexPrintf("%s -- Vertex weight vector must be numeric, full, and length=%d.\n", + THISFUNCTION,nvtxs); + mexErrMsgTxt(" "); + } + } + + if (nrhs >= 3 && !mxIsEmpty(EWGTS_IN)) { + if (mxIsNumeric(EWGTS_IN) && mxIsSparse(EWGTS_IN) && + (nterms=mxGetNzmax(EWGTS_IN)) == nedges) { + ewgts = (float *) mxCalloc(nedges, sizeof(float)); + p = mxGetPr(A_IN); + for (i = 0; i < nedges; ewgts[i++] = (float) *p++); + } + else { + mexPrintf("%s -- Edge weight matrix must be numeric, sparse, and nonzeroes=%d.\n", + THISFUNCTION,nedges); + mexErrMsgTxt(" "); + } + } + + if (nrhs >= 4 && (ncols = mxGetN(XYZ_IN)) >= 1) { + if (mxIsNumeric(XYZ_IN) && !mxIsSparse(XYZ_IN) && + mxGetM(XYZ_IN) == nvtxs) { + x = (float *) mxCalloc(nvtxs, sizeof(float)); + p = mxGetPr(XYZ_IN); + for (i = 0; i < nvtxs; x[i++] = (float) *p++); + } + else { + mexPrintf("%s -- XYZ coordinate matrix must be numeric, full, and length=%d.\n", + THISFUNCTION,nvtxs); + mexErrMsgTxt(" "); + } + if ((ncols ) >= 2) { + y = (float *) mxCalloc(nvtxs, sizeof(float)); + for (i = 0; i < nvtxs; y[i++] = (float) *p++); + if ((ncols ) >= 3) { + z = (float *) mxCalloc(nvtxs, sizeof(float)); + for (i = 0; i < nvtxs; z[i++] = (float) *p++); + } + } + } + + if (nrhs >= 5 && !mxIsEmpty(OPTNS_IN)) { + if (mxIsNumeric(OPTNS_IN) && !mxIsSparse(OPTNS_IN) && + (nterms=mxGetM(OPTNS_IN)*mxGetN(OPTNS_IN))) { + p = mxGetPr(OPTNS_IN); + for (i = 0; i < (nterms<10 ? nterms : 10); options[i++] = *p++); + } + else { + mexPrintf("%s -- Options vector must be numeric and full.\n", + THISFUNCTION); + mexErrMsgTxt(" "); + } + } + + if (nrhs >= 6 && !mxIsEmpty(NPARTS_IN)) { + if (mxIsNumeric(NPARTS_IN) && !mxIsSparse(NPARTS_IN) && + (nterms=mxGetM(NPARTS_IN)*mxGetN(NPARTS_IN))) { + nparts = (int *) mxCalloc(nterms, sizeof(int)); + p = mxGetPr(NPARTS_IN); + for (i = 0; i < nterms; nparts[i++] = (int) *p++); + } + else { + mexPrintf("%s -- Parts vector must be numeric and full.\n", + THISFUNCTION); + mexErrMsgTxt(" "); + } + } + + if (nrhs >= 7 && !mxIsEmpty(GOAL_IN)) { + if (mxIsNumeric(GOAL_IN) && !mxIsSparse(GOAL_IN) && + (nterms=mxGetM(GOAL_IN)*mxGetN(GOAL_IN))) { + goal = (double *) mxCalloc(nterms, sizeof(double)); + p = mxGetPr(GOAL_IN); + for (i = 0; i < nterms; goal[i++] = *p++); + } + else { + mexPrintf("%s -- Goal vector must be numeric and full.\n", + THISFUNCTION); + mexErrMsgTxt(" "); + } + } + + assignment = (short *) mxCalloc(nvtxs, sizeof(short)); + + /* Do the actual computations in a subroutine */ + + ierr = Chacox(nvtxs, start, adjacency, vwgts, ewgts, x, y, z, + assignment, options, nparts, goal); + + /* Create matrices for the return arguments */ + + if (!ierr) { + ASSGN_OUT = mxCreateDoubleMatrix(1,nvtxs,mxREAL); + p = mxGetPr(ASSGN_OUT); + for (i = 0; i < nvtxs; *p++ = (double) assignment[i++]); + } + else + ASSGN_OUT = mxCreateDoubleMatrix(0,0,mxREAL); + + /* Free what we allocated */ + + if (!assignment) mxFree((void *) assignment); + if (!goal) mxFree((void *) goal); + if (!nparts) mxFree((void *) nparts); + if (!z) mxFree((void *) z); + if (!y) mxFree((void *) y); + if (!x) mxFree((void *) x); + if (!ewgts) mxFree((void *) ewgts); + if (!vwgts) mxFree((void *) vwgts); + if (!adjacency) mxFree((void *) adjacency); + if (!start) mxFree((void *) start); + + clock1=clock(); + time1 =time(NULL); + mexPrintf("Chaco Module -- %f CPU seconds; %f elapsed seconds.\n\n", + ((double)(clock1-clock0))/CLOCKS_PER_SEC,difftime(time1,time0)); + + return; +} + +void ChacoUsage( void ) +{ + mexPrintf("\n"); + mexPrintf("Usage: [assgn] = Chaco(A,vwgts,ewgts,xyz,options,nparts,goal);\n"); + mexPrintf("\n"); + + return; +} + Index: /issm/trunk-jpl-damage/externalpackages/chaco/mex/Chaco_m.m =================================================================== --- /issm/trunk-jpl-damage/externalpackages/chaco/mex/Chaco_m.m (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/chaco/mex/Chaco_m.m (revision 11330) @@ -0,0 +1,217 @@ +function [part1,part2,chaco_time] = chaco(A,xy,method,nparts,goal) +% CHACO : Hendrickson/Leland's graph partitioner. +% +% [part1,part2,chaco_time] = chaco(A) returns a 50/50 vertex partition of the mesh +% whose symmetric adjacency matrix is A. +% +% Optional arguments: +% map = chaco(A, xy, method, nparts, goal); +% map = chaco(A, xy, method, inmap, goal); +% +% A: Depending on "method", A may contain vertex and edge weights. +% +% xy: Each row of xy is the coordinates of a vertex. +% If xy is non-null and there is no output, draw a picture. +% +% method: Scalar or vector describing the desired method. +% Default is multilevel Kernighan-Lin; other possibilities below. +% +% nparts Number of parts to divide into. Default is 2. If nparts is +% or present, the output is a "map vector", see below. (If method(5) +% inmap: is specified, nparts is interpreted differently; see below. In +% any case, the default is to divide into two parts.) +% If method(1) = 7 (see below), this argument is a map vector +% specifying an initial 2-way partition, and Chaco refines it. +% +% goal: Optionally, a vector of desired sizes (or total vertex weights) +% for each of the nparts parts. Default is all sizes equal. +% +% map: If nparts and inmap are not present, the output is a vector of +% the n/2 vertex numbers in one part of the 2-way partition, for +% compatibility with geopart and specpart. +% If nparts or imap is present, the output is a vector of the +% n part numbers, from 0 to nparts-1, assigned to the vertices. +% +% This is a Matlab interface to the graph partitioning software described +% in B. Hendrickson and R. Leland, "The Chaco User's Guide (Version 2.0)", +% Sandia National Laboratories report SAND94-2692, October 1994. +% This interface was written by John Gilbert, Xerox PARC, and is +% Copyright (c) 1994-1996 by Xerox Corporation. All rights reserved. +% HELP COPYRIGHT for complete copyright and licensing notice. +% +% Modified by Tim Davis, for Matlab 5.1. July 6, 1998. +% 05/28/10 jes Reorganization into Matlab-layer and x-layer. +% +% See also GEOPART, SPECPART. +% +% "method" is a vector of flags as follows. Not all combinations are supported. +% See Section 6.10 of the Chaco manual for more details on all the arguments. +% If "method" is shorter than 10, we use the defaults for unspecified entries. +% +% method(1): Global partitioning method ("global_method" in the Chaco manual). +% 1 Multilevel Kernighan-Lin (default) +% 2 Spectral +% 3 Inertial +% 4 Linear +% 5 Random +% 6 Scattered +% 7 Use "inmap" as the global (2-way) partition +% +% method(2): Local refinement method ("local_method" in the Chaco manual). +% 1 Kernighan-Lin (default) +% 2 None +% +% method(3): Vertex weighting. +% 0 No weights (default) +% 1 Use diag(A) as (positive integer) vertex weights +% +% method(4): Edge weighting. +% 0 No weights (default) +% 1 Use off-diagonals of A as (positive integer) edge weights +% +% method(5): Target architecture ("architecture" in the Chaco manual). +% If method(5) = 0, the target is a hypercube, "nparts" is the +% number of dimensions, and the partition is into 2^nparts parts. +% If method(5) = 1, 2, or 3, the target is a 1-, 2-, or 3-D grid, +% "nparts" is a vector of the sizes of the grid in each dimension, +% and the partition is into prod(nparts) parts. +% Default is method(5) = 1, so nparts is the number of parts. +% +% method(6): Partitioning dimension ("ndims" in the Chaco manual). +% 1 Bisection (default) +% 2 Quadrisection +% 3 Octasection +% +% method(7): Number of vertices to coarsen to ("vmax" in the Chaco manual). +% Default is 50. +% +% method(8): Eigensolver ("rqi_flag" in the Chaco manual). +% 0 RQI/Symmlq (default) +% 1 Lanczos +% +% method(9): Eigensolver convergence tolerance ("eigtol" in the Chaco manual). +% Default is .001 +% +% method(10): Seed for random number generator ("seed" in the Chaco manual). +% Default is 7654321. +% +% Many esoteric details of Chaco's behavior can be changed by placing a file +% called "User_Params" in the same directory as the executable mlchaco.mex. +% As always, see the manual for details. + +DefaultMethod = [1 1 0 0 1 1 50 0 .001 7654321]; + +% Fill in default arguments. +if nargin < 2, xy = []; end; +if nargin < 3, method = DefaultMethod; end; +if nargin < 4, nparts = []; end; +if nargin < 5, goal = []; end; +if length(method) < length(DefaultMethod) + method = [method DefaultMethod(length(method)+1 : length(DefaultMethod))]; +end; + +% Decide on output and graphics. +if (isempty (nparts)) + mapvector = 0; +else + mapvector = 1; +end; +picture = (nargout == 0) & (size(xy,2) >= 2); + +% Chaco numbers vertices from 1 and the Matlab sparse data structure +% numbers rows from 0, so we add an empty first row to make things line up. +% This code also makes sure the arg to Chaco will be sparse. +[n,n] = size(A); +Adiag = diag(diag(A)); +%Aout = [sparse(1,n) ; A-Adiag]; +Aout = sparse(A-Adiag); + +% Make sure all args except the adj matrix are full; +if issparse(xy) + xy = full(xy); +end; +if issparse(method) + method = full(method); +end; +if issparse(nparts) + nparts = full(nparts); +end; +if issparse(goal) + goal = full(goal); +end; + +% Decode "method" to get the actual args to Chaco. +% Note that "nparts" may correspond to any of several Chaco +% parameters, depending on the method. + +if method(3) + vwgts = full(diag(A)); + totalvwgt = sum(vwgts); +else + vwgts = []; + totalvwgt = size(A,2); +end; +if method(4) + ewgts = Aout; +else + ewgts = []; +end; +if method(1) == 7 + % Refine an input partition: "nparts" is the input partition. + % This seems to work only for hypercube architecture, + % so we force a 1-D hypercube with 2-way partitioning. + nsets = 2; +elseif method(5) == 0 + % Partition for hypercube: "nparts" is # of dimensions (default 1). + if (isempty (nparts)) + nsets = 2^1; + else + nsets = 2^nparts; + end; +else + % Partition for mesh: "nparts" is vector of mesh sizes in each + % dimension, default [2 1 ... 1] with "architecture" dimensions. + if (isempty (nparts)) + nsets = prod(2); + else + nsets = prod(nparts); + end; +end; +if length(goal) ~= nsets + goal = totalvwgt/nsets * ones(1,nsets); +end; + +[map,chaco_time]=Chaco(Aout, vwgts, ewgts, xy, method, nparts, goal); + +% Draw the picture. +if picture + if size(xy,2) >= 3 && unique(xy(:,3)) == 0 + xy=xy(:,1:2); + end + if length(unique(map)) == 2 + gplotpart(A,xy,find(map==0)); + else + gplotmap(A,xy,map); + end; + if method(1)==1, heading = 'Multilevel Kernighan-Lin'; + elseif method(1)==2, heading = 'Spectral'; + elseif method(1)==3, heading = 'Inertial'; + elseif method(1)==4, heading = 'Linear'; + elseif method(1)==5, heading = 'Random'; + elseif method(1)==6, heading = 'Scattered'; + elseif method(1)==7, heading = 'Input'; + end; + heading = [heading ' Partition']; + if method(2)==1 & method(1) ~= 1 + heading =[heading ' Refined by KL']; + end; + title(heading); +end; + +% Put output in the right form. +if mapvector + part1 = map; +else + part1 = find(map==0); + part2 = find(map==1); +end; Index: /issm/trunk-jpl-damage/externalpackages/chaco/mex/Chacox.c =================================================================== --- /issm/trunk-jpl-damage/externalpackages/chaco/mex/Chacox.c (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/chaco/mex/Chacox.c (revision 11330) @@ -0,0 +1,471 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +#include +#include +#include "defs.h" +#include "params.h" + +#define THISFUNCTION "Chacox" + +#define OPT_GLOBAL 0 +#define OPT_LOCAL 1 +#define OPT_VWGTS 2 +#define OPT_EWGTS 3 +#define OPT_ARCH 4 +#define OPT_NDIMS 5 +#define OPT_VMAX 6 +#define OPT_RQI 7 +#define OPT_EIGTOL 8 +#define OPT_SEED 9 + +int input_parse( + char *outassignname, /* name of assignment output file */ + char *outfilename, /* name of file for outputing run results */ + int *architecture, /* 0=> hypercube, d=> d-dimensional mesh */ + int *ndims_tot, /* target number of hypercube dimensions */ + int mesh_dims[3], /* mesh dimensions */ + int *global_method, /* what global partitioning strategy to use? */ + int *local_method, /* what local refinement strategy to use? */ + int *rqi_flag, /* should I use multilevel eigensolver? */ + int *vmax, /* if so, how far should I coarsen? */ + int *ndims, /* number of divisions at each stage */ + int *nprocs, /* number of processors being divided into */ + double options[10], /* architecture and partitioning options */ + int *nparts /* number of parts options */ +); + + +int Chacox( + int nvtxs, /* number of vertices in graph */ + int *start, /* start of edge list for each vertex */ + int *adjacency, /* edge list data */ + int *vwgts, /* weights for all vertices */ + float *ewgts, /* weights for all edges */ + float *x, + float *y, + float *z, /* coordinates for inertial method */ + short *assignment, /* set number of each vtx (length nvtxs+1) */ + double options[10], /* architecture and partitioning options */ + int *nparts, /* number of parts options */ + double *goal /* desired set sizes */ +) +{ + extern int Using_Main; /* is main routine being called? */ + extern char *PARAMS_FILENAME; /* name of file with parameter updates */ + extern double EIGEN_TOLERANCE; /* tolerance for eigen calculations */ + extern int OUTPUT_ASSIGN; /* whether to write assignment to file */ + extern int DEBUG_MEMORY; /* debug memory allocation and freeing? */ + extern int DEBUG_TRACE; /* trace main execution path */ + extern int DEBUG_PARAMS; /* debug flag for reading parameters */ + extern long RANDOM_SEED; /* seed for random number generators */ + extern int ECHO; /* controls amount of output */ + extern int PROMPT; /* prompt for input or not? */ + extern int PRINT_HEADERS; /* print lines for output sections? */ + extern int MATCH_TYPE; /* matching routine to call */ + extern double input_time; /* times data file input */ + extern double start_time; /* time partitioning starts */ + FILE *params_file; /* file with parameter value updates */ + int global_method; /* global partitioning method */ + int local_method; /* local partitioning method */ + double eigtol; /* tolerance in eigenvector calculation */ + int ndims; /* dimension of recursive partitioning */ + int architecture; /* 0 => hypercube, d => d-dimensional mesh */ + int ndims_tot; /* total number of cube dimensions to divide */ + int mesh_dims[3]; /* dimensions of mesh of processors */ + long seed; /* for random graph mutations */ + int rqi_flag; /* use RQI/Symmlq eigensolver? */ + int vmax; /* if so, how many vertices to coarsen down to? */ + char outassignname[NAME_LENGTH]; /* assignment output file name */ + char outfilename[NAME_LENGTH]; /* name of output file */ + char *outassignptr; /* name or null pointer for output assignment */ + char *outfileptr; /* name or null pointer for output file */ + int nprocs; /* number of processors being divided into */ + double time; /* timing marker */ + int flag; /* return code from input routines */ + double *smalloc(); /* safe version of malloc */ + double seconds(); /* returns elapsed time in seconds */ + int sfree(), interface(), affirm(); + void input_queries(), smalloc_stats(), read_params(), clear_timing(); + + int i,tvwgt; + double tgoal; + + if (DEBUG_TRACE > 0) { + printf("\n"); + } + + if (PRINT_HEADERS) { + printf("\n Chaco 2.0\n"); + printf(" Sandia National Laboratories\n\n"); + } + + Using_Main = TRUE; + params_file = fopen(PARAMS_FILENAME, "r"); + if (params_file == NULL && DEBUG_PARAMS > 1) { + printf("Parameter file `%s' not found; using default parameters.\n", + PARAMS_FILENAME); + } + + start_time = time = seconds(); + + read_params(params_file); + + flag = input_parse(outassignname, outfilename, + &architecture, &ndims_tot, mesh_dims, + &global_method, &local_method, &rqi_flag, &vmax, &ndims, &nprocs, + options, nparts); + if (flag) + return(flag); + + if (OUTPUT_ASSIGN > 0) + outassignptr = outassignname; + else + outassignptr = NULL; + + if (ECHO < 0) + outfileptr = outfilename; + else + outfileptr = NULL; + + if ((int)options[OPT_VWGTS] && vwgts) { + printf("%s -- Applying weights for %d vertices.\n", + THISFUNCTION,nvtxs); + tvwgt = 0.; + for (i=0; i 0) + eigtol = options[OPT_EIGTOL]; + else + eigtol = EIGEN_TOLERANCE; + if ((int)options[OPT_SEED] > 0) + seed = (int)options[OPT_SEED]; + else + seed = RANDOM_SEED; + +/* Chaco numbers vertices from 1 and the Matlab sparse data structure + numbers rows from 0, so increment the row indices for each column. */ + + for (i=0; i 0) { + printf("\n"); + smalloc_stats(); + } + + if (params_file != NULL) + fclose(params_file); + + if (DEBUG_TRACE > 1) { + printf("\n"); + } + + return(0); +} + + +int input_parse( + char *outassignname, /* name of assignment output file */ + char *outfilename, /* name of file for outputing run results */ + int *architecture, /* 0=> hypercube, d=> d-dimensional mesh */ + int *ndims_tot, /* target number of hypercube dimensions */ + int mesh_dims[3], /* mesh dimensions */ + int *global_method, /* what global partitioning strategy to use? */ + int *local_method, /* what local refinement strategy to use? */ + int *rqi_flag, /* should I use multilevel eigensolver? */ + int *vmax, /* if so, how far should I coarsen? */ + int *ndims, /* number of divisions at each stage */ + int *nprocs, /* number of processors being divided into */ + double options[10], /* architecture and partitioning options */ + int *nparts /* number of parts options */ +) +{ + extern int SEQUENCE; /* sequence instead of partition graph? */ + extern int ARCHITECTURE; /* 0=> hypercube, d=> d-dimensional mesh */ + extern int OUTPUT_ASSIGN; /* write assignments to file? */ + extern int ECHO; /* copy input to screen? results to file? */ + extern int DEBUG_TRACE; /* trace main execution path */ + extern int PROMPT; /* prompt for input? */ + extern int MATCH_TYPE; /* max-matching routine to call */ + int eigensolver; /* which kind of eigensolver to use */ + + if (DEBUG_TRACE > 0) { + printf("\n"); + } + + if (PROMPT) { + printf("Parallel machine architecture:\n"); + printf(" (0) Hypercube\n"); + printf(" (1) One-dimensional mesh\n"); + printf(" (2) Two-dimensional mesh\n"); + printf(" (3) Three-dimensional mesh\n"); + } + *architecture = (int)options[OPT_ARCH]; + if (*architecture < 0 || *architecture > 3) { + printf("%s -- Architecture %d must be between 0 and 3.\n", + THISFUNCTION,options[OPT_ARCH]); + return(-1); + } + + /* Name output assignment file. */ + if (PROMPT) + printf("Assignment output file: "); + outassignname = NULL; + + /* Name output results file. */ + if (PROMPT) + printf("File name for saving run results: "); + outfilename = NULL; + + /* Initialize the method flags */ + *rqi_flag = 0; + *global_method = 0; + + /* Get global method, if any. */ + if (SEQUENCE) { + *global_method = 2; + } + else { + if (PROMPT) { + printf("Global partitioning method:\n"); + printf(" (1) Multilevel-KL\n"); + printf(" (2) Spectral\n"); + printf(" (3) Inertial\n"); + printf(" (4) Linear\n"); + printf(" (5) Random\n"); + printf(" (6) Scattered\n"); + printf(" (7) Read-from-file\n"); + } + *global_method = (int)options[OPT_GLOBAL]; + if (*global_method < 1 || *global_method > 7) { + printf("%s -- Global method %d must be between 1 and 7.\n", + THISFUNCTION,options[OPT_GLOBAL]); + return(-1); + } + } + + if (*global_method == 7) { /* Name and open input assignment file. */ + if (PROMPT) + printf("Assignment input file: "); + } + + else if (*global_method == 3) { + if (PROMPT) + printf("Geometry input file name: "); + } + + else if (*global_method == 2) { + if (PROMPT) { + printf("Eigensolver:\n"); + printf(" (1) Multilevel RQI/Symmlq\n"); + printf(" (2) Lanczos\n"); + } + eigensolver = (int)options[OPT_RQI]; + if (eigensolver < 0 || eigensolver > 2) { + printf("%s -- RQI/Symmlq flag %d must be between 0 and 2.\n", + THISFUNCTION,options[OPT_RQI]); + return(-1); + } + if (eigensolver == 1) { + if (MATCH_TYPE == 5) { /* geometric matching */ + if (PROMPT) + printf("Geometry input file name: "); + } + *rqi_flag = 1; + if (PROMPT) + printf("Number of vertices to coarsen down to: "); + *vmax = (int)options[OPT_VMAX]; + if (*vmax <= 0) { + printf("%s -- Vmax %d must be greater then 0.\n", + THISFUNCTION,options[OPT_VMAX]); + return(-1); + } + } + else if (eigensolver == 0 || eigensolver == 2) { + *rqi_flag = 0; + } + } + + else if (*global_method == 1) { + if (MATCH_TYPE == 5) { /* geometric matching */ + if (PROMPT) + printf("Geometry input file name: "); + } + if (PROMPT) + printf("Number of vertices to coarsen down to: "); + *vmax = (int)options[OPT_VMAX]; + if (*vmax <= 0) { + printf("%s -- Vmax %d must be greater then 0.\n", + THISFUNCTION,options[OPT_VMAX]); + return(-1); + } + } + + if (SEQUENCE) { + *local_method = 2; + if (*architecture == 0) { + *ndims_tot = 1; + } + else if (*architecture > 0) { + mesh_dims[0] = 2; + mesh_dims[1] = mesh_dims[2] = 1; + } + *ndims = 1; + goto End_Label; + } + + /* Get local method, if any */ + *local_method = 0; + if (*global_method == 1) + *local_method = 1; + else { + if (PROMPT) { + printf("Local refinement method:\n"); + printf(" (1) Kernighan-Lin\n"); + printf(" (2) None\n"); + } + *local_method = (int)options[OPT_LOCAL]; + if (*local_method < 1 || *local_method > 2) { + printf("%s -- Local method %d must be 1 and 2.\n", + THISFUNCTION,options[OPT_LOCAL]); + return(-1); + } + } + + /* Now learn about the parallel architecture. */ + if (*architecture == 0) { + /* Get total number of hypercube dimensions in which to partition. */ + *ndims_tot = 0; + if (PROMPT) + printf("Total number of target hypercube dimensions: "); + *ndims_tot = nparts[0]; + if (*ndims_tot < 1) { + printf(" Number of divisions must be at least 1\n"); + printf("%s -- Number of divisions %d must be at least 1.\n", + THISFUNCTION,nparts[0]); + return(-1); + } + *nprocs = 1 << (*ndims_tot); + } + + else { /* Get dimensions of mesh. */ + mesh_dims[1] = mesh_dims[2] = 1; + if (*architecture == 2) { + if (PROMPT) + printf("X and Y extent of of 2-D mesh: "); + mesh_dims[0] = nparts[0]; + mesh_dims[1] = nparts[1]; + } + else if (*architecture == 3) { + if (PROMPT) + printf("X, Y and Z extent of 3-D mesh: "); + mesh_dims[0] = nparts[0]; + mesh_dims[1] = nparts[1]; + mesh_dims[2] = nparts[2]; + } + else { /* Anything else => 1-D mesh */ + if (PROMPT) + printf("Size of 1-D mesh: "); + mesh_dims[0] = nparts[0]; + *architecture = 1; + } + *nprocs = mesh_dims[0] * mesh_dims[1] * mesh_dims[2]; + } + + /* Get number of dimensions in which to partition at each level. */ + *ndims = 0; + if (*nprocs <= 3) { + *ndims = 1; + } + else if (*nprocs <= 7) { + if (PROMPT) { + printf("Partitioning dimension: \n"); + printf(" (1) Bisection\n"); + printf(" (2) Quadrisection\n"); + } + *ndims = (int)options[OPT_NDIMS]; + if (*ndims < 1 || *ndims > 2) { + printf("%s -- Ndims %d must be 1 or 2 for %d processors.\n", + THISFUNCTION,options[OPT_NDIMS],*nprocs); + return(-1); + } + } + else { + if (PROMPT) { + printf("Partitioning dimension: \n"); + printf(" (1) Bisection\n"); + printf(" (2) Quadrisection\n"); + printf(" (3) Octasection\n"); + } + *ndims = (int)options[OPT_NDIMS]; + if (*ndims < 1 || *ndims > 3) { + printf("%s -- Ndims %d must be between 1 and 3 for %d processors.\n", + THISFUNCTION,options[OPT_NDIMS],*nprocs); + return(-1); + } + } +End_Label: + + if (*global_method == 1 || *rqi_flag) { + if (*vmax < 2 * (1 << *ndims)) { + *vmax = 2 * (1 << *ndims); + } + } + + return(0); +} Index: /issm/trunk-jpl-damage/externalpackages/chaco/mex/Makefile =================================================================== --- /issm/trunk-jpl-damage/externalpackages/chaco/mex/Makefile (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/chaco/mex/Makefile (revision 11330) @@ -0,0 +1,293 @@ +# This is the Makefile for the mex-file version of Chaco, to be dynamically +# linked with Matlab using the interface in the "meshpart" toolbox. +# See file "README" for more information. +# +# You may need to change the following variables: +# +# MATLAB Matlab's top-level directory, often "/usr/matlab" or similar. +# CHACO Chaco's source directory, normally the "code" subdirectory +# of the Chaco distribution. +# MLCHACO Directory with Chaco files modified for Matlab, normally +# the directory containing this Makefile. +# DEST_DIR Directory for the executable mlchaco.mex, normally the +# "meshpart" directory, which is normally the parent of the +# directory containing this Makefile. +# CC Choice of C compiler. gcc seems to work best for Matlab for me. +# IFLAGS, CFLAGS, OFLAGS Flags to go with the compiler and linker. +# +# This Makefile works under Solaris 2. To use it with a different Unix, +# you may need to change the references to "ar" and/or "ranlib" and +# possibly other things. +# +# John Gilbert, 1996. +# Copyright (c) 1990-1996 by Xerox Corporation. All rights reserved. +# See file ../copyright.m for complete copyright and licensing notice. + +#MATLAB = /import/matlab +#MATLAB = /usr/local/libexec/matlab +#MATLAB = /usr/local/pkgs/matlab-7.6 +MATLAB = ${MATLAB_DIR} + +#CHACO = /project/sparse/chaco/version2/code +#CHACO = ../../Chaco-2.0/code +#CHACO = ../../Chaco-2.2/code +#CHACO = ../../../chaco/src/code +CHACO = ${CHACO_DIR}/../src/code + +MLCHACO = . +DEST_DIR = .. +CC = gcc +#CC = cc +IFLAGS = -I${MATLAB}/extern/include -I${CHACO}/main +#CFLAGS = -Xa -G -xO4 -xcg92 +#CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -DMATLAB +CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions +#OFLAGS = -xO4 -xcg92 +OFLAGS = -O2 +#AR = /usr/ccs/bin/ar rcv # for solaris 2 +AR = /usr/bin/ar rcv # for solaris 2 +#RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +RANLIB = /usr/bin/ranlib # for solaris 2 + + +MLFILES.c= ${MLCHACO}/Chacox.c \ + ${MLCHACO}/user_params.c +# ${MLCHACO}/bail.c \ # redefined original with -DMATLAB +# ${MLCHACO}/chaco_check_graph.c \ # redefined original with -DMATLAB +# ${MLCHACO}/check_input.c \ # redefined original with -DMATLAB +# ${MLCHACO}/smalloc.c \ # redefined original with -DMATLAB + +CHFILES.c= ${CHACO}/main/interface.c \ + ${CHACO}/main/main.c \ + ${CHACO}/submain/balance.c \ + ${CHACO}/submain/divide.c \ + ${CHACO}/submain/submain.c \ + ${CHACO}/input/input_assign.c \ + ${CHACO}/input/check_input.c \ + ${CHACO}/input/input.c \ + ${CHACO}/input/input_geom.c \ + ${CHACO}/input/input_graph.c \ + ${CHACO}/input/read_params.c \ + ${CHACO}/input/reflect_input.c \ + ${CHACO}/input/read_val.c \ + ${CHACO}/graph/check_graph.c \ + ${CHACO}/graph/free_graph.c \ + ${CHACO}/graph/reformat.c \ + ${CHACO}/graph/subgraph.c \ + ${CHACO}/graph/graph_out.c \ + ${CHACO}/inertial/eigenvec2.c \ + ${CHACO}/inertial/eigenvec3.c \ + ${CHACO}/inertial/inertial.c \ + ${CHACO}/inertial/inertial1d.c \ + ${CHACO}/inertial/inertial2d.c \ + ${CHACO}/inertial/inertial3d.c \ + ${CHACO}/inertial/make_subgeom.c \ + ${CHACO}/klspiff/buckets.c \ + ${CHACO}/klspiff/buckets_bi.c \ + ${CHACO}/klspiff/buckets1.c \ + ${CHACO}/klspiff/bilistops.c \ + ${CHACO}/klspiff/coarsen_kl.c \ + ${CHACO}/klspiff/count_weights.c \ + ${CHACO}/klspiff/compress_ewgts.c \ + ${CHACO}/klspiff/kl_init.c \ + ${CHACO}/klspiff/kl_output.c \ + ${CHACO}/klspiff/klspiff.c \ + ${CHACO}/klspiff/make_bndy_list.c \ + ${CHACO}/klspiff/make_kl_list.c \ + ${CHACO}/klspiff/nway_kl.c \ + ${CHACO}/klvspiff/bpm_improve.c \ + ${CHACO}/klvspiff/bucketsv.c \ + ${CHACO}/klvspiff/clear_dvals.c \ + ${CHACO}/klvspiff/coarsen_klv.c \ + ${CHACO}/klvspiff/countup_vtx_sep.c \ + ${CHACO}/klvspiff/find_bndy.c \ + ${CHACO}/klvspiff/flow.c \ + ${CHACO}/klvspiff/klv_init.c \ + ${CHACO}/klvspiff/klvspiff.c \ + ${CHACO}/klvspiff/make_bpgraph.c \ + ${CHACO}/klvspiff/make_sep_list.c \ + ${CHACO}/klvspiff/matching.c \ + ${CHACO}/klvspiff/nway_klv.c \ + ${CHACO}/klvspiff/flatten.c \ + ${CHACO}/coarsen/coarsen.c \ + ${CHACO}/coarsen/interpolate.c \ + ${CHACO}/coarsen/makefgraph.c \ + ${CHACO}/coarsen/makeccoords.c \ + ${CHACO}/coarsen/coarsen1.c \ + ${CHACO}/coarsen/makev2cv.c \ + ${CHACO}/coarsen/maxmatch.c \ + ${CHACO}/coarsen/maxmatch1.c \ + ${CHACO}/coarsen/maxmatch2.c \ + ${CHACO}/coarsen/maxmatch3.c \ + ${CHACO}/coarsen/maxmatch4.c \ + ${CHACO}/coarsen/maxmatch5.c \ + ${CHACO}/connect/add_edges.c \ + ${CHACO}/connect/connected.c \ + ${CHACO}/connect/find_edges.c \ + ${CHACO}/eigen/bidir.c \ + ${CHACO}/eigen/bisect.c \ + ${CHACO}/eigen/checkeig.c \ + ${CHACO}/eigen/checkeig_ext.c \ + ${CHACO}/eigen/checkorth.c \ + ${CHACO}/eigen/cksturmcnt.c \ + ${CHACO}/eigen/mkeigvecs.c\ + ${CHACO}/eigen/eigensolve.c \ + ${CHACO}/eigen/get_extval.c \ + ${CHACO}/eigen/get_ritzvals.c \ + ${CHACO}/eigen/lanczos_FO.c \ + ${CHACO}/eigen/lanczos_SO.c \ + ${CHACO}/eigen/lanczos_SO_float.c \ + ${CHACO}/eigen/lanczos_ext.c \ + ${CHACO}/eigen/lanczos_ext_float.c \ + ${CHACO}/eigen/lanc_seconds.c\ + ${CHACO}/eigen/lanpause.c \ + ${CHACO}/eigen/makeorthlnk.c \ + ${CHACO}/eigen/mkscanlist.c \ + ${CHACO}/eigen/orthog1.c \ + ${CHACO}/eigen/orthogonalize.c \ + ${CHACO}/eigen/orthogvec.c \ + ${CHACO}/eigen/ql.c \ + ${CHACO}/eigen/rqi.c \ + ${CHACO}/eigen/rqi_ext.c \ + ${CHACO}/eigen/scale_diag.c \ + ${CHACO}/eigen/scanmax.c \ + ${CHACO}/eigen/scanmin.c \ + ${CHACO}/eigen/solistout.c \ + ${CHACO}/eigen/sorthog.c \ + ${CHACO}/eigen/splarax.c \ + ${CHACO}/eigen/sturmcnt.c \ + ${CHACO}/eigen/Tevec.c \ + ${CHACO}/eigen/tri_solve.c \ + ${CHACO}/eigen/warnings.c \ + ${CHACO}/symmlq/aprod.c \ + ${CHACO}/symmlq/msolve.c \ + ${CHACO}/symmlq/pow_dd.c \ + ${CHACO}/symmlq/symmlq.c \ + ${CHACO}/symmlq/symmlqblas.c \ + ${CHACO}/tinvit/tinvit.c \ + ${CHACO}/tinvit/pythag.c \ + ${CHACO}/tinvit/epslon.c \ + ${CHACO}/optimize/determinant.c \ + ${CHACO}/optimize/func2d.c \ + ${CHACO}/optimize/func3d.c \ + ${CHACO}/optimize/opt2d.c \ + ${CHACO}/optimize/opt3d.c \ + ${CHACO}/assign/assign.c \ + ${CHACO}/assign/assign_out.c \ + ${CHACO}/assign/mapper.c \ + ${CHACO}/assign/median.c \ + ${CHACO}/assign/merge_assign.c \ + ${CHACO}/assign/rec_median.c \ + ${CHACO}/assign/rotate.c \ + ${CHACO}/assign/y2x.c \ + ${CHACO}/bpmatch/checkbp.c \ + ${CHACO}/bpmatch/inits2d.c \ + ${CHACO}/bpmatch/inits3d.c \ + ${CHACO}/bpmatch/genvals2d.c \ + ${CHACO}/bpmatch/genvals3d.c \ + ${CHACO}/bpmatch/map2d.c \ + ${CHACO}/bpmatch/map3d.c \ + ${CHACO}/bpmatch/movevtxs.c \ + ${CHACO}/bpmatch/sorts2d.c \ + ${CHACO}/bpmatch/sorts3d.c \ + ${CHACO}/refine_map/compute_cube_edata.c \ + ${CHACO}/refine_map/compute_cube_vdata.c \ + ${CHACO}/refine_map/refine_cube.c \ + ${CHACO}/refine_map/update_cube_edata.c \ + ${CHACO}/refine_map/update_cube_vdata.c \ + ${CHACO}/refine_map/find_edge_cube.c \ + ${CHACO}/refine_map/init_cube_edata.c \ + ${CHACO}/refine_map/compute_mesh_edata.c \ + ${CHACO}/refine_map/compute_mesh_vdata.c \ + ${CHACO}/refine_map/find_edge_mesh.c \ + ${CHACO}/refine_map/init_mesh_edata.c \ + ${CHACO}/refine_map/refine_mesh.c \ + ${CHACO}/refine_map/update_mesh_edata.c \ + ${CHACO}/refine_map/update_mesh_vdata.c \ + ${CHACO}/refine_map/refine_map.c \ + ${CHACO}/refine_map/make_comm_graph.c \ + ${CHACO}/refine_part/refine_part.c \ + ${CHACO}/refine_part/kl_refine.c \ + ${CHACO}/refine_part/make_maps_ref.c \ + ${CHACO}/refine_part/make_terms_ref.c \ + ${CHACO}/internal/force_internal.c \ + ${CHACO}/internal/improve_internal.c \ + ${CHACO}/internal/check_internal.c \ + ${CHACO}/misc/define_subcubes.c \ + ${CHACO}/misc/define_submeshes.c \ + ${CHACO}/misc/divide_procs.c \ + ${CHACO}/misc/merge_goals.c \ + ${CHACO}/misc/make_term_props.c \ + ${CHACO}/misc/count.c \ + ${CHACO}/misc/countup.c \ + ${CHACO}/misc/countup_cube.c \ + ${CHACO}/misc/countup_mesh.c \ + ${CHACO}/misc/make_subgoal.c \ + ${CHACO}/misc/find_maxdeg.c \ + ${CHACO}/misc/make_maps.c \ + ${CHACO}/misc/make_setlists.c \ + ${CHACO}/misc/sequence.c \ + ${CHACO}/misc/perturb.c \ + ${CHACO}/misc/simple_part.c \ + ${CHACO}/misc/time_kernels.c \ + ${CHACO}/misc/timing.c \ + ${CHACO}/util/affirm.c \ + ${CHACO}/util/array_alloc_2D.c \ + ${CHACO}/util/bit_reverse.c \ + ${CHACO}/util/checkpnt.c \ + ${CHACO}/util/cpvec.c \ + ${CHACO}/util/dot.c \ + ${CHACO}/util/doubleout.c \ + ${CHACO}/util/input_int.c \ + ${CHACO}/util/gray.c \ + ${CHACO}/util/machine_params.c \ + ${CHACO}/util/makevwsqrt.c \ + ${CHACO}/util/mkvec.c \ + ${CHACO}/util/norm.c \ + ${CHACO}/util/normalize.c \ + ${CHACO}/util/mergesort.c \ + ${CHACO}/util/randomize.c \ + ${CHACO}/util/smalloc.c \ + ${CHACO}/util/bail.c \ + ${CHACO}/util/scadd.c \ + ${CHACO}/util/seconds.c \ + ${CHACO}/util/setvec.c \ + ${CHACO}/util/shell_sort.c \ + ${CHACO}/util/strout.c \ + ${CHACO}/util/tri_prod.c \ + ${CHACO}/util/true_or_false.c \ + ${CHACO}/util/update.c \ + ${CHACO}/util/vecout.c \ + ${CHACO}/util/vecran.c \ + ${CHACO}/util/vecscale.c +# ${CHACO}/main/user_params.c \ + +MLFILES.o= $(MLFILES.c:.c=.o) + +CHFILES.o= $(CHFILES.c:.c=.o) + +#mlchaco: ${MLFILES.o} chaco.a Makefile +# ${MATLAB}/bin/cmex CC='gcc -G' -lm ${OFLAGS} ${MLFILES.o} chaco.a; \ +# mv mlchaco.mex* ${DEST_DIR} + +#mlchaco: ${MLFILES.c} chaco.a Makefile +# mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +# mv mlchaco.mex* ${DEST_DIR} + +#mlchaco: ${MLFILES.c} ${CHFILES.c} ${CHACO}/chaco.a Makefile +# ${MATLAB}/bin/mex mlchaco.c -largeArrayDims -DMATLAB ${MLFILES.c} ${CHACO}/chaco.a -I${CHACO}/main +# mv mlchaco.mex* ${DEST_DIR} + +Chaco: ${MLFILES.c} ${CHFILES.c} ${CHACO}/chaco.a Makefile + ${MATLAB}/bin/mex Chaco.c -largeArrayDims ${MLFILES.c} ${CHACO}/chaco.a -I${CHACO}/main +# mv Chaco.mex* ${DEST_DIR} + +chaco.a: ${CHFILES.o} + ${AR} ${CHACO}/chaco.a ${CHFILES.o} ; ${RANLIB} ${CHACO}/chaco.a + +clean: + rm -f ${CHACO}/*/*.o chaco.a ${MLCHACO}/*.o ${DEST_DIR}/core + +.c.o: + ${CC} -c ${IFLAGS} ${CFLAGS} -o $*.o $*.c + Index: /issm/trunk-jpl-damage/externalpackages/chaco/mex/User_Params.debug =================================================================== --- /issm/trunk-jpl-damage/externalpackages/chaco/mex/User_Params.debug (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/chaco/mex/User_Params.debug (revision 11330) @@ -0,0 +1,27 @@ +% This file, User_Params, is read at runtime to modify Chaco's defaults. +% The purpose of this version is to turn on some debugging stuff that +% the Matlab version will normally have off. + +ECHO = 2 +OUTPUT_METRICS = 2 +OUTPUT_TIME = 2 +PRINT_HEADERS = 1 + +DEBUG_EVECS = 1 +DEBUG_KL = 1 +DEBUG_INERTIAL = 1 +DEBUG_CONNECTED = 1 +DEBUG_PERTURB = 1 +DEBUG_ASSIGN = 1 +DEBUG_OPTIMIZE = 1 +DEBUG_BPMATCH = 1 +DEBUG_COARSEN = 1 +DEBUG_MEMORY = 1 +DEBUG_INPUT = 0 +DEBUG_PARAMS = 1 +DEBUG_INTERNAL = 1 +DEBUG_REFINE_PART = 1 +DEBUG_REFINE_MAP = 1 +DEBUG_SIMULATOR = 1 +DEBUG_TRACE = 1 +DEBUG_MACH_PARAMS = 1 Index: /issm/trunk-jpl-damage/externalpackages/chaco/mex/User_Params.verbose =================================================================== --- /issm/trunk-jpl-damage/externalpackages/chaco/mex/User_Params.verbose (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/chaco/mex/User_Params.verbose (revision 11330) @@ -0,0 +1,8 @@ +% This file, User_Params, is read at runtime to modify Chaco's defaults. +% The purpose of this version is to turn on some verbose output that +% the Matlab version will normally have off. + +ECHO = 1 +OUTPUT_METRICS = 1 +OUTPUT_TIME = 1 +PRINT_HEADERS = 1 Index: /issm/trunk-jpl-damage/externalpackages/chaco/mex/user_params.c =================================================================== --- /issm/trunk-jpl-damage/externalpackages/chaco/mex/user_params.c (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/chaco/mex/user_params.c (revision 11330) @@ -0,0 +1,142 @@ +/* This software was developed by Bruce Hendrickson and Robert Leland * + * at Sandia National Laboratories under US Department of Energy * + * contract DE-AC04-76DP00789 and is copyrighted by Sandia Corporation. */ + +/* Modified by John Gilbert 25 Aug 1995 for Matlab mex-file interface */ +/* Modified by Tim Davis, July 6, 1998, for Matlab 5.1 interface, and */ +/* a more picky compiler (cc) that complains about duplicate global */ +/* declarations. */ + +#include "params.h" + +#define TRUE 1 +#define FALSE 0 + + +/* Input and ouput control parameters */ + +int CHECK_INPUT = TRUE; /* Check input for consistency? (TRUE/FALSE) */ +int ECHO = 0; /* Print input/param options? to file? (-2..2) */ +int OUTPUT_METRICS = 0; /* Controls displaying of results (-2..2) */ +int OUTPUT_TIME = 0; /* At what level to display timings (0..2) */ +int OUTPUT_ASSIGN = FALSE; /* Write assignments to file? (TRUE/FALSE) */ +int OUT_ASSIGN_INV = FALSE;/* If so, use inverse form? (TRUE/FALSE) */ +int IN_ASSIGN_INV = FALSE; /* Input file in inverse form? (TRUE/FALSE) */ +int PROMPT = FALSE; /* Prompt for input? (TRUE/FALSE) */ +int PRINT_HEADERS = FALSE; /* Print pretty output headers (TRUE/FALSE) */ + + +/* Eigenvector calculation parameters */ + +int LANCZOS_TYPE = 3; /* type of Lanczos to use */ + /* 1 => full orthog, 2 => full inverse operator */ + /* 3 => selective orthogonalization */ +double EIGEN_TOLERANCE = 1e-3; /* Numerical eigen-tolerance */ +double SRESTOL = -1.; /* Rel resid tol on T evec; autoset if <= 0 */ +int LANCZOS_SO_INTERVAL = 10; /* Itns. between SO orthog checks; set >= 2 */ +int LANCZOS_MAXITNS = -1; /* Max Lanczos its; autoset if <= 0 */ +double BISECTION_SAFETY = 10; /* Divides Lanczos bisection tol */ +int LANCZOS_CONVERGENCE_MODE = 0; /* Lanczos convergence test type: */ + /* 0=> residual, 1=> partition */ +int RQI_CONVERGENCE_MODE = 1; /* RQI convergence test type: */ + /* 0=> residual, 1=> partition */ +int LANCZOS_SO_PRECISION = 2; /* 2 => double Lanczos, 1 => float */ +int WARNING_EVECS = 2; /* Warnings in eigenvector generation (0..3) */ +double WARNING_ORTHTOL = 2; /* Warning if Ares and bjitol have this ratio */ +double WARNING_MISTOL = 100; /* Warning if Ares and bjitol have this ratio */ +int LANCZOS_TIME = FALSE; /* Detailed Lanczos times? (TRUE/FALSE) */ +int TIME_KERNELS = FALSE; /* Time numerical kernels? (TRUE/FALSE) */ + + +/* Other parameters for spectral methods */ + +int MAKE_CONNECTED = TRUE;/* Connect graph if using spectral method? */ +int PERTURB = TRUE; /* Randomly perturb matrix in spectral method? */ +int NPERTURB = 2; /* If so, how many edges to modify? */ +double PERTURB_MAX = 3.0e-3; /* Largest value for perturbation */ +int MAPPING_TYPE = 1; /* How to map from eigenvectors to partition */ + /* 0 => cut at origin, 1 => min-cost assign */ +int COARSE_NLEVEL_RQI = 2;/* # levels between RQI calls in uncoarsening */ +int OPT3D_NTRIES = 5; /* # local opts to look for global min in opt3d */ + + +/* Kernighan--Lin/Fiduccia--Mattheyses parameters */ + +int KL_METRIC = 2; /* KL interset cost: 1=>cuts, 2=>hops */ +int KL_RANDOM = TRUE; /* Use randomness in Kernighan-Lin? (TRUE/FALSE)*/ +int KL_BAD_MOVES = 20; /* Number of unhelpful moves in a row allowed */ +int KL_NTRIES_BAD = 1; /* # unhelpful passes before quitting KL */ +int KL_UNDO_LIST = TRUE; /* Only resort changed vtxs? (TRUE/FALSE) */ +double KL_IMBALANCE = 0.0; /* Fractional imbalance allowed by KL */ + + +/* Coarsening parameters */ + +double COARSEN_RATIO_MIN = .7; /* Min vtx reduction each coarsen stage */ +int COARSE_NLEVEL_KL = 2; /* # levels between KL calls in uncoarsening */ +int MATCH_TYPE = 1; /* Type of contraction matching (1..4) */ +int HEAVY_MATCH = FALSE; /* Encourage heavy match edges? (TRUE/FALSE) */ +int COARSE_KL_BOTTOM = TRUE; /* Force KL at lowest level (TRUE/FALSE) */ +int COARSEN_VWGTS = TRUE; /* Sum vtx weights in coarsening? (TRUE/FALSE) */ +int COARSEN_EWGTS = TRUE; /* Sum edge weights in coarsening? (TRUE/FALSE) */ +int KL_ONLY_BNDY = TRUE; /* Start moving vtxs on boundary? (TRUE/FALSE) */ + + +/* Parameters for post-processing options */ + +int REFINE_PARTITION = FALSE; /* Postprocess to improve cuts? */ +int INTERNAL_VERTICES = FALSE; /* ... to up internal vtxs? (TRUE/FALSE) */ +int REFINE_MAP = FALSE; /* ... to reduce hops? (TRUE/FALSE) */ + + +/* Architecture and simulator parameters */ + +int ARCHITECTURE = 0; /* 0=> hypercube, d=> d-dimensional mesh (0..3)*/ + +/* Modified by Tim Davis: remove duplicate definitions */ +#ifdef DUPLICATE_DEFINITIONS_REMOVED +int SIMULATOR = 0; /* Run simulator? In what mode? */ +int SIMULATION_ITNS = 1; /* # iterations simulator is to imitate. */ +int PERCENTAGE_OUTPUT = FALSE; /* Output in percent? (TRUE/FALSE) */ +double CUT_COST = 0.0; /* Communication cost of a cut-edge. */ +double HOP_COST = 0.0; /* Communication cost of a hop. */ +double BDY_COST = 0.0; /* Cost associated with boundary vertices. */ +double BDY_HOP_COST = 0.0; /* Cost associated with boundary hops. */ +double STARTUP_COST = 0.0; /* Communication cost of a message startup. */ + /* Note: nCUBE2 startup: 112e-6, per byte: 4.6e-6, buffering 5.6e-6 */ + /* Intel Paragon startup: 70e-6, per byte: 5.3e-8 */ +#endif + +/* Miscellaneous parameters */ + +int TERM_PROP = FALSE; /* Invoke terminal propagation? (TRUE/FALSE) */ +double CUT_TO_HOP_COST = 1; /* ..if so, relative importance of cuts/hops */ +int SEQUENCE = FALSE; /* Only do spectral ordering? (TRUE/FALSE) */ +char SEQ_FILENAME[NAME_LENGTH] = "Sequence.out"; /* If so, file name */ +long RANDOM_SEED = 7654321L; /* Seed for random number generator */ +int NSQRTS = 1000; /* # square roots to precompute if coarsening */ +int MAKE_VWGTS = FALSE; /* Make vtx weights degrees+1? (TRUE/FALSE) */ +int FREE_GRAPH = FALSE; /* Free input graph data? (TRUE/FALSE) */ +char *PARAMS_FILENAME = "User_Params"; /* File of parameter changes */ + + +/* Parameters that control debugging output */ + +int DEBUG_EVECS = 0; /* Debug flag for eigenvector generation (0..5) */ +int DEBUG_KL = 0; /* Debug flag for Kernighan-Lin (0..3) */ +int DEBUG_INERTIAL = 0; /* Debug flag for inertial method (0..1) */ +int DEBUG_CONNECTED = 0; /* Debug flag for connected components (0..1) */ +int DEBUG_PERTURB = 0; /* Debug flag for matrix perturbation (0..1) */ +int DEBUG_ASSIGN = 0; /* Debug flag for assignment to sets (0..1) */ +int DEBUG_OPTIMIZE = 0; /* Debug flag for optimization/rotation (0..2) */ +int DEBUG_BPMATCH = 0; /* Debug flag for bipartite matching code (0..2) */ +int DEBUG_COARSEN = 0; /* Debug flag for coarsening/uncoarsening (0..1) */ +int DEBUG_MEMORY = 0; /* Debug flag for smalloc/sfree (0..3) */ +int DEBUG_INPUT = 0; /* Debug flag for having read input files (0..1) */ +int DEBUG_PARAMS = 1; /* Debug flag for reading parameter file (0..2) */ +int DEBUG_INTERNAL = 0; /* Debug flag for internal vertices (0..2) */ +int DEBUG_REFINE_PART = 0;/* Debug flag for refine partition (0..1) */ +int DEBUG_REFINE_MAP = 0; /* Debug flag for refining mapping (0..1) */ +int DEBUG_SIMULATOR = 0; /* Debug flag for comm simulator (0..2) */ +int DEBUG_TRACE = 0; /* Trace main execution path (0..2) */ +int DEBUG_MACH_PARAMS = 0;/* Print computed machine params? (0..1) */ Index: /issm/trunk-jpl-damage/externalpackages/chaco/mlchaco_README.txt =================================================================== --- /issm/trunk-jpl-damage/externalpackages/chaco/mlchaco_README.txt (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/chaco/mlchaco_README.txt (revision 11330) @@ -0,0 +1,136 @@ +mlchaco (from meshpartdist.tar, 2/08/02) +http://www.cerfacs.fr/algor/Softs/MESHPART/ + + +[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c +34a35 [CLK_TCK undefined, so use CLOCKS_PER_SEC] +> #include /* CLOCKS_PER_SEC */ +56,61c57,62 [update for current Matlab] +< void mexFunction( +< int nlhs, /* number of expected outputs */ +< Matrix *plhs[], /* matrix pointer array returning outputs */ +< int nrhs, /* number of inputs */ +< Matrix *prhs[] /* matrix pointer array for inputs */ +< ) +--- +> void mexFunction( +> int nlhs, /* number of expected outputs */ +> mxArray *plhs[], /* array of pointers to output arguments +> */ +> int nrhs, /* number of inputs */ +> const mxArray *prhs[] /* array of pointers to input arguments */ +> ) +87a89 [update for current Matlab] +> mwIndex *mwstart,*mwadjacency; +104c106,110 [update for current Matlab] +< start = mxGetJc(A_in); +--- +> /* start = mxGetJc(A_in);*/ +> mwstart = mxGetJc(A_in); +> start = mxMalloc((mxGetN(A_in)+1)*sizeof(int)); +> for (i=0; i<(mxGetN(A_in)+1); i++) +> start[i]= (int)mwstart[i]; +106c112,116 [update for current Matlab] +< adjacency = mxGetIr(A_in); +--- +> /* adjacency = mxGetIr(A_in);*/ +> mwadjacency = mxGetIr(A_in); +> adjacency = mxMalloc(mxGetNzmax(A_in)*sizeof(int)); +> for (i=0; i adjacency[i]= (int)mwadjacency[i]; +131,132c141,144 [provide default filenames, since no way to input] +< outassignname = NULL; +< outfilename = NULL; +--- +> /* outassignname = NULL; +> outfilename = NULL;*/ +> outassignname = "chaco_assign.txt"; +> outfilename = "chaco_out.txt"; +169c181 [update for current Matlab] +< plhs [1] = mxCreateFull (1, 1, REAL) ; +--- +> plhs [1] = mxCreateDoubleMatrix (1, 1, mxREAL) ; +173c185 [CLK_TCK undefined, so use CLOCKS_PER_SEC] +< ((double) CLK_TCK) ; +--- +> ((double) CLOCKS_PER_SEC) ; +179c191 [update for current Matlab] +< map_out = mxCreateFull(1,nvtxs,REAL); +--- +> map_out = mxCreateDoubleMatrix(1,nvtxs,mxREAL); +185a198,199 [update for current Matlab] +> if (start != NULL) mxFree((char *) start); +> if (adjacency != NULL) mxFree((char *) adjacency); + + +[jschierm@astrid chaco]$ diff Makefile_old Makefile +27c27,28 [current Matlab location] +< MATLAB = /usr/local/libexec/matlab +--- +> #MATLAB = /usr/local/libexec/matlab +> MATLAB = /usr/local/pkgs/matlab-7.6 +30c31,32 [current Chaco 2.2 location] +< CHACO = ../../Chaco-2.0/code +--- +> #CHACO = ../../Chaco-2.0/code +> CHACO = ../../Chaco-2.2/code +34,35c36,37 [use gcc instead of cc] +< #CC = gcc +< CC = cc +--- +> CC = gcc +> #CC = cc +37c39,40 [add MATLAB flag to compile for mex-function] +< CFLAGS = -Xa -G -xO4 -xcg92 +--- +> #CFLAGS = -Xa -G -xO4 -xcg92 +> CFLAGS = -Xa -G -xO4 -xcg92 -DMATLAB +39,40c42,45 [current function locations] +< AR = /usr/ccs/bin/ar rcv # for solaris 2 +< RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +--- +> #AR = /usr/ccs/bin/ar rcv # for solaris 2 +> AR = /usr/bin/ar rcv # for solaris 2 +> #RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +> RANLIB = /usr/bin/ranlib # for solaris 2 +45,47d49 [use Chaco versions with MATLAB switch rather than local versions] +< ${MLCHACO}/chaco_check_graph.c \ +< ${MLCHACO}/check_input.c \ +< ${MLCHACO}/smalloc.c \ +48a51,53 +> # ${MLCHACO}/chaco_check_graph.c \ +> # ${MLCHACO}/check_input.c \ +> # ${MLCHACO}/smalloc.c \ +55a61 [update CHLIST to match Chaco 2.2] +> ${CHACO}/input/check_input.c \ +61a68 [update CHLIST to match Chaco 2.2] +> ${CHACO}/graph/check_graph.c \ +91a99 [update CHLIST to match Chaco 2.2] +> ${CHACO}/klvspiff/flow.c \ +97a106 [update CHLIST to match Chaco 2.2] +> ${CHACO}/klvspiff/flatten.c \ +100c109,110 [update CHLIST to match Chaco 2.2] +< ${CHACO}/coarsen/makecgraph.c \ +--- +> ${CHACO}/coarsen/makefgraph.c \ +> ${CHACO}/coarsen/makeccoords.c \ +102d111 [update CHLIST to match Chaco 2.2] +< ${CHACO}/coarsen/countcedges.c \ +108a118 [update CHLIST to match Chaco 2.2] +> ${CHACO}/coarsen/maxmatch5.c \ +234a245 [update CHLIST to match Chaco 2.2] +> ${CHACO}/util/smalloc.c \ +245a257,258 [use local versions rather than Chaco versions (added for clarity)] +> # ${CHACO}/main/user_params.c \ +> # ${CHACO}/util/bail.c \ +254a268,271 [update for current mex] +> #mlchaco: ${MLFILES.c} chaco.a Makefile +> # mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +> # mv mlchaco.mex* ${DEST_DIR} +> +256c273 [update for current mex] +< mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +--- +> mex -output mlchaco -largeArrayDims -DMATLAB ${MLFILES.c} +> chaco.a -I${CHACO}/main + Index: /issm/trunk-jpl-damage/externalpackages/chaco/mlchaco_jes_notes.txt =================================================================== --- /issm/trunk-jpl-damage/externalpackages/chaco/mlchaco_jes_notes.txt (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/chaco/mlchaco_jes_notes.txt (revision 11330) @@ -0,0 +1,182 @@ +7/15/09: + +[jschierm@astrid chaco]$ diff Makefile_old Makefile +27c27,28 +< MATLAB = /usr/local/libexec/matlab +--- +> #MATLAB = /usr/local/libexec/matlab +> MATLAB = /usr/local/matlab780 +30c31,32 +< CHACO = ../../Chaco-2.0/code +--- +> #CHACO = ../../Chaco-2.0/code +> CHACO = ../../Chaco-2.2/code +34,35c36,37 +< #CC = gcc +< CC = cc +--- +> CC = gcc +> #CC = cc +39,40c41,44 +< AR = /usr/ccs/bin/ar rcv # for solaris 2 +< RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +--- +> #AR = /usr/ccs/bin/ar rcv # for solaris 2 +> AR = /usr/bin/ar rcv # for solaris 2 +> #RANLIB = /usr/ccs/bin/ranlib # for solaris 2 +> RANLIB = /usr/bin/ranlib # for solaris 2 +91a96,97 [missing symbols] +> ${CHACO}/klvspiff/flatten.c \ +> ${CHACO}/klvspiff/flow.c \ +99a106 [missing symbols] +> ${CHACO}/coarsen/makeccoords.c \ +102a110 [missing symbols] +> ${CHACO}/coarsen/makefgraph.c \ +108a117 [missing symbols] +> ${CHACO}/coarsen/maxmatch5.c \ +254a264,267 +> #mlchaco: ${MLFILES.c} chaco.a Makefile +> # mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +> # mv mlchaco.mex* ${DEST_DIR} +> +256c269 +< mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +--- +> mex -output mlchaco -largeArrayDims ${MLFILES.c} chaco.a -I${CHACO}/main + +[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c +34a35 +> #include /* CLOCKS_PER_SEC */ +56,61c57,62 +< void mexFunction( +< int nlhs, /* number of expected outputs */ +< Matrix *plhs[], /* matrix pointer array returning outputs */ +< int nrhs, /* number of inputs */ +< Matrix *prhs[] /* matrix pointer array for inputs */ +< ) +--- +> void mexFunction( +> int nlhs, /* number of expected outputs */ +> mxArray *plhs[], /* array of pointers to output arguments +> */ +> int nrhs, /* number of inputs */ +> const mxArray *prhs[] /* array of pointers to input arguments */ +> ) +87a89 +> mwIndex *mwstart,*mwadjacency; +104c106,110 +< start = mxGetJc(A_in); +--- +> /* start = mxGetJc(A_in);*/ +> mwstart = mxGetJc(A_in); +> start = mxMalloc((mxGetN(A_in)+1)*sizeof(int)); +> for (i=0; i<(mxGetN(A_in)+1); i++) +> start[i]= (int)mwstart[i]; +106c112,116 +< adjacency = mxGetIr(A_in); +--- +> /* adjacency = mxGetIr(A_in);*/ +> mwadjacency = mxGetIr(A_in); +> adjacency = mxMalloc(mxGetNzmax(A_in)*sizeof(int)); +> for (i=0; i adjacency[i]= (int)mwadjacency[i]; +169c181 +< plhs [1] = mxCreateFull (1, 1, REAL) ; +--- +> plhs [1] = mxCreateDoubleMatrix (1, 1, mxREAL) ; +173c185 +< ((double) CLK_TCK) ; +--- +> ((double) CLOCKS_PER_SEC) ; +179c191 +< map_out = mxCreateFull(1,nvtxs,REAL); +--- +> map_out = mxCreateDoubleMatrix(1,nvtxs,mxREAL); +185a198,199 +> if (start != NULL) mxFree((char *) start); +> if (adjacency != NULL) mxFree((char *) adjacency); + + +7/29/09: + +[jschierm@astrid chaco]$ diff mlchaco_old.c mlchaco.c +131,132c141,144 +< outassignname = NULL; +< outfilename = NULL; +--- +> /* outassignname = NULL; +> outfilename = NULL;*/ +> outassignname = "chaco_assign.txt"; +> outfilename = "chaco_out.txt"; + +7/30/09: + +[jschierm@astrid chaco]$ diff Makefile_old Makefile +27c27,28 +< MATLAB = /usr/local/libexec/matlab +--- +> #MATLAB = /usr/local/libexec/matlab +> MATLAB = /usr/local/pkgs/matlab-7.6 +37c39,40 +< CFLAGS = -Xa -G -xO4 -xcg92 +--- +> #CFLAGS = -Xa -G -xO4 -xcg92 +> CFLAGS = -Xa -G -xO4 -xcg92 -DMATLAB +45,47d49 [using Chaco versions with MATLAB switch] +< ${MLCHACO}/chaco_check_graph.c \ +< ${MLCHACO}/check_input.c \ +< ${MLCHACO}/smalloc.c \ +48a51,53 +> # ${MLCHACO}/chaco_check_graph.c \ +> # ${MLCHACO}/check_input.c \ +> # ${MLCHACO}/smalloc.c \ +55a61 +> ${CHACO}/input/check_input.c \ +61a68 +> ${CHACO}/graph/check_graph.c \ +91a99 [compared CHFILES with Chaco Makefile CHFILES] +> ${CHACO}/klvspiff/flow.c \ +97a106 [compared CHFILES with Chaco Makefile CHFILES] +> ${CHACO}/klvspiff/flatten.c \ +100c109,110 [compared CHFILES with Chaco Makefile CHFILES] +< ${CHACO}/coarsen/makecgraph.c \ +--- +> ${CHACO}/coarsen/makefgraph.c \ +> ${CHACO}/coarsen/makeccoords.c \ +102d111 [compared CHFILES with Chaco Makefile CHFILES] +< ${CHACO}/coarsen/countcedges.c \ +108a118 [compared CHFILES with Chaco Makefile CHFILES] +> ${CHACO}/coarsen/maxmatch5.c \ +234a245 +> ${CHACO}/util/smalloc.c \ +245a257,258 +> # ${CHACO}/main/user_params.c \ +> # ${CHACO}/util/bail.c \ +254a268,271 +> #mlchaco: ${MLFILES.c} chaco.a Makefile +> # mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +> # mv mlchaco.mex* ${DEST_DIR} +> +256c273 +< mex -V4 -output mlchaco ${MLFILES.c} chaco.a -I${CHACO}/main +--- +> mex -output mlchaco -largeArrayDims -DMATLAB ${MLFILES.c} +> chaco.a -I${CHACO}/main + +5/25/10: + +- reorganized chaco.m and mlchaco.c drivers into Chaco.c matlab-layer (independent of chaco) and Chacox.c x-layer (independent of matlab). + +5/26/10: + +- added mexchaco target to Makefile (and related changes). + +5/27/10 + +- added define for exit(status) to ${CHACO}/main/defs.h so that local bail.c is + unnecessary. + +6/15/10: + +- separated chaco x-layer from meshpart build. + Index: /issm/trunk-jpl-damage/externalpackages/cmake/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/cmake/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/cmake/install.sh (revision 11330) @@ -0,0 +1,22 @@ +#!/bin/bash + +#Some cleanup +rm -rf install cmake-2.8.5 +mkdir install + +#Untar +tar -zxvf cmake-2.8.5.tar.gz + +#Move cmake into install directory +mv cmake-2.8.5/* install +rm -rf cmake-2.8.5 + +#Compile cmake +cd install +./bootstrap --prefix=$ISSM_TIER/externalpackages/cmake/install +if [ -z $1 ]; then + make +else + make -j $1; +fi +make install Index: /issm/trunk-jpl-damage/externalpackages/colpack/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/colpack/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/colpack/install.sh (revision 11330) @@ -0,0 +1,22 @@ +#!/bin/bash + +#Erase install +rm -rf install src ColPack + +#install directory +mkdir src +tar -zxvf ColPack-1.0.3.tar.gz +mv ColPack/* src +rm -rf ColPack + +#compile +cd src +if [ -z $1 ]; then + make +else + make -j $1 +fi +cd .. + +#install +ln -s src/build ./install Index: /issm/trunk-jpl-damage/externalpackages/cppcheck/README =================================================================== --- /issm/trunk-jpl-damage/externalpackages/cppcheck/README (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/cppcheck/README (revision 11330) @@ -0,0 +1,2 @@ +Cppcheck: static analysis of source code. +Obtained code from http://sourceforge.net/projects/cppcheck/ Index: /issm/trunk-jpl-damage/externalpackages/cppcheck/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/cppcheck/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/cppcheck/install.sh (revision 11330) @@ -0,0 +1,20 @@ +#!/bin/bash + +#Erase install +rm -rf install src cppcheck-1.48 +mkdir src + +tar -xvf cppcheck-1.48.tar + +mv cppcheck-1.48/* src +rm -rf cppcheck-1.48 + +#compile +cd src +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install PREFIX=$ISSM_TIER/externalpackages/cppcheck/install +cd .. Index: /issm/trunk-jpl-damage/externalpackages/dace/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dace/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dace/install.sh (revision 11330) @@ -0,0 +1,12 @@ +#!/bin/bash + +#Some cleanup +rm -rf install dace +mkdir install + +#uncompress +unzip dace.zip + +#move to install directory +mv dace/* install +rm -rf dace Index: /issm/trunk-jpl-damage/externalpackages/dakota/LHSDriver.cpp.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dakota/LHSDriver.cpp.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dakota/LHSDriver.cpp.patch (revision 11330) @@ -0,0 +1,8 @@ +766c766 +< /*char output_string[32], message_string[32], title_string[32], +--- +> char output_string[32], message_string[32], title_string[32], +802c802 +< check_error(err_code, "lhs_files");*/ +--- +> check_error(err_code, "lhs_files"); Index: /issm/trunk-jpl-damage/externalpackages/dakota/NIDRProblemDescDB.C.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dakota/NIDRProblemDescDB.C.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dakota/NIDRProblemDescDB.C.patch (revision 11330) @@ -0,0 +1,4 @@ +95a96,98 +> +> //close the input file +> fclose(nidrin); Index: /issm/trunk-jpl-damage/externalpackages/dakota/NonDLocalReliability.C.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dakota/NonDLocalReliability.C.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dakota/NonDLocalReliability.C.patch (revision 11330) @@ -0,0 +1,7 @@ +2276a2277 +> // add sensitivity output to importance factors (jes, 8/06/10) +2280c2281,2282 +< << impFactor[i][j] << '\n'; +--- +> << impFactor[i][j] << " Sensitivity = " << setw(write_precision+7) +> << fnGradsMeanX(i, j) << '\n'; Index: /issm/trunk-jpl-damage/externalpackages/dakota/NonDSampling.C.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dakota/NonDSampling.C.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dakota/NonDSampling.C.patch (revision 11330) @@ -0,0 +1,15 @@ +656a657,658 +> +> +659a662,663 +> +> return; //don't compute for now, too expensive. +705c709 +< //calculate simple rank correlation coeff +--- +> //calculate simple correlation coeff +710a715 +> +1071a1077,1078 +> +> return; //don't output for now. Index: /issm/trunk-jpl-damage/externalpackages/dakota/NonDUnilevelRBDO.C.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dakota/NonDUnilevelRBDO.C.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dakota/NonDUnilevelRBDO.C.patch (revision 11330) @@ -0,0 +1,10 @@ +1052,1053c1052,1057 +< s << " Importance Factor for variable " << setw(11) +< << uv_labels[j].data() << " = " << impFactor[i][j] << '\n'; +--- +> // add sensitivity output to importance factors (jes, 8/06/10) +> s << " Importance Factor for variable " << setiosflags(ios::left) +> << setw(11) << uv_labels[j].data() << " = " +> << resetiosflags(ios::adjustfield) << setw(write_precision+7) +> << impFactor[i][j] << " Sensitivity = " << setw(write_precision+7) +> << fnGradsMeanX(i, j) << '\n'; Index: /issm/trunk-jpl-damage/externalpackages/dakota/ParallelLibrary.C.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dakota/ParallelLibrary.C.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dakota/ParallelLibrary.C.patch (revision 11330) @@ -0,0 +1,34 @@ +134a135 +> initialized=0; //we run serially all the time! +165a167,197 +> /** This constructor is provided for the Issm software, to run serial +> * Dakota in a parallel MPI ring: */ +> ParallelLibrary::ParallelLibrary(char* serial_mode): worldRank(0), worldSize(1), +> mpirunFlag(false), ownMPIFlag(false), dryRunFlag(false), dummyFlag(false), +> stdOutputFlag(false), stdErrorFlag(false), startClock(0), +> stdOutputFilename(NULL), stdErrorFilename(NULL), readRestartFilename(NULL), +> writeRestartFilename(NULL), stopRestartEvals(0), +> currPLIter(parallelLevels.end()), currPCIter(parallelConfigurations.end()) +> { +> startClock = clock(); +> #ifdef DAKOTA_UTILIB +> utilib::exception_mngr::set_mode(utilib::exception_mngr::Abort); +> startCPUTime = CPUSeconds(); // see utilib/src/sys/seconds.cpp +> startWCTime = WallClockSeconds(); // see utilib/src/sys/seconds.cpp +> #endif // DAKOTA_UTILIB +> +> // do not initialize MPI. Get worldRank/worldSize if available +> ParallelLevel pl; +> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota! +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota in serial mode on CPU 0, inside an MPI ring."; +> #else // mpi not available +> pl.serverIntraComm = MPI_COMM_NULL; +> Cout << "Running Dakota in serial mode.\n"; +> #endif // HAVE_MPI +> +> parallelLevels.insert(pl); +> currPLIter = parallelLevels.begin(); +> increment_parallel_configuration(); +> } +> Index: /issm/trunk-jpl-damage/externalpackages/dakota/ParallelLibrary.H.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dakota/ParallelLibrary.H.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dakota/ParallelLibrary.H.patch (revision 11330) @@ -0,0 +1,3 @@ +346a347,348 +> /// library mode constructor, serial mode +> ParallelLibrary(char* serial_mode); Index: /issm/trunk-jpl-damage/externalpackages/dakota/README =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dakota/README (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dakota/README (revision 11330) @@ -0,0 +1,9 @@ +version 4.3 of dakota is not yet released. The 4.3 version +here refers to the VOTD release on May 12th 2009. While waiting +for 4.3, we consider the develpment version to be 4.3. +4.2 is replaced by 4.3, to handle fnEvalId extra arguemnt to the Dakota +structure. + +Be sure to set FC and F77 variable names to point to your fortran compiler, otherwise, + the LHS packages will pick up gfortran as its fortran compiler, which can create serious + troubles. Index: /issm/trunk-jpl-damage/externalpackages/dakota/install-altix64-cosmos.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dakota/install-altix64-cosmos.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dakota/install-altix64-cosmos.sh (revision 11330) @@ -0,0 +1,96 @@ +#!/bin/bash + +#Get number of cpus +NUMCPUS=$1; + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C ./NonDSampling.C.patch +patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_TIER/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas=/opt/intel/mkl/9.1.023/lib/64/libmkl.so \ + --with-lapack=/opt/intel/mkl/9.1.023/lib/64/libmkl_lapack.so +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ -z $NUMCPUS ]; +then + make + make install +else + make -j $NUMCPUS + make -j $NUMCPUS install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk-jpl-damage/externalpackages/dakota/install-linux64-astrid.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dakota/install-linux64-astrid.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dakota/install-linux64-astrid.sh (revision 11330) @@ -0,0 +1,96 @@ +#!/bin/bash + +#Get number of cpus +NUMCPUS=$1; + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C ./NonDSampling.C.patch +patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_TIER/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas=/usr/lib64/libblas.so.3.0.3 \ + --with-lapack=/usr/lib64/liblapack.so.3.0.3 +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ -z $NUMCPUS ]; +then + make + make install +else + make -j $NUMCPUS + make -j $NUMCPUS install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk-jpl-damage/externalpackages/dakota/install-macosx64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dakota/install-macosx64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dakota/install-macosx64.sh (revision 11330) @@ -0,0 +1,94 @@ +#!/bin/bash + +#Get number of cpus +NUMCPUS=$1; + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C ./NonDSampling.C.patch +patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_TIER/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ -z $NUMCPUS ]; +then + make + make install +else + make -j $NUMCPUS + make -j $NUMCPUS install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk-jpl-damage/externalpackages/dakota/install-pleiades.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dakota/install-pleiades.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dakota/install-pleiades.sh (revision 11330) @@ -0,0 +1,96 @@ +#!/bin/bash + +#Get number of cpus +NUMCPUS=$1; + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf install +mkdir src install + +#Untar +tar -zxvf Dakota_4_3.src.tar.gz + +#Move Dakota to src directory +mv Dakota/* src +rm -rf Dakota + +#Apply patches +patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch +patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch +patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch +patch src/src/NonDSampling.C ./NonDSampling.C.patch +patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch +patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? +#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch + +#Configure dakota +cd src +./configure \ + --prefix="$ISSM_TIER/externalpackages/dakota/install" \ + --without-graphics \ + --with-pic \ + --disable-mpi \ + --with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \ + --with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" +cd .. + +#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC +#flag to the compilation. +cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/NCSUOpt/Makefile + +cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-nappspack/Makefile + +cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-cddlib/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-shared/Makefile + +cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-conveyor/Makefile + +cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/methods/hopspack/src-appspack/Makefile + +cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/colin/src/Makefile + +cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/coliny/src/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp +mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +mv temp ./src/packages/ampl/Makefile + +#Compile and install dakota +cd src +if [ -z $NUMCPUS ]; +then + make + make install +else + make -j $NUMCPUS + make -j $NUMCPUS install +fi +cd .. + +#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! +cd install/lib +mv libamplsolver.a libamplsolver.a.bak +ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a Index: /issm/trunk-jpl-damage/externalpackages/doxygen/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/doxygen/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/doxygen/install.sh (revision 11330) @@ -0,0 +1,19 @@ +#!/bin/bash + +#Some cleanup +rm -rf install + +#Download latest version +svn co https://doxygen.svn.sourceforge.net/svnroot/doxygen/trunk install + +#Configure doxygen +cd install && ./configure --prefix "$ISSM_TIER/externalpackages/doxygen/install" +if [ -z $1 ]; then + make +else + make -j $1 +fi + +#Install doxygen +make install +make install_docs Index: /issm/trunk-jpl-damage/externalpackages/dyson/ldap.pl =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dyson/ldap.pl (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dyson/ldap.pl (revision 11330) @@ -0,0 +1,25 @@ +#!/usr/bin/perl +# +# LDAP.PL - Acquire JPL LDAP data and pare down to user IDs - 2011-08-01 +# +$cat="/bin/cat"; $srt="/bin/sort"; $ldb="/usr/bin/ldapsearch"; # Binary locations (change as needed) +$lds="ldap.jpl.nasa.gov"; $ou="ou=personnel,dc=dir,dc=jpl,dc=nasa,dc=gov"; # Define LDAP server & organization +$bn="jplbadgenumber"; $txt="$bn".".txt"; $db="jplusers.db"; # Initialize values +# +system(`$ldb -x -h $lds -b $ou uid=* filter $bn > $txt`); # Execute LDAPsearch, write to file +# +open(I,"<$txt"); # Open input file handle + open(O,">badges.tmp"); # Open output file handle + while () { chomp($_); # Spool through input file + if ($_=~"^uid=") { # If line begins with UID value, + $_=~s/uid=//; $_=~s/,(.*)$//; $_=~s/\n//; # strip line of extraneous data + if (!($_=~/^\d\d\d\d\d\d/)) { print O "$_\n"; } # If UID is non-numeric, print output + } # Close condition + } # Close spool + close(O); # Close output file handle +close(I); # Close input file handle +# +system(`$cat badges.tmp |$srt -u > $db 2>/dev/null`); # Sort output +unlink("badges.tmp"); unlink("$txt"); # Unlink temp files +# +# EOF - 2011-08-01 - Jay Dyson Index: /issm/trunk-jpl-damage/externalpackages/dyson/readme.txt =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dyson/readme.txt (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dyson/readme.txt (revision 11330) @@ -0,0 +1,38 @@ +-- ARCHIVE MANIFEST ------------------------------------------ 2011-08-19 -- + + Filename Description + -------------- ---------------------------------------------------------- + readme.txt This file: describes script functions. + ldap.pl PERL script for acquiring JPL user IDs via cron job. + source_seek.sh Code-scanning script. Surveys scripts for hard-coded IP + addresses, password callouts, and user IDs. + +-- SCRIPT INFORMATION ------------------------------------------------------ + + LDAP.PL (requires PERL, UNIX ldapsearch, and related utilities) + -------------------------------------------------------------------------- + The LDAP.PL script is intended solely for twice-daily invocation via cron. + This script should be run once at noon, once at midnight. This script + generates the jplusers.db file on which the SOURCE_SEEK.SH shell script + relies for its scanning of source files. + + SOURCE_SEEK.SH (requires UNIX shell and related utilities) + -------------------------------------------------------------------------- + The SOURCE_SEEK.SH shell script is intended for regular cron invocation, + but may be run at system administrator discretion. This script uses UNIX + 'find' and 'grep' utilities to scan code files for hard-coded JPL Internet + Protocol (IP) addresses, password callouts, and JPL user IDs. This script + accepts the path where source code files reside as a command line + argument (e.g., ./source_seek.sh /path/to/sourcecode/files). + +-- AUTHOR CONTACT INFO ----------------------------------------------------- + + Please direct questions regarding these files to the developer. + + Name : Jay Dyson, CISSP + Role : IT Security Engineer + Group : JPL IT Security + E-mail : jdyson@jpl.nasa.gov + Phone : 818-397-4960 + +------------------------------------------------ LAST UPDATED: 2011-08-19 -- Index: /issm/trunk-jpl-damage/externalpackages/dyson/source_seek.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/dyson/source_seek.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/dyson/source_seek.sh (revision 11330) @@ -0,0 +1,26 @@ +#!/bin/sh +# +# SOURCE_SEEK.SH - Look for IP addresses and mention of 'password' in source files - 2009-10-05 +# +if [ -n "${1}" ]; then + clear + echo "Checking for IP addresses" + echo "--------------------------------------------" + find $1 -name "*" -exec grep -il "128\.149\." {} \; + find $1 -name "*" -exec grep -il "137\.78\." {} \; + find $1 -name "*" -exec grep -il "137\.79\." {} \; + find $1 -name "*" -exec grep -il "137\.228\." {} \; + echo "--------------------------------------------" + echo "\nChecking for 'password'" + echo "--------------------------------------------" + find $1 -name "*" -exec grep -il "password" {} \; + echo "--------------------------------------------" + echo "\nChecking for JPL user IDs" + echo "--------------------------------------------" + find $1 -name "*" -exec grep -ilf jplusers.db {} \; + echo "--------------------------------------------" +else + echo -e "\nUSE: $0 \n"; +fi +# +# EOF - 2011-08-05 - Jay Dyson Index: /issm/trunk-jpl-damage/externalpackages/export_fig/eps2pdf.m =================================================================== --- /issm/trunk-jpl-damage/externalpackages/export_fig/eps2pdf.m (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/export_fig/eps2pdf.m (revision 11330) @@ -0,0 +1,104 @@ +%EPS2PDF Convert an eps file to pdf format using ghostscript +% +% Examples: +% eps2pdf source dest +% eps2pdf(source, dest, crop) +% eps2pdf(source, dest, crop, append) +% eps2pdf(source, dest, crop, append, gray) +% eps2pdf(source, dest, crop, append, gray, quality) +% +% This function converts an eps file to pdf format. The output can be +% optionally cropped and also converted to grayscale. If the output pdf +% file already exists then the eps file can optionally be appended as a new +% page on the end of the eps file. The level of bitmap compression can also +% optionally be set. +% +% This function requires that you have ghostscript installed on your +% system. Ghostscript can be downloaded from: http://www.ghostscript.com +% +%IN: +% source - filename of the source eps file to convert. The filename is +% assumed to already have the extension ".eps". +% dest - filename of the destination pdf file. The filename is assumed to +% already have the extension ".pdf". +% crop - boolean indicating whether to crop the borders off the pdf. +% Default: true. +% append - boolean indicating whether the eps should be appended to the +% end of the pdf as a new page (if the pdf exists already). +% Default: false. +% gray - boolean indicating whether the output pdf should be grayscale or +% not. Default: false. +% quality - scalar indicating the level of image bitmap quality to +% output. A larger value gives a higher quality. quality > 100 +% gives lossless output. Default: ghostscript prepress default. + +% Copyright (C) Oliver Woodford 2009-2010 + +% Suggestion of appending pdf files provided by Matt C at: +% http://www.mathworks.com/matlabcentral/fileexchange/23629 + +% Thank you to Fabio Viola for pointing out compression artifacts, leading +% to the quality setting. +% Thank you to Scott for pointing out the subsampling of very small images, +% which was fixed for lossless compression settings. + +function eps2pdf(source, dest, crop, append, gray, quality) +% Intialise the options string for ghostscript +options = ['-q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress -sOutputFile="' dest '"']; +% Set crop option +if nargin < 3 || crop + options = [options ' -dEPSCrop']; +end +% Set the grayscale option +if nargin > 4 && gray + options = [options ' -sColorConversionStrategy=Gray -dProcessColorModel=/DeviceGray']; +end +% Set the bitmap quality +if nargin > 5 && ~isempty(quality) + options = [options ' -dAutoFilterColorImages=false -dAutoFilterGrayImages=false']; + if quality > 100 + options = [options ' -dColorImageFilter=/FlateEncode -dGrayImageFilter=/FlateEncode -c ".setpdfwrite << /ColorImageDownsampleThreshold 10 /GrayImageDownsampleThreshold 10 >> setdistillerparams"']; + else + options = [options ' -dColorImageFilter=/DCTEncode -dGrayImageFilter=/DCTEncode']; + v = 1 + (quality < 80); + quality = 1 - quality / 100; + s = sprintf('<< /QFactor %.2f /Blend 1 /HSample [%d 1 1 %d] /VSample [%d 1 1 %d] >>', quality, v, v, v, v); + options = sprintf('%s -c ".setpdfwrite << /ColorImageDict %s /GrayImageDict %s >> setdistillerparams"', options, s, s); + end +end +% Check if the output file exists +if nargin > 3 && append && exist(dest, 'file') == 2 + % File exists - append current figure to the end + tmp_nam = tempname; + % Copy the file + copyfile(dest, tmp_nam); + % Add the output file names + options = [options ' -f "' tmp_nam '" "' source '"']; + try + % Convert to pdf using ghostscript + [status message] = ghostscript(options); + catch + % Delete the intermediate file + delete(tmp_nam); + rethrow(lasterror); + end + % Delete the intermediate file + delete(tmp_nam); +else + % File doesn't exist or should be over-written + % Add the output file names + options = [options ' -f "' source '"']; + % Convert to pdf using ghostscript + [status message] = ghostscript(options); +end +% Check for error +if status + % Report error + if isempty(message) + error('Unable to generate pdf. Check destination directory is writable.'); + else + error(message); + end +end +return + Index: /issm/trunk-jpl-damage/externalpackages/export_fig/export_fig.m =================================================================== --- /issm/trunk-jpl-damage/externalpackages/export_fig/export_fig.m (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/export_fig/export_fig.m (revision 11330) @@ -0,0 +1,720 @@ +%EXPORT_FIG Exports figures suitable for publication +% +% Examples: +% im = export_fig +% [im alpha] = export_fig +% export_fig filename +% export_fig filename -format1 -format2 +% export_fig ... -nocrop +% export_fig ... -transparent +% export_fig ... -native +% export_fig ... -m +% export_fig ... -r +% export_fig ... -a +% export_fig ... -q +% export_fig ... - +% export_fig ... - +% export_fig ... -append +% export_fig(..., handle) +% +% This function saves a figure or single axes to one or more vector and/or +% bitmap file formats, and/or outputs a rasterized version to the +% workspace, with the following properties: +% - Figure/axes reproduced as it appears on screen +% - Cropped borders (optional) +% - Embedded fonts (vector formats) +% - Improved line and grid line styles +% - Anti-aliased graphics (bitmap formats) +% - Render images at native resolution (optional for bitmap formats) +% - Transparent background supported (pdf, eps, png) +% - Semi-transparent patch objects supported (png only) +% - RGB, CMYK or grayscale output (CMYK only with pdf, eps, tiff) +% - Variable image compression, including lossless (pdf, eps, jpg) +% - Optionally append to file (pdf, tiff) +% - Vector formats: pdf, eps +% - Bitmap formats: png, tiff, jpg, bmp, export to workspace +% +% This function is especially suited to exporting figures for use in +% publications and presentations, because of the high quality and +% portability of media produced. +% +% Note that the background color and figure dimensions are reproduced +% (the latter approximately, and ignoring cropping & magnification) in the +% output file. For transparent background (and semi-transparent patch +% objects), use the -transparent option or set the figure 'Color' property +% to 'none'. To make axes transparent set the axes 'Color' property to +% 'none'. Pdf, eps and png are the only file formats to support a +% transparent background, whilst the png format alone supports transparency +% of patch objects. +% +% The choice of renderer (opengl, zbuffer or painters) has a large impact +% on the quality of output. Whilst the default value (opengl for bitmaps, +% painters for vector formats) generally gives good results, if you aren't +% satisfied then try another renderer. Notes: 1) For vector formats (eps, +% pdf), only painters generates vector graphics. 2) For bitmaps, only +% opengl can render transparent patch objects correctly. 3) For bitmaps, +% only painters will correctly scale line dash and dot lengths when +% magnifying or anti-aliasing. 4) Fonts may be substitued with Courier when +% using painters. +% +% When exporting to vector format (pdf & eps) and bitmap format using the +% painters renderer, this function requires that ghostscript is installed +% on your system. You can download this from: +% http://www.ghostscript.com +% When exporting to eps it additionally requires pdftops, from the Xpdf +% suite of functions. You can download this from: +% http://www.foolabs.com/xpdf +% +%IN: +% filename - string containing the name (optionally including full or +% relative path) of the file the figure is to be saved as. If +% a path is not specified, the figure is saved in the current +% directory. If no name and no output arguments are specified, +% the default name, 'export_fig_out', is used. If neither a +% file extension nor a format are specified, a ".png" is added +% and the figure saved in that format. +% -format1, -format2, etc. - strings containing the extensions of the +% file formats the figure is to be saved as. +% Valid options are: '-pdf', '-eps', '-png', +% '-tif', '-jpg' and '-bmp'. All combinations +% of formats are valid. +% -nocrop - option indicating that the borders of the output are not to +% be cropped. +% -transparent - option indicating that the figure background is to be +% made transparent (png, pdf and eps output only). +% -m - option where val indicates the factor to magnify the +% on-screen figure dimensions by when generating bitmap +% outputs. Default: '-m1'. +% -r - option val indicates the resolution (in pixels per inch) to +% export bitmap outputs at, keeping the dimensions of the +% on-screen figure. Default: sprintf('-r%g', get(0, +% 'ScreenPixelsPerInch')). Note that the -m and -r options +% change the same property. +% -native - option indicating that the output resolution (when outputting +% a bitmap format) should be such that the vertical resolution +% of the first suitable image found in the figure is at the +% native resolution of that image. To specify a particular +% image to use, give it the tag 'export_fig_native'. Notes: +% This overrides any value set with the -m and -r options. It +% also assumes that the image is displayed front-to-parallel +% with the screen. The output resolution is approximate and +% should not be relied upon. Anti-aliasing can have adverse +% effects on image quality (disable with the -a1 option). +% -a1, -a2, -a3, -a4 - option indicating the amount of anti-aliasing to +% use for bitmap outputs. '-a1' means no anti- +% aliasing; '-a4' is the maximum amount (default). +% - - option to force a particular renderer (painters, opengl +% or zbuffer) to be used over the default: opengl for +% bitmaps; painters for vector formats. +% - - option indicating which colorspace color figures should +% be saved in: RGB (default), CMYK or gray. CMYK is only +% supported in pdf, eps and tiff output. +% -q - option to vary bitmap image quality (in pdf, eps and jpg +% files only). Larger val, in the range 0-100, gives higher +% quality/lower compression. val > 100 gives lossless +% compression. Default: '-q95' for jpg, ghostscript prepress +% default for pdf & eps. Note: lossless compression can +% sometimes give a smaller file size than the default lossy +% compression, depending on the type of images. +% -append - option indicating that if the file (pdfs only) already +% exists, the figure is to be appended as a new page, instead +% of being overwritten (default). +% handle - The handle of the figure or axes (can be an array of handles +% of several axes, but these must be in the same figure) to be +% saved. Default: gcf. +% +%OUT: +% im - MxNxC uint8 image array of the figure. +% alpha - MxN single array of alphamatte values in range [0,1], for the +% case when the background is transparent. +% +% Some helpful examples and tips can be found at: +% http://sites.google.com/site/oliverwoodford/software/export_fig +% +% See also PRINT, SAVEAS. + +% Copyright (C) Oliver Woodford 2008-2011 + +% The idea of using ghostscript is inspired by Peder Axensten's SAVEFIG +% (fex id: 10889) which is itself inspired by EPS2PDF (fex id: 5782). +% The idea for using pdftops came from the MATLAB newsgroup (id: 168171). +% The idea of editing the EPS file to change line styles comes from Jiro +% Doke's FIXPSLINESTYLE (fex id: 17928). +% The idea of changing dash length with line width came from comments on +% fex id: 5743, but the implementation is mine :) +% The idea of anti-aliasing bitmaps came from Anders Brun's MYAA (fex id: +% 20979). +% The idea of appending figures in pdfs came from Matt C in comments on the +% FEX (id: 23629) + +% Thanks to Roland Martin for pointing out the colour MATLAB +% bug/feature with colorbar axes and transparent backgrounds. +% Thanks also to Andrew Matthews for describing a bug to do with the figure +% size changing in -nodisplay mode. I couldn't reproduce it, but included a +% fix anyway. +% Thanks to Tammy Threadgill for reporting a bug where an axes is not +% isolated from gui objects. + +function [im alpha] = export_fig(varargin) +% Parse the input arguments +[fig options] = parse_args(nargout, varargin{:}); +% Isolate the subplot, if it is one +cls = strcmp(get(fig(1), 'Type'), 'axes'); +if cls + % Given handles of one or more axes, so isolate them from the rest + fig = isolate_axes(fig); +else + old_mode = get(fig, 'InvertHardcopy'); +end +% Hack the font units where necessary (due to a font rendering bug in +% print?). This may not work perfectly in all cases. Also it can change the +% figure layout if reverted, so use a copy. +magnify = options.magnify * options.aa_factor; +if isbitmap(options) && magnify ~= 1 + fontu = findobj(fig, 'FontUnits', 'normalized'); + if ~isempty(fontu) + % Some normalized font units found + if ~cls + fig = copyfig(fig); + set(fig, 'Visible', 'off'); + fontu = findobj(fig, 'FontUnits', 'normalized'); + cls = true; + end + set(fontu, 'FontUnits', 'points'); + end +end +% Set to print exactly what is there +set(fig, 'InvertHardcopy', 'off'); +% Set the renderer +switch options.renderer + case 1 + renderer = '-opengl'; + case 2 + renderer = '-zbuffer'; + case 3 + renderer = '-painters'; + otherwise + renderer = '-opengl'; % Default for bitmaps +end +% Do the bitmap formats first +if isbitmap(options) + % Get the background colour + if options.transparent && (options.png || options.alpha) + % Get out an alpha channel + % MATLAB "feature": black colorbar axes can change to white and vice versa! + hCB = findobj(fig, 'Type', 'axes', 'Tag', 'Colorbar'); + if isempty(hCB) + yCol = []; + xCol = []; + else + yCol = get(hCB, 'YColor'); + xCol = get(hCB, 'XColor'); + if iscell(yCol) + yCol = cell2mat(yCol); + xCol = cell2mat(xCol); + end + yCol = sum(yCol, 2); + xCol = sum(xCol, 2); + end + % MATLAB "feature": apparently figure size can change when changing + % colour in -nodisplay mode + pos = get(fig, 'Position'); + % Set the background colour to black, and set size in case it was + % changed internally + tcol = get(fig, 'Color'); + set(fig, 'Color', 'k', 'Position', pos); + % Correct the colorbar axes colours + set(hCB(yCol==0), 'YColor', [0 0 0]); + set(hCB(xCol==0), 'XColor', [0 0 0]); + % Print large version to array + B = print2array(fig, magnify, renderer); + % Downscale the image + B = downsize(single(B), options.aa_factor); + % Set background to white (and set size) + set(fig, 'Color', 'w', 'Position', pos); + % Correct the colorbar axes colours + set(hCB(yCol==3), 'YColor', [1 1 1]); + set(hCB(xCol==3), 'XColor', [1 1 1]); + % Print large version to array + A = print2array(fig, magnify, renderer); + % Downscale the image + A = downsize(single(A), options.aa_factor); + % Set the background colour (and size) back to normal + set(fig, 'Color', tcol, 'Position', pos); + % Compute the alpha map + alpha = round(sum(B - A, 3)) / (255 * 3) + 1; + A = alpha; + A(A==0) = 1; + A = B ./ A(:,:,[1 1 1]); + clear B + % Convert to greyscale + if options.colourspace == 2 + A = rgb2grey(A); + end + A = uint8(A); + % Crop the background + if options.crop + [alpha v] = crop_background(alpha, 0); + A = A(v(1):v(2),v(3):v(4),:); + end + if options.png + % Compute the resolution + res = options.magnify * get(0, 'ScreenPixelsPerInch') / 25.4e-3; + % Save the png + imwrite(A, [options.name '.png'], 'Alpha', alpha, 'ResolutionUnit', 'meter', 'XResolution', res, 'YResolution', res); + % Clear the png bit + options.png = false; + end + % Return only one channel for greyscale + if isbitmap(options) + A = check_greyscale(A); + end + if options.alpha + % Store the image + im = A; + % Clear the alpha bit + options.alpha = false; + end + % Get the non-alpha image + if isbitmap(options) + alph = alpha(:,:,ones(1, size(A, 3))); + A = uint8(single(A) .* alph + 255 * (1 - alph)); + clear alph + end + if options.im + % Store the new image + im = A; + end + else + % Print large version to array + if options.transparent + % MATLAB "feature": apparently figure size can change when changing + % colour in -nodisplay mode + pos = get(fig, 'Position'); + tcol = get(fig, 'Color'); + set(fig, 'Color', 'w', 'Position', pos); + A = print2array(fig, magnify, renderer); + set(fig, 'Color', tcol, 'Position', pos); + tcol = 255; + else + [A tcol] = print2array(fig, magnify, renderer); + end + % Crop the background + if options.crop + A = crop_background(A, tcol); + end + % Downscale the image + A = downsize(A, options.aa_factor); + if options.colourspace == 2 + % Convert to greyscale + A = rgb2grey(A); + else + % Return only one channel for greyscale + A = check_greyscale(A); + end + % Outputs + if options.im + im = A; + end + if options.alpha + im = A; + alpha = zeros(size(A, 1), size(A, 2), 'single'); + end + end + % Save the images + if options.png + res = options.magnify * get(0, 'ScreenPixelsPerInch') / 25.4e-3; + imwrite(A, [options.name '.png'], 'ResolutionUnit', 'meter', 'XResolution', res, 'YResolution', res); + end + if options.bmp + imwrite(A, [options.name '.bmp']); + end + % Save jpeg with given quality + if options.jpg + quality = options.quality; + if isempty(quality) + quality = 95; + end + if quality > 100 + imwrite(A, [options.name '.jpg'], 'Mode', 'lossless'); + else + imwrite(A, [options.name '.jpg'], 'Quality', quality); + end + end + % Save tif images in cmyk if wanted (and possible) + if options.tif + if options.colourspace == 1 && size(A, 3) == 3 + A = double(255 - A); + K = min(A, [], 3); + K_ = 255 ./ max(255 - K, 1); + C = (A(:,:,1) - K) .* K_; + M = (A(:,:,2) - K) .* K_; + Y = (A(:,:,3) - K) .* K_; + A = uint8(cat(3, C, M, Y, K)); + clear C M Y K K_ + end + append_mode = {'overwrite', 'append'}; + imwrite(A, [options.name '.tif'], 'Resolution', options.magnify*get(0, 'ScreenPixelsPerInch'), 'WriteMode', append_mode{options.append+1}); + end +end +% Now do the vector formats +if isvector(options) + % Set the default renderer to painters + if ~options.renderer + renderer = '-painters'; + end + % Generate some filenames + tmp_nam = [tempname '.eps']; + if options.pdf + pdf_nam = [options.name '.pdf']; + else + pdf_nam = [tempname '.pdf']; + end + % Generate the options for print + p2eArgs = {renderer}; + if options.colourspace == 1 + p2eArgs = [p2eArgs {'-cmyk'}]; + end + if ~options.crop + p2eArgs = [p2eArgs {'-loose'}]; + end + try + % Generate an eps + print2eps(tmp_nam, fig, p2eArgs{:}); + % Remove the background, if desired + if options.transparent && ~isequal(get(fig, 'Color'), 'none') + eps_remove_background(tmp_nam); + end + % Generate a pdf + eps2pdf(tmp_nam, pdf_nam, 1, options.append, options.colourspace==2, options.quality); + catch ex + % Delete the eps + delete(tmp_nam); + rethrow(ex); + end + % Delete the eps + delete(tmp_nam); + if options.eps + try + % Generate an eps from the pdf + pdf2eps(pdf_nam, [options.name '.eps']); + catch ex + if ~options.pdf + % Delete the pdf + delete(pdf_nam); + end + rethrow(ex); + end + if ~options.pdf + % Delete the pdf + delete(pdf_nam); + end + end +end +if cls + % Close the created figure + close(fig); +else + % Reset the hardcopy mode + set(fig, 'InvertHardcopy', old_mode); +end +return + +function [fig options] = parse_args(nout, varargin) +% Parse the input arguments +% Set the defaults +fig = get(0, 'CurrentFigure'); +options = struct('name', 'export_fig_out', ... + 'crop', true, ... + 'transparent', false, ... + 'renderer', 0, ... % 0: default, 1: OpenGL, 2: ZBuffer, 3: Painters + 'pdf', false, ... + 'eps', false, ... + 'png', false, ... + 'tif', false, ... + 'jpg', false, ... + 'bmp', false, ... + 'colourspace', 0, ... % 0: RGB/gray, 1: CMYK, 2: gray + 'append', false, ... + 'im', nout == 1, ... + 'alpha', nout == 2, ... + 'aa_factor', 3, ... + 'magnify', 1, ... + 'quality', []); +native = false; % Set resolution to native of an image + +% Go through the other arguments +for a = 1:nargin-1 + if all(ishandle(varargin{a})) + fig = varargin{a}; + elseif ischar(varargin{a}) && ~isempty(varargin{a}) + if varargin{a}(1) == '-' + switch lower(varargin{a}(2:end)) + case 'nocrop' + options.crop = false; + case {'trans', 'transparent'} + options.transparent = true; + case 'opengl' + options.renderer = 1; + case 'zbuffer' + options.renderer = 2; + case 'painters' + options.renderer = 3; + case 'pdf' + options.pdf = true; + case 'eps' + options.eps = true; + case 'png' + options.png = true; + case {'tif', 'tiff'} + options.tif = true; + case {'jpg', 'jpeg'} + options.jpg = true; + case 'bmp' + options.bmp = true; + case 'rgb' + options.colourspace = 0; + case 'cmyk' + options.colourspace = 1; + case {'gray', 'grey'} + options.colourspace = 2; + case {'a1', 'a2', 'a3', 'a4'} + options.aa_factor = str2double(varargin{a}(3)); + case 'append' + options.append = true; + case 'native' + native = true; + otherwise + val = str2double(regexp(varargin{a}, '(?<=-(m|M|r|R|q|Q))(\d*\.)?\d+(e-?\d+)?', 'match')); + if ~isscalar(val) + error('option %s not recognised', varargin{a}); + end + switch lower(varargin{a}(2)) + case 'm' + options.magnify = val; + case 'r' + options.magnify = val ./ get(0, 'ScreenPixelsPerInch'); + case 'q' + options.quality = max(val, 0); + end + end + else + [p options.name ext] = fileparts(varargin{a}); + if ~isempty(p) + options.name = [p filesep options.name]; + end + switch lower(ext) + case {'.tif', '.tiff'} + options.tif = true; + case {'.jpg', '.jpeg'} + options.jpg = true; + case '.png' + options.png = true; + case '.bmp' + options.bmp = true; + case '.eps' + options.eps = true; + case '.pdf' + options.pdf = true; + otherwise + options.name = varargin{a}; + end + end + end +end + +% Check we have a figure handle +if isempty(fig) + error('No figure found'); +end + +% Set the default format +if ~isvector(options) && ~isbitmap(options) + options.png = true; +end + +% Check whether transparent background is wanted (old way) +if isequal(get(fig, 'Color'), 'none') + options.transparent = true; +end + +% If requested, set the resolution to the native vertical resolution of the +% first suitable image found +if native && isbitmap(options) + % Find a suitable image + list = findobj(fig, 'Type', 'image', 'Tag', 'export_fig_native'); + if isempty(list) + list = findobj(fig, 'Type', 'image', 'Visible', 'on'); + end + for hIm = list(:)' + % Check height is >= 2 + height = size(get(hIm, 'CData'), 1); + if height < 2 + continue + end + % Account for the image filling only part of the axes, or vice + % versa + yl = get(hIm, 'YData'); + if isscalar(yl) + yl = [yl(1)-0.5 yl(1)+height+0.5]; + else + if ~diff(yl) + continue + end + yl = yl + [-0.5 0.5] * (diff(yl) / (height - 1)); + end + hAx = get(hIm, 'Parent'); + yl2 = get(hAx, 'YLim'); + % Find the pixel height of the axes + oldUnits = get(hAx, 'Units'); + set(hAx, 'Units', 'pixels'); + pos = get(hAx, 'Position'); + set(hAx, 'Units', oldUnits); + if ~pos(4) + continue + end + % Found a suitable image + % Account for stretch-to-fill being disabled + pbar = get(hAx, 'PlotBoxAspectRatio'); + pos = min(pos(4), pbar(2)*pos(3)/pbar(1)); + % Set the magnification to give native resolution + options.magnify = (height * diff(yl2)) / (pos * diff(yl)); + break + end +end +return + +function A = downsize(A, factor) +% Downsample an image +if factor == 1 + % Nothing to do + return +end +try + % Faster, but requires image processing toolbox + A = imresize(A, 1/factor, 'bilinear'); +catch + % No image processing toolbox - resize manually + % Lowpass filter - use Gaussian as is separable, so faster + % Compute the 1d Gaussian filter + filt = (-factor-1:factor+1) / (factor * 0.6); + filt = exp(-filt .* filt); + % Normalize the filter + filt = single(filt / sum(filt)); + % Filter the image + padding = floor(numel(filt) / 2); + for a = 1:size(A, 3) + A(:,:,a) = conv2(filt, filt', single(A([ones(1, padding) 1:end repmat(end, 1, padding)],[ones(1, padding) 1:end repmat(end, 1, padding)],a)), 'valid'); + end + % Subsample + A = A(1+floor(mod(end-1, factor)/2):factor:end,1+floor(mod(end-1, factor)/2):factor:end,:); +end +return + +function A = rgb2grey(A) +A = cast(reshape(reshape(single(A), [], 3) * single([0.299; 0.587; 0.114]), size(A, 1), size(A, 2)), class(A)); +return + +function A = check_greyscale(A) +% Check if the image is greyscale +if size(A, 3) == 3 && ... + all(reshape(A(:,:,1) == A(:,:,2), [], 1)) && ... + all(reshape(A(:,:,2) == A(:,:,3), [], 1)) + A = A(:,:,1); % Save only one channel for 8-bit output +end +return + +function [A v] = crop_background(A, bcol) +% Map the foreground pixels +[h w c] = size(A); +if isscalar(bcol) && c > 1 + bcol = bcol(ones(1, c)); +end +bail = false; +for l = 1:w + for a = 1:c + if ~all(A(:,l,a) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end +end +bail = false; +for r = w:-1:l + for a = 1:c + if ~all(A(:,r,a) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end +end +bail = false; +for t = 1:h + for a = 1:c + if ~all(A(t,:,a) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end +end +bail = false; +for b = h:-1:t + for a = 1:c + if ~all(A(b,:,a) == bcol(a)) + bail = true; + break; + end + end + if bail + break; + end +end +% Crop the background, leaving one boundary pixel to avoid bleeding on +% resize +v = [max(t-1, 1) min(b+1, h) max(l-1, 1) min(r+1, w)]; +A = A(v(1):v(2),v(3):v(4),:); +return + +function eps_remove_background(fname) +% Remove the background of an eps file +% Open the file +fh = fopen(fname, 'r+'); +if fh == -1 + error('Not able to open file %s.', fname); +end +% Read the file line by line +while true + % Get the next line + l = fgets(fh); + if isequal(l, -1) + break; % Quit, no rectangle found + end + % Check if the line contains the background rectangle + if isequal(regexp(l, ' *0 +0 +\d+ +\d+ +rf *[\n\r]+', 'start'), 1) + % Set the line to whitespace and quit + l(1:regexp(l, '[\n\r]', 'start', 'once')-1) = ' '; + fseek(fh, -numel(l), 0); + fprintf(fh, l); + break; + end +end +% Close the file +fclose(fh); +return + +function b = isvector(options) +b = options.pdf || options.eps; +return + +function b = isbitmap(options) +b = options.png || options.tif || options.jpg || options.bmp || options.im || options.alpha; +return Index: /issm/trunk-jpl-damage/externalpackages/export_fig/fix_lines.m =================================================================== --- /issm/trunk-jpl-damage/externalpackages/export_fig/fix_lines.m (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/export_fig/fix_lines.m (revision 11330) @@ -0,0 +1,154 @@ +function fix_lines(fname, fname2) +%FIX_LINES Improves the line style of eps files generated by print +% +% Examples: +% fix_lines fname +% fix_lines fname fname2 +% +% This function improves the style of lines in eps files generated by +% MATLAB's print function, making them more similar to those seen on +% screen. Grid lines are also changed from a dashed style to a dotted +% style, for greater differentiation from dashed lines. +% +% The function also places embedded fonts after the postscript header, in +% versions of MATLAB which place the fonts first (R2006b and earlier), in +% order to allow programs such as Ghostscript to find the bounding box +% information. +% +% IN: +% fname - Name or path of source eps file. +% fname2 - Name or path of destination eps file. Default: same as fname. + +% Copyright: (C) Oliver Woodford, 2008-2010 + +% The idea of editing the EPS file to change line styles comes from Jiro +% Doke's FIXPSLINESTYLE (fex id: 17928) +% The idea of changing dash length with line width came from comments on +% fex id: 5743, but the implementation is mine :) + +% Thank you to Sylvain Favrot for bringing the embedded font/bounding box +% interaction in older versions of MATLAB to my attention. +% Thank you to D Ko for bringing an error with eps files with tiff previews +% to my attention. +% Thank you to Laurence K for suggesting the check to see if the file was +% opened. + +% Read in the file +fh = fopen(fname, 'r'); +if fh == -1 + error('File %s not found.', fname); +end +try + fstrm = fread(fh, '*char')'; +catch ex + fclose(fh); + rethrow(ex); +end +fclose(fh); + +% Move any embedded fonts after the postscript header +if strcmp(fstrm(1:15), '%!PS-AdobeFont-') + % Find the start and end of the header + ind = regexp(fstrm, '[\n\r]%!PS-Adobe-'); + [ind2 ind2] = regexp(fstrm, '[\n\r]%%EndComments[\n\r]+'); + % Put the header first + if ~isempty(ind) && ~isempty(ind2) && ind(1) < ind2(1) + fstrm = fstrm([ind(1)+1:ind2(1) 1:ind(1) ind2(1)+1:end]); + end +end + +% Make sure all line width commands come before the line style definitions, +% so that dash lengths can be based on the correct widths +% Find all line style sections +ind = [regexp(fstrm, '[\n\r]SO[\n\r]'),... % This needs to be here even though it doesn't have dots/dashes! + regexp(fstrm, '[\n\r]DO[\n\r]'),... + regexp(fstrm, '[\n\r]DA[\n\r]'),... + regexp(fstrm, '[\n\r]DD[\n\r]')]; +ind = sort(ind); +% Find line width commands +[ind2 ind3] = regexp(fstrm, '[\n\r]\d* w[\n\r]'); +% Go through each line style section and swap with any line width commands +% near by +b = 1; +m = numel(ind); +n = numel(ind2); +for a = 1:m + % Go forwards width commands until we pass the current line style + while b <= n && ind2(b) < ind(a) + b = b + 1; + end + if b > n + % No more width commands + break; + end + % Check we haven't gone past another line style (including SO!) + if a < m && ind2(b) > ind(a+1) + continue; + end + % Are the commands close enough to be confident we can swap them? + if (ind2(b) - ind(a)) > 8 + continue; + end + % Move the line style command below the line width command + fstrm(ind(a)+1:ind3(b)) = [fstrm(ind(a)+4:ind3(b)) fstrm(ind(a)+1:ind(a)+3)]; + b = b + 1; +end + +% Find any grid line definitions and change to GR format +% Find the DO sections again as they may have moved +ind = int32(regexp(fstrm, '[\n\r]DO[\n\r]')); +if ~isempty(ind) + % Find all occurrences of what are believed to be axes and grid lines + ind2 = int32(regexp(fstrm, '[\n\r] *\d* *\d* *mt *\d* *\d* *L[\n\r]')); + if ~isempty(ind2) + % Now see which DO sections come just before axes and grid lines + ind2 = repmat(ind2', [1 numel(ind)]) - repmat(ind, [numel(ind2) 1]); + ind2 = any(ind2 > 0 & ind2 < 12); % 12 chars seems about right + ind = ind(ind2); + % Change any regions we believe to be grid lines to GR + fstrm(ind+1) = 'G'; + fstrm(ind+2) = 'R'; + end +end + +% Isolate line style definition section +first_sec = strfind(fstrm, '% line types:'); +[second_sec remaining] = strtok(fstrm(first_sec+1:end), '/'); +[remaining remaining] = strtok(remaining, '%'); + +% Define the new styles, including the new GR format +% Dot and dash lengths have two parts: a constant amount plus a line width +% variable amount. The constant amount comes after dpi2point, and the +% variable amount comes after currentlinewidth. If you want to change +% dot/dash lengths for a one particular line style only, edit the numbers +% in the /DO (dotted lines), /DA (dashed lines), /DD (dot dash lines) and +% /GR (grid lines) lines for the style you want to change. +new_style = {'/dom { dpi2point 1 currentlinewidth 0.08 mul add mul mul } bdef',... % Dot length macro based on line width + '/dam { dpi2point 2 currentlinewidth 0.04 mul add mul mul } bdef',... % Dash length macro based on line width + '/SO { [] 0 setdash 0 setlinecap } bdef',... % Solid lines + '/DO { [1 dom 1.2 dom] 0 setdash 0 setlinecap } bdef',... % Dotted lines + '/DA { [4 dam 1.5 dam] 0 setdash 0 setlinecap } bdef',... % Dashed lines + '/DD { [1 dom 1.2 dom 4 dam 1.2 dom] 0 setdash 0 setlinecap } bdef',... % Dot dash lines + '/GR { [0 dpi2point mul 4 dpi2point mul] 0 setdash 1 setlinecap } bdef'}; % Grid lines - dot spacing remains constant + +if nargin < 2 + % Overwrite the input file + fname2 = fname; +end + +% Save the file with the section replaced +fh = fopen(fname2, 'w'); +if fh == -1 + error('Unable to open %s for writing.', fname2); +end +try + fwrite(fh, fstrm(1:first_sec), 'char*1'); + fwrite(fh, second_sec, 'char*1'); + fprintf(fh, '%s\r', new_style{:}); + fwrite(fh, remaining, 'char*1'); +catch ex + fclose(fh); + rethrow(ex); +end +fclose(fh); +return Index: /issm/trunk-jpl-damage/externalpackages/export_fig/ghostscript.m =================================================================== --- /issm/trunk-jpl-damage/externalpackages/export_fig/ghostscript.m (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/export_fig/ghostscript.m (revision 11330) @@ -0,0 +1,140 @@ +function varargout = ghostscript(cmd) +%GHOSTSCRIPT Calls a local GhostScript executable with the input command +% +% Example: +% [status result] = ghostscript(cmd) +% +% Attempts to locate a ghostscript executable, finally asking the user to +% specify the directory ghostcript was installed into. The resulting path +% is stored for future reference. +% +% Once found, the executable is called with the input command string. +% +% This function requires that you have Ghostscript installed on your +% system. You can download this from: http://www.ghostscript.com +% +% IN: +% cmd - Command string to be passed into ghostscript. +% +% OUT: +% status - 0 iff command ran without problem. +% result - Output from ghostscript. + +% Copyright: Oliver Woodford, 2009-2010 + +% Thanks to Jonas Dorn for the fix for the title of the uigetdir window on +% Mac OS. + +% Thanks to Nathan Childress for the fix to the default location on 64-bit +% Windows systems. + +% 27/4/11 - Find 64-bit Ghostscript on Windows. Thanks to Paul Durack and +% Shaun Kline for pointing out the issue + +% 4/5/11 - Thanks to David Chorlian for pointing out an alternative +% location for gs on linux. + +% Call ghostscript +[varargout{1:nargout}] = system(sprintf('"%s" %s', gs_path, cmd)); +return + +function path = gs_path +% Return a valid path +% Start with the currently set path +path = user_string('ghostscript'); +% Check the path works +if check_gs_path(path) + return +end +% Check whether the binary is on the path +if ispc + bin = {'gswin32c.exe', 'gswin64c.exe'}; +else + bin = {'gs'}; +end +for a = 1:numel(bin) + path = bin{a}; + if check_store_gs_path(path) + return + end +end +% Search the obvious places +if ispc + default_location = 'C:\Program Files\gs\'; + dir_list = dir(default_location); + if isempty(dir_list) + default_location = 'C:\Program Files (x86)\gs\'; % Possible location on 64-bit systems + dir_list = dir(default_location); + end + executable = {'\bin\gswin32c.exe', '\bin\gswin64c.exe'}; + ver_num = 0; + % If there are multiple versions, use the newest + for a = 1:numel(dir_list) + ver_num2 = sscanf(dir_list(a).name, 'gs%g'); + if ~isempty(ver_num2) && ver_num2 > ver_num + for b = 1:numel(executable) + path2 = [default_location dir_list(a).name executable{b}]; + if exist(path2, 'file') == 2 + path = path2; + ver_num = ver_num2; + end + end + end + end + if check_store_gs_path(path) + return + end +else + bin = {'/usr/bin/gs', '/usr/local/bin/gs'}; + for a = 1:numel(bin) + path = bin{a}; + if check_store_gs_path(path) + return + end + end +end +% Ask the user to enter the path +while 1 + if strncmp(computer, 'MAC', 3) % Is a Mac + % Give separate warning as the uigetdir dialogue box doesn't have a + % title + uiwait(warndlg('Ghostscript not found. Please locate the program.')) + end + base = uigetdir('/', 'Ghostcript not found. Please locate the program.'); + if isequal(base, 0) + % User hit cancel or closed window + break; + end + base = [base filesep]; + bin_dir = {'', ['bin' filesep], ['lib' filesep]}; + for a = 1:numel(bin_dir) + for b = 1:numel(bin) + path = [base bin_dir{a} bin{b}]; + if exist(path, 'file') == 2 + if check_store_gs_path(path) + return + end + end + end + end +end +error('Ghostscript not found. Have you installed it from www.ghostscript.com?'); + +function good = check_store_gs_path(path) +% Check the path is valid +good = check_gs_path(path); +if ~good + return +end +% Update the current default path to the path found +if ~user_string('ghostscript', path) + warning('Path to ghostscript installation could not be saved. Enter it manually in ghostscript.txt.'); + return +end +return + +function good = check_gs_path(path) +% Check the path is valid +[good message] = system(sprintf('"%s" -h', path)); +good = good == 0; +return Index: /issm/trunk-jpl-damage/externalpackages/export_fig/isolate_axes.m =================================================================== --- /issm/trunk-jpl-damage/externalpackages/export_fig/isolate_axes.m (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/export_fig/isolate_axes.m (revision 11330) @@ -0,0 +1,122 @@ +%ISOLATE_AXES Isolate the specified axes in a figure on their own +% +% Examples: +% fh = isolate_axes(ah) +% fh = isolate_axes(ah, vis) +% +% This function will create a new figure containing the axes specified, and +% also their associated legends and colorbars. The axes specified must all +% be in the same figure, but they will generally only be a subset of the +% axes in the figure. +% +% IN: +% ah - An array of axes handles, which must come from the same figure. +% vis - A boolean indicating whether the new figure should be visible. +% Default: false. +% +% OUT: +% fh - The handle of the created figure. + +% Copyright (C) Oliver Woodford 2011 + +% Thank you to Rosella Blatt for reporting a bug to do with axes in GUIs + +function fh = isolate_axes(ah, vis) +% Make sure we have an array of handles +if ~all(ishandle(ah)) + error('ah must be an array of handles'); +end +% Check that the handles are all for axes, and are all in the same figure +fh = ancestor(ah(1), 'figure'); +nAx = numel(ah); +for a = 1:nAx + if ~strcmp(get(ah(a), 'Type'), 'axes') + error('All handles must be axes handles.'); + end + if ~isequal(ancestor(ah(a), 'figure'), fh) + error('Axes must all come from the same figure.'); + end +end +% Tag the axes so we can find them in the copy +old_tag = get(ah, 'Tag'); +if nAx == 1 + old_tag = {old_tag}; +end +set(ah, 'Tag', 'ObjectToCopy'); +% Create a new figure exactly the same as the old one +fh = copyfig(fh); %copyobj(fh, 0); +if nargin < 2 || ~vis + set(fh, 'Visible', 'off'); +end +% Reset the axes tags +for a = 1:nAx + set(ah(a), 'Tag', old_tag{a}); +end +% Find the objects to save +ah = findall(fh, 'Tag', 'ObjectToCopy'); +if numel(ah) ~= nAx + close(fh); + error('Incorrect number of axes found.'); +end +% Set the axes tags to what they should be +for a = 1:nAx + set(ah(a), 'Tag', old_tag{a}); +end +% Keep any legends and colorbars which overlap the subplots +lh = findall(fh, 'Type', 'axes', '-and', {'Tag', 'legend', '-or', 'Tag', 'Colorbar'}); +nLeg = numel(lh); +if nLeg > 0 + ax_pos = get(ah, 'OuterPosition'); + if nAx > 1 + ax_pos = cell2mat(ax_pos(:)); + end + ax_pos(:,3:4) = ax_pos(:,3:4) + ax_pos(:,1:2); + leg_pos = get(lh, 'OuterPosition'); + if nLeg > 1; + leg_pos = cell2mat(leg_pos); + end + leg_pos(:,3:4) = leg_pos(:,3:4) + leg_pos(:,1:2); + for a = 1:nAx + % Overlap test + ah = [ah; lh(leg_pos(:,1) < ax_pos(a,3) & leg_pos(:,2) < ax_pos(a,4) &... + leg_pos(:,3) > ax_pos(a,1) & leg_pos(:,4) > ax_pos(a,2))]; + end +end +% Get all the objects in the figure +axs = findall(fh); +% Delete everything except for the input axes and associated items +delete(axs(~ismember(axs, [ah; allchildren(ah); allancestors(ah)]))); +return + +function ah = allchildren(ah) +ah = allchild(ah); +if iscell(ah) + ah = cell2mat(ah); +end +ah = ah(:); +return + +function ph = allancestors(ah) +ph = []; +for a = 1:numel(ah) + h = get(ah(a), 'parent'); + while h ~= 0 + ph = [ph; h]; + h = get(h, 'parent'); + end +end +return + +function fh = copyfig(fh) +% Is there a legend? +if isempty(findobj(fh, 'Type', 'axes', 'Tag', 'legend')) + % Safe to copy using copyobj + fh = copyobj(fh, 0); +else + % copyobj will change the figure, so save and then load it instead + tmp_nam = [tempname '.fig']; + hgsave(fh, tmp_nam); + fh = hgload(tmp_nam); + delete(tmp_nam); +end +return Index: /issm/trunk-jpl-damage/externalpackages/export_fig/license.txt =================================================================== --- /issm/trunk-jpl-damage/externalpackages/export_fig/license.txt (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/export_fig/license.txt (revision 11330) @@ -0,0 +1,24 @@ +Copyright (c) 2011, Oliver Woodford +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are +met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in + the documentation and/or other materials provided with the distribution + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. Index: /issm/trunk-jpl-damage/externalpackages/export_fig/pdf2eps.m =================================================================== --- /issm/trunk-jpl-damage/externalpackages/export_fig/pdf2eps.m (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/export_fig/pdf2eps.m (revision 11330) @@ -0,0 +1,51 @@ +%PDF2EPS Convert a pdf file to eps format using pdftops +% +% Examples: +% pdf2eps source dest +% +% This function converts a pdf file to eps format. +% +% This function requires that you have pdftops, from the Xpdf suite of +% functions, installed on your system. This can be downloaded from: +% http://www.foolabs.com/xpdf +% +%IN: +% source - filename of the source pdf file to convert. The filename is +% assumed to already have the extension ".pdf". +% dest - filename of the destination eps file. The filename is assumed to +% already have the extension ".eps". + +% Copyright (C) Oliver Woodford 2009-2010 + +% Thanks to Aldebaro Klautau for reporting a bug when saving to +% non-existant directories. + +function pdf2eps(source, dest) +% Construct the options string for pdftops +options = ['-q -paper match -eps -level2 "' source '" "' dest '"']; +% Convert to eps using pdftops +[status message] = pdftops(options); +% Check for error +if status + % Report error + if isempty(message) + error('Unable to generate eps. Check destination directory is writable.'); + else + error(message); + end +end +% Fix the DSC error created by pdftops +fid = fopen(dest, 'r+'); +if fid == -1 + % Cannot open the file + return +end +fgetl(fid); % Get the first line +str = fgetl(fid); % Get the second line +if strcmp(str(1:min(13, end)), '% Produced by') + fseek(fid, -numel(str)-1, 'cof'); + fwrite(fid, '%'); % Turn ' ' into '%' +end +fclose(fid); +return + Index: /issm/trunk-jpl-damage/externalpackages/export_fig/pdftops.m =================================================================== --- /issm/trunk-jpl-damage/externalpackages/export_fig/pdftops.m (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/export_fig/pdftops.m (revision 11330) @@ -0,0 +1,107 @@ +function varargout = pdftops(cmd) +%PDFTOPS Calls a local pdftops executable with the input command +% +% Example: +% [status result] = pdftops(cmd) +% +% Attempts to locate a pdftops executable, finally asking the user to +% specify the directory pdftops was installed into. The resulting path is +% stored for future reference. +% +% Once found, the executable is called with the input command string. +% +% This function requires that you have pdftops (from the Xpdf package) +% installed on your system. You can download this from: +% http://www.foolabs.com/xpdf +% +% IN: +% cmd - Command string to be passed into pdftops. +% +% OUT: +% status - 0 iff command ran without problem. +% result - Output from pdftops. + +% Copyright: Oliver Woodford, 2009-2010 + +% Thanks to Jonas Dorn for the fix for the title of the uigetdir window on +% Mac OS. +% Thanks to Christoph Hertel for pointing out a bug in check_xpdf_path +% under linux. + +% Call pdftops +[varargout{1:nargout}] = system(sprintf('"%s" %s', xpdf_path, cmd)); +return + +function path = xpdf_path +% Return a valid path +% Start with the currently set path +path = user_string('pdftops'); +% Check the path works +if check_xpdf_path(path) + return +end +% Check whether the binary is on the path +if ispc + bin = 'pdftops.exe'; +else + bin = 'pdftops'; +end +if check_store_xpdf_path(bin) + path = bin; + return +end +% Search the obvious places +if ispc + path = 'C:\Program Files\xpdf\pdftops.exe'; +else + path = '/usr/local/bin/pdftops'; +end +if check_store_xpdf_path(path) + return +end +% Ask the user to enter the path +while 1 + if strncmp(computer,'MAC',3) % Is a Mac + % Give separate warning as the uigetdir dialogue box doesn't have a + % title + uiwait(warndlg('Pdftops not found. Please locate the program, or install xpdf-tools from http://users.phg-online.de/tk/MOSXS/.')) + end + base = uigetdir('/', 'Pdftops not found. Please locate the program.'); + if isequal(base, 0) + % User hit cancel or closed window + break; + end + base = [base filesep]; + bin_dir = {'', ['bin' filesep], ['lib' filesep]}; + for a = 1:numel(bin_dir) + path = [base bin_dir{a} bin]; + if exist(path, 'file') == 2 + break; + end + end + if check_store_xpdf_path(path) + return + end +end +error('pdftops executable not found.'); + +function good = check_store_xpdf_path(path) +% Check the path is valid +good = check_xpdf_path(path); +if ~good + return +end +% Update the current default path to the path found +if ~user_string('pdftops', path) + warning('Path to pdftops executable could not be saved. Enter it manually in pdftops.txt.'); + return +end +return + +function good = check_xpdf_path(path) +% Check the path is valid +[good message] = system(sprintf('"%s" -h', path)); +% system returns good = 1 even when the command runs +% Look for something distinct in the help text +good = ~isempty(strfind(message, 'PostScript')); +return Index: /issm/trunk-jpl-damage/externalpackages/export_fig/print2array.m =================================================================== --- /issm/trunk-jpl-damage/externalpackages/export_fig/print2array.m (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/export_fig/print2array.m (revision 11330) @@ -0,0 +1,157 @@ +%PRINT2ARRAY Exports a figure to an image array +% +% Examples: +% A = print2array +% A = print2array(figure_handle) +% A = print2array(figure_handle, resolution) +% A = print2array(figure_handle, resolution, renderer) +% [A bcol] = print2array(...) +% +% This function outputs a bitmap image of the given figure, at the desired +% resolution. +% +% If renderer is '-painters' then ghostcript needs to be installed. This +% can be downloaded from: http://www.ghostscript.com +% +% IN: +% figure_handle - The handle of the figure to be exported. Default: gcf. +% resolution - Resolution of the output, as a factor of screen +% resolution. Default: 1. +% renderer - string containing the renderer paramater to be passed to +% print. Default: '-opengl'. +% +% OUT: +% A - MxNx3 uint8 image of the figure. +% bcol - 1x3 uint8 vector of the background color + +% Copyright (C) Oliver Woodford 2008-2011 + +% 5/9/2011 Set EraseModes to normal when using opengl or zbuffer renderers. +% Thanks to Pawel Kocieniewski for reporting the issue. + +% 21/9/2011 Bug fix: unit8 -> uint8! +% Thanks to Tobias Lamour for reporting the issue. + +% 14/11/2011 Bug fix: stop using hardcopy(), as it interfered with figure +% size and erasemode settings. Makes it a bit slower, but more reliable. +% Thanks to Phil Trinh and Meelis Lootus for reporting the issues. + +function [A bcol] = print2array(fig, res, renderer) +% Generate default input arguments, if needed +if nargin < 2 + res = 1; + if nargin < 1 + fig = gcf; + end +end +% Warn if output is large +old_mode = get(fig, 'Units'); +set(fig, 'Units', 'pixels'); +px = get(fig, 'Position'); +set(fig, 'Units', old_mode); +npx = prod(px(3:4)*res)/1e6; +if npx > 30 + % 30M pixels or larger! + warning('MATLAB:LargeImage', 'print2array generating a %.1fM pixel image. This could be slow and might also cause memory problems.', npx); +end +% Retrieve the background colour +bcol = get(fig, 'Color'); +% Set the resolution parameter +res_str = ['-r' num2str(ceil(get(0, 'ScreenPixelsPerInch')*res))]; +% Generate temporary file name +tmp_nam = [tempname '.tif']; +if nargin > 2 && strcmp(renderer, '-painters') + % Print to eps file + tmp_eps = [tempname '.eps']; + print2eps(tmp_eps, fig, renderer, '-loose'); + try + % Export to tiff using ghostscript + ghostscript(['-dEPSCrop -q -dNOPAUSE -dBATCH ' res_str ' -sDEVICE=tiff24nc -sOutputFile="' tmp_nam '" "' tmp_eps '"']); + catch + % Delete the intermediate file + delete(tmp_eps); + rethrow(lasterror); + end + % Delete the intermediate file + delete(tmp_eps); + % Read in the generated bitmap + A = imread(tmp_nam); + % Delete the temporary bitmap file + delete(tmp_nam); + % Set border pixels to the correct colour + if isequal(bcol, 'none') + bcol = []; + elseif isequal(bcol, [1 1 1]) + bcol = uint8([255 255 255]); + else + for l = 1:size(A, 2) + if ~all(reshape(A(:,l,:) == 255, [], 1)) + break; + end + end + for r = size(A, 2):-1:l + if ~all(reshape(A(:,r,:) == 255, [], 1)) + break; + end + end + for t = 1:size(A, 1) + if ~all(reshape(A(t,:,:) == 255, [], 1)) + break; + end + end + for b = size(A, 1):-1:t + if ~all(reshape(A(b,:,:) == 255, [], 1)) + break; + end + end + bcol = median([reshape(A(:,[l r],:), [], size(A, 3)); reshape(A(:,[t b],:), [], size(A, 3))], 1); + for c = 1:size(A, 3) + A(:,[1:l-1, r+1:end],c) = bcol(c); + A([1:t-1, b+1:end],:,c) = bcol(c); + end + end +else + if nargin < 3 + renderer = '-opengl'; + end + err = false; + % Set paper size + old_mode = get(fig, 'PaperPositionMode'); + set(fig, 'PaperPositionMode', 'auto'); + try + % Print to tiff file + print(fig, renderer, res_str, '-dtiff', tmp_nam); + % Read in the printed file + A = imread(tmp_nam); + % Delete the temporary file + delete(tmp_nam); + catch ex + err = true; + end + % Reset paper size + set(fig, 'PaperPositionMode', old_mode); + % Throw any error that occurred + if err + rethrow(ex); + end + % Set the background color + if isequal(bcol, 'none') + bcol = []; + else + bcol = bcol * 255; + if isequal(bcol, round(bcol)) + bcol = uint8(bcol); + else + bcol = squeeze(A(1,1,:)); + end + end +end +% Check the output size is correct +if isequal(res, round(res)) + px = [px([4 3])*res 3]; + if ~isequal(size(A), px) + % Correct the output size + A = A(1:min(end,px(1)),1:min(end,px(2)),:); + end +end +return Index: /issm/trunk-jpl-damage/externalpackages/export_fig/print2eps.m =================================================================== --- /issm/trunk-jpl-damage/externalpackages/export_fig/print2eps.m (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/export_fig/print2eps.m (revision 11330) @@ -0,0 +1,71 @@ +%PRINT2EPS Prints figures to eps with improved line styles +% +% Examples: +% print2eps filename +% print2eps(filename, fig_handle) +% print2eps(filename, fig_handle, options) +% +% This function saves a figure as an eps file, and improves the line style, +% making dashed lines more like those on screen and giving grid lines their +% own dotted style. +% +%IN: +% filename - string containing the name (optionally including full or +% relative path) of the file the figure is to be saved as. A +% ".eps" extension is added if not there already. If a path is +% not specified, the figure is saved in the current directory. +% fig_handle - The handle of the figure to be saved. Default: gcf. +% options - Additional parameter strings to be passed to print. + +% Copyright (C) Oliver Woodford 2008-2011 + +% The idea of editing the EPS file to change line styles comes from Jiro +% Doke's FIXPSLINESTYLE (fex id: 17928) +% The idea of changing dash length with line width came from comments on +% fex id: 5743, but the implementation is mine :) + +% 14/11/2011 Fix a MATLAB bug rendering black or white text incorrectly. +% Thanks to Mathieu Morlighem for reporting the issue and obtaining a fix +% from TMW. + +function print2eps(name, fig, varargin) +options = {'-depsc2'}; +if nargin < 2 + fig = gcf; +elseif nargin > 2 + options = [options varargin]; +end +% Construct the filename +if numel(name) < 5 || ~strcmpi(name(end-3:end), '.eps') + name = [name '.eps']; % Add the missing extension +end +% Set paper size +old_mode = get(fig, 'PaperPositionMode'); +set(fig, 'PaperPositionMode', 'auto'); +% MATLAB bug fix - black and white text can come out inverted sometimes +% Find the white and black text +white_text_handles = findobj(fig, 'Type', 'text'); +M = get(white_text_handles, 'Color'); +if iscell(M) + M = cell2mat(M); +end +M = sum(M, 2); +black_text_handles = white_text_handles(M == 0); +white_text_handles = white_text_handles(M == 3); +% Set the font colors slightly off their correct values +set(black_text_handles, 'Color', [0 0 0] + eps); +set(white_text_handles, 'Color', [1 1 1] - eps); +% Print to eps file +print(fig, options{:}, name); +% Reset the font colors +set(black_text_handles, 'Color', [0 0 0]); +set(white_text_handles, 'Color', [1 1 1]); +% Reset paper size +set(fig, 'PaperPositionMode', old_mode); +% Fix the line styles +try + fix_lines(name); +catch + warning('fix_lines() failed. This is usually because the figure contains a large number of patch objects. Consider exporting to a bitmap format in this case.'); +end +return Index: /issm/trunk-jpl-damage/externalpackages/export_fig/user_string.m =================================================================== --- /issm/trunk-jpl-damage/externalpackages/export_fig/user_string.m (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/export_fig/user_string.m (revision 11330) @@ -0,0 +1,84 @@ +%USER_STRING Get/set a user specific string +% +% Examples: +% string = user_string(string_name) +% saved = user_string(string_name, new_string) +% +% Function to get and set a string in a system or user specific file. This +% enables, for example, system specific paths to binaries to be saved. +% +% IN: +% string_name - String containing the name of the string required. The +% string is extracted from a file called (string_name).txt, +% stored in the same directory as user_string.m. +% new_string - The new string to be saved under the name given by +% string_name. +% +% OUT: +% string - The currently saved string. Default: ''. +% saved - Boolean indicating whether the save was succesful + +% Copyright (C) Oliver Woodford 2011 + +% This method of saving paths avoids changing .m files which might be in a +% version control system. Instead it saves the user dependent paths in +% separate files with a .txt extension, which need not be checked in to +% the version control system. Thank you to Jonas Dorn for suggesting this +% approach. + +function string = user_string(string_name, string) +if ~ischar(string_name) + error('string_name must be a string.'); +end +% Create the full filename +string_name = fullfile(fileparts(mfilename('fullpath')), '.ignore', [string_name '.txt']); +if nargin > 1 + % Set string + if ~ischar(string) + error('new_string must be a string.'); + end + % Make sure the save directory exists + dname = fileparts(string_name); + if ~exist(dname, 'dir') + % Create the directory + try + if ~mkdir(dname) + string = false; + return + end + catch + string = false; + return + end + % Make it hidden + try + fileattrib(dname, '+h'); + catch + end + end + % Write the file + fid = fopen(string_name, 'w'); + if fid == -1 + string = false; + return + end + try + fwrite(fid, string, '*char'); + catch + fclose(fid); + string = false; + return + end + fclose(fid); + string = true; +else + % Get string + fid = fopen(string_name, 'r'); + if fid == -1 + string = ''; + return + end + string = fread(fid, '*char')'; + fclose(fid); +end +return Index: /issm/trunk-jpl-damage/externalpackages/findbugs/README =================================================================== --- /issm/trunk-jpl-damage/externalpackages/findbugs/README (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/findbugs/README (revision 11330) @@ -0,0 +1,2 @@ +Fingbugs for Java programs. +Downloaded from http://findbugs.sourceforge.net/downloads.html Index: /issm/trunk-jpl-damage/externalpackages/findbugs/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/findbugs/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/findbugs/install.sh (revision 11330) @@ -0,0 +1,10 @@ +#!/bin/bash + +#Erase install +rm -rf install findbugs-1.3.9 +mkdir install + +tar -zxvf findbugs-1.3.9.tar.gz + +mv findbugs-1.3.9/* install +rm -rf findbugs-1.3.9 Index: /issm/trunk-jpl-damage/externalpackages/flaim/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/flaim/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/flaim/install.sh (revision 11330) @@ -0,0 +1,7 @@ +#!/bin/bash + +#Erase symlink +rm -rf install + +#symlink to flaim directory +ln -s /home/jschierm/flaim/svn/trunk ./install Index: /issm/trunk-jpl-damage/externalpackages/gdal/GDALmake.opt.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/gdal/GDALmake.opt.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/gdal/GDALmake.opt.patch (revision 11330) @@ -0,0 +1,8 @@ +31c31 +< LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib -lexpat -ljpeg -lpng -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ +--- +> LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib64 -lexpat -ljpeg -lpng -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ +225c225 +< CURL_LIB = -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz +--- +> CURL_LIB = -L/usr/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz Index: /issm/trunk-jpl-damage/externalpackages/gdal/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/gdal/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/gdal/install.sh (revision 11330) @@ -0,0 +1,36 @@ +#!/bin/bash + +#Some cleanup +rm -rf src +rm -rf install +rm -rf gdal-1.6.0 +mkdir src install + +#Untar +tar -zxvf gdal-1.6.0.tar.gz + +#Move gdal into src directory +mv gdal-1.6.0/* src +rm -rf gdal-1.6.0 + +#Configure gdal +cd src +./configure \ + --prefix="$ISSM_TIER/externalpackages/gdal/install" \ + --without-python \ + --with-netcdf=no \ + --with-jasper=no \ + --without-ld-shared \ + --with-unix-stdio-64=no \ + --with-expat-lib=/usr/lib64/libexpat.so + +#Patch GDALmake.opt +patch GDALmake.opt ../GDALmake.opt.patch + +#Compile and install gdal +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk-jpl-damage/externalpackages/gfortran/README =================================================================== --- /issm/trunk-jpl-damage/externalpackages/gfortran/README (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/gfortran/README (revision 11330) @@ -0,0 +1,7 @@ +For Mac users, you can download a fortran compiler on: +http://gcc.gnu.org/wiki/GFortranBinaries + +Other websites: +http://www.macresearch.org/gfortran-leopard +http://hpc.sourceforge.net/ +http://r.research.att.com/tools/ or http://cran.r-project.org/bin/macosx/tools/ Index: /issm/trunk-jpl-damage/externalpackages/googleearthtoolbox/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/googleearthtoolbox/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/googleearthtoolbox/install.sh (revision 11330) @@ -0,0 +1,7 @@ +#!/bin/bash + +#Some cleanup +rm -rf install + +#Download code: +svn checkout http://googleearthtoolbox.googlecode.com/svn/trunk/ install Index: /issm/trunk-jpl-damage/externalpackages/graphviz/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/graphviz/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/graphviz/install.sh (revision 11330) @@ -0,0 +1,27 @@ +#!/bin/bash + +#Some cleanup +rm -rf install src +mkdir install src + +#Untar +tar -zxvf graphviz-2.24.0.tar.gz + +#Move Dakota to src directory +mv graphviz-2.24.0/* src/ +rm -rf graphviz-2.24.0 + +#Configure dakota +cd src +./configure --prefix="$ISSM_TIER/externalpackages/graphviz/install" +cd .. + +#Compile and install +cd src +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install +cd .. Index: /issm/trunk-jpl-damage/externalpackages/intel/intel.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/intel/intel.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/intel/intel.sh (revision 11330) @@ -0,0 +1,16 @@ + export CPATH="C:\\IntelInstall\\Compiler\\11.1\\038\\ipp\\ia32\\include;C:\\IntelInstall\\Compiler\\11.1\\038\\mkl\\include;" + export DEVENVDIR="C:\\MicrosoftVisualStudio 9.0\\Common7\\IDE" + export FPATH="C:\\IntelInstall\\Compiler\\11.1\\038\\mkl\\include;" + export FRAMEWORK35VERSION="v3.5" + export FRAMEWORKDIR="C:\\WINDOWS\\Microsoft.NET\\Framework" + export FRAMEWORKVERSION="v2.0.50727" + export INCLUDE="C:\\IntelInstall\\Compiler\\11.1\\038\\ipp\\ia32\\include;C:\\IntelInstall\\Compiler\\11.1\\038\\mkl\\include;C:\\IntelInstall\\Compiler\\11.1\\038\\tbb\\include;C:\\IntelInstall\\Compiler\\11.1\\038\\include;C:\\MicrosoftVisualStudio 9.0\\VC\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v6.0A\\include;" + export IPPROOT="C:\\IntelInstall\\Compiler\\11.1\\038\\ipp\\ia32" + export LIB="C:\\IntelInstall\\Compiler\\11.1\\038\\ipp\\ia32\\lib;C:\\IntelInstall\\Compiler\\11.1\\038\\ipp\\ia32\\stublib;C:\\IntelInstall\\Compiler\\11.1\\038\\mkl\\ia32\\lib;C:\\IntelInstall\\Compiler\\11.1\\038\\tbb\\ia32\\vc9\\lib;C:\\IntelInstall\\Compiler\\11.1\\038\\Lib\\ia32;C:\\MicrosoftVisualStudio 9.0\\VC\\LIB;C:\\Program Files\\Microsoft SDKs\\Windows\\v6.0A\\lib;" + export LIBPATH="C:\\WINDOWS\\Microsoft.NET\\Framework\\v3.5;C:\\WINDOWS\\Microsoft.NET\\Framework\\v2.0.50727;C:\\MicrosoftVisualStudio 9.0\\VC\\LIB;" + export LIBRARY_PATH="C:\\IntelInstall\\Compiler\\11.1\\038\\ipp\\ia32\\lib;C:\\IntelInstall\\Compiler\\11.1\\038\\ipp\\ia32\\stublib;C:\\IntelInstall\\Compiler\\11.1\\038\\mkl\\ia32\\lib;" + export PATH="$PATH:/cygdrive/c/IntelInstall/Compiler/11.1/038/Bin/ia32:/cygdrive/c/MicrosoftVisualStudio 9.0/Common7/IDE:/cygdrive/c/MicrosoftVisualStudio 9.0/VC/BIN:/cygdrive/c/MicrosoftVisualStudio 9.0/Common7/Tools:/cygdrive/c/WINDOWS/Microsoft.NET/Framework/v3.5:/cygdrive/c/WINDOWS/Microsoft.NET/Framework/v2.0.50727:/cygdrive/c/MicrosoftVisualStudio 9.0/VC/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v6.0A/bin:/cygdrive/c/WINDOWS" + export TBB_ARCH_PLATFORM="ia32\\vc9" + export VCINSTALLDIR="C:\\MicrosoftVisualStudio 9.0\\VC" + export VSINSTALLDIR="C:\\MicrosoftVisualStudio 9.0" + export WINDOWSSDKDIR="C:\\Program Files\\Microsoft SDKs\\Windows\\v6.0A\\" Index: /issm/trunk-jpl-damage/externalpackages/intel/readme =================================================================== --- /issm/trunk-jpl-damage/externalpackages/intel/readme (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/intel/readme (revision 11330) @@ -0,0 +1,42 @@ +How to install intel compiler to work on cygwin at the command line: + +This is what I got from the following post on google: + +----------------------------------------------------- +All necessary paths and environment variables are set if you put the Microsoft linker path in ICL.CFG, and open the Intel +compiler command line window on the Start menu. Then you can run cygwin.bat so that bash inherits the ICL paths, +without breaking ICL. You will sometimes get the bash warning about finding Windows style paths in the environment, +but those are necessary for ICL and Microsoft link. Needless to say, the Windows environment variable forgetfulness + point will be reached sooner with this setup. + +After I run cygwin.bat, and try to run icl, it says: + +link: invalid option -- o +Try `ling --help' for more information. + +I verified that icl compiles without any problems before I run cygwin.bat + +What am I missing? + + + +This would indicate that you ignored my advice about icl.cfg, and so you are getting the wrong link.exe. It should have said "link" not "ling." +For a VC9 installation, /windows/C/Program Files/Intel/Compiler/11.1/026/bin/ia32/icl.cfg: +-Qlocation,link,"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin" +-Qprec-div -Qprec-sqrt -Qansi_alias +---------------------------------------------------------- + + + + + +So here is what you do: +edit /cygdrive/c/IntelInstall/Compiler/11.1/026/bin/ia32/icl.cfg + +add: +-Qlocation,link,"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin" +-Qprec-div -Qprec-sqrt -Qansi_alias + + +Then run the intel compiler command window. Go to C:\Cygwin and run Cygwin.bat. +you are now running cygwin with the correct paths. Type "export" at the command line, and figure out which variables have been set that relate to the intel compiler and visual studio environment. Build a file containing specific export commands and source it from your .bashrc. intel.sh is an example of such file on a Windows XP 32 build. Index: /issm/trunk-jpl-damage/externalpackages/latex2rtf/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/latex2rtf/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/latex2rtf/install.sh (revision 11330) @@ -0,0 +1,13 @@ +#!/bin/bash + +#Some cleanup +rm -rf latex2rtf-2.0.0 cfg install + +#untar +tar -zxvf latex2rtf-2.0.0.tar.gz +mv latex2rtf-2.0.0 install + +#Compile +cd install +export PREFIX="$ISSM_TIER/externalpackages/latex2rtf/install/" +make Index: /issm/trunk-jpl-damage/externalpackages/libtool/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/libtool/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/libtool/install.sh (revision 11330) @@ -0,0 +1,17 @@ +#!/bin/bash + +#Some cleanup +rm -rf install libtool-2.2.6b src +mkdir install + +#Untar +tar -zxvf libtool-2.2.6b.tar.gz + +#Move libtool into src directory +mv libtool-2.2.6b src + +#Compile libtool +cd src +./configure --prefix="$ISSM_TIER/externalpackages/libtool/install" +make +make install Index: /issm/trunk-jpl-damage/externalpackages/m2html/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/m2html/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/m2html/install.sh (revision 11330) @@ -0,0 +1,17 @@ +#!/bin/bash + +#Some cleanup +rm -rf install m2html +mkdir install + +#uncompress +unzip m2html.zip + +#move to install directory +mv m2html/* install +rm -rf m2html + +#patch m2html +cd install +patch m2html.m ../m2html.m.patch +cd .. Index: /issm/trunk-jpl-damage/externalpackages/m2html/m2html.m.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/m2html/m2html.m.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/m2html/m2html.m.patch (revision 11330) @@ -0,0 +1,114 @@ +*** m2html.m 2011-08-12 10:57:45.000000000 -0700 +--- install/m2html.m 2011-08-12 10:58:26.000000000 -0700 +*************** +*** 306,311 **** +--- 306,325 ---- + end + + mdir = unique(mdirs); ++ ++ %add root directories ++ for i=1:length(mdir) ++ path=strsplit(mdir{i},'/'); ++ string=path{1}; ++ mdir{end+1}=string; ++ for j=2:length(path), ++ string=[string '/' path{j}]; ++ mdir{end+1}=string; ++ end ++ end ++ ++ mdir=unique(mdir); ++ + if options.verbose, + fprintf('Found %d unique Matlab directories.\n',length(mdir)); + end +*************** +*** 423,429 **** + %- Set some template variables + tpl = set(tpl,'var','DATE',[datestr(now,8) ' ' datestr(now,1) ' ' ... + datestr(now,13)]); +! tpl = set(tpl,'var','MASTERPATH', './'); + tpl = set(tpl,'var','DIRS', sprintf('%s ',mdir{:})); + + %- Print list of unique directories +--- 437,443 ---- + %- Set some template variables + tpl = set(tpl,'var','DATE',[datestr(now,8) ' ' datestr(now,1) ' ' ... + datestr(now,13)]); +! tpl = set(tpl,'var','MASTERPATH', ''); + tpl = set(tpl,'var','DIRS', sprintf('%s ',mdir{:})); + + %- Print list of unique directories +*************** +*** 555,561 **** + tpl = set(tpl,'var','subfold',''); + d = dir(mdir{i}); + d = {d([d.isdir]).name}; +! d = {d{~ismember(d,{'.' '..'})}}; + for j=1:length(d) + if ismember(fullfile(mdir{i},d{j}),mdir) + tpl = set(tpl,'var','SUBDIRECTORY',... +--- 569,575 ---- + tpl = set(tpl,'var','subfold',''); + d = dir(mdir{i}); + d = {d([d.isdir]).name}; +! d = {d{~ismember(d,{'.' '..' 'CVS' '.svn'})}}; + for j=1:length(d) + if ismember(fullfile(mdir{i},d{j}),mdir) + tpl = set(tpl,'var','SUBDIRECTORY',... +*************** +*** 687,695 **** + % Path should look like: ...;C:\WINNT\System32;...;C:\GraphViz\bin + % (Note that this should have been done automatically during GraphViz installation) + +! eval(['!' dot_exec ' -Tcmap -Tpng ' mdotfile ... + ' -o ' fullfile(options.htmlDir,mdir{i},[dotbase '.map']) ... +! ' -o ' fullfile(options.htmlDir,mdir{i},[dotbase '.png'])]) + % use '!' rather than 'system' for backward compability + catch + fprintf('failed.'); +--- 701,709 ---- + % Path should look like: ...;C:\WINNT\System32;...;C:\GraphViz\bin + % (Note that this should have been done automatically during GraphViz installation) + +! eval(['!' dot_exec ' -Tcmap -Tgif ' mdotfile ... + ' -o ' fullfile(options.htmlDir,mdir{i},[dotbase '.map']) ... +! ' -o ' fullfile(options.htmlDir,mdir{i},[dotbase '.gif'])]) + % use '!' rather than 'system' for backward compability + catch + fprintf('failed.'); +*************** +*** 700,706 **** + tpl = set(tpl,'var','INDEX',[options.indexFile options.extension]); + tpl = set(tpl,'var','MASTERPATH', backtomaster(mdir{i})); + tpl = set(tpl,'var','MDIR', mdir{i}); +! tpl = set(tpl,'var','GRAPH_IMG', [dotbase '.png']); + fmap = openfile(fullfile(options.htmlDir,mdir{i},[dotbase '.map']),'r'); + tpl = set(tpl,'var','GRAPH_MAP', fscanf(fmap,'%c')); + fclose(fmap); +--- 714,720 ---- + tpl = set(tpl,'var','INDEX',[options.indexFile options.extension]); + tpl = set(tpl,'var','MASTERPATH', backtomaster(mdir{i})); + tpl = set(tpl,'var','MDIR', mdir{i}); +! tpl = set(tpl,'var','GRAPH_IMG', [dotbase '.gif']); + fmap = openfile(fullfile(options.htmlDir,mdir{i},[dotbase '.map']),'r'); + tpl = set(tpl,'var','GRAPH_MAP', fscanf(fmap,'%c')); + fclose(fmap); +*************** +*** 1032,1038 **** + if recursive + d = dir(mdirs{i}); + d = {d([d.isdir]).name}; +! d = {d{~ismember(d,{'.' '..'})}}; + for j=1:length(d) + mfiles = getmfiles(cellstr(fullfile(mdirs{i},d{j})),... + mfiles,recursive); +--- 1046,1052 ---- + if recursive + d = dir(mdirs{i}); + d = {d([d.isdir]).name}; +! d = {d{~ismember(d,{'.' '..' 'CVS' '.svn'})}}; + for j=1:length(d) + mfiles = getmfiles(cellstr(fullfile(mdirs{i},d{j})),... + mfiles,recursive); Index: /issm/trunk-jpl-damage/externalpackages/matlab/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/matlab/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/matlab/install.sh (revision 11330) @@ -0,0 +1,15 @@ +#!/bin/bash + +#Erase symlink +rm -rf install + +#Select or create a new simlink +ln -s /usr/local/pkgs/matlab-7.6/ install +#ln -s /usr/local/matlab704/ install +#ln -s /usr/local/matlab711/ install +ln -s /usr/local/matlab712/ install +#ln -s /usr/local/pkgs/matlab-7.6/ install +#ln -s /Applications/MATLAB_R2008a/ install +#ln -s /Applications/MATLAB_R2009a.app/ install +#ln -s /Applications/MATLAB_R2010a.app/ install +#ln -s /Applications/MATLAB_R2011b.app/ install Index: /issm/trunk-jpl-damage/externalpackages/mercurial/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mercurial/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mercurial/install.sh (revision 11330) @@ -0,0 +1,20 @@ +#!/bin/bash + +#Some cleanup +rm -rf install mercurial-1.7.3 +mkdir install + +#Untar +tar -zxvf mercurial-1.7.3.tar.gz + +#Move mercurial into install directory +mv mercurial-1.7.3/* install +rm -rf mercurial-1.7.3 + +#Apply patches +cd install +#patch Lib/Makefile ../lib_Makefile.patch +exit + +#Compile mercurial +make Index: /issm/trunk-jpl-damage/externalpackages/merge/mergesort.c =================================================================== --- /issm/trunk-jpl-damage/externalpackages/merge/mergesort.c (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/merge/mergesort.c (revision 11330) @@ -0,0 +1,196 @@ +/****************************************************************************** +* FILE: mergesort.c +* DESCRIPTION: +* The master task distributes an array to the workers in chunks, zero pads for equal load balancing +* The workers sort and return to the master, which does a final merge +******************************************************************************/ + +#include +#include +#include +#include + + + +#define N 100000 +#define MASTER 0 /* taskid of first task */ + +void showVector(int *v, int n, int id); +int * merge(int *A, int asize, int *B, int bsize); +void swap(int *v, int i, int j); +void m_sort(int *A, int min, int max); + +double startT, stopT; + +double startTime; + +/*function to print a vector*/ +void showVector(int *v, int n, int id) +{ + int i; + printf("%d: ",id); + for(i=0;i= asize) /*if A is shorter*/ + for (i = ci; i < csize; i++, bi++) + C[i] = B[bi]; + else if (bi >= bsize) /*if B is shorter*/ + for (i = ci; i < csize; i++, ai++) + C[i] = A[ai]; + + for (i = 0; i < asize; i++) + A[i] = C[i]; + for (i = 0; i < bsize; i++) + B[i] = C[asize+i]; + + /* showVector(C, csize, 0); */ + return C; +} + +void swap(int *v, int i, int j) +{ + int t; + t = v[i]; + v[i] = v[j]; + v[j] = t; +} + +void m_sort(int *A, int min, int max) +{ + int *C; /* dummy, just to fit the function */ + int mid = (min+max)/2; + int lowerCount = mid - min + 1; + int upperCount = max - mid; + + /* If the range consists of a single element, it's already sorted */ + if (max == min) { + return; + } else { + /* Otherwise, sort the first half */ + m_sort(A, min, mid); + /* Now sort the second half */ + m_sort(A, mid+1, max); + /* Now merge the two halves */ + C = merge(A + min, lowerCount, A + mid + 1, upperCount); + } +} + +main(int argc, char **argv) +{ + int * data; + int * chunk; + int * other; + int m,n=N; + int id,p; + int s = 0; + int i; + int step; + MPI_Status status; + + MPI_Init(&argc,&argv); + MPI_Comm_rank(MPI_COMM_WORLD,&id); + MPI_Comm_size(MPI_COMM_WORLD,&p); + + startT = MPI_Wtime(); + +/**************************** master task ************************************/ + if(id == MASTER) + { + int r; + srandom(MPI_Wtime()); + s = n/p; + r = n%p; + data = (int *)malloc((n+s-r)*sizeof(int)); + for(i=0;i CC = cc +8c6 +< OPTFLAGS = -DLINUX -fPIC +--- +> OPTFLAGS = -O2 Index: /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/cosmos/Makefile.in.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/cosmos/Makefile.in.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/cosmos/Makefile.in.patch (revision 11330) @@ -0,0 +1,10 @@ +3,5c3 +< CC = icc +< OBJ_EXT=o +< LIB_EXT=a +--- +> CC = cc +8c6 +< OPTFLAGS = -DLINUX -fPIC +--- +> OPTFLAGS = -O2 Index: /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch (revision 11330) @@ -0,0 +1,10 @@ +3,5c3 +< CC = gcc +< OBJ_EXT=o +< LIB_EXT=a +--- +> CC = cc +8c6 +< OPTFLAGS = -DLINUX -fPIC +--- +> OPTFLAGS = -O2 Index: /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/macosx32/Makefile.in.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/macosx32/Makefile.in.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/macosx32/Makefile.in.patch (revision 11330) @@ -0,0 +1,10 @@ +3,5c3 +< CC = gcc +< OBJ_EXT=o +< LIB_EXT=a +--- +> CC = cc +8c6 +< OPTFLAGS = -DLINUX -fPIC +--- +> OPTFLAGS = -O2 -m32 Index: /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/macosx64/Makefile.in.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/macosx64/Makefile.in.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/macosx64/Makefile.in.patch (revision 11330) @@ -0,0 +1,10 @@ +3,5c3 +< CC = gcc +< OBJ_EXT=o +< LIB_EXT=a +--- +> CC = cc +8c6 +< OPTFLAGS = -DLINUX -fPIC +--- +> OPTFLAGS = -O2 -m64 Index: /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/pleiades/Makefile.in.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/pleiades/Makefile.in.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/pleiades/Makefile.in.patch (revision 11330) @@ -0,0 +1,10 @@ +3,5c3 +< CC = gcc +< OBJ_EXT=o +< LIB_EXT=a +--- +> CC = icc +8c6 +< OPTFLAGS = -DLINUX -fPIC +--- +> OPTFLAGS = -O2 Index: /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/win32/Makefile.in.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/win32/Makefile.in.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/configs/4.0/win32/Makefile.in.patch (revision 11330) @@ -0,0 +1,14 @@ +3,5c3,5 +< CC = gcc +< OBJ_EXT=o +< LIB_EXT=a +--- +> CC = icl +> OBJ_EXT=obj +> LIB_EXT=lib +8c8 +< OPTFLAGS = -DLINUX -fPIC +--- +> OPTFLAGS = -DWIN32 -D__VC__ +22d21 +< #RANLIB = Index: /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-altix64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-altix64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-altix64.sh (revision 11330) @@ -0,0 +1,20 @@ +#!/bin/bash + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/altix64/Makefile.in.patch + +#Compile +make Index: /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-cosmos.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-cosmos.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-cosmos.sh (revision 11330) @@ -0,0 +1,20 @@ +#!/bin/bash + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/cosmos/Makefile.in.patch + +#Compile +make Index: /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-linux64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-linux64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-linux64.sh (revision 11330) @@ -0,0 +1,20 @@ +#!/bin/bash + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/linux64/Makefile.in.patch + +#Compile +make Index: /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-macosx32.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-macosx32.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-macosx32.sh (revision 11330) @@ -0,0 +1,20 @@ +#!/bin/bash + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/macosx32/Makefile.in.patch + +#Compile +make Index: /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-macosx64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-macosx64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-macosx64.sh (revision 11330) @@ -0,0 +1,20 @@ +#!/bin/bash + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/macosx64/Makefile.in.patch + +#Compile +make Index: /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-pleiades.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-pleiades.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-pleiades.sh (revision 11330) @@ -0,0 +1,20 @@ +#!/bin/bash + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/pleiades/Makefile.in.patch + +#Compile +make Index: /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-win32.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-win32.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/install-4.0-win32.sh (revision 11330) @@ -0,0 +1,20 @@ +#!/bin/bash + +#Some cleanup +rm -rf install metis-4.0 +mkdir install + +#Untar +tar -zxvf metis-4.0.tar.gz + +#Move metis into install directory +mv metis-4.0/* install +rm -rf metis-4.0 + +#Apply patches +cd install +patch -p1 < ../metis-4.0.patch +patch Makefile.in ../configs/4.0/win32/Makefile.in.patch + +#Compile +make Index: /issm/trunk-jpl-damage/externalpackages/metis/install-5.0.1-linux64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/install-5.0.1-linux64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/install-5.0.1-linux64.sh (revision 11330) @@ -0,0 +1,20 @@ +#!/bin/bash +#metis 5.0 should be used: srand48 and drand48 are being redefined in conflict to the stdlib equivalent functions. + +#Some cleanup +rm -rf install metis-5.0.1 +mkdir install + +#Untar +tar -zxvf metis-5.0.1.tar.gz + +#Move metis into install directory +mv metis-5.0.1/* install +rm -rf metis-5.0.1 + +#Apply patches +cd install + +#Compile metis +make config prefix="$ISSM_TIER/externalpackages/metis/install" +make install Index: /issm/trunk-jpl-damage/externalpackages/metis/metis-4.0.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/metis/metis-4.0.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/metis/metis-4.0.patch (revision 11330) @@ -0,0 +1,263 @@ +diff -crB install/Lib/kmetis.c install2/Lib/kmetis.c +*** install/Lib/kmetis.c 1998-11-30 08:26:47.000000000 -0800 +--- install2/Lib/kmetis.c 2011-06-08 15:47:33.911358942 -0700 +*************** +*** 66,72 **** + ctrl.dbglvl = options[OPTION_DBGLVL]; + } + ctrl.optype = OP_KMETIS; +! ctrl.CoarsenTo = amax((*nvtxs)/(40*log2(*nparts)), 20*(*nparts)); + ctrl.maxvwgt = 1.5*((graph.vwgt ? idxsum(*nvtxs, graph.vwgt) : (*nvtxs))/ctrl.CoarsenTo); + + InitRandom(-1); +--- 66,72 ---- + ctrl.dbglvl = options[OPTION_DBGLVL]; + } + ctrl.optype = OP_KMETIS; +! ctrl.CoarsenTo = amax((*nvtxs)/(40*log2_function(*nparts)), 20*(*nparts)); + ctrl.maxvwgt = 1.5*((graph.vwgt ? idxsum(*nvtxs, graph.vwgt) : (*nvtxs))/ctrl.CoarsenTo); + + InitRandom(-1); +diff -crB install/Lib/kvmetis.c install2/Lib/kvmetis.c +*** install/Lib/kvmetis.c 1998-11-30 08:26:47.000000000 -0800 +--- install2/Lib/kvmetis.c 2011-06-08 15:47:33.916358976 -0700 +*************** +*** 66,72 **** + ctrl.dbglvl = options[OPTION_DBGLVL]; + } + ctrl.optype = OP_KVMETIS; +! ctrl.CoarsenTo = amax((*nvtxs)/(40*log2(*nparts)), 20*(*nparts)); + ctrl.maxvwgt = 1.5*((graph.vwgt ? idxsum(*nvtxs, graph.vwgt) : (*nvtxs))/ctrl.CoarsenTo); + + InitRandom(-1); +--- 66,72 ---- + ctrl.dbglvl = options[OPTION_DBGLVL]; + } + ctrl.optype = OP_KVMETIS; +! ctrl.CoarsenTo = amax((*nvtxs)/(40*log2_function(*nparts)), 20*(*nparts)); + ctrl.maxvwgt = 1.5*((graph.vwgt ? idxsum(*nvtxs, graph.vwgt) : (*nvtxs))/ctrl.CoarsenTo); + + InitRandom(-1); +diff -crB install/Lib/Makefile install2/Lib/Makefile +*** install/Lib/Makefile 1998-09-22 05:08:29.000000000 -0700 +--- install2/Lib/Makefile 2011-06-08 15:19:00.551540482 -0700 +*************** +*** 6,31 **** + LD = $(CC) -L. + + +! OBJS = coarsen.o fm.o initpart.o match.o ccgraph.o memory.o \ +! pmetis.o pqueue.o refine.o util.o timing.o debug.o \ +! bucketsort.o graph.o stat.o kmetis.o kwayrefine.o \ +! kwayfm.o balance.o ometis.o srefine.o sfm.o separator.o \ +! mincover.o mmd.o mesh.o meshpart.o frename.o fortran.o \ +! myqsort.o compress.o parmetis.o estmem.o \ +! mpmetis.o mcoarsen.o mmatch.o minitpart.o mbalance.o \ +! mrefine.o mutil.o mfm.o mkmetis.o mkwayrefine.o mkwayfmh.o \ +! mrefine2.o minitpart2.o mbalance2.o mfm2.o \ +! kvmetis.o kwayvolrefine.o kwayvolfm.o subdomains.o + +! .c.o: +! $(CC) $(CFLAGS) -c $*.c + +! ../libmetis.a: $(OBJS) + $(AR) $@ $(OBJS) + $(RANLIB) $@ + + clean: +! rm -f *.o + + realclean: +! rm -f *.o ; rm -f ../libmetis.a +--- 6,31 ---- + LD = $(CC) -L. + + +! OBJS = coarsen.$(OBJ_EXT) fm.$(OBJ_EXT) initpart.$(OBJ_EXT) match.$(OBJ_EXT) ccgraph.$(OBJ_EXT) memory.$(OBJ_EXT) \ +! pmetis.$(OBJ_EXT) pqueue.$(OBJ_EXT) refine.$(OBJ_EXT) util.$(OBJ_EXT) timing.$(OBJ_EXT) debug.$(OBJ_EXT) \ +! bucketsort.$(OBJ_EXT) graph.$(OBJ_EXT) stat.$(OBJ_EXT) kmetis.$(OBJ_EXT) kwayrefine.$(OBJ_EXT) \ +! kwayfm.$(OBJ_EXT) balance.$(OBJ_EXT) ometis.$(OBJ_EXT) srefine.$(OBJ_EXT) sfm.$(OBJ_EXT) separator.$(OBJ_EXT) \ +! mincover.$(OBJ_EXT) mmd.$(OBJ_EXT) mesh.$(OBJ_EXT) meshpart.$(OBJ_EXT) frename.$(OBJ_EXT) fortran.$(OBJ_EXT) \ +! myqsort.$(OBJ_EXT) compress.$(OBJ_EXT) parmetis.$(OBJ_EXT) estmem.$(OBJ_EXT) \ +! mpmetis.$(OBJ_EXT) mcoarsen.$(OBJ_EXT) mmatch.$(OBJ_EXT) minitpart.$(OBJ_EXT) mbalance.$(OBJ_EXT) \ +! mrefine.$(OBJ_EXT) mutil.$(OBJ_EXT) mfm.$(OBJ_EXT) mkmetis.$(OBJ_EXT) mkwayrefine.$(OBJ_EXT) mkwayfmh.$(OBJ_EXT) \ +! mrefine2.$(OBJ_EXT) minitpart2.$(OBJ_EXT) mbalance2.$(OBJ_EXT) mfm2.$(OBJ_EXT) \ +! kvmetis.$(OBJ_EXT) kwayvolrefine.$(OBJ_EXT) kwayvolfm.$(OBJ_EXT) subdomains.$(OBJ_EXT) + +! %.$(OBJ_EXT) : %.c +! $(CC) -c $(CFLAGS) -o $@ $< + +! ../libmetis.$(LIB_EXT): $(OBJS) + $(AR) $@ $(OBJS) + $(RANLIB) $@ + + clean: +! rm -f *.$(OBJ_EXT) + + realclean: +! rm -f *.$(OBJ_EXT) ; rm -f ../libmetis.$(LIB_EXT) +diff -crB install/Lib/metis.h install2/Lib/metis.h +*** install/Lib/metis.h 1998-11-30 08:26:50.000000000 -0800 +--- install2/Lib/metis.h 2011-06-08 15:19:00.544540433 -0700 +*************** +*** 18,24 **** +--- 18,26 ---- + #else + #include + #endif ++ #ifndef WIN32 + #include ++ #endif + #include + #include + #include +diff -crB install/Lib/mkmetis.c install2/Lib/mkmetis.c +*** install/Lib/mkmetis.c 1998-11-30 08:26:48.000000000 -0800 +--- install2/Lib/mkmetis.c 2011-06-08 15:47:33.921359010 -0700 +*************** +*** 47,53 **** + ctrl.dbglvl = options[OPTION_DBGLVL]; + } + ctrl.optype = OP_KMETIS; +! ctrl.CoarsenTo = amax((*nvtxs)/(20*log2(*nparts)), 30*(*nparts)); + + ctrl.nmaxvwgt = 1.5/(1.0*ctrl.CoarsenTo); + +--- 47,53 ---- + ctrl.dbglvl = options[OPTION_DBGLVL]; + } + ctrl.optype = OP_KMETIS; +! ctrl.CoarsenTo = amax((*nvtxs)/(20*log2_function(*nparts)), 30*(*nparts)); + + ctrl.nmaxvwgt = 1.5/(1.0*ctrl.CoarsenTo); + +diff -crB install/Lib/proto.h install2/Lib/proto.h +*** install/Lib/proto.h 1998-11-30 08:26:50.000000000 -0800 +--- install2/Lib/proto.h 2011-06-08 15:47:34.009359613 -0700 +*************** +*** 230,237 **** +--- 230,243 ---- + void QUADNODALMETIS(int, int, idxtype *, idxtype *, idxtype *adjncy); + + /* meshpart.c */ ++ #ifdef __cplusplus ++ extern "C" { ++ #endif + void METIS_PartMeshNodal(int *, int *, idxtype *, int *, int *, int *, int *, idxtype *, idxtype *); + void METIS_PartMeshDual(int *, int *, idxtype *, int *, int *, int *, int *, idxtype *, idxtype *); ++ #ifdef __cplusplus ++ } ++ #endif + + /* mfm.c */ + void MocFM_2WayEdgeRefine(CtrlType *, GraphType *, float *, int); +*************** +*** 459,465 **** + void srand48(long); + int ispow2(int); + void InitRandom(int); +! int log2(int); + + + +--- 465,471 ---- + void srand48(long); + int ispow2(int); + void InitRandom(int); +! int log2_function(int); + + + +diff -crB install/Lib/rename.h install2/Lib/rename.h +*** install/Lib/rename.h 1998-11-30 08:26:50.000000000 -0800 +--- install2/Lib/rename.h 2011-06-08 15:47:34.014359647 -0700 +*************** +*** 410,416 **** + #define RandomPermute __RandomPermute + #define ispow2 __ispow2 + #define InitRandom __InitRandom +! #define log2 __log2 + + + +--- 410,417 ---- + #define RandomPermute __RandomPermute + #define ispow2 __ispow2 + #define InitRandom __InitRandom +! /* Correction bug Nadir SOUALEM*/ +! #define log2_function __log2_function + + + +diff -crB install/Lib/util.c install2/Lib/util.c +*** install/Lib/util.c 1998-11-30 08:26:50.000000000 -0800 +--- install2/Lib/util.c 2011-06-08 15:47:34.018359675 -0700 +*************** +*** 507,515 **** + } + + /************************************************************************* +! * This function returns the log2(x) + **************************************************************************/ +! int log2(int a) + { + int i; + +--- 507,515 ---- + } + + /************************************************************************* +! * This function returns the log2_function(x) + **************************************************************************/ +! int log2_function(int a) + { + int i; + +diff -crB install/Makefile install2/Makefile +*** install/Makefile 1998-09-20 11:15:31.000000000 -0700 +--- install2/Makefile 2011-06-08 15:19:00.511540204 -0700 +*************** +*** 2,9 **** + + default: + (cd Lib ; make ) +! (cd Programs ; make ) +! (cd Test ; make ) + + clean: + (cd Lib ; make clean ) +--- 2,9 ---- + + default: + (cd Lib ; make ) +! # (cd Programs ; make ) +! # (cd Test ; make ) + + clean: + (cd Lib ; make clean ) +diff -crB install/Makefile.in install2/Makefile.in +*** install/Makefile.in 1998-10-02 14:28:35.000000000 -0700 +--- install2/Makefile.in 2011-06-08 15:19:00.536540378 -0700 +*************** +*** 1,9 **** + + # Which compiler to use +! CC = cc + + # What optimization level to use +! OPTFLAGS = -O2 + + # What options to be used by the compiler + COPTIONS = +--- 1,11 ---- + + # Which compiler to use +! CC = gcc +! OBJ_EXT=o +! LIB_EXT=a + + # What optimization level to use +! OPTFLAGS = -DLINUX -fPIC + + # What options to be used by the compiler + COPTIONS = Index: /issm/trunk-jpl-damage/externalpackages/mitgcm/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mitgcm/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mitgcm/install.sh (revision 11330) @@ -0,0 +1,25 @@ +#!/bin/bash + +#Do these commands once: +# cvs -d:pserver:cvsanon@mitgcm.org:/u/gcmpack login +# ( enter the CVS password: "cvsanon" ) + +#Some cleanup +rm -rf install + +#add cvs repository +export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' + +#Download code from server +cvs co -P MITgcm_code + +#move +mv MITgcm install + +#compile code +cd install +mkdir bin exe +cd bin +../tools/genmake2 -mods=../../code +make depend +make -j 8 Index: /issm/trunk-jpl-damage/externalpackages/mitgcm/readme_mitgcm.txt =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mitgcm/readme_mitgcm.txt (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mitgcm/readme_mitgcm.txt (revision 11330) @@ -0,0 +1,84 @@ +Instructions for getting MITgcm: http://mitgcm.org/ + + +(1) +add to your .bashrc file +# CVS +export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' + +source .bashrc + +cvs login + ( enter the CVS password: "cvsanon" ) + +cvs co -P MITgcm + +( +or if you don't want the verification packages +cvs co -P MITgcm_code +) + + +(2) +and if you don't like CVS go to : + +http://mitgcm.org/download/ + +and download the most recent checkpoint: +e.g. + MITgcm_c62w.tar.gz + + + + + +========================================================== +Instructions for generating and running a 1-CPU experiment +========================================================== + + cd MITgcm/verification/lab_sea + cd build + cp ../code/*.h ../code/packages.conf . + ../../../tools/genmake2 + make depend + make + cd ../input + ../build/mitgcmuv > output.txt + +Use matlab script to look at the output + cd ../../../verification/lab_sea/matlab + matlab + lookat_ice (you might have to modify the script) + + + +================================================================ +Instructions for running the "weddell" 200x160x50 configuration +================================================================ +face=6; ix=101:300; jx=290:449; kx=1:50; + +1. Obtain copies of following directories: + ftp://ecco2.jpl.nasa.gov/data1/weddell/code + ftp://ecco2.jpl.nasa.gov/data1/weddell/run_template + ftp://ecco2.jpl.nasa.gov/data1/data/era40/era40_ecmwf_blend + ftp://ecco2.jpl.nasa.gov/data1/data/blend_forcing/cube59_GPCP + +2. Get and compile code: + cvs co MITgcm_code + cd MITgcm + mkdir bin exe + cd bin + ../tools/genmake2 -mods=../../code + make depend + make -j + +3. Model execution: + cd ../exe + cp ../../run_template/* . + cp ../bin/mitgcmuv . + ./mitgcmuv >& output.txt & + + + + + Index: /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/altix64/Examples.Makefile.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/altix64/Examples.Makefile.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/altix64/Examples.Makefile.patch (revision 11330) @@ -0,0 +1,6 @@ +72,73c72,73 +< cpi: cpi.o ../lib/lib${MPILIBNAME}.a +< $(C_LINK) $(LDFLAGS) -o cpi cpi.o -lm ${LIBS} +--- +> cpi: cpi.o ../lib/lib${MPILIBNAME}.a +> $(C_LINK) $(LDFLAGS) -o cpi cpi.o -lm ${LIBS} ../lib/libmpich.a Index: /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/altix64/mpicxx.h.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/altix64/mpicxx.h.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/altix64/mpicxx.h.patch (revision 11330) @@ -0,0 +1,12 @@ +26c26 +< //#error "SEEK_SET is #defined but must not be for the C++ binding of MPI" +--- +> #error "SEEK_SET is #defined but must not be for the C++ binding of MPI" +30c30 +< //#error "SEEK_CUR is #defined but must not be for the C++ binding of MPI" +--- +> #error "SEEK_CUR is #defined but must not be for the C++ binding of MPI" +35c35 +< //#error "SEEK_END is #defined but must not be for the C++ binding of MPI" +--- +> #error "SEEK_END is #defined but must not be for the C++ binding of MPI" Index: /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/linux64/Examples.Makefile.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/linux64/Examples.Makefile.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/linux64/Examples.Makefile.patch (revision 11330) @@ -0,0 +1,6 @@ +72,73c72,73 +< cpi: cpi.o ../lib/lib${MPILIBNAME}.a +< $(C_LINK) $(LDFLAGS) -o cpi cpi.o -lm ${LIBS} +--- +> cpi: cpi.o ../lib/lib${MPILIBNAME}.a +> $(C_LINK) $(LDFLAGS) -o cpi cpi.o -lm ${LIBS} ../lib/libmpich.a Index: /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/linux64/mpicxx.h.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/linux64/mpicxx.h.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/linux64/mpicxx.h.patch (revision 11330) @@ -0,0 +1,12 @@ +26c26 +< //#error "SEEK_SET is #defined but must not be for the C++ binding of MPI" +--- +> #error "SEEK_SET is #defined but must not be for the C++ binding of MPI" +30c30 +< //#error "SEEK_CUR is #defined but must not be for the C++ binding of MPI" +--- +> #error "SEEK_CUR is #defined but must not be for the C++ binding of MPI" +35c35 +< //#error "SEEK_END is #defined but must not be for the C++ binding of MPI" +--- +> #error "SEEK_END is #defined but must not be for the C++ binding of MPI" Index: /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/macosx32/Examples.Makefile.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/macosx32/Examples.Makefile.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/macosx32/Examples.Makefile.patch (revision 11330) @@ -0,0 +1,6 @@ +72,73c72,73 +< cpi: cpi.o ../lib/lib${MPILIBNAME}.a +< $(C_LINK) $(LDFLAGS) -o cpi cpi.o -lm ${LIBS} +--- +> cpi: cpi.o ../lib/lib${MPILIBNAME}.a +> $(C_LINK) $(LDFLAGS) -o cpi cpi.o -lm ${LIBS} ../lib/libmpich.a Index: /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/macosx32/mpicxx.h.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/macosx32/mpicxx.h.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/macosx32/mpicxx.h.patch (revision 11330) @@ -0,0 +1,12 @@ +26c26 +< //#error "SEEK_SET is #defined but must not be for the C++ binding of MPI" +--- +> #error "SEEK_SET is #defined but must not be for the C++ binding of MPI" +30c30 +< //#error "SEEK_CUR is #defined but must not be for the C++ binding of MPI" +--- +> #error "SEEK_CUR is #defined but must not be for the C++ binding of MPI" +35c35 +< //#error "SEEK_END is #defined but must not be for the C++ binding of MPI" +--- +> #error "SEEK_END is #defined but must not be for the C++ binding of MPI" Index: /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/win32/Examples.Makefile.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/win32/Examples.Makefile.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/win32/Examples.Makefile.patch (revision 11330) @@ -0,0 +1,6 @@ +72,73c72,73 +< cpi: cpi.o ../lib/lib${MPILIBNAME}.a +< $(C_LINK) $(LDFLAGS) -o cpi cpi.o -lm ${LIBS} +--- +> cpi: cpi.o ../lib/lib${MPILIBNAME}.a +> $(C_LINK) $(LDFLAGS) -o cpi cpi.o -lm ${LIBS} ../lib/libmpich.a Index: /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/win32/mpicxx.h.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/win32/mpicxx.h.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/configs/1.0.2/win32/mpicxx.h.patch (revision 11330) @@ -0,0 +1,12 @@ +26c26 +< //#error "SEEK_SET is #defined but must not be for the C++ binding of MPI" +--- +> #error "SEEK_SET is #defined but must not be for the C++ binding of MPI" +30c30 +< //#error "SEEK_CUR is #defined but must not be for the C++ binding of MPI" +--- +> #error "SEEK_CUR is #defined but must not be for the C++ binding of MPI" +35c35 +< //#error "SEEK_END is #defined but must not be for the C++ binding of MPI" +--- +> #error "SEEK_END is #defined but must not be for the C++ binding of MPI" Index: /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-altix64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-altix64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-altix64.sh (revision 11330) @@ -0,0 +1,39 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install mpich2-1.0.2p1 +mkdir src install + +#Untar +tar -zxvf mpich2-1.0.2p1.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.0.2p1/* src +rm -rf mpich2-1.0.2p1 + +#Configure mpich2 +cd src +make distclean +export CFLAGS="$CFLAGS -fPIC" +export FFLAGS="$FFLAGS -fPIC" +./configure \ + --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ + --enable-sharedlibs=gcc \ + --enable-f91=gfortran + +#Apply Patch to examples +patch ./examples/Makefile ../configs/1.0.2/altix64/Examples.Makefile.patch +patch -R ./src/binding/cxx/mpicxx.h ../configs/1.0.2/altix64/mpicxx.h.patch +patch -R ./src/include/mpicxx.h ../configs/1.0.2/altix64/mpicxx.h.patch + +#Compile mpich2 +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install + +#remove so files +cd ../install/lib +rm -rf *.so Index: /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-linux64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-linux64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-linux64.sh (revision 11330) @@ -0,0 +1,35 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install mpich2-1.0.2p1 +mkdir src install + +#Untar +tar -zxvf mpich2-1.0.2p1.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.0.2p1/* src +rm -rf mpich2-1.0.2p1 + +#Configure mpich2 +cd src +make distclean +export CFLAGS="$CFLAGS -fPIC" +export FFLAGS="$FFLAGS -fPIC" +./configure \ + --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ + --enable-sharedlibs=gcc \ + --enable-f91=gfortran + +#Apply Patch to examples +patch ./examples/Makefile ../configs/1.0.2/linux64/Examples.Makefile.patch +patch -R ./src/binding/cxx/mpicxx.h ../configs/1.0.2/linux64/mpicxx.h.patch +patch -R ./src/include/mpicxx.h ../configs/1.0.2/linux64/mpicxx.h.patch + +#Compile mpich2 +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-macosx32.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-macosx32.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-macosx32.sh (revision 11330) @@ -0,0 +1,38 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install mpich2-1.0.2p1 +mkdir src install + +#Untar +tar -zxvf mpich2-1.0.2p1.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.0.2p1/* src +rm -rf mpich2-1.0.2p1 + +#Configure mpich2 +cd src +make distclean +export CFLAGS=" -m32" +./configure \ + --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ + --enable-f91=gfortran \ + --enable-sharedlibs=osx-gcc + +#Apply Patch to examples +patch ./examples/Makefile ../configs/1.0.2/macosx32/Examples.Makefile.patch +patch -R ./src/binding/cxx/mpicxx.h ../configs/1.0.2/macosx32/mpicxx.h.patch +patch -R ./src/include/mpicxx.h ../configs/1.0.2/macosx32/mpicxx.h.patch + +#Compile mpich2 +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install + +#remove so files +cd ../install/lib +rm -rf *.so Index: /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-win32.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-win32.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.0.2-win32.sh (revision 11330) @@ -0,0 +1,36 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install mpich2-1.0.2p1 +mkdir src install + +#Untar +tar -zxvf mpich2-1.0.2p1.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.0.2p1/* src +rm -rf mpich2-1.0.2p1 + +#Configure mpich2 +cd src +make distclean +export CFLAGS="$CFLAGS -fPIC" +export FFLAGS="$FFLAGS -fPIC" +./configure --prefix="$ISSM_TIER/externalpackages/mpich2/install" + +#Apply Patch to examples +patch ./examples/Makefile ../configs/1.0.2/win32/Examples.Makefile.patch +patch -R ./src/binding/cxx/mpicxx.h ../configs/1.0.2/win32/mpicxx.h.patch +patch -R ./src/include/mpicxx.h ../configs/1.0.2/win32/mpicxx.h.patch + +#Compile mpich2 +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install + +#remove so files +cd ../install/lib +rm -rf *.so Index: /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.4-linux64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.4-linux64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.4-linux64.sh (revision 11330) @@ -0,0 +1,34 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install mpich2-1.4 +mkdir src install + +#Untar +tar -zxvf mpich2-1.4.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.4/* src +rm -rf mpich2-1.4 + +#Configure mpich2 +cd src +export CFLAGS="$CFLAGS -fPIC" +export FFLAGS="$FFLAGS -fPIC" +./configure \ + --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ + --enable-shared \ + --enable-sharedlibs=gcc \ + --enable-f91=gfortran + +#Compile mpich2 +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install + +#remove so files +cd ../install/lib +rm -rf *.so Index: /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx32.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx32.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx32.sh (revision 11330) @@ -0,0 +1,37 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install mpich2-1.4 +mkdir src install + +#Untar +tar -zxvf mpich2-1.4.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.4/* src +rm -rf mpich2-1.4 + +#Configure mpich2 +cd src +export CFLAGS=" -arch i386" +export CXXFLAGS=" -arch i386" +export CPPFLAGS=" -arch i386" +export FFLAGS=" -arch i386" +./configure \ + --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ + --enable-f91=gfortran \ + --enable-sharedlibs=osx-gcc \ + --enable-shared \ + --enable-fc="/usr/local/bin/gfortran" + +#Compile mpich2 +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install + +#remove so files +cd ../install/lib +rm -rf *.so Index: /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/mpich2/install-1.4-macosx64.sh (revision 11330) @@ -0,0 +1,37 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install mpich2-1.4 +mkdir src install + +#Untar +tar -zxvf mpich2-1.4.tar.gz + +#Move mpich2 into src directory +mv mpich2-1.4/* src +rm -rf mpich2-1.4 + +#Configure mpich2 +cd src +export FCFLAGS=" -m64" +export FFLAGS=" -m64" +export CFLAGS=" -arch x86_64" +export CXXFLAGS=" -arch x86_64" +./configure \ + --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ + --enable-f91 \ + --enable-sharedlibs=osx-gcc \ + --enable-shared \ + --enable-fc + +#Compile mpich2 +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install + +#remove so files +cd ../install/lib +rm -rf *.so Index: /issm/trunk-jpl-damage/externalpackages/ncview/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/ncview/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/ncview/install.sh (revision 11330) @@ -0,0 +1,24 @@ +#!/bin/bash + +#Some cleanup +rm -rf install +mkdir install + +#Untar +tar -zxvf ncview-1.93g.tar.gz + +#Move doxygen into src directory +mv ncview-1.93g/* install +rmdir ncview-1.93g + +#Configure doxygen +cd install +./configure \ + --prefix "$ISSM_TIER/externalpackages/ncview/install" \ + --x-libraries=/usr/X11/lib/ \ + --x-includes=/usr/X11/include/ \ + --with-netcdf_incdir="$ISSM_TIER/externalpackages/netcdf/install/include/" \ + --with-netcdf_libdir="$ISSM_TIER/externalpackages/netcdf/install/lib/" + +make +make install Index: /issm/trunk-jpl-damage/externalpackages/netcdf/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/netcdf/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/netcdf/install.sh (revision 11330) @@ -0,0 +1,23 @@ +#!/bin/bash + +#Some cleanup +rm -rf install netcdf-4.0.1 +mkdir install + +#Untar +tar -zxvf netcdf-4.0.1.tar.gz + +#Move netcdf to install directory +rm -rf install/* +mv netcdf-4.0.1/* install/ +rm -rf netcdf-4.0.1 + +#Configure and compile +cd install +./configure --prefix="$ISSM_TIER/externalpackages/netcdf/install" +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk-jpl-damage/externalpackages/oofem/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/oofem/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/oofem/install.sh (revision 11330) @@ -0,0 +1,32 @@ +#!/bin/bash + +#Some cleanup +rm -rf src +rm -rf oofem-2.0 +mkdir src + +#Untar +tar -zxvf oofem-2.0.tar.gz + +#Move oofem into src directory +mv oofem-2.0/* src +rm -rf oofem-2.0 + +# currently a basic serial configuration, see http://www.oofem.org/wiki/doku.php?id=installation +# for details on enabling the IML++ and PETSc libraries, and for configuring the parallel version +cd src +./configure OOFEM_TARGET=oofem-2.0 --enable-dss + +#Compile oofem +cd targets/oofem-2.0 +if [ -z $1 ]; then + make +else + make -j $1 +fi + +# build verification tools +cd ../../tools && make all + +# testing solver +cd ../targets/oofem-2.0 && make tests && less ./test_results Index: /issm/trunk-jpl-damage/externalpackages/openanalysis/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/openanalysis/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/openanalysis/install.sh (revision 11330) @@ -0,0 +1,13 @@ +#!/bin/bash + +#Some cleanup +rm -rf openanalysis + +#download openanalysis +svn co http://svn.berlios.de/svnroot/repos/openanalysis/OpenAnalysis/trunk openanalysis + +#Configure +cd openanalysis + +make -f Makefile.quick all +make -f Makefile.quick install Index: /issm/trunk-jpl-damage/externalpackages/pcre/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/pcre/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/pcre/install.sh (revision 11330) @@ -0,0 +1,17 @@ +#!/bin/bash + +#Cleaning +rm -rf install +rm -rf pcre-8.21 +mkdir install + +#Untar and move python into install directory +tar -zxvf pcre-8.21.tar.gz +mv pcre-8.21/* install +rm -rf pcre-8.21 + +#Configure doxygen +cd install +./configure --prefix "$ISSM_TIER/externalpackages/python/install" +make +make install Index: /issm/trunk-jpl-damage/externalpackages/petsc/README =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/README (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/README (revision 11330) @@ -0,0 +1,27 @@ +petsc carries a version of Blas that uses int arguments (int32) type, while +Matlab carries a version of Blas that uses int64_t arguments (hidden behing +a ptrdiff_t type (check MATLAB_DIR/extern/include/blas.h). +In serial mode, Matlab discards the Petsc Blas library (even when it was statically +linked against the mex files!) symbols, and replaces them with its version. +Because the prototypes conflict (32 vs 64), crashes ensue whenever using a Blas +routine (for ex: VecAXPY calls BLASaxpy_, which calls daxpy). + +To avoid that, we have to recompile Petsc with a 64 bit prototype. Luckily, +Petsc did a good job, and hid the Blas int type into the typedef BLASint (check +in include/petsc.h). Just typedef it back from int to int64_t, and recompile, +and that does the trick. Don't forget the #include "inttypes.h" at the top of petsc.h, +otherwise, crashes during the compile. + +Same problem may arise for using the lapack library. + +Now, Petsc pretends it can compile in --with-64-bit-pointers. That sets PetscInt to long long +The only problem, it says MUMPS, Scalapack, blacs, Plapack don't support 64 bit indexing. +Mumps looks like it might. + +If compiling --with-64-bit-pointers, all prototypes in Petsc ask for PetscInt = long long +which Issm does not know. Can't compile with this option. Unless we switch to 64 bit integers +in ISSM. Started to put this framework into place: we now have IssmInt, IssmDouble, IssmChar +in types.h. They rely on ISSM_USE_64_BIT_INDEXING symbol, define in config.h, instantiated by +autotools with --with-64bit-pointers=1 in configure.sh + +Recomendation: wait until MUMPS implements 64 bit indexing. Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-altix64-castor.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-altix64-castor.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-altix64-castor.sh (revision 11330) @@ -0,0 +1,61 @@ +#!/bin/bash +#Step 1: unzip and install +#Step 2: After Plapack implodes +STEP=0 + +if [ $STEP -eq 1 ]; then + #Some cleanup + rm -rf install petsc-2.3.2-p3 src + mkdir install src + + #Untar and move petsc to install directory + tar -zxvf petsc-2.3.2-p3.tar.gz + mv petsc-2.3.2-p3/* install/ + rm -rf petsc-2.3.2-p3 + + #configure + cd install + ./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --with-batch=1 \ + --ISSM_ARCH=$ISSM_ARCH \ + --PETSC_DIR=$PETSC_DIR \ + --with-debugging=no \ + --with-shared=0 COPTFLAGS=-O3 FOPTFLAGS=-O3 \ + --with-blas-lapack-dir=/opt/intel/mkl/9.1.023 \ + --with-mpi-lib=/usr/lib/libmpi.so \ + --with-mpi-include=/usr/include \ + --with-mpi-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-plapack=yes \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort + + echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/installation/compilationtroubleshooting/petsc232/) ==" + echo "== Then run STEP=2 ==" +fi +if [ $STEP -eq 2 ]; then + cd install + ./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --with-batch=1 \ + --ISSM_ARCH=$ISSM_ARCH \ + --PETSC_DIR=$PETSC_DIR \ + --with-debugging=no \ + --with-shared=0 COPTFLAGS=-O3 FOPTFLAGS=-O3 \ + --with-blas-lapack-dir=/opt/intel/mkl/9.1.023 \ + --with-mpi-lib=/usr/lib/libmpi.so \ + --with-mpi-include=/usr/include \ + --with-mpi-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --with-plapack-dir=$PETSC_DIR/externalpackages/PLAPACKR32-hg/$ISSM_ARCH \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort + echo "== Follow PETSc's instructions" +fi Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-cosmos.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-cosmos.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-cosmos.sh (revision 11330) @@ -0,0 +1,32 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-2.3.2-p3 src +mkdir install src + +#Untar and move petsc to install directory +tar -zxvf petsc-2.3.2-p3.tar.gz +mv petsc-2.3.2-p3/* install/ +rm -rf petsc-2.3.2-p3 + +#configure +cd install +PETSC_DIR=$ISSM_TIER/externalpackages/petsc/install +./config/configure.py \ + --prefix=$PETSC_DIR \ + --with-batch=1 \ + --ISSM_ARCH=$ISSM_ARCH \ + --PETSC_DIR=$PETSC_DIR \ + --with-debugging=no COPTFLAGS=-O3 FOPTFLAGS=-O3 \ + --with-blas-lapack-dir=/opt/intel/mkl/10.0.5.025/ \ + --with-mpi-dir=/opt/mpich/gm/intel10.1/ \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-plapack=yes \ + --FFLAGS=-I/usr/include \ + --with-mpi-shared=0 + +#Compile petsc and install it +make +make install Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-linux64-astrid.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-linux64-astrid.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-linux64-astrid.sh (revision 11330) @@ -0,0 +1,35 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-2.3.2-p3 src +mkdir install src + +#Untar and move petsc to install directory +tar -zxvf petsc-2.3.2-p3.tar.gz +mv petsc-2.3.2-p3/* install/ +rm -rf petsc-2.3.2-p3 + +#configure +cd install +./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --PETSC_ARCH=linux-gnu-amd64 \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ + --with-fc=gfortran \ + --with-debugging=1 \ + --with-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --FFLAGS=-I$ISSM_TIER/externalpackages/mpich2/install/include \ + --download-plapack=yes \ + --COPTFLAGS="-march=opteron -O2" \ + --FOPTFLAGS="-march=opteron -O2" \ + --CXXOPTFLAGS="-march=opteron -O2" + +#Compile petsc and install it +make +make install Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-eric.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-eric.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-eric.sh (revision 11330) @@ -0,0 +1,68 @@ +#!/bin/bash +#Step 1: unzip and install +#Step 2: After MUMPS Crashes +STEP=0 + +if [ $STEP -eq 1 ]; then + #Some cleanup + rm -rf install petsc-2.3.2-p3 src + mkdir install src + + #Untar and move petsc to install directory + tar -zxvf petsc-2.3.2-p3.tar.gz + mv petsc-2.3.2-p3/* install/ + rm -rf petsc-2.3.2-p3 + + #configure + cd install + ./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --PETSC_ARCH=macosx-gnu \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ + --with-fc=/usr/local/bin/gfortran \ + --with-debugging=0 \ + --with-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran -fPIC -arch i386" \ + --download-plapack=yes \ + --CXXFLAGS=" -fPIC -arch i386" \ + --CFLAGS=" -fPIC -arch i386" \ + --with-pic \ + --with-fc="gfortran -arch i386 " \ + --LDFLAGS="-arch i386" + echo "== Fix MUMPS compilation manually (http://issm.jpl.nasa.gov/installation/compilationtroubleshooting/petsc232/) ==" + echo "== Then run STEP=2 ==" +fi + +if [ $STEP -eq 2 ]; then + cd install + ./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --PETSC_ARCH=macosx-gnu \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ + --with-fc=/usr/local/bin/gfortran \ + --with-debugging=0 \ + --with-shared=0 \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3 \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran -fPIC -arch i386" \ + --download-plapack=yes \ + --CXXFLAGS=" -fPIC -arch i386" \ + --CFLAGS=" -fPIC -arch i386" \ + --with-pic \ + --with-fc="gfortran -arch i386 " \ + --LDFLAGS="-arch i386" + + #Compile petsc and install it + make + make install +fi Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh (revision 11330) @@ -0,0 +1,31 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-2.3.2-p3 src +mkdir install src + +#Untar and move petsc to install directory +tar -zxvf petsc-2.3.2-p3.tar.gz +mv petsc-2.3.2-p3/* install/ +rm -rf petsc-2.3.2-p3 + +#configure +cd install +./config/configure.py --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --PETSC_ARCH=macosx-gnu \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ + --with-fc=/usr/local/bin/gfortran \ + --with-debugging=0 \ + --with-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran" \ + --download-plapack=yes + +#Compile petsc and install it +make +make install Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-pleiades.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-pleiades.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-pleiades.sh (revision 11330) @@ -0,0 +1,67 @@ +#!/bin/bash +#Step 1: unzip and install +#Step 2: After Plapack implodes +STEP=0 + +if [ $STEP -eq 1 ]; then + #Some cleanup + rm -rf install petsc-2.3.2-p3 src + mkdir install src + + #Untar and move petsc to install directory + tar -zxvf petsc-2.3.2-p3.tar.gz + mv petsc-2.3.2-p3/* install/ + rm -rf petsc-2.3.2-p3 + + #configure + cd install + ./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH=$ISSM_ARCH \ + --PETSC_DIR=$PETSC_DIR \ + --with-debugging=no \ + --with-shared=0 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ + --with-mpi-lib=/nasa/sgi/mpt/1.23.nas/lib64/libmpi.so \ + --with-mpi-include=/nasa/sgi/mpt/1.23.nas/include \ + --with-mpi-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-plapack=yes \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --COPTFLAGS=" -O3 -xS" \ + --FOPTFLAGS=" -O3 -xS" \ + --CXXOPTFLAGS=" -O3 -xS" + + echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/installation/compilationtroubleshooting/petsc232/) ==" + echo "== Then run STEP=2 ==" +fi +if [ $STEP -eq 2 ]; then + cd install + ./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH=$ISSM_ARCH \ + --PETSC_DIR=$PETSC_DIR \ + --with-debugging=no \ + --with-shared=0 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ + --with-mpi-lib=/nasa/sgi/mpt/1.23.nas/lib64/libmpi.so \ + --with-mpi-include=/nasa/sgi/mpt/1.23.nas/include \ + --with-mpi-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --with-plapack-dir=$PETSC_DIR/externalpackages/PLAPACKR32-hg/$ISSM_ARCH \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --COPTFLAGS=" -O3 -xS" \ + --FOPTFLAGS=" -O3 -xS" \ + --CXXOPTFLAGS=" -O3 -xS" + echo "== Follow PETSc's instructions" +fi Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win32-eric.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win32-eric.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-2.3.2-win32-eric.sh (revision 11330) @@ -0,0 +1,25 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-2.3.2-p3 src +mkdir install src + +#Untar and move petsc to install directory +tar -zxvf petsc-2.3.2-p3.tar.gz +mv petsc-2.3.2-p3/* install/ +rm -rf petsc-2.3.2-p3 + +#configure +cd install +./config/configure.py \ + --with-parallel-no \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --PETSC_ARCH=cygwin-intel \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \ + --with-debugging=0 \ + --with-mpi=0 \ + --download-c-blas-lapack=1 + +#Compile petsc and install it +make +make install Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-altix64-castor.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-altix64-castor.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-altix64-castor.sh (revision 11330) @@ -0,0 +1,62 @@ +#!/bin/bash +#Step 1: unzip and install +#Step 2: After Plapack implodes +STEP=0 + +if [ $STEP -eq 1 ]; then + #Some cleanup + rm -rf install petsc-3.1-p7 src + mkdir install src + + #Untar and move petsc to install directory + tar -zxvf petsc-3.1-p7.tar.gz + mv petsc-3.1-p7/* install/ + rm -rf petsc-3.1-p7 + + #configure + cd src + ./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --ISSM_ARCH=$ISSM_ARCH \ + --with-debugging=no \ + --with-shared=0 COPTFLAGS=-O3 FOPTFLAGS=-O3 \ + --with-blas-lapack-dir=/opt/intel/mkl/9.1.023 \ + --with-mpi-lib=/usr/lib/libmpi.so \ + --with-mpi-include=/usr/include \ + --with-mpi-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-plapack=yes \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --download-parmetis=yes + + echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/installation/compilationtroubleshooting/petsc31/) ==" + echo "== Then run STEP=2 ==" +fi +if [ $STEP -eq 2 ]; then + cd src + ./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --with-batch=1 \ + --ISSM_ARCH=$ISSM_ARCH \ + --with-debugging=no \ + --with-shared=0 COPTFLAGS=-O3 FOPTFLAGS=-O3 \ + --with-blas-lapack-dir=/opt/intel/mkl/9.1.023 \ + --with-mpi-lib=/usr/lib/libmpi.so \ + --with-mpi-include=/usr/include \ + --with-mpi-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --with-plapack-dir=$PETSC_DIR/externalpackages/PLAPACKR32-hg/$ISSM_ARCH \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --download-parmetis=yes + echo "== Follow PETSc's instructions" +fi Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-cosmos.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-cosmos.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-cosmos.sh (revision 11330) @@ -0,0 +1,32 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.1-p7 src +mkdir install src + +#Untar and move petsc to install directory +tar -zxvf petsc-3.1-p7.tar.gz +mv petsc-3.1-p7/* src/ +rm -rf petsc-3.1-p7 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --with-batch=1 \ + --ISSM_ARCH=$ISSM_ARCH \ + --with-debugging=no COPTFLAGS=-O3 FOPTFLAGS=-O3 \ + --with-blas-lapack-dir=/opt/intel/mkl/10.0.5.025/ \ + --with-mpi-dir=/opt/mpich/gm/intel10.1/ \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-plapack=yes \ + --FFLAGS=-I/usr/include \ + --with-mpi-shared=0 \ + --download-parmetis=yes + +#Compile petsc and install it +make +make install Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-linux64-astrid.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-linux64-astrid.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-linux64-astrid.sh (revision 11330) @@ -0,0 +1,36 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.1-p7 src +mkdir install src + +#Untar and move petsc to install directory +tar -zxvf petsc-3.1-p7.tar.gz +mv petsc-3.1-p7/* src/ +rm -rf petsc-3.1-p7 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --PETSC_ARCH=linux-gnu-amd64 \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-parmetis=yes \ + --FFLAGS=-I$ISSM_TIER/externalpackages/mpich2/install/include \ + --download-plapack=yes \ + --COPTFLAGS="-march=opteron -O2" \ + --FOPTFLAGS="-march=opteron -O2" \ + --CXXOPTFLAGS="-march=opteron -O2" \ + --with-pic=1 + +#Compile petsc and install it +make +make install Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-mathieu.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-mathieu.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-mathieu.sh (revision 11330) @@ -0,0 +1,35 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.1-p7 src +mkdir install src + +#Untar and move petsc to install directory +tar -zxvf petsc-3.1-p7.tar.gz +mv petsc-3.1-p7/* src/ +rm -rf petsc-3.1-p7 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --PETSC_ARCH=macosx-gnu \ + --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --with-debugging=0 \ + --with-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-plapack=yes \ + --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -arch i386" \ + --COPTFLAGS="-march=opteron -O2 -arch i386" \ + --FOPTFLAGS="-march=opteron -O2 -arch i386" \ + --CXXOPTFLAGS="-march=opteron -O2 -arch i386" \ + --download-parmetis=yes + +#Compile petsc and install it +make +make install Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-ogive.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-ogive.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-macosx32-ogive.sh (revision 11330) @@ -0,0 +1,36 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.1-p7 src +mkdir install src + +#Untar and move petsc to install directory +tar -zxvf petsc-3.1-p7.tar.gz +mv petsc-3.1-p7/* src/ +rm -rf petsc-3.1-p7 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --PETSC_ARCH=macosx-gnu \ + --with-fc=/usr/local/bin/gfortran \ + --with-debugging=0 \ + --with-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-plapack=yes \ + --download-parmetis=yes \ + --download-f-blas-lapack=yes \ + --COPTFLAGS="-march=opteron -O2 " \ + --FOPTFLAGS="-march=opteron -O2 " \ + --CXXOPTFLAGS="-march=opteron -O2 " \ + --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran " + +#Compile petsc and install it +make +make install Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-pleiades.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-pleiades.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-3.1-pleiades.sh (revision 11330) @@ -0,0 +1,69 @@ +#!/bin/bash +#Step 1: unzip and install +#Step 2: After Plapack implodes +STEP=0 + +if [ $STEP -eq 1 ]; then + #Some cleanup + rm -rf install petsc-3.1-p7 src + mkdir install src + + #Untar and move petsc to install directory + tar -zxvf petsc-3.1-p7.tar.gz + mv petsc-3.1-p7/* install/ + rm -rf petsc-3.1-p7 + + #configure + cd src + ./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --with-debugging=no \ + --with-shared=0 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ + --with-mpi-lib=/nasa/sgi/mpt/1.25/lib/libmpi.so \ + --with-mpi-include=/nasa/sgi/mpt/1.25/include \ + --known-mpi-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-plapack=yes \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --COPTFLAGS=" -O3 -xS" \ + --FOPTFLAGS=" -O3 -xS" \ + --CXXOPTFLAGS=" -O3 -xS" \ + --with-pic=1 + echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/installation/compilationtroubleshooting/petsc31/) ==" + echo "== Then run STEP=2 ==" +fi +if [ $STEP -eq 2 ]; then + cd src + ./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --with-debugging=no \ + --with-shared=0 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ + --with-mpi-lib=/nasa/sgi/mpt/1.25/lib/libmpi.so \ + --with-mpi-include=/nasa/sgi/mpt/1.25/include \ + --known-mpi-shared=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --with-plapack-dir=$ISSM_TIER/externalpackages/petsc/src/$ISSM_ARCH \ + --download-parmetis=yes \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --COPTFLAGS=" -O3 -xS" \ + --FOPTFLAGS=" -O3 -xS" \ + --CXXOPTFLAGS=" -O3 -xS" \ + --with-pic=1 + echo "== Follow PETSc's instructions" +fi Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-3.2-linux64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-3.2-linux64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-3.2-linux64.sh (revision 11330) @@ -0,0 +1,33 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.2-p3 src +mkdir install src + +#Untar and move petsc to install directory +tar -zxvf petsc-3.2-p3.tar.gz +mv petsc-3.2-p3/* src/ +rm -rf petsc-3.2-p3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \ + --with-clanguage=C++ \ + --PETSC_ARCH=linux-gnu-amd64 \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-f-blas-lapack=yes \ + --download-plapack=yes \ + --download-parmetis=yes \ + --with-pic=1 + +#Compile petsc and install it +make +make install Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-3.2-macosx64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-3.2-macosx64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-3.2-macosx64.sh (revision 11330) @@ -0,0 +1,31 @@ +#!/bin/bash + +#Some cleanup +rm -rf install petsc-3.2-p3 src +mkdir install src + +#Untar and move petsc to install directory +tar -zxvf petsc-3.2-p3.tar.gz +mv petsc-3.2-p3/* src/ +rm -rf petsc-3.2-p3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --PETSC_ARCH=macosx-gnu \ + --with-mpi-dir="$ISSM_TIER/externalpackages/mpich2/install" \ + --with-debugging=0 \ + --with-shared-libraries=0 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-blas=yes \ + --download-plapack=yes \ + --download-parmetis=yes \ + --download-f-blas-lapack=yes + +#Compile petsc and install it +make +make install Index: /issm/trunk-jpl-damage/externalpackages/petsc/install-3.2-pleiades.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/petsc/install-3.2-pleiades.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/petsc/install-3.2-pleiades.sh (revision 11330) @@ -0,0 +1,69 @@ +#!/bin/bash +#Step 1: unzip and install +#Step 2: After Plapack implodes +STEP=2 + +if [ $STEP -eq 1 ]; then + #Some cleanup + rm -rf install petsc-3.2-p3 src + mkdir install src + + #Untar and move petsc to install directory + tar -zxvf petsc-3.2-p3.tar.gz + mv petsc-3.2-p3/* src/ + rm -rf petsc-3.2-p3 + + #configure + cd src + ./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=0 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ + --known-mpi-shared-libraries=1 \ + --with-mpi-lib=/nasa/sgi/mpt/1.25/lib/libmpi.so \ + --with-mpi-include=/nasa/sgi/mpt/1.25/include \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --download-plapack=yes \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --COPTFLAGS=" -O3 -xS" \ + --FOPTFLAGS=" -O3 -xS" \ + --CXXOPTFLAGS=" -O3 -xS" \ + --with-pic=1 + echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/installation/compilationtroubleshooting/petsc31/) ==" + echo "== Then run STEP=2 ==" +fi +if [ $STEP -eq 2 ]; then + cd src + ./config/configure.py \ + --prefix="$ISSM_TIER/externalpackages/petsc/install" \ + --with-batch=1 \ + --PETSC_ARCH="$ISSM_ARCH" \ + --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ + --with-debugging=0 \ + --with-shared-libraries=0 \ + --with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \ + --with-mpi-lib=/nasa/sgi/mpt/1.25/lib/libmpi.so \ + --with-mpi-include=/nasa/sgi/mpt/1.25/include \ + --known-mpi-shared-libraries=1 \ + --download-mumps=yes \ + --download-scalapack=yes \ + --download-blacs=yes \ + --with-plapack-dir=$ISSM_TIER/externalpackages/petsc/src/$ISSM_ARCH \ + --download-parmetis=yes \ + --FFLAGS=-I/usr/include \ + --with-cc=icc \ + --with-fc=ifort \ + --COPTFLAGS=" -O3 -xS" \ + --FOPTFLAGS=" -O3 -xS" \ + --CXXOPTFLAGS=" -O3 -xS" \ + --with-pic=1 + echo "== Follow PETSc's instructions" +fi Index: /issm/trunk-jpl-damage/externalpackages/polygonclipper/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/polygonclipper/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/polygonclipper/install.sh (revision 11330) @@ -0,0 +1,15 @@ +#!/bin/bash + +#Some cleanup +rm -rf install + +#install +mkdir install +cd install +cp ../PolygonClipper.zip . + +#uncompress +unzip PolygonClipper.zip + +#Make +mex gpc.c gpc_mexfile.c -O -output PolygonClip Index: /issm/trunk-jpl-damage/externalpackages/python/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/python/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/python/install.sh (revision 11330) @@ -0,0 +1,22 @@ +#!/bin/bash +#wget http://python.org/ftp/python/3.2.2/Python-3.2.2.tgz + +#Some cleanup +rm -rf install +rm -rf Python-3.2.2 +mkdir install + +#Untar and move python into install directory +tar -zxvf Python-3.2.2.tgz +mv Python-3.2.2/* install +rm -rf Python-3.2.2 + +#Configure doxygen +cd install +./configure --prefix "$ISSM_TIER/externalpackages/python/install" +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk-jpl-damage/externalpackages/qhull/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/qhull/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/qhull/install.sh (revision 11330) @@ -0,0 +1,19 @@ +#!/bin/bash + +#Some cleanup +rm -rf src install qhull-2003.1 +mkdir src install + +#Untar +tar -zxvf qhull-2003.1.tar.gz + +#Move qhull to src directory +rm -rf src/* +mv qhull-2003.1/* src/ +rm -rf qhull-2003.1 + +#Configure qhull +cd src +./configure --prefix="$ISSM_TIER/externalpackages/qhull/install" +make +make install Index: /issm/trunk-jpl-damage/externalpackages/rats/README =================================================================== --- /issm/trunk-jpl-damage/externalpackages/rats/README (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/rats/README (revision 11330) @@ -0,0 +1,3 @@ +Rought Auditing Tools for Software +Obtained code from https://www.fortify.com/ssa-elements/threat-intelligence/rats.html + Index: /issm/trunk-jpl-damage/externalpackages/rats/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/rats/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/rats/install.sh (revision 11330) @@ -0,0 +1,17 @@ +#!/bin/bash + +#Erase install +rm -rf install src rats-2.3 + +#install directory +mkdir src +tar -zxvf rats-2.3.tar.gz +mv rats-2.3/* src +rm -rf rats-2.3 + +#compile +cd src +./configure --prefix=$ISSM_TIER/externalpackages/rats/install +make +make install +cd .. Index: /issm/trunk-jpl-damage/externalpackages/rose/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/rose/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/rose/install.sh (revision 11330) @@ -0,0 +1,26 @@ +#!/bin/bash + +#Some cleanup +rm -rf source build install +mkdir install source build + +#Untar +tar -zxvf rose-0.9.5a-13219.tar.gz + +#Move rose into install directory +mv rose-0.9.5a-13219/* source +rm -rf rose-0.9.5a-13219 + +#Configure +cd build +../source/configure \ + --prefix=$ISSM_TIER/externalpackages/rose/install \ + --with-boost=$ISSM_TIER/externalpackages/boost/install\ + --srcdir=$ISSM_TIER/externalpackages/rose/source + +if [ -z $1 ]; then + make +else + make -j $1 +fi +make install Index: /issm/trunk-jpl-damage/externalpackages/satstress/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/satstress/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/satstress/install.sh (revision 11330) @@ -0,0 +1,16 @@ +#!/bin/bash + +#Some cleanup +rm -rf install SatStress-0.1.2 +mkdir install + +#Untar +tar -zxvf SatStress-0.1.2.tar.gz + +#Move SatStress into install directory +mv SatStress-0.1.2/* install +rm -rf SatStress-0.1.2 + +#Compile SatStress +cd install +make test Index: /issm/trunk-jpl-damage/externalpackages/scotch/Makefile.inc =================================================================== --- /issm/trunk-jpl-damage/externalpackages/scotch/Makefile.inc (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/scotch/Makefile.inc (revision 11330) @@ -0,0 +1,26 @@ +EXE = +LIB = .a +OBJ = .o +MEX = .mexa64 + +MAKE = make +AR = ar +ARFLAGS = -ruv +CAT = cat +CCS = gcc +CCP = mpicc +CCD = mpicc +CCM = ${MATLAB_DIR}/bin/mex +#CFLAGS = -m64 -O3 -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DCOMMON_TIMING_OLD -DMATLAB -fPIC -I${MATLAB_DIR}/extern/include +CFLAGS = -m64 -O3 -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DCOMMON_TIMING_OLD -fPIC +#LDFLAGS = -lz -lm -lrt -L${MATLAB_DIR}/bin/glnxa64 -lmex -lmat +#LDFLAGS = -lz -lm -lrt -Wl,-rpath-link,${MATLAB_DIR}/bin/glnxa64 -L${MATLAB_DIR}/bin/glnxa64 -lmex -lmat +LDFLAGS = -lz -lm -lrt +MFLAGS = -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DCOMMON_TIMING_OLD -DNOFILEIO -DMATLAB -I${MATLAB_DIR}/extern/include -largeArrayDims +CP = cp +LEX = flex +LN = ln +MKDIR = mkdir +MV = mv +RANLIB = ranlib +YACC = yacc Index: /issm/trunk-jpl-damage/externalpackages/scotch/gmap.m =================================================================== --- /issm/trunk-jpl-damage/externalpackages/scotch/gmap.m (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/scotch/gmap.m (revision 11330) @@ -0,0 +1,66 @@ +% +% function to call the gmap module of the scotch partitioner. +% +% [maptab]=gmap(adj_mat,vlist,vwgt,ewgt,atype,apar,... +% options) +% +% where the required input is: +% adj_mat (double [sparse nv x nv], vertex adjacency matrix) +% vlist (double [nv], vertex labels or []) +% vwgt (double [nv], vertex weights (integers) or []) +% ewgt (double [sparse nv x nv], edge weights (integers) or []) +% atype (character, architecture type) +% 'cmplt' complete graph +% 'cmpltw' weighted complete graph +% 'hcub' binary hypercube +% 'leaf' tree-leaf architecture +% 'mesh2d' bidimensional array +% 'mesh3d' tridimensional array +% 'torus2d' bidimensional array with wraparound edges +% 'torus3d' tridimensional array with wraparound edges +% apars (double, architecture params (corresponding to atype)) +% [size] cmplt +% [size load0 load1 ...] cmpltw +% [dim] hcub +% [height cluster weight] leaf +% [dimX dimY] mesh2d +% [dimX dimY dimZ] mesh3d +% [dimX dimY] torus2d +% [dimX dimY dimZ] torus3d +% +% the required output is: +% maptab (double [nv x 2], vertex labels and partitions) +% +% the optional input is: +% options (character, options to gmap) +% " -h : Display this help" +% " -m : Set mapping strategy (see user's manual)" +% " -s : Force unity weights on :" +% " e : edges" +% " v : vertices" +% " -V : Print program version and copyright" +% " -v : Set verbose mode to :" +% " m : mapping information" +% " s : strategy information" +% " t : timing information" +% "" +% "See default strategy with option '-vs'" +% +function [maptab]=gmap(adj_mat,vlist,vwgt,ewgt,atype,apars,... + varargin) + +if ~nargin + help gmap + return +end + +% gmap_mex uses static variables, so clear those out before every run +clear gmap_mex + +[maptab]=gmap_mex(adj_mat,vlist,vwgt,ewgt,atype,apars,... + varargin{:}); + +% doesn't hurt to clear out after every run, too +clear gmap_mex + +end Index: /issm/trunk-jpl-damage/externalpackages/scotch/gmap_mex.c =================================================================== --- /issm/trunk-jpl-damage/externalpackages/scotch/gmap_mex.c (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/scotch/gmap_mex.c (revision 11330) @@ -0,0 +1,286 @@ + +#define THISFUNCTION "Gmap" + +/* Gmap structures and prototypes */ + +#ifdef MATLAB + #include "mat.h" + #include "mex.h" + #include "matrix.h" + + #define printf mexPrintf + #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) + #define malloc mxMalloc + #define calloc mxCalloc + #define realloc mxRealloc + #define free mxFree + #define exit(status) mexErrMsgTxt("exit=" #status) +#endif + +void GmapUsage( void ); + + +int +gmapx ( + int (**pmaptabi)[2], + int argcm, + char *argvm[], + int nvi, + int ne2i, + int *ir, + int *jc, + int *vli, + int *vwi, + int *ewi, + char archtyp[], + int nai, + int *api); + +/******************************/ +/* */ +/* This is the main function. */ +/* */ +/******************************/ + +void mexFunction( int nlhs, + mxArray *plhs[], + int nrhs, + const mxArray *prhs[] ) +{ + int argcm; + char **argvm=NULL; + int nvert =0,nedge2=0,napar =0; + mwIndex *ir=NULL,*jc=NULL; + int *adjir=NULL,*adjjc=NULL; + double *vld=NULL,*vwd=NULL,*ewd=NULL,*apd=NULL; + int *vli=NULL,*vwi=NULL,*ewi=NULL,*api=NULL; + char *archtyp=NULL; + int (*maptabi)[2]=NULL; + double* maptabd=NULL; + int i,j,k,imi=0,imo=0,isi=0,ierr; + + /* Check for proper number of arguments */ + + if (nrhs == 0 && nlhs == 0) { + GmapUsage(); + return; + } + else if (nrhs < 6 || nlhs > 1) { + GmapUsage(); + mexErrMsgTxt(" "); + } + +/* load matlab argument list and convert to integer (note that converting here + and in the x-layer is inefficient, but it makes the x-layer more general) */ + + argvm = (char **) calloc(nrhs,sizeof(char *)); + + if (!(mxIsNumeric(prhs[imi]) && + (mxGetM(prhs[imi]) == 1 && mxGetN(prhs[imi]) == 1))) { + argvm[isi] = (char *) calloc(4+1,sizeof(char)); + strcpy(argvm[isi],"gmap"); + mexPrintf("%s -- Using \"%s\" entry point.\n", + THISFUNCTION,argvm[isi]); + isi++; + } + else { + argvm[isi] = (char *) calloc(5+1,sizeof(char)); + strcpy(argvm[isi],"gpart"); + mexPrintf("%s -- Using \"%s\" entry point.\n", + THISFUNCTION,argvm[isi]); + isi++; + + argvm[isi] = (char *) calloc(17,sizeof(char)); + sprintf(argvm[isi],"%d",(int)mxGetScalar(prhs[imi])); + mexPrintf("%s -- Number of parts is %s.\n", + THISFUNCTION,argvm[isi]); + isi++; + imi++; + } + + if (!mxIsNumeric(prhs[imi]) || (!mxIsEmpty(prhs[imi]) && !mxIsSparse(prhs[imi]))) { + mexPrintf("%s -- Adjacency matrix must be numeric and sparse.\n",THISFUNCTION); + mexErrMsgTxt(" "); + } + else { + nvert =mxGetM(prhs[imi]); + nedge2=mxGetNzmax(prhs[imi]); + if (mxGetNzmax(prhs[imi])) { + ir =mxGetIr(prhs[imi]); + adjir = (int *) malloc(mxGetNzmax(prhs[imi])*sizeof(int)); + for (i=0; i= 5) && + (strncmp (argvm[0] + strlen (argvm[0]) - 5, "gpart", 5) == 0))) { + if (!mxIsChar(prhs[imi])) { + mexPrintf("%s -- Architecture type must be character.\n",THISFUNCTION); + mexErrMsgTxt(" "); + } + else { + if (mxGetM(prhs[imi])*mxGetN(prhs[imi])) { + archtyp = (char *) calloc(mxGetM(prhs[imi])*mxGetN(prhs[imi])+1,sizeof(char)); + mxGetString(prhs[imi],archtyp,mxGetM(prhs[imi])*mxGetN(prhs[imi])+1); + } + mexPrintf("%s -- Architecture type is \"%s\".\n", + THISFUNCTION,archtyp); + } + imi++; + + if (!mxIsNumeric(prhs[imi])) { + mexPrintf("%s -- Architecture parameter vector must be numeric.\n",THISFUNCTION); + mexErrMsgTxt(" "); + } + else { + napar =mxGetM(prhs[imi])*mxGetN(prhs[imi]); + if (mxGetM(prhs[imi])*mxGetN(prhs[imi])) { + apd=mxGetPr(prhs[imi]); + api = (int *) malloc(mxGetM(prhs[imi])*mxGetN(prhs[imi])*sizeof(int)); + for (i=0; i=0; i--) + free(argvm[i]); + if (api) free(api); + if (archtyp) free(archtyp); + if (ewi) free(ewi); + if (vwi) free(vwi); + if (vli) free(vli); + if (adjjc) free(adjjc); + if (adjir) free(adjir); + + return; +} + +void GmapUsage( void ) +{ + + mexPrintf("\n"); + mexPrintf("Usage: [maptab]=Gmap_mex(adjmat,vertlb,vertwt,edgewt,archtyp,archpar,\n"); + mexPrintf(" Scotch-specific parameters);\n"); + mexPrintf("\n"); + + return; +} + Index: /issm/trunk-jpl-damage/externalpackages/scotch/gmapx.c =================================================================== --- /issm/trunk-jpl-damage/externalpackages/scotch/gmapx.c (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/scotch/gmapx.c (revision 11330) @@ -0,0 +1,385 @@ +/* Copyright 2004,2007,2008 ENSEIRB, INRIA & CNRS +** +** This file is part of the Scotch software package for static mapping, +** graph partitioning and sparse matrix ordering. +** +** This software is governed by the CeCILL-C license under French law +** and abiding by the rules of distribution of free software. You can +** use, modify and/or redistribute the software under the terms of the +** CeCILL-C license as circulated by CEA, CNRS and INRIA at the following +** URL: "http://www.cecill.info". +** +** As a counterpart to the access to the source code and rights to copy, +** modify and redistribute granted by the license, users are provided +** only with a limited warranty and the software's author, the holder of +** the economic rights, and the successive licensors have only limited +** liability. +** +** In this respect, the user's attention is drawn to the risks associated +** with loading, using, modifying and/or developing or reproducing the +** software by the user in light of its specific status of free software, +** that may mean that it is complicated to manipulate, and that also +** therefore means that it is reserved for developers and experienced +** professionals having in-depth computer knowledge. Users are therefore +** encouraged to load and test the software's suitability as regards +** their requirements in conditions enabling the security of their +** systems and/or data to be ensured and, more generally, to use and +** operate it in the same conditions as regards security. +** +** The fact that you are presently reading this means that you have had +** knowledge of the CeCILL-C license and that you accept its terms. +*/ +/************************************************************/ +/** **/ +/** NAME : gmap.c **/ +/** **/ +/** AUTHOR : Francois PELLEGRINI **/ +/** **/ +/** FUNCTION : Part of a graph mapping software. **/ +/** This module contains the main function. **/ +/** **/ +/** DATES : # Version 0.0 : from : 05 jan 1993 **/ +/** to 12 may 1993 **/ +/** # Version 1.1 : from : 15 oct 1993 **/ +/** to 15 oct 1993 **/ +/** # Version 1.3 : from : 06 apr 1994 **/ +/** to 18 may 1994 **/ +/** # Version 2.0 : from : 06 jun 1994 **/ +/** to 17 nov 1994 **/ +/** # Version 2.1 : from : 07 apr 1995 **/ +/** to 18 jun 1995 **/ +/** # Version 3.0 : from : 01 jul 1995 **/ +/** to 02 oct 1995 **/ +/** # Version 3.1 : from : 07 nov 1995 **/ +/** to 25 apr 1996 **/ +/** # Version 3.2 : from : 24 sep 1996 **/ +/** to 26 may 1998 **/ +/** # Version 3.3 : from : 19 oct 1998 **/ +/** to : 30 mar 1999 **/ +/** # Version 3.4 : from : 03 feb 2000 **/ +/** to : 03 feb 2000 **/ +/** # Version 4.0 : from : 16 jan 2004 **/ +/** to : 27 dec 2004 **/ +/** # Version 5.0 : from : 23 dec 2007 **/ +/** to : 18 jun 2008 **/ +/** **/ +/************************************************************/ + +/* +** The defines and includes. +*/ + +#define GMAP + +#include "module.h" +#include "common.h" +#include "scotch.h" +#include "gmap.h" + +/* +** The static variables. +*/ + +static int C_partNbr = 2; /* Default number of parts */ +static int C_paraNum = 0; /* Number of parameters */ +static int C_paraNbr = 0; /* No parameters for mapping */ +static int C_fileNum = 0; /* Number of file in arg list */ +static int C_fileNbr = 4; /* Number of files for mapping */ +static File C_fileTab[C_FILENBR] = { /* File array */ + { "-", NULL, "r" }, + { "-", NULL, "r" }, + { "-", NULL, "w" }, + { "-", NULL, "w" } }; + +static const char * C_usageList[] = { /* Usage */ + "gmap [ [ [ []]]] ", + "gpart [] [ [ []]] ", + " -h : Display this help", + " -m : Set mapping strategy (see user's manual)", + " -s : Force unity weights on :", + " e : edges", + " v : vertices", + " -V : Print program version and copyright", + " -v : Set verbose mode to :", + " m : mapping information", + " s : strategy information", + " t : timing information", + "", + "See default strategy with option '-vs'", + NULL }; + +/******************************/ +/* */ +/* This is the main function. */ +/* */ +/******************************/ + +int +gmapx ( + int (**pmaptabi)[2], + int argcm, + char *argvm[], + int nvi, + int ne2i, + int *ir, + int *jc, + int *vli, + int *vwi, + int *ewi, + char archtyp[], + int nai, + int *api) +{ + SCOTCH_Graph grafdat; /* Source graph */ + SCOTCH_Num grafflag; /* Source graph properties */ + SCOTCH_Arch archdat; /* Target architecture */ + SCOTCH_Strat stradat; /* Mapping strategy */ + SCOTCH_Mapping mapdat; /* Mapping data */ + Clock runtime[2]; /* Timing variables */ + SCOTCH_Num nvert =0; + SCOTCH_Num nedge2=0; + SCOTCH_Num* adjir =NULL; + SCOTCH_Num* adjjc =NULL; + SCOTCH_Num* vertlab=NULL; + SCOTCH_Num* vertwgt=NULL; + SCOTCH_Num* edgewgt=NULL; + SCOTCH_Num napar =0; + SCOTCH_Num* archpar=NULL; + SCOTCH_Num (*maptab)[2]=NULL; + int (*maptabi)[2]=NULL; + int flagval; + int i,j,k; + +/* reset static variables from previous runs (jes, 4/27/10) */ + + C_partNbr = 2; /* Default number of parts */ + C_paraNum = 0; /* Number of parameters */ + C_paraNbr = 0; /* No parameters for mapping */ + C_fileNum = 0; /* Number of file in arg list */ + C_fileNbr = 4; /* Number of files for mapping */ + for (i=0; i= 5) && (strncmp (argvm[0] + i - 5, "gpart", 5) == 0)) { + flagval |= C_FLAGPART; + C_paraNbr = 1; /* One more parameter */ + C_fileNbr = 3; /* One less file to provide */ + errorProg ("gpart"); + } + else + errorProg ("gmap"); + + intRandResetStatic (); + intRandInit (); + + if ((argcm >= 2) && (argvm[1][0] == '?')) { /* If need for help */ + usagePrint (stdout, C_usageList); + return (0); + } + + grafflag = 0; /* Use vertex and edge weights */ + SCOTCH_stratInit (&stradat); /* Set default mapping strategy */ + + for (i = 0; i < C_FILENBR; i ++) /* Set default stream pointers */ + C_fileTab[i].pntr = (C_fileTab[i].mode[0] == 'r') ? stdin : stdout; + for (i = 1; i < argcm; i ++) { /* Loop for all option codes */ + if ((argvm[i][0] != '-') || (argvm[i][1] == '\0') || (argvm[i][1] == '.')) { /* If found a file name */ + if (C_paraNum < C_paraNbr) { /* If number of parameters not reached */ + if ((C_partNbr = atoi (argvm[i])) < 1) /* Get the number of parts */ + errorPrint ("main: invalid number of parts (\"%s\")", argvm[i]); + C_paraNum ++; + continue; /* Process the other parameters */ + } + if (C_fileNum < C_fileNbr) /* A file name has been given */ + C_fileTab[C_fileNum ++].name = argvm[i]; + else + errorPrint ("main: too many file names given"); + } + else { /* If found an option name */ + switch (argvm[i][1]) { + case 'H' : /* Give the usage message */ + case 'h' : + usagePrint (stdout, C_usageList); + return (0); + case 'M' : + case 'm' : + SCOTCH_stratExit (&stradat); + SCOTCH_stratInit (&stradat); + SCOTCH_stratGraphMap (&stradat, &argvm[i][2]); + break; + case 'S' : + case 's' : /* Source graph parameters */ + for (j = 2; argvm[i][j] != '\0'; j ++) { + switch (argvm[i][j]) { + case 'E' : + case 'e' : + grafflag |= 2; /* Do not load edge weights */ + break; + case 'V' : + case 'v' : + grafflag |= 1; /* Do not load vertex weights */ + break; + default : + errorPrint ("main: invalid source graph option (\"%c\")", argvm[i][j]); + } + } + break; + case 'V' : + fprintf (stderr, "gmap/gpart, version %s - F. Pellegrini\n", SCOTCH_VERSION); + fprintf (stderr, "Copyright 2004,2007,2008 ENSEIRB, INRIA & CNRS, France\n"); + fprintf (stderr, "This software is libre/free software under CeCILL-C -- see the user's manual for more information\n"); + return (0); + case 'v' : /* Output control info */ + for (j = 2; argvm[i][j] != '\0'; j ++) { + switch (argvm[i][j]) { + case 'M' : + case 'm' : + flagval |= C_FLAGVERBMAP; + break; + case 'S' : + case 's' : + flagval |= C_FLAGVERBSTR; + break; + case 'T' : + case 't' : + flagval |= C_FLAGVERBTIM; + break; + default : + errorPrint ("main: unprocessed parameter \"%c\" in \"%s\"", argvm[i][j], argvm[i]); + } + } + break; + default : + errorPrint ("main: unprocessed option (\"%s\")", argvm[i]); + } + } + } + if ((flagval & C_FLAGPART) != 0) { /* If program run as the partitioner */ + C_fileTab[3].name = C_fileTab[2].name; /* Put provided file names at their right place */ + C_fileTab[2].name = C_fileTab[1].name; + C_fileTab[1].name = "-"; + } + + fileBlockOpen (C_fileTab, C_FILENBR); /* Open all files */ + + clockInit (&runtime[0]); + clockStart (&runtime[0]); + + SCOTCH_graphInit (&grafdat); /* Create graph structure */ + SCOTCH_graphLoad (&grafdat, C_filepntrsrcinp, -1, grafflag, nvert, nedge2, adjir, adjjc, vertlab, vertwgt, edgewgt); /* Read source graph */ + + SCOTCH_archInit (&archdat); /* Create architecture structure */ + if ((flagval & C_FLAGPART) != 0) /* If program run as the partitioner */ + SCOTCH_archCmplt (&archdat, C_partNbr); /* Create a complete graph of proper size */ + else + SCOTCH_archLoad (&archdat, C_filepntrtgtinp, archtyp, napar, archpar); /* Read target architecture */ + + clockStop (&runtime[0]); /* Get input time */ + clockInit (&runtime[1]); + clockStart (&runtime[1]); + + SCOTCH_graphMapInit (&grafdat, &mapdat, &archdat, NULL); + SCOTCH_graphMapCompute (&grafdat, &mapdat, &stradat); /* Perform mapping */ + + clockStop (&runtime[1]); /* Get computation time */ + clockStart (&runtime[0]); + + SCOTCH_graphMapSave (&nvert, &maptab, &grafdat, &mapdat, C_filepntrmapout); /* Write mapping */ + +/* convert output arguments from scotch data types */ + + if (maptab) { + *pmaptabi = (int (*)[2]) malloc(nvert*2*sizeof(int)); + maptabi = *pmaptabi; + for (j=0; j<2; j++) + for (i=0; i : Set mapping strategy (see user's manual)" +% " -s : Force unity weights on :" +% " e : edges" +% " v : vertices" +% " -V : Print program version and copyright" +% " -v : Set verbose mode to :" +% " m : mapping information" +% " s : strategy information" +% " t : timing information" +% "" +% "See default strategy with option '-vs'" +% +function [maptab]=gpart(npart,adj_mat,vlist,vwgt,ewgt,... + varargin) + +if ~nargin + help gpart + return +end + +% gmap_mex uses static variables, so clear those out before every run +clear gmap_mex + +[maptab]=gmap_mex(npart,adj_mat,vlist,vwgt,ewgt,... + varargin{:}); + +% doesn't hurt to clear out after every run, too +clear gmap_mex + +end Index: /issm/trunk-jpl-damage/externalpackages/scotch/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/scotch/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/scotch/install.sh (revision 11330) @@ -0,0 +1,51 @@ +#!/bin/bash + +# Some cleanup +rm -rf scotch_5.1 +rm -rf src +rm -rf install + +# Create src and install directories +mkdir src install + +# Untar +tar -xvzf scotch_5.1.6.tar.gz + +# Move scotch to src directory +mv scotch_5.1/* src +rm -rf scotch_5.1 + +# Apply patches (all at once, since many) +# (written by diff -rc old_src new_src > scotch.patch) +patch -p0 < scotch.patch + +# Build scotch +cp -p Makefile.inc src/src +cp -p gmap_mex.c src/src/scotch +cp -p gmapx.c src/src/scotch +cd src/src +# For stand-alone scotch modules: +make scotch +make clean +# For no-file-io scotch modules: +make nfioscotch +# Clean up +make clean +cd ../.. + +# Populate install directory +cp -pr src/grf install +cp -pr src/tgt install +cp -pr src/doc install +cp -pr src/man install +mkdir install/include +cp -p src/src/libscotch/module.h install/include/scotch_module.h +cp -p src/src/libscotch/common.h install/include/scotch_common.h +cp -p src/include/scotch.h install/include/ +cp -p src/src/scotch/gmap.h install/include/scotch_gmap.h +mkdir install/lib +mv src/lib/* install/lib +mkdir install/bin +mv src/bin/* install/bin +#cp -p gmap.m install/bin +#cp -p gpart.m install/bin Index: /issm/trunk-jpl-damage/externalpackages/scotch/mex/Gmap.c =================================================================== --- /issm/trunk-jpl-damage/externalpackages/scotch/mex/Gmap.c (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/scotch/mex/Gmap.c (revision 11330) @@ -0,0 +1,278 @@ + +#define THISFUNCTION "Gmap" + +/* Gmap structures and prototypes */ + +#include "mat.h" +#include "mex.h" +#include "matrix.h" + +void GmapUsage( void ); + + +int +Gmapx ( + int (**pmaptabi)[2], + int argcm, + char *argvm[], + int nvi, + int ne2i, + int *ir, + int *jc, + int *vli, + int *vwi, + int *ewi, + char archtyp[], + int nai, + int *api); + +/******************************/ +/* */ +/* This is the main function. */ +/* */ +/******************************/ + +void mexFunction( int nlhs, + mxArray *plhs[], + int nrhs, + const mxArray *prhs[] ) +{ + int argcm; + char **argvm=NULL; + int nvert =0,nedge2=0,napar =0; + mwIndex *ir=NULL,*jc=NULL; + int *adjir=NULL,*adjjc=NULL; + double *vld=NULL,*vwd=NULL,*ewd=NULL,*apd=NULL; + int *vli=NULL,*vwi=NULL,*ewi=NULL,*api=NULL; + char *archtyp=NULL; + int (*maptabi)[2]=NULL; + double* maptabd=NULL; + int i,j,k,imi=0,imo=0,isi=0,ierr; + + /* Check for proper number of arguments */ + + if (nrhs == 0 && nlhs == 0) { + GmapUsage(); + return; + } + else if (nrhs < 6 || nlhs > 1) { + GmapUsage(); + mexErrMsgTxt(" "); + } + +/* load matlab argument list and convert to integer (note that converting here + and in the x-layer is inefficient, but it makes the x-layer more general) */ + + argvm = (char **) calloc(nrhs,sizeof(char *)); + + if (!(mxIsNumeric(prhs[imi]) && + (mxGetM(prhs[imi]) == 1 && mxGetN(prhs[imi]) == 1))) { + argvm[isi] = (char *) calloc(4+1,sizeof(char)); + strcpy(argvm[isi],"Gmap"); + mexPrintf("%s -- Using \"%s\" entry point.\n", + THISFUNCTION,argvm[isi]); + isi++; + } + else { + argvm[isi] = (char *) calloc(5+1,sizeof(char)); + strcpy(argvm[isi],"Gpart"); + mexPrintf("%s -- Using \"%s\" entry point.\n", + THISFUNCTION,argvm[isi]); + isi++; + + argvm[isi] = (char *) calloc(17,sizeof(char)); + sprintf(argvm[isi],"%d",(int)mxGetScalar(prhs[imi])); + mexPrintf("%s -- Number of parts is %s.\n", + THISFUNCTION,argvm[isi]); + isi++; + imi++; + } + + if (!mxIsNumeric(prhs[imi]) || (!mxIsEmpty(prhs[imi]) && !mxIsSparse(prhs[imi]))) { + mexPrintf("%s -- Adjacency matrix must be numeric and sparse.\n",THISFUNCTION); + mexErrMsgTxt(" "); + } + else { + nvert =mxGetM(prhs[imi]); + nedge2=mxGetNzmax(prhs[imi]); + if (mxGetNzmax(prhs[imi])) { + ir =mxGetIr(prhs[imi]); + adjir = (int *) malloc(mxGetNzmax(prhs[imi])*sizeof(int)); + for (i=0; i= 5) && + (strncmp (argvm[0] + strlen (argvm[0]) - 5, "Gpart", 5) == 0))) { + if (!mxIsChar(prhs[imi])) { + mexPrintf("%s -- Architecture type must be character.\n",THISFUNCTION); + mexErrMsgTxt(" "); + } + else { + if (mxGetM(prhs[imi])*mxGetN(prhs[imi])) { + archtyp = (char *) calloc(mxGetM(prhs[imi])*mxGetN(prhs[imi])+1,sizeof(char)); + mxGetString(prhs[imi],archtyp,mxGetM(prhs[imi])*mxGetN(prhs[imi])+1); + } + mexPrintf("%s -- Architecture type is \"%s\".\n", + THISFUNCTION,archtyp); + } + imi++; + + if (!mxIsNumeric(prhs[imi])) { + mexPrintf("%s -- Architecture parameter vector must be numeric.\n",THISFUNCTION); + mexErrMsgTxt(" "); + } + else { + napar =mxGetM(prhs[imi])*mxGetN(prhs[imi]); + if (mxGetM(prhs[imi])*mxGetN(prhs[imi])) { + apd=mxGetPr(prhs[imi]); + api = (int *) malloc(mxGetM(prhs[imi])*mxGetN(prhs[imi])*sizeof(int)); + for (i=0; i=0; i--) + free(argvm[i]); + free(argvm); + } + + return; +} + +void GmapUsage( void ) +{ + + mexPrintf("\n"); + mexPrintf("Usage: [maptab]=Gmap(adjmat,vertlb,vertwt,edgewt,archtyp,archpar,\n"); + mexPrintf(" Scotch-specific parameters);\n"); + mexPrintf("\n"); + + return; +} + Index: /issm/trunk-jpl-damage/externalpackages/scotch/mex/Gmapx.c =================================================================== --- /issm/trunk-jpl-damage/externalpackages/scotch/mex/Gmapx.c (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/scotch/mex/Gmapx.c (revision 11330) @@ -0,0 +1,385 @@ +/* Copyright 2004,2007,2008 ENSEIRB, INRIA & CNRS +** +** This file is part of the Scotch software package for static mapping, +** graph partitioning and sparse matrix ordering. +** +** This software is governed by the CeCILL-C license under French law +** and abiding by the rules of distribution of free software. You can +** use, modify and/or redistribute the software under the terms of the +** CeCILL-C license as circulated by CEA, CNRS and INRIA at the following +** URL: "http://www.cecill.info". +** +** As a counterpart to the access to the source code and rights to copy, +** modify and redistribute granted by the license, users are provided +** only with a limited warranty and the software's author, the holder of +** the economic rights, and the successive licensors have only limited +** liability. +** +** In this respect, the user's attention is drawn to the risks associated +** with loading, using, modifying and/or developing or reproducing the +** software by the user in light of its specific status of free software, +** that may mean that it is complicated to manipulate, and that also +** therefore means that it is reserved for developers and experienced +** professionals having in-depth computer knowledge. Users are therefore +** encouraged to load and test the software's suitability as regards +** their requirements in conditions enabling the security of their +** systems and/or data to be ensured and, more generally, to use and +** operate it in the same conditions as regards security. +** +** The fact that you are presently reading this means that you have had +** knowledge of the CeCILL-C license and that you accept its terms. +*/ +/************************************************************/ +/** **/ +/** NAME : gmap.c **/ +/** **/ +/** AUTHOR : Francois PELLEGRINI **/ +/** **/ +/** FUNCTION : Part of a graph mapping software. **/ +/** This module contains the main function. **/ +/** **/ +/** DATES : # Version 0.0 : from : 05 jan 1993 **/ +/** to 12 may 1993 **/ +/** # Version 1.1 : from : 15 oct 1993 **/ +/** to 15 oct 1993 **/ +/** # Version 1.3 : from : 06 apr 1994 **/ +/** to 18 may 1994 **/ +/** # Version 2.0 : from : 06 jun 1994 **/ +/** to 17 nov 1994 **/ +/** # Version 2.1 : from : 07 apr 1995 **/ +/** to 18 jun 1995 **/ +/** # Version 3.0 : from : 01 jul 1995 **/ +/** to 02 oct 1995 **/ +/** # Version 3.1 : from : 07 nov 1995 **/ +/** to 25 apr 1996 **/ +/** # Version 3.2 : from : 24 sep 1996 **/ +/** to 26 may 1998 **/ +/** # Version 3.3 : from : 19 oct 1998 **/ +/** to : 30 mar 1999 **/ +/** # Version 3.4 : from : 03 feb 2000 **/ +/** to : 03 feb 2000 **/ +/** # Version 4.0 : from : 16 jan 2004 **/ +/** to : 27 dec 2004 **/ +/** # Version 5.0 : from : 23 dec 2007 **/ +/** to : 18 jun 2008 **/ +/** **/ +/************************************************************/ + +/* +** The defines and includes. +*/ + +#define GMAP + +#include "module.h" +#include "common.h" +#include "scotch.h" +#include "gmap.h" + +/* +** The static variables. +*/ + +static int C_partNbr = 2; /* Default number of parts */ +static int C_paraNum = 0; /* Number of parameters */ +static int C_paraNbr = 0; /* No parameters for mapping */ +static int C_fileNum = 0; /* Number of file in arg list */ +static int C_fileNbr = 4; /* Number of files for mapping */ +static File C_fileTab[C_FILENBR] = { /* File array */ + { "-", NULL, "r" }, + { "-", NULL, "r" }, + { "-", NULL, "w" }, + { "-", NULL, "w" } }; + +static const char * C_usageList[] = { /* Usage */ + "gmap [ [ [ []]]] ", + "gpart [] [ [ []]] ", + " -h : Display this help", + " -m : Set mapping strategy (see user's manual)", + " -s : Force unity weights on :", + " e : edges", + " v : vertices", + " -V : Print program version and copyright", + " -v : Set verbose mode to :", + " m : mapping information", + " s : strategy information", + " t : timing information", + "", + "See default strategy with option '-vs'", + NULL }; + +/******************************/ +/* */ +/* This is the main function. */ +/* */ +/******************************/ + +int +Gmapx ( + int (**pmaptabi)[2], + int argcm, + char *argvm[], + int nvi, + int ne2i, + int *ir, + int *jc, + int *vli, + int *vwi, + int *ewi, + char archtyp[], + int nai, + int *api) +{ + SCOTCH_Graph grafdat; /* Source graph */ + SCOTCH_Num grafflag; /* Source graph properties */ + SCOTCH_Arch archdat; /* Target architecture */ + SCOTCH_Strat stradat; /* Mapping strategy */ + SCOTCH_Mapping mapdat; /* Mapping data */ + Clock runtime[2]; /* Timing variables */ + SCOTCH_Num nvert =0; + SCOTCH_Num nedge2=0; + SCOTCH_Num* adjir =NULL; + SCOTCH_Num* adjjc =NULL; + SCOTCH_Num* vertlab=NULL; + SCOTCH_Num* vertwgt=NULL; + SCOTCH_Num* edgewgt=NULL; + SCOTCH_Num napar =0; + SCOTCH_Num* archpar=NULL; + SCOTCH_Num (*maptab)[2]=NULL; + int (*maptabi)[2]=NULL; + int flagval; + int i,j,k; + +/* reset static variables from previous runs (jes, 4/27/10) */ + + C_partNbr = 2; /* Default number of parts */ + C_paraNum = 0; /* Number of parameters */ + C_paraNbr = 0; /* No parameters for mapping */ + C_fileNum = 0; /* Number of file in arg list */ + C_fileNbr = 4; /* Number of files for mapping */ + for (i=0; i= 5) && (strncmp (argvm[0] + i - 5, "Gpart", 5) == 0)) { + flagval |= C_FLAGPART; + C_paraNbr = 1; /* One more parameter */ + C_fileNbr = 3; /* One less file to provide */ + errorProg ("Gpart"); + } + else + errorProg ("Gmap"); + + intRandResetStatic (); + intRandInit (); + + if ((argcm >= 2) && (argvm[1][0] == '?')) { /* If need for help */ + usagePrint (stdout, C_usageList); + return (0); + } + + grafflag = 0; /* Use vertex and edge weights */ + SCOTCH_stratInit (&stradat); /* Set default mapping strategy */ + + for (i = 0; i < C_FILENBR; i ++) /* Set default stream pointers */ + C_fileTab[i].pntr = (C_fileTab[i].mode[0] == 'r') ? stdin : stdout; + for (i = 1; i < argcm; i ++) { /* Loop for all option codes */ + if ((argvm[i][0] != '-') || (argvm[i][1] == '\0') || (argvm[i][1] == '.')) { /* If found a file name */ + if (C_paraNum < C_paraNbr) { /* If number of parameters not reached */ + if ((C_partNbr = atoi (argvm[i])) < 1) /* Get the number of parts */ + errorPrint ("main: invalid number of parts (\"%s\")", argvm[i]); + C_paraNum ++; + continue; /* Process the other parameters */ + } + if (C_fileNum < C_fileNbr) /* A file name has been given */ + C_fileTab[C_fileNum ++].name = argvm[i]; + else + errorPrint ("main: too many file names given"); + } + else { /* If found an option name */ + switch (argvm[i][1]) { + case 'H' : /* Give the usage message */ + case 'h' : + usagePrint (stdout, C_usageList); + return (0); + case 'M' : + case 'm' : + SCOTCH_stratExit (&stradat); + SCOTCH_stratInit (&stradat); + SCOTCH_stratGraphMap (&stradat, &argvm[i][2]); + break; + case 'S' : + case 's' : /* Source graph parameters */ + for (j = 2; argvm[i][j] != '\0'; j ++) { + switch (argvm[i][j]) { + case 'E' : + case 'e' : + grafflag |= 2; /* Do not load edge weights */ + break; + case 'V' : + case 'v' : + grafflag |= 1; /* Do not load vertex weights */ + break; + default : + errorPrint ("main: invalid source graph option (\"%c\")", argvm[i][j]); + } + } + break; + case 'V' : + fprintf (stderr, "Gmap/Gpart, version %s - F. Pellegrini\n", SCOTCH_VERSION); + fprintf (stderr, "Copyright 2004,2007,2008 ENSEIRB, INRIA & CNRS, France\n"); + fprintf (stderr, "This software is libre/free software under CeCILL-C -- see the user's manual for more information\n"); + return (0); + case 'v' : /* Output control info */ + for (j = 2; argvm[i][j] != '\0'; j ++) { + switch (argvm[i][j]) { + case 'M' : + case 'm' : + flagval |= C_FLAGVERBMAP; + break; + case 'S' : + case 's' : + flagval |= C_FLAGVERBSTR; + break; + case 'T' : + case 't' : + flagval |= C_FLAGVERBTIM; + break; + default : + errorPrint ("main: unprocessed parameter \"%c\" in \"%s\"", argvm[i][j], argvm[i]); + } + } + break; + default : + errorPrint ("main: unprocessed option (\"%s\")", argvm[i]); + } + } + } + if ((flagval & C_FLAGPART) != 0) { /* If program run as the partitioner */ + C_fileTab[3].name = C_fileTab[2].name; /* Put provided file names at their right place */ + C_fileTab[2].name = C_fileTab[1].name; + C_fileTab[1].name = "-"; + } + + fileBlockOpen (C_fileTab, C_FILENBR); /* Open all files */ + + clockInit (&runtime[0]); + clockStart (&runtime[0]); + + SCOTCH_graphInit (&grafdat); /* Create graph structure */ + SCOTCH_graphLoad (&grafdat, C_filepntrsrcinp, -1, grafflag, nvert, nedge2, adjir, adjjc, vertlab, vertwgt, edgewgt); /* Read source graph */ + + SCOTCH_archInit (&archdat); /* Create architecture structure */ + if ((flagval & C_FLAGPART) != 0) /* If program run as the partitioner */ + SCOTCH_archCmplt (&archdat, C_partNbr); /* Create a complete graph of proper size */ + else + SCOTCH_archLoad (&archdat, C_filepntrtgtinp, archtyp, napar, archpar); /* Read target architecture */ + + clockStop (&runtime[0]); /* Get input time */ + clockInit (&runtime[1]); + clockStart (&runtime[1]); + + SCOTCH_graphMapInit (&grafdat, &mapdat, &archdat, NULL); + SCOTCH_graphMapCompute (&grafdat, &mapdat, &stradat); /* Perform mapping */ + + clockStop (&runtime[1]); /* Get computation time */ + clockStart (&runtime[0]); + + SCOTCH_graphMapSave (&nvert, &maptab, &grafdat, &mapdat, C_filepntrmapout); /* Write mapping */ + +/* convert output arguments from scotch data types */ + + if (maptab) { + *pmaptabi = (int (*)[2]) malloc(nvert*2*sizeof(int)); + maptabi = *pmaptabi; + for (j=0; j<2; j++) + for (i=0; i +#include /* strcasecmp */ +#include /* clock,time,difftime */ +#include "mex.h" + + +/* Input Arguments */ + +#define IR_IN prhs[0] +#define JC_IN prhs[1] +#define PR_IN prhs[2] +#define M_IN prhs[3] +#define N_IN prhs[4] + +/* Output Arguments */ + +#define A_OUT plhs[0] + + +void VectorToSparseUsage( void ); + + +void mexFunction( int nlhs, + mxArray *plhs[], + int nrhs, + const mxArray *prhs[] ) +{ + int min,nin; + mwIndex *ir =NULL,*jc =NULL; + double *ird=NULL,*jcd=NULL,*pr=NULL,*prd=NULL; + int i,mrow; + + /* Check for proper number of arguments */ + + if (nrhs == 0 && nlhs == 0) { + VectorToSparseUsage(); + return; + } + else if (nrhs < 2 || nlhs != 1) { + VectorToSparseUsage(); + mexErrMsgTxt(" "); + } + + /* Create matrices for the return arguments */ + + if (!mxIsNumeric(IR_IN) || !mxIsNumeric(JC_IN)) { + mexPrintf("%s -- Input matrices IR and JC must be numeric.\n",THISFUNCTION); + mexErrMsgTxt(" "); + } + + mrow = 0; + ird = mxGetPr(IR_IN); + for (i=0; i mrow) + mrow=(int)ird[i]+1; + + if (nrhs >= 4 && mxIsNumeric(M_IN) && !mxIsEmpty(M_IN)) + min = mxGetScalar(M_IN); + else { + min = mrow; + } + + if (mrow > min) { + mexPrintf("%s -- Number of rows specified by M (%d) and IR (%d) is inconsistent.\n", + THISFUNCTION,min,mrow); + mexErrMsgTxt(" "); + } + + if (nrhs >= 5 && mxIsNumeric(N_IN) && !mxIsEmpty(N_IN)) + nin = mxGetScalar(N_IN); + else + nin = mxGetM(JC_IN)*mxGetN(JC_IN)-1; + + if (mxGetM(JC_IN)*mxGetN(JC_IN)-1 != nin) { + mexPrintf("%s -- Number of columns specified by N (%d) and JC (%d) is inconsistent.\n", + THISFUNCTION,nin,mxGetM(JC_IN)*mxGetN(JC_IN)-1); + mexErrMsgTxt(" "); + } + + A_OUT = mxCreateSparse(min, nin, mxGetM(IR_IN)*mxGetN(IR_IN), mxREAL); + if (mxGetM(IR_IN)*mxGetN(IR_IN)) { + ird = mxGetPr(IR_IN); + ir = mxGetIr(A_OUT); + for (i=0; i= 3 && mxIsNumeric(PR_IN) && !mxIsEmpty(PR_IN)) { + if (mxGetM(PR_IN)*mxGetN(PR_IN) != mxGetM(IR_IN)*mxGetN(IR_IN)) { + mexPrintf("%s -- Number of terms specified by IR (%d) and PR (%d) is inconsistent.\n", + THISFUNCTION,mxGetM(IR_IN)*mxGetN(IR_IN),mxGetM(PR_IN)*mxGetN(PR_IN)); + mexErrMsgTxt(" "); + } + + if (mxGetM(PR_IN)*mxGetN(PR_IN)) { + prd = mxGetPr(PR_IN); + pr = mxGetPr(A_OUT); + for (i=0; iarchLoad != NULL) { /* If class has loading function */ ++ #ifndef NOFILEIO + if (class->archLoad (&archptr->data, stream) != 0) { /* Load class data */ ++ #else /* NOFILEIO */ ++ if (class->archLoad (&archptr->data, stream, napar, archpar) != 0) { /* Load class data */ ++ #endif /* NOFILEIO */ + errorPrint ("archLoad: cannot load architecture data"); + memset (archptr, 0, sizeof (Arch)); /* Initialize architecture body */ + return (1); +diff -rc src/src/libscotch/arch_cmplt.c new5/src/libscotch/arch_cmplt.c +*** src/src/libscotch/arch_cmplt.c 2008-05-22 06:44:41.000000000 -0700 +--- new5/src/libscotch/arch_cmplt.c 2010-07-21 17:13:15.585257133 -0700 +*************** +*** 90,99 **** + int + archCmpltArchLoad ( + ArchCmplt * restrict const archptr, +! FILE * restrict const stream) + { + long numnbr; + + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchCmplt) > sizeof (ArchDummy)) || + (sizeof (ArchCmpltDom) > sizeof (ArchDomDummy))) { +--- 90,109 ---- + int + archCmpltArchLoad ( + ArchCmplt * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) + { + long numnbr; + ++ #ifdef NOFILEIO ++ // printf("archCmpltArchLoad - napar=%d,archpar=%p\n",napar,archpar); ++ #endif /* NOFILEIO */ ++ + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchCmplt) > sizeof (ArchDummy)) || + (sizeof (ArchCmpltDom) > sizeof (ArchDomDummy))) { +*************** +*** 102,109 **** +--- 112,124 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((fscanf (stream, "%ld", &numnbr) != 1) || + (numnbr < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 1) || ++ ((numnbr=(long)archpar[0]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archCmpltArchLoad: bad input"); + return (1); + } +diff -rc src/src/libscotch/arch_cmplt.h new5/src/libscotch/arch_cmplt.h +*** src/src/libscotch/arch_cmplt.h 2008-05-22 06:44:41.000000000 -0700 +--- new5/src/libscotch/arch_cmplt.h 2010-07-21 17:13:15.588257154 -0700 +*************** +*** 87,93 **** +--- 87,97 ---- + #define static + #endif + ++ #ifndef NOFILEIO + int archCmpltArchLoad (ArchCmplt * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archCmpltArchLoad (ArchCmplt * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archCmpltArchSave (const ArchCmplt * const, FILE * restrict const); + #define archCmpltArchFree NULL + ArchDomNum archCmpltDomNum (const ArchCmplt * const, const ArchCmpltDom * const); +diff -rc src/src/libscotch/arch_cmpltw.c new5/src/libscotch/arch_cmpltw.c +*** src/src/libscotch/arch_cmpltw.c 2008-08-27 14:22:22.000000000 -0700 +--- new5/src/libscotch/arch_cmpltw.c 2010-07-21 17:13:15.590257168 -0700 +*************** +*** 200,211 **** + int + archCmpltwArchLoad ( + ArchCmpltw * restrict const archptr, +! FILE * restrict const stream) + { + long vertnbr; + Gnum velosum; + Anum vertnum; + + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchCmpltw) > sizeof (ArchDummy)) || + (sizeof (ArchCmpltwDom) > sizeof (ArchDomDummy))) { +--- 200,221 ---- + int + archCmpltwArchLoad ( + ArchCmpltw * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) + { + long vertnbr; + Gnum velosum; + Anum vertnum; + ++ #ifdef NOFILEIO ++ // printf("archCmpltwArchLoad - napar=%d,archpar=%p\n",napar,archpar); ++ #endif /* NOFILEIO */ ++ + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchCmpltw) > sizeof (ArchDummy)) || + (sizeof (ArchCmpltwDom) > sizeof (ArchDomDummy))) { +*************** +*** 214,221 **** +--- 224,236 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((fscanf (stream, "%ld", &vertnbr) != 1) || + (vertnbr < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 1) || ++ ((vertnbr=(long)archpar[0]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archCmpltwArchLoad: bad input (1)"); + return (1); + } +*************** +*** 230,237 **** +--- 245,257 ---- + long veloval; + Gnum velotmp; + ++ #ifndef NOFILEIO + if ((fscanf (stream, "%ld", &veloval) != 1) || + (veloval < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 1+(vertnum+1)) || ++ ((veloval=(long)archpar[1+(vertnum+1)]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archCmpltwArchLoad: bad input (2)"); + return (1); + } +diff -rc src/src/libscotch/arch_cmpltw.h new5/src/libscotch/arch_cmpltw.h +*** src/src/libscotch/arch_cmpltw.h 2008-05-22 06:44:41.000000000 -0700 +--- new5/src/libscotch/arch_cmpltw.h 2010-07-21 17:13:15.592257181 -0700 +*************** +*** 86,92 **** +--- 86,96 ---- + #endif + + int archCmpltwArchBuild (ArchCmpltw * restrict const archptr, const Gnum, const Gnum * restrict const); ++ #ifndef NOFILEIO + int archCmpltwArchLoad (ArchCmpltw * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archCmpltwArchLoad (ArchCmpltw * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archCmpltwArchSave (const ArchCmpltw * const, FILE * restrict const); + int archCmpltwArchFree (ArchCmpltw * restrict const); + ArchDomNum archCmpltwDomNum (const ArchCmpltw * const, const ArchCmpltwDom * const); +diff -rc src/src/libscotch/arch_deco.c new5/src/libscotch/arch_deco.c +*** src/src/libscotch/arch_deco.c 2008-09-28 06:35:27.000000000 -0700 +--- new5/src/libscotch/arch_deco.c 2010-07-21 17:13:15.595257202 -0700 +*************** +*** 211,217 **** + int + archDecoArchLoad ( + ArchDeco * restrict const archptr, +! FILE * restrict const stream) + { + INT decotype; /* Type of decomposition */ + INT termdomnbr; /* Number of terminal domains (ie processors) */ +--- 211,223 ---- + int + archDecoArchLoad ( + ArchDeco * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) + { + INT decotype; /* Type of decomposition */ + INT termdomnbr; /* Number of terminal domains (ie processors) */ +*************** +*** 220,225 **** +--- 226,237 ---- + Anum * restrict termdisttab; /* Table of terminal-to-terminal distances */ + INT i, j; + ++ #ifdef NOFILEIO ++ // printf("archDecoArchLoad - napar=%d,archpar=%p\n",napar,archpar); ++ errorPrint ("archDecoArchLoad - not yet converted to matlab matrices"); ++ return (1); ++ #endif /* NOFILEIO */ ++ + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchDeco) > sizeof (ArchDummy)) || + (sizeof (ArchDecoDom) > sizeof (ArchDomDummy))) { +diff -rc src/src/libscotch/arch_deco.h new5/src/libscotch/arch_deco.h +*** src/src/libscotch/arch_deco.h 2008-09-27 07:49:46.000000000 -0700 +--- new5/src/libscotch/arch_deco.h 2010-07-21 17:13:15.597257216 -0700 +*************** +*** 113,119 **** +--- 113,123 ---- + #endif + + int archDecoArchBuild (ArchDeco * const, const Anum, const Anum, const ArchDecoTermVert * const, const Anum * const); ++ #ifndef NOFILEIO + int archDecoArchLoad (ArchDeco * const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archDecoArchLoad (ArchDeco * const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archDecoArchSave (const ArchDeco * const, FILE * restrict const); + int archDecoArchFree (ArchDeco * const); + Anum archDecoArchSize (ArchDeco * const, const Anum); +diff -rc src/src/libscotch/arch.h new5/src/libscotch/arch.h +*** src/src/libscotch/arch.h 2009-04-28 08:11:27.000000000 -0700 +--- new5/src/libscotch/arch.h 2010-07-21 17:13:15.600257237 -0700 +*************** +*** 175,181 **** +--- 175,185 ---- + int archInit (Arch * restrict const); + int archExit (Arch * restrict const); + int archFree (Arch * restrict const); ++ #ifndef NOFILEIO + int archLoad (Arch * restrict const, FILE * const); ++ #else /* NOFILEIO */ ++ int archLoad (Arch * restrict const, FILE * const, const char *, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archSave (const Arch * const, FILE * const); + char * archName (const Arch * const); + const ArchClass * archClass (const char * const); +diff -rc src/src/libscotch/arch_hcub.c new5/src/libscotch/arch_hcub.c +*** src/src/libscotch/arch_hcub.c 2008-05-22 06:44:41.000000000 -0700 +--- new5/src/libscotch/arch_hcub.c 2010-07-21 17:13:15.602257251 -0700 +*************** +*** 88,95 **** + int + archHcubArchLoad ( + ArchHcub * restrict const archptr, +! FILE * restrict const stream) +! { + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchHcub) > sizeof (ArchDummy)) || + (sizeof (ArchHcubDom) > sizeof (ArchDomDummy))) { +--- 88,105 ---- + int + archHcubArchLoad ( + ArchHcub * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) +! { +! #ifdef NOFILEIO +! // printf("archHcubArchLoad - napar=%d,archpar=%p\n",napar,archpar); +! #endif /* NOFILEIO */ +! + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchHcub) > sizeof (ArchDummy)) || + (sizeof (ArchHcubDom) > sizeof (ArchDomDummy))) { +*************** +*** 98,105 **** +--- 108,120 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((intLoad (stream, &archptr->dimmax) != 1) || + (archptr->dimmax < 1) || ++ #else /* NOFILEIO */ ++ if ((napar < 1) || ++ ((archptr->dimmax=archpar[0]) < 1) || ++ #endif /* NOFILEIO */ + (archptr->dimmax > (sizeof (archptr->dimmax) << 3))) { + errorPrint ("archHcubArchLoad: bad input"); + return (1); +diff -rc src/src/libscotch/arch_hcub.h new5/src/libscotch/arch_hcub.h +*** src/src/libscotch/arch_hcub.h 2008-05-22 06:44:41.000000000 -0700 +--- new5/src/libscotch/arch_hcub.h 2010-07-21 17:13:15.604257265 -0700 +*************** +*** 85,91 **** +--- 85,95 ---- + #define static + #endif + ++ #ifndef NOFILEIO + int archHcubArchLoad (ArchHcub * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archHcubArchLoad (ArchHcub * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archHcubArchSave (const ArchHcub * const, FILE * restrict const); + #define archHcubArchFree NULL + ArchDomNum archHcubDomNum (const ArchHcub * const, const ArchHcubDom * const); +diff -rc src/src/libscotch/arch_mesh.c new5/src/libscotch/arch_mesh.c +*** src/src/libscotch/arch_mesh.c 2008-05-22 06:44:41.000000000 -0700 +--- new5/src/libscotch/arch_mesh.c 2010-07-21 17:13:15.607257286 -0700 +*************** +*** 96,103 **** + int + archMesh2ArchLoad ( + ArchMesh2 * restrict const archptr, +! FILE * restrict const stream) +! { + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchMesh2) > sizeof (ArchDummy)) || + (sizeof (ArchMesh2Dom) > sizeof (ArchDomDummy))) { +--- 96,113 ---- + int + archMesh2ArchLoad ( + ArchMesh2 * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) +! { +! #ifdef NOFILEIO +! // printf("archMesh2ArchLoad - napar=%d,archpar=%p\n",napar,archpar); +! #endif /* NOFILEIO */ +! + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchMesh2) > sizeof (ArchDummy)) || + (sizeof (ArchMesh2Dom) > sizeof (ArchDomDummy))) { +*************** +*** 106,114 **** +--- 116,130 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((intLoad (stream, &archptr->c[0]) != 1) || + (intLoad (stream, &archptr->c[1]) != 1) || + (archptr->c[0] < 1) || (archptr->c[1] < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 2) || ++ ((archptr->c[0]=archpar[0]) < 1) || ++ ((archptr->c[1]=archpar[1]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archMesh2ArchLoad: bad input"); + return (1); + } +*************** +*** 421,428 **** + int + archMesh3ArchLoad ( + ArchMesh3 * restrict const archptr, +! FILE * restrict const stream) +! { + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchMesh3) > sizeof (ArchDummy)) || + (sizeof (ArchMesh3Dom) > sizeof (ArchDomDummy))) { +--- 437,454 ---- + int + archMesh3ArchLoad ( + ArchMesh3 * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) +! { +! #ifdef NOFILEIO +! // printf("archMesh3ArchLoad - napar=%d,archpar=%p\n",napar,archpar); +! #endif /* NOFILEIO */ +! + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchMesh3) > sizeof (ArchDummy)) || + (sizeof (ArchMesh3Dom) > sizeof (ArchDomDummy))) { +*************** +*** 431,440 **** +--- 457,473 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((intLoad (stream, &archptr->c[0]) != 1) || + (intLoad (stream, &archptr->c[1]) != 1) || + (intLoad (stream, &archptr->c[2]) != 1) || + (archptr->c[0] < 1) || (archptr->c[1] < 1) || (archptr->c[2] < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 3) || ++ ((archptr->c[0]=archpar[0]) < 1) || ++ ((archptr->c[1]=archpar[1]) < 1) || ++ ((archptr->c[2]=archpar[2]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archMesh3ArchLoad: bad input"); + return (1); + } +diff -rc src/src/libscotch/arch_mesh.h new5/src/libscotch/arch_mesh.h +*** src/src/libscotch/arch_mesh.h 2008-05-22 06:44:41.000000000 -0700 +--- new5/src/libscotch/arch_mesh.h 2010-07-21 17:13:15.610257307 -0700 +*************** +*** 96,102 **** +--- 96,106 ---- + #define static + #endif + ++ #ifndef NOFILEIO + int archMesh2ArchLoad (ArchMesh2 * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archMesh2ArchLoad (ArchMesh2 * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archMesh2ArchSave (const ArchMesh2 * const, FILE * restrict const); + #define archMesh2ArchFree NULL + ArchDomNum archMesh2DomNum (const ArchMesh2 * const, const ArchMesh2Dom * const); +*************** +*** 114,120 **** +--- 118,128 ---- + int archMesh2DomMpiType (const ArchMesh2 * const, MPI_Datatype * const); + #endif /* SCOTCH_PTSCOTCH */ + ++ #ifndef NOFILEIO + int archMesh3ArchLoad (ArchMesh3 * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archMesh3ArchLoad (ArchMesh3 * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archMesh3ArchSave (const ArchMesh3 * const, FILE * restrict const); + #define archMesh3ArchFree NULL + ArchDomNum archMesh3DomNum (const ArchMesh3 * const, const ArchMesh3Dom * const); +diff -rc src/src/libscotch/arch_tleaf.c new5/src/libscotch/arch_tleaf.c +*** src/src/libscotch/arch_tleaf.c 2008-05-22 06:44:41.000000000 -0700 +--- new5/src/libscotch/arch_tleaf.c 2010-07-21 17:13:15.612257320 -0700 +*************** +*** 92,99 **** + int + archTleafArchLoad ( + ArchTleaf * restrict const archptr, +! FILE * restrict const stream) +! { + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchTleaf) > sizeof (ArchDummy)) || + (sizeof (ArchTleafDom) > sizeof (ArchDomDummy))) { +--- 92,109 ---- + int + archTleafArchLoad ( + ArchTleaf * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) +! { +! #ifdef NOFILEIO +! // printf("archTleafArchLoad - napar=%d,archpar=%p\n",napar,archpar); +! #endif /* NOFILEIO */ +! + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchTleaf) > sizeof (ArchDummy)) || + (sizeof (ArchTleafDom) > sizeof (ArchDomDummy))) { +*************** +*** 102,107 **** +--- 112,118 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((intLoad (stream, &archptr->leafdep) != 1) || + (intLoad (stream, &archptr->clusdep) != 1) || + (intLoad (stream, &archptr->linkval) != 1) || +*************** +*** 109,114 **** +--- 120,132 ---- + (archptr->clusdep < 0) || + (archptr->clusdep > archptr->leafdep) || + (archptr->linkval < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 3) || ++ ((archptr->leafdep=archpar[0]) < 1) || ++ ((archptr->clusdep=archpar[1]) < 0) || ++ ( archptr->clusdep > archptr->leafdep) || ++ ((archptr->linkval=archpar[2]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archTleafArchLoad: bad input"); + return (1); + } +diff -rc src/src/libscotch/arch_tleaf.h new5/src/libscotch/arch_tleaf.h +*** src/src/libscotch/arch_tleaf.h 2008-05-22 06:44:41.000000000 -0700 +--- new5/src/libscotch/arch_tleaf.h 2010-07-21 17:13:15.615257341 -0700 +*************** +*** 89,95 **** +--- 89,99 ---- + #define static + #endif + ++ #ifndef NOFILEIO + int archTleafArchLoad (ArchTleaf * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archTleafArchLoad (ArchTleaf * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archTleafArchSave (const ArchTleaf * const, FILE * restrict const); + #define archTleafArchFree NULL + ArchDomNum archTleafDomNum (const ArchTleaf * const, const ArchTleafDom * const); +diff -rc src/src/libscotch/arch_torus.c new5/src/libscotch/arch_torus.c +*** src/src/libscotch/arch_torus.c 2008-05-22 06:44:41.000000000 -0700 +--- new5/src/libscotch/arch_torus.c 2010-07-21 17:13:15.618257362 -0700 +*************** +*** 90,97 **** + int + archTorus2ArchLoad ( + ArchTorus2 * restrict const archptr, +! FILE * restrict const stream) +! { + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchTorus2) > sizeof (ArchDummy)) || + (sizeof (ArchTorus2Dom) > sizeof (ArchDomDummy))) { +--- 90,107 ---- + int + archTorus2ArchLoad ( + ArchTorus2 * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) +! { +! #ifdef NOFILEIO +! // printf("archTorus2ArchLoad - napar=%d,archpar=%p\n",napar,archpar); +! #endif /* NOFILEIO */ +! + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchTorus2) > sizeof (ArchDummy)) || + (sizeof (ArchTorus2Dom) > sizeof (ArchDomDummy))) { +*************** +*** 100,108 **** +--- 110,124 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((intLoad (stream, &archptr->c[0]) != 1) || + (intLoad (stream, &archptr->c[1]) != 1) || + (archptr->c[0] < 1) || (archptr->c[1] < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 2) || ++ ((archptr->c[0]=archpar[0]) < 1) || ++ ((archptr->c[1]=archpar[1]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archTorus2ArchLoad: bad input"); + return (1); + } +*************** +*** 363,370 **** + int + archTorus3ArchLoad ( + ArchTorus3 * restrict const archptr, +! FILE * restrict const stream) +! { + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchTorus3) > sizeof (ArchDummy)) || + (sizeof (ArchTorus3Dom) > sizeof (ArchDomDummy))) { +--- 379,396 ---- + int + archTorus3ArchLoad ( + ArchTorus3 * restrict const archptr, +! FILE * restrict const stream +! #ifdef NOFILEIO +! , +! const Anum napar, +! const Anum * archpar +! #endif /* NOFILEIO */ +! ) +! { +! #ifdef NOFILEIO +! // printf("archTorus3ArchLoad - napar=%d,archpar=%p\n",napar,archpar); +! #endif /* NOFILEIO */ +! + #ifdef SCOTCH_DEBUG_ARCH1 + if ((sizeof (ArchTorus3) > sizeof (ArchDummy)) || + (sizeof (ArchTorus3Dom) > sizeof (ArchDomDummy))) { +*************** +*** 373,382 **** +--- 399,415 ---- + } + #endif /* SCOTCH_DEBUG_ARCH1 */ + ++ #ifndef NOFILEIO + if ((intLoad (stream, &archptr->c[0]) != 1) || + (intLoad (stream, &archptr->c[1]) != 1) || + (intLoad (stream, &archptr->c[2]) != 1) || + (archptr->c[0] < 1) || (archptr->c[1] < 1) || (archptr->c[2] < 1)) { ++ #else /* NOFILEIO */ ++ if ((napar < 3) || ++ ((archptr->c[0]=archpar[0]) < 1) || ++ ((archptr->c[1]=archpar[1]) < 1) || ++ ((archptr->c[2]=archpar[2]) < 1)) { ++ #endif /* NOFILEIO */ + errorPrint ("archTorus3ArchLoad: bad input"); + return (1); + } +diff -rc src/src/libscotch/arch_torus.h new5/src/libscotch/arch_torus.h +*** src/src/libscotch/arch_torus.h 2008-05-22 06:44:41.000000000 -0700 +--- new5/src/libscotch/arch_torus.h 2010-07-21 17:13:15.620257376 -0700 +*************** +*** 96,102 **** +--- 96,106 ---- + #define static + #endif + ++ #ifndef NOFILEIO + int archTorus2ArchLoad (ArchTorus2 * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archTorus2ArchLoad (ArchTorus2 * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archTorus2ArchSave (const ArchTorus2 * const, FILE * restrict const); + #define archTorus2ArchFree NULL + ArchDomNum archTorus2DomNum (const ArchTorus2 * const, const ArchTorus2Dom * const); +*************** +*** 114,120 **** +--- 118,128 ---- + int archTorus2DomMpiType (const ArchTorus2 * const, MPI_Datatype * const); + #endif /* SCOTCH_PTSCOTCH */ + ++ #ifndef NOFILEIO + int archTorus3ArchLoad (ArchTorus3 * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int archTorus3ArchLoad (ArchTorus3 * restrict const, FILE * restrict const, const Anum, const Anum *); ++ #endif /* NOFILEIO */ + int archTorus3ArchSave (const ArchTorus3 * const, FILE * restrict const); + #define archTorus3ArchFree NULL + ArchDomNum archTorus3DomNum (const ArchTorus3 * const, const ArchTorus3Dom * const); +diff -rc src/src/libscotch/common.c new5/src/libscotch/common.c +*** src/src/libscotch/common.c 2008-05-22 06:44:41.000000000 -0700 +--- new5/src/libscotch/common.c 2010-07-21 17:13:15.622257390 -0700 +*************** +*** 100,106 **** +--- 100,112 ---- + { + const char ** cptr; + ++ #ifndef MATLAB + fprintf (stream, "Usage is:\n"); + for (cptr = data; *cptr != NULL; cptr ++) + fprintf (stream, " %s\n", *cptr); ++ #else /* MATLAB */ ++ mexPrintf ("Usage is:\n"); ++ for (cptr = data; *cptr != NULL; cptr ++) ++ mexPrintf (" %s\n", *cptr); ++ #endif /* MATLAB */ + } +diff -rc src/src/libscotch/common.h new5/src/libscotch/common.h +*** src/src/libscotch/common.h 2009-02-06 14:20:55.000000000 -0800 +--- new5/src/libscotch/common.h 2010-07-21 17:15:06.061025001 -0700 +*************** +*** 1,3 **** +--- 1,5 ---- ++ #ifndef _SCOTCH_COMMON_H_ ++ #define _SCOTCH_COMMON_H_ + /* Copyright 2004,2007-2009 ENSEIRB, INRIA & CNRS + ** + ** This file is part of the Scotch software package for static mapping, +*************** +*** 79,84 **** +--- 81,87 ---- + #include + #endif /* COMMON_TIMING_OLD */ + #include ++ #include + + #ifdef SCOTCH_PTSCOTCH + #include +*************** +*** 106,113 **** + #define memCpy(dst,src,siz) memcpy((dst),(src),(siz)) + #define memMov(dst,src,siz) memmove((dst),(src),(siz)) + +- #define MIN(x,y) (((x) < (y)) ? (x) : (y)) +- #define MAX(x,y) (((x) < (y)) ? (y) : (x)) + #define ABS(x) MAX ((x), -(x)) + #define SIGN(x) (((x) < 0) ? -1 : 1) + +--- 109,114 ---- +*************** +*** 190,216 **** + size_t memMax (); + #endif /* COMMON_MEMORY_TRACE */ + +- void usagePrint (FILE * const, const char (* [])); + +- int fileBlockOpen (File * const, const int); + int fileBlockOpenDist (File * const, const int, const int, const int, const int); +- void fileBlockClose (File * const, const int); + FILE * fileCompress (FILE * const, const int); + int fileCompressType (const char * const); + FILE * fileUncompress (FILE * const, const int); + int fileUncompressType (const char * const); + int fileNameDistExpand (char ** const, const int, const int, const int); + + void errorProg (const char * const); + void errorPrint (const char * const, ...); + void errorPrintW (const char * const, ...); + + int intLoad (FILE * const, INT * const); + int intSave (FILE * const, const INT); + void intAscn (INT * const, const INT, const INT); + void intPerm (INT * const, const INT); + void intRandReset (void); +- void intRandInit (void); + INT intRandVal (INT); + void intSort1asc1 (void * const, const INT); + void intSort2asc1 (void * const, const INT); +--- 191,227 ---- + size_t memMax (); + #endif /* COMMON_MEMORY_TRACE */ + + + int fileBlockOpenDist (File * const, const int, const int, const int, const int); + FILE * fileCompress (FILE * const, const int); + int fileCompressType (const char * const); + FILE * fileUncompress (FILE * const, const int); + int fileUncompressType (const char * const); + int fileNameDistExpand (char ** const, const int, const int, const int); + ++ #ifdef __cplusplus ++ extern "C" { ++ #endif /* __cplusplus */ ++ + void errorProg (const char * const); + void errorPrint (const char * const, ...); + void errorPrintW (const char * const, ...); ++ double clockGet (void); ++ void usagePrint (FILE * const, const char (* [])); ++ void intRandInit (void); ++ int fileBlockOpen (File * const, const int); ++ void fileBlockClose (File * const, const int); ++ void intRandResetStatic (void); ++ ++ #ifdef __cplusplus ++ } ++ #endif /* __cplusplus */ + + int intLoad (FILE * const, INT * const); + int intSave (FILE * const, const INT); + void intAscn (INT * const, const INT, const INT); + void intPerm (INT * const, const INT); + void intRandReset (void); + INT intRandVal (INT); + void intSort1asc1 (void * const, const INT); + void intSort2asc1 (void * const, const INT); +*************** +*** 221,227 **** + void clockStart (Clock * const); + void clockStop (Clock * const); + double clockVal (Clock * const); +- double clockGet (void); + + /* + ** Macro definitions. +--- 232,237 ---- +*************** +*** 249,251 **** +--- 259,263 ---- + void nl##__ pl \ + { nu pc; } \ + void nu pl ++ ++ #endif //#ifndef _SCOTCH_COMMON_H_ +diff -rc src/src/libscotch/common_integer.c new5/src/libscotch/common_integer.c +*** src/src/libscotch/common_integer.c 2009-01-21 01:32:32.000000000 -0800 +--- new5/src/libscotch/common_integer.c 2010-07-21 17:13:15.628257432 -0700 +*************** +*** 191,196 **** +--- 191,209 ---- + static volatile int intrandflag = 0; /*+ Flag set if generator already initialized +*/ + static unsigned int intrandseed = 1; /*+ Random seed +*/ + ++ void ++ intRandResetStatic (void) ++ { ++ #ifdef MATLAB ++ // printf("intRandResetStatic begin - intrandflag=%d,intrandseed=%d\n",intrandflag,intrandseed); ++ #endif /* MATLAB */ ++ intrandflag = 0; /*+ Flag set if generator already initialized +*/ ++ intrandseed = 1; /*+ Random seed +*/ ++ #ifdef MATLAB ++ // printf("intRandResetStatic end - intrandflag=%d,intrandseed=%d\n",intrandflag,intrandseed); ++ #endif /* MATLAB */ ++ } ++ + /* This routine initializes the pseudo-random + ** generator if necessary. In order for multi-sequential + ** programs to have exactly the same behavior on any +*************** +*** 205,210 **** +--- 218,226 ---- + void + intRandInit (void) + { ++ #ifdef MATLAB ++ // printf("intRandInit begin - intrandflag=%d,intrandseed=%d\n",intrandflag,intrandseed); ++ #endif /* MATLAB */ + if (intrandflag == 0) { /* If generator not yet initialized */ + #if ! ((defined COMMON_DEBUG) || (defined COMMON_RANDOM_FIXED_SEED) || (defined SCOTCH_DETERMINISTIC)) + intrandseed = time (NULL); /* Set random seed if needed */ +*************** +*** 216,221 **** +--- 232,240 ---- + #endif /* COMMON_RANDOM_RAND */ + intrandflag = 1; /* Generator has been initialized */ + } ++ #ifdef MATLAB ++ // printf("intRandInit end - intrandflag=%d,intrandseed=%d\n",intrandflag,intrandseed); ++ #endif /* MATLAB */ + } + + /* This routine reinitializes the pseudo-random +*************** +*** 228,233 **** +--- 247,255 ---- + void + intRandReset (void) + { ++ #ifdef MATLAB ++ // printf("intRandReset begin - intrandflag=%d,intrandseed=%d\n",intrandflag,intrandseed); ++ #endif /* MATLAB */ + if (intrandflag != 0) { /* Keep seed computed during first initialization */ + #ifdef COMMON_RANDOM_RAND + srand (intrandseed); +*************** +*** 237,242 **** +--- 259,267 ---- + } + else + intRandInit (); ++ #ifdef MATLAB ++ // printf("intRandReset end - intrandflag=%d,intrandseed=%d\n",intrandflag,intrandseed); ++ #endif /* MATLAB */ + } + + /*********************/ +diff -rc src/src/libscotch/common_memory.c new5/src/libscotch/common_memory.c +*** src/src/libscotch/common_memory.c 2009-01-03 02:16:11.000000000 -0800 +--- new5/src/libscotch/common_memory.c 2010-07-21 17:13:15.630257445 -0700 +*************** +*** 87,93 **** +--- 87,95 ---- + size_t newadd; + byte * newptr; + ++ printf("memAllocRecord begin -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) ++ printf("memAllocRecord begin -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + if (muteflag != 0) { /* Unsafe code with respect to race conditions but should work as first allocs are sequential */ + muteflag = 0; + pthread_mutex_init (&mutelocdat, NULL); /* Initialize local mutex */ +*************** +*** 109,116 **** +--- 111,120 ---- + + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) + pthread_mutex_unlock (&mutelocdat); /* Unlock local mutex */ ++ printf("memAllocRecord end -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + #endif /* (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) */ + ++ printf("memAllocRecord end -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + return ((void *) newptr); /* Return skewed pointer or NULL */ + } + +*************** +*** 124,133 **** +--- 128,139 ---- + size_t oldsiz; + size_t newadd; + ++ printf("memReallocRecord begin -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + tmpptr = ((byte *) oldptr) - COMMON_MEMORY_SKEW; + oldsiz = *((size_t *) tmpptr); + + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) ++ printf("memReallocRecord begin -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + pthread_mutex_lock (&mutelocdat); /* Lock local mutex */ + #endif /* (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) */ + +*************** +*** 145,152 **** +--- 151,160 ---- + + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) + pthread_mutex_unlock (&mutelocdat); /* Unlock local mutex */ ++ printf("memReallocRecord end -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + #endif /* (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) */ + ++ printf("memReallocRecord end -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + return ((void *) newptr); /* Return skewed pointer or NULL */ + } + +*************** +*** 157,166 **** +--- 165,176 ---- + byte * tmpptr; + size_t oldsiz; + ++ printf("memFreeRecord begin -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + tmpptr = ((byte *) oldptr) - COMMON_MEMORY_SKEW; + oldsiz = *((size_t *) tmpptr); + + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) ++ printf("memFreeRecord begin -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + pthread_mutex_lock (&mutelocdat); /* Lock local mutex */ + #endif /* (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) */ + +*************** +*** 169,175 **** +--- 179,187 ---- + + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) + pthread_mutex_unlock (&mutelocdat); /* Unlock local mutex */ ++ printf("memFreeRecord end -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + #endif /* (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) */ ++ printf("memFreeRecord end -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + } + + size_t +*************** +*** 177,183 **** +--- 189,197 ---- + { + size_t curmax; + ++ printf("memMax begin -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) ++ printf("memMax begin -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + pthread_mutex_lock (&mutelocdat); /* Lock local mutex */ + #endif /* (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) */ + +*************** +*** 185,192 **** +--- 199,208 ---- + + #if (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) + pthread_mutex_unlock (&mutelocdat); /* Unlock local mutex */ ++ printf("memMax end -- muteflag=%d,mutelocdat=%p\n",muteflag,mutelocdat); + #endif /* (defined (COMMON_PTHREAD) || defined (SCOTCH_PTHREAD)) */ + ++ printf("memMax end -- memorysiz=%d,memorymax=%d\n",memorysiz,memorymax); + return (curmax); + } + #endif /* COMMON_MEMORY_TRACE */ +diff -rc src/src/libscotch/dummysizes.c new5/src/libscotch/dummysizes.c +*** src/src/libscotch/dummysizes.c 2009-05-09 16:08:02.000000000 -0700 +--- new5/src/libscotch/dummysizes.c 2010-07-21 17:13:15.633257466 -0700 +*************** +*** 267,271 **** +--- 267,273 ---- + } + #endif /* SCOTCH_DEBUG_MAIN1 */ + ++ #ifndef MATLAB + exit (0); ++ #endif /* MATLAB */ + } +diff -rc src/src/libscotch/graph.c new5/src/libscotch/graph.c +*** src/src/libscotch/graph.c 2008-05-22 06:44:42.000000000 -0700 +--- new5/src/libscotch/graph.c 2010-07-21 17:13:15.635257480 -0700 +*************** +*** 135,141 **** + if ((grafptr->velotax != NULL) && /* Free graph tables */ + ((grafptr->flagval & GRAPHVERTGROUP) == 0)) + memFree (grafptr->velotax + grafptr->baseval); +! if (grafptr->vlbltax != NULL) + memFree (grafptr->vlbltax + grafptr->baseval); + if ((grafptr->edlotax != NULL) && + ((grafptr->flagval & GRAPHEDGEGROUP) == 0)) +--- 135,144 ---- + if ((grafptr->velotax != NULL) && /* Free graph tables */ + ((grafptr->flagval & GRAPHVERTGROUP) == 0)) + memFree (grafptr->velotax + grafptr->baseval); +! /* vlbltax must also check GRAPHVERTGROUP (jes, 12/11/09) */ +! // if (grafptr->vlbltax != NULL) +! if ((grafptr->vlbltax != NULL) && +! ((grafptr->flagval & GRAPHVERTGROUP) == 0)) + memFree (grafptr->vlbltax + grafptr->baseval); + if ((grafptr->edlotax != NULL) && + ((grafptr->flagval & GRAPHEDGEGROUP) == 0)) +diff -rc src/src/libscotch/graph.h new5/src/libscotch/graph.h +*** src/src/libscotch/graph.h 2008-06-01 02:49:11.000000000 -0700 +--- new5/src/libscotch/graph.h 2010-07-21 17:13:15.637257494 -0700 +*************** +*** 159,165 **** +--- 159,169 ---- + int graphInit (Graph * const); + void graphExit (Graph * const); + void graphFree (Graph * const); ++ #ifndef NOFILEIO + int graphLoad (Graph * const, FILE * const, const Gnum, const GraphFlag); ++ #else /* NOFILEIO */ ++ int graphLoad (Graph * const, FILE * const, const Gnum, const GraphFlag, const Gnum, const Gnum, const Gnum*, const Gnum*, const Gnum*, const Gnum*, const Gnum*); ++ #endif /* NOFILEIO */ + int graphLoad2 (const Gnum, const Gnum, const Gnum * const, const Gnum * const, Gnum * restrict const, const Gnum, const Gnum * const); + int graphSave (const Graph * const, FILE * const); + Gnum graphBase (Graph * const, const Gnum); +diff -rc src/src/libscotch/graph_io.c new5/src/libscotch/graph_io.c +*** src/src/libscotch/graph_io.c 2008-05-22 06:44:42.000000000 -0700 +--- new5/src/libscotch/graph_io.c 2010-07-21 17:13:15.639257508 -0700 +*************** +*** 86,92 **** + Graph * restrict const grafptr, /* Graph structure to fill */ + FILE * const stream, /* Stream from which to read graph data */ + const Gnum baseval, /* Base value (-1 means keep file base) */ +! const GraphFlag flagval) /* Graph loading flags */ + { + Gnum edgenum; /* Number of edges really allocated */ + Gnum edgennd; +--- 86,103 ---- + Graph * restrict const grafptr, /* Graph structure to fill */ + FILE * const stream, /* Stream from which to read graph data */ + const Gnum baseval, /* Base value (-1 means keep file base) */ +! const GraphFlag flagval /* Graph loading flags */ +! #ifdef NOFILEIO +! , +! const Gnum nvert, +! const Gnum nedge2, +! const Gnum* adjir, +! const Gnum* adjjc, +! const Gnum* vertlab, +! const Gnum* vertwgt, +! const Gnum* edgewgt +! #endif /* NOFILEIO */ +! ) + { + Gnum edgenum; /* Number of edges really allocated */ + Gnum edgennd; +*************** +*** 104,120 **** +--- 115,141 ---- + char proptab[4]; + Gnum vertnum; + ++ #ifdef NOFILEIO ++ // printf("graphLoad - stream=%p; nvert=%d,nedge2=%d\n",stream,nvert,nedge2); ++ // printf("graphLoad - adjir=%p,adjjc=%p,vertlab=%p,vertwgt=%p,edgewgt=%p\n", ++ // adjir,adjjc,vertlab,vertwgt,edgewgt); ++ #endif /* NOFILEIO */ + memSet (grafptr, 0, sizeof (Graph)); + ++ #ifndef NOFILEIO + if (intLoad (stream, &versval) != 1) { /* Read version number */ + errorPrint ("graphLoad: bad input (1)"); + return (1); + } ++ #else /* NOFILEIO */ ++ versval=0; ++ #endif /* NOFILEIO */ + if (versval != 0) { /* If version not zero */ + errorPrint ("graphLoad: old-style graph format no longer supported"); + return (1); + } + ++ #ifndef NOFILEIO + if ((intLoad (stream, &grafptr->vertnbr) != 1) || /* Read rest of header */ + (intLoad (stream, &grafptr->edgenbr) != 1) || + (intLoad (stream, &baseadj) != 1) || +*************** +*** 124,129 **** +--- 145,159 ---- + errorPrint ("graphLoad: bad input (2)"); + return (1); + } ++ #else /* NOFILEIO */ ++ grafptr->vertnbr=nvert; ++ grafptr->edgenbr=nedge2; ++ baseadj=1; ++ propval=0; ++ if (vertlab) propval+=100; ++ if (edgewgt) propval+= 10; ++ if (vertwgt) propval+= 1; ++ #endif /* NOFILEIO */ + sprintf (proptab, "%3.3d", (int) propval); /* Compute file properties */ + proptab[0] -= '0'; /* Vertex labels flag */ + proptab[1] -= '0'; /* Edge weights flag */ +*************** +*** 140,145 **** +--- 170,179 ---- + } + if (proptab[0] != 0) /* If vertex labels, no base adjust */ + baseadj = 0; ++ #ifdef NOFILEIO ++ // printf("graphLoad - baseadj=%d,baseval=%d,grafptr->baseval=%d\n", ++ // baseadj,baseval,grafptr->baseval); ++ #endif /* NOFILEIO */ + + velonbr = ((proptab[2] != 0) && ((flagval & GRAPHIONOLOADVERT) == 0)) ? grafptr->vertnbr : 0; + vlblnbr = (proptab[0] != 0) ? grafptr->vertnbr : 0; +*************** +*** 178,188 **** +--- 212,226 ---- + if (grafptr->vlbltax != NULL) { /* If must read label */ + Gnum vlblval; /* Value where to read vertex label */ + ++ #ifndef NOFILEIO + if (intLoad (stream, &vlblval) != 1) { /* Read label data */ + errorPrint ("graphLoad: bad input (3)"); + graphFree (grafptr); + return (1); + } ++ #else /* NOFILEIO */ ++ vlblval=vertlab[vertnum-grafptr->baseval]; ++ #endif /* NOFILEIO */ + grafptr->vlbltax[vertnum] = vlblval; + if (grafptr->vlbltax[vertnum] > vlblmax) /* Get maximum vertex label */ + vlblmax = grafptr->vlbltax[vertnum]; +*************** +*** 190,209 **** +--- 228,257 ---- + if (proptab[2] != 0) { /* If must read vertex load */ + Gnum veloval; /* Value where to read vertex load */ + ++ #ifndef NOFILEIO + if (intLoad (stream, &veloval) != 1) { /* Read vertex load data */ + errorPrint ("graphLoad: bad input (4)"); + graphFree (grafptr); + return (1); + } ++ #else /* NOFILEIO */ ++ veloval=vertwgt[vertnum-grafptr->baseval]; ++ #endif /* NOFILEIO */ + if (grafptr->velotax != NULL) + velosum += + grafptr->velotax[vertnum] = veloval; + } ++ #ifndef NOFILEIO + if (intLoad (stream, °rval) != 1) { /* Read vertex degree */ + errorPrint ("graphLoad: bad input (5)"); + graphFree (grafptr); + return (1); + } ++ #else /* NOFILEIO */ ++ // printf("old degrval=%d; new degrval=%d\n", ++ // degrval,adjjc[vertnum-grafptr->baseval+1]-adjjc[vertnum-grafptr->baseval]); ++ degrval=adjjc[vertnum-grafptr->baseval+1]-adjjc[vertnum-grafptr->baseval]; ++ #endif /* NOFILEIO */ + if (degrmax < degrval) /* Set maximum degree */ + degrmax = degrval; + +*************** +*** 219,238 **** +--- 267,301 ---- + if (proptab[1] != 0) { /* If must read edge load */ + Gnum edloval; /* Value where to read edge load */ + ++ #ifndef NOFILEIO + if (intLoad (stream, &edloval) != 1) { /* Read edge load data */ + errorPrint ("graphLoad: bad input (6)"); + graphFree (grafptr); + return (1); + } ++ #else /* NOFILEIO */ ++ edloval=edgewgt[edgenum-grafptr->baseval]; ++ #endif /* NOFILEIO */ + if (grafptr->edlotax != NULL) + edlosum += + grafptr->edlotax[edgenum] = (Gnum) edloval; + } ++ #ifndef NOFILEIO + if (intLoad (stream, &edgeval) != 1) { /* Read edge data */ + errorPrint ("graphLoad: bad input (7)"); + graphFree (grafptr); + return (1); + } ++ #else /* NOFILEIO */ ++ // printf("edgenum=%d: old edgeval=%d; new edgeval[%d]=%d\n", ++ // edgenum,edgeval,edgenum-grafptr->baseval,adjir[edgenum-grafptr->baseval]+1); ++ /* if vertex labels are supplied, they must be referenced (jes, 1/05/10) */ ++ // edgeval=adjir[edgenum-grafptr->baseval]+1; ++ if (vertlab) ++ edgeval=vertlab[adjir[edgenum-grafptr->baseval] ]; ++ else ++ edgeval= adjir[edgenum-grafptr->baseval]+1; ++ #endif /* NOFILEIO */ + grafptr->edgetax[edgenum] = edgeval + baseadj; + } + } +*************** +*** 279,284 **** +--- 342,351 ---- + Gnum vertnum; /* Number of current vertex */ + Gnum * restrict indxtab; /* Vertex label/number index table */ + ++ #ifdef NOFILEIO ++ printf("graphLoad2 - baseval=%d,vertnnd=%d,vlblmax=%d\n", ++ baseval,vertnnd,vlblmax); ++ #endif /* NOFILEIO */ + if ((indxtab = (Gnum *) memAlloc ((vlblmax + 1) * sizeof (Gnum))) == NULL) { + errorPrint ("graphLoad2: out of memory"); + return (1); +*************** +*** 286,291 **** +--- 353,362 ---- + + memSet (indxtab, ~0, (vlblmax + 1) * sizeof (Gnum)); /* Assume labels not used */ + for (vertnum = baseval; vertnum < vertnnd; vertnum ++) { ++ #ifdef NOFILEIO ++ // printf("graphLoad2 - vertnum=%d; vlbltax=%d,indxtab=%d\n", ++ // vertnum,vlbltax[vertnum],indxtab[vlbltax[vertnum]]); ++ #endif /* NOFILEIO */ + if (indxtab[vlbltax[vertnum]] != ~0) { /* If vertex label already used */ + errorPrint ("graphLoad2: duplicate vertex label"); + memFree (indxtab); +*************** +*** 294,299 **** +--- 365,374 ---- + indxtab[vlbltax[vertnum]] = vertnum; /* Set vertex number index */ + } + for (vertnum = baseval; vertnum < vertnnd; vertnum ++) { ++ #ifdef NOFILEIO ++ // printf("graphLoad2 - vertnum=%d; vlbltax=%d,indxtab=%d\n", ++ // vertnum,vlbltax[vertnum],indxtab[vlbltax[vertnum]]); ++ #endif /* NOFILEIO */ + Gnum edgenum; /* Number of current edge */ + + for (edgenum = verttax[vertnum]; edgenum < vendtax[vertnum]; edgenum ++) { +*************** +*** 307,313 **** +--- 382,396 ---- + memFree (indxtab); + return (1); + } ++ #ifdef NOFILEIO ++ // printf("graphLoad2 - edgenum=%d; old edgetax=%d,", ++ // edgenum,edgetax[edgenum]); ++ #endif /* NOFILEIO */ + edgetax[edgenum] = indxtab[edgetax[edgenum]]; /* Replace label by number */ ++ #ifdef NOFILEIO ++ // printf("new edgetax=%d\n", ++ // edgetax[edgenum]); ++ #endif /* NOFILEIO */ + } + } + +diff -rc src/src/libscotch/graph_io_scot.c new5/src/libscotch/graph_io_scot.c +*** src/src/libscotch/graph_io_scot.c 2008-05-22 06:44:42.000000000 -0700 +--- new5/src/libscotch/graph_io_scot.c 2010-07-21 17:13:15.641257522 -0700 +*************** +*** 89,95 **** +--- 89,99 ---- + int o; + + if (filesrcptr != NULL) { ++ #ifndef NOFILEIO + if (graphLoad (grafptr, filesrcptr, -1, 0) != 0) ++ #else /* NOFILEIO */ ++ if (graphLoad (grafptr, filesrcptr, -1, 0, 0, 0, NULL, NULL, NULL, NULL, NULL) != 0) ++ #endif /* NOFILEIO */ + return (1); + } + +diff -rc src/src/libscotch/library_arch.c new5/src/libscotch/library_arch.c +*** src/src/libscotch/library_arch.c 2008-05-22 06:44:42.000000000 -0700 +--- new5/src/libscotch/library_arch.c 2010-07-21 17:13:15.643257536 -0700 +*************** +*** 120,128 **** + int + SCOTCH_archLoad ( + SCOTCH_Arch * const archptr, +! FILE * const stream) + { + return (archLoad ((Arch *) archptr, stream)); + } + + /*+ This routine saves the given opaque +--- 120,139 ---- + int + SCOTCH_archLoad ( + SCOTCH_Arch * const archptr, +! FILE * const stream +! #ifdef NOFILEIO +! , +! const char * archtyp, +! const SCOTCH_Num napar, +! const SCOTCH_Num * archpar +! #endif /* NOFILEIO */ +! ) + { ++ #ifndef NOFILEIO + return (archLoad ((Arch *) archptr, stream)); ++ #else /* NOFILEIO */ ++ return (archLoad ((Arch *) archptr, stream, archtyp, napar, archpar)); ++ #endif /* NOFILEIO */ + } + + /*+ This routine saves the given opaque +diff -rc src/src/libscotch/library_arch_f.c new5/src/libscotch/library_arch_f.c +*** src/src/libscotch/library_arch_f.c 2008-05-22 06:44:42.000000000 -0700 +--- new5/src/libscotch/library_arch_f.c 2010-07-21 17:13:15.645257550 -0700 +*************** +*** 121,127 **** +--- 121,131 ---- + } + setbuf (stream, NULL); /* Do not buffer on input */ + ++ #ifndef NOFILEIO + o = SCOTCH_archLoad (archptr, stream); ++ #else /* NOFILEIO */ ++ o = SCOTCH_archLoad (archptr, stream, "", 0, NULL); ++ #endif /* NOFILEIO */ + + fclose (stream); /* This closes filenum too */ + +diff -rc src/src/libscotch/library_error_exit.c new5/src/libscotch/library_error_exit.c +*** src/src/libscotch/library_error_exit.c 2009-01-20 00:36:33.000000000 -0800 +--- new5/src/libscotch/library_error_exit.c 2010-07-21 17:13:15.648257570 -0700 +*************** +*** 114,119 **** +--- 114,120 ---- + int proclocnum; + #endif /* SCOTCH_PTSCOTCH */ + ++ #ifndef MATLAB + fprintf (stderr, "%s", _SCOTCHerrorProgName); + #ifdef SCOTCH_PTSCOTCH + if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && +*************** +*** 131,136 **** +--- 132,155 ---- + fprintf (stderr, "\n"); + fflush (stderr); /* In case it has been set to buffered mode */ + ++ #else /* MATLAB */ ++ mexPrintf ("%s", _SCOTCHerrorProgName); ++ #ifdef SCOTCH_PTSCOTCH ++ if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && ++ (proclocnum != 0) && ++ (MPI_Comm_rank (MPI_COMM_WORLD, &proclocnum) == MPI_SUCCESS)) ++ mexPrintf ("(%d): ", proclocnum); ++ #else /* SCOTCH_PTSCOTCH */ ++ if (_SCOTCHerrorProgName[0] != '\0') ++ mexPrintf (": "); ++ #endif /* SCOTCH_PTSCOTCH */ ++ mexPrintf ("ERROR: "); ++ va_start (errlist, errstr); ++ mexPrintf (errstr, errlist); /* Print arguments */ ++ va_end (errlist); ++ mexPrintf ("\n"); ++ #endif /* MATLAB */ ++ + #ifdef SCOTCH_ERROR_SLEEP + sleep (SCOTCH_ERROR_SLEEP); /* Wait for messages to be propagated */ + #endif /* SCOTCH_ERROR_SLEEP */ +*************** +*** 155,160 **** +--- 174,180 ---- + int proclocnum; + #endif /* SCOTCH_PTSCOTCH */ + ++ #ifndef MATLAB + fprintf (stderr, "%s", _SCOTCHerrorProgName); + #ifdef SCOTCH_PTSCOTCH + if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && +*************** +*** 171,174 **** +--- 191,212 ---- + va_end (errlist); + fprintf (stderr, "\n"); + fflush (stderr); /* In case it has been set to buffered mode */ ++ ++ #else /* MATLAB */ ++ mexPrintf ("%s", _SCOTCHerrorProgName); ++ #ifdef SCOTCH_PTSCOTCH ++ if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && ++ (proclocnum != 0) && ++ (MPI_Comm_rank (MPI_COMM_WORLD, &proclocnum) == MPI_SUCCESS)) ++ mexPrintf ("(%d): ", proclocnum); ++ #else /* SCOTCH_PTSCOTCH */ ++ if (_SCOTCHerrorProgName[0] != '\0') ++ mexPrintf (": "); ++ #endif /* SCOTCH_PTSCOTCH */ ++ mexPrintf ("WARNING: "); ++ va_start (errlist, errstr); ++ mexPrintf (errstr, errlist); /* Print arguments */ ++ va_end (errlist); ++ mexPrintf ("\n"); ++ #endif /* MATLAB */ + } +diff -rc src/src/libscotch/library_graph.c new5/src/libscotch/library_graph.c +*** src/src/libscotch/library_graph.c 2008-05-22 07:28:12.000000000 -0700 +--- new5/src/libscotch/library_graph.c 2010-07-21 17:13:15.650257584 -0700 +*************** +*** 137,143 **** + SCOTCH_Graph * const grafptr, + FILE * const stream, + const SCOTCH_Num baseval, +! const SCOTCH_Num flagval) + { + GraphFlag srcgrafflag; /* Graph flags */ + +--- 137,154 ---- + SCOTCH_Graph * const grafptr, + FILE * const stream, + const SCOTCH_Num baseval, +! const SCOTCH_Num flagval +! #ifdef NOFILEIO +! , +! const SCOTCH_Num nvert, +! const SCOTCH_Num nedge2, +! const SCOTCH_Num* adjir, +! const SCOTCH_Num* adjjc, +! const SCOTCH_Num* vertlab, +! const SCOTCH_Num* vertwgt, +! const SCOTCH_Num* edgewgt +! #endif /* NOFILEIO */ +! ) + { + GraphFlag srcgrafflag; /* Graph flags */ + +*************** +*** 153,159 **** +--- 164,174 ---- + srcgrafflag = (((flagval & 1) != 0) ? GRAPHIONOLOADVERT : 0) + + (((flagval & 2) != 0) ? GRAPHIONOLOADEDGE : 0); + ++ #ifndef NOFILEIO + return (graphLoad ((Graph * const) grafptr, stream, (Gnum) baseval, srcgrafflag)); ++ #else /* NOFILEIO */ ++ return (graphLoad ((Graph * const) grafptr, stream, (Gnum) baseval, srcgrafflag, (const Gnum) nvert, (const Gnum) nedge2, (const Gnum *) adjir, (const Gnum *) adjjc, (const Gnum *) vertlab, (const Gnum *) vertwgt, (const Gnum *) edgewgt)); ++ #endif /* NOFILEIO */ + } + + /*+ This routine saves the contents of the given +diff -rc src/src/libscotch/library_graph_f.c new5/src/libscotch/library_graph_f.c +*** src/src/libscotch/library_graph_f.c 2008-05-22 06:44:43.000000000 -0700 +--- new5/src/libscotch/library_graph_f.c 2010-07-21 17:13:15.652257598 -0700 +*************** +*** 136,142 **** +--- 136,146 ---- + } + setbuf (stream, NULL); /* Do not buffer on input */ + ++ #ifndef NOFILEIO + o = SCOTCH_graphLoad (grafptr, stream, *baseptr, *flagptr); ++ #else /* NOFILEIO */ ++ o = SCOTCH_graphLoad (grafptr, stream, *baseptr, *flagptr, 0, 0, NULL, NULL, NULL, NULL, NULL); ++ #endif /* NOFILEIO */ + + fclose (stream); /* This closes filenum too */ + +diff -rc src/src/libscotch/library_graph_map.c new5/src/libscotch/library_graph_map.c +*** src/src/libscotch/library_graph_map.c 2008-09-28 04:04:05.000000000 -0700 +--- new5/src/libscotch/library_graph_map.c 2010-07-21 17:13:15.654257612 -0700 +*************** +*** 182,192 **** +--- 182,200 ---- + + int + SCOTCH_graphMapSave ( ++ #ifdef NOFILEIO ++ Gnum *pnvert, ++ Gnum (**pmaptab)[2], ++ #endif /* NOFILEIO */ + const SCOTCH_Graph * const grafptr, /*+ Graph to order +*/ + const SCOTCH_Mapping * const mappptr, /*+ Mapping to save +*/ + FILE * const stream) /*+ Output stream +*/ + { ++ #ifndef NOFILEIO + return (mapSave (&((LibMapping *) mappptr)->m, ((Graph *) grafptr)->vlbltax, stream)); ++ #else /* NOFILEIO */ ++ return (mapSave (pnvert, pmaptab, &((LibMapping *) mappptr)->m, ((Graph *) grafptr)->vlbltax, stream)); ++ #endif /* NOFILEIO */ + } + + /*+ This routine computes a mapping +diff -rc src/src/libscotch/library_graph_map_f.c new5/src/libscotch/library_graph_map_f.c +*** src/src/libscotch/library_graph_map_f.c 2008-06-28 03:44:26.000000000 -0700 +--- new5/src/libscotch/library_graph_map_f.c 2010-07-21 17:13:15.656257626 -0700 +*************** +*** 183,189 **** +--- 183,193 ---- + return; + } + ++ #ifndef NOFILEIO + o = SCOTCH_graphMapSave (grafptr, mapptr, stream); ++ #else /* NOFILEIO */ ++ o = SCOTCH_graphMapSave (NULL, NULL, grafptr, mapptr, stream); ++ #endif /* NOFILEIO */ + + fclose (stream); /* This closes filenum too */ + +diff -rc src/src/libscotch/library.h new5/src/libscotch/library.h +*** src/src/libscotch/library.h 2009-05-09 16:08:03.000000000 -0700 +--- new5/src/libscotch/library.h 2010-07-21 17:13:15.660257654 -0700 +*************** +*** 1,3 **** +--- 1,5 ---- ++ #ifndef _SCOTCH_H_ ++ #define _SCOTCH_H_ + /* Copyright 2004,2007-2009 ENSEIRB, INRIA & CNRS + ** + ** This file is part of the Scotch software package for static mapping, +*************** +*** 134,140 **** +--- 136,146 ---- + + int SCOTCH_archInit (SCOTCH_Arch * const); + void SCOTCH_archExit (SCOTCH_Arch * const); ++ #ifndef NOFILEIO + int SCOTCH_archLoad (SCOTCH_Arch * const, FILE * const); ++ #else /* NOFILEIO */ ++ int SCOTCH_archLoad (SCOTCH_Arch * const, FILE * const, const char *, const SCOTCH_Num, const SCOTCH_Num *); ++ #endif /* NOFILEIO */ + int SCOTCH_archSave (const SCOTCH_Arch * const, FILE * const); + int SCOTCH_archBuild (SCOTCH_Arch * const, const SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_Num * const, const SCOTCH_Strat * const); + int SCOTCH_archCmplt (SCOTCH_Arch * const, const SCOTCH_Num); +*************** +*** 191,197 **** +--- 197,207 ---- + int SCOTCH_graphInit (SCOTCH_Graph * const); + void SCOTCH_graphExit (SCOTCH_Graph * const); + void SCOTCH_graphFree (SCOTCH_Graph * const); ++ #ifndef NOFILEIO + int SCOTCH_graphLoad (SCOTCH_Graph * const, FILE * const, const SCOTCH_Num, const SCOTCH_Num); ++ #else /* NOFILEIO */ ++ int SCOTCH_graphLoad (SCOTCH_Graph * const, FILE * const, const SCOTCH_Num, const SCOTCH_Num, const SCOTCH_Num, const SCOTCH_Num, const SCOTCH_Num *, const SCOTCH_Num *, const SCOTCH_Num *, const SCOTCH_Num *, const SCOTCH_Num *); ++ #endif /* NOFILEIO */ + int SCOTCH_graphSave (const SCOTCH_Graph * const, FILE * const); + int SCOTCH_graphBuild (SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_Num, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num, const SCOTCH_Num * const, const SCOTCH_Num * const); + SCOTCH_Num SCOTCH_graphBase (SCOTCH_Graph * const, const SCOTCH_Num baseval); +*************** +*** 210,216 **** +--- 220,230 ---- + int SCOTCH_graphMapInit (const SCOTCH_Graph * const, SCOTCH_Mapping * const, const SCOTCH_Arch * const, SCOTCH_Num * const); + void SCOTCH_graphMapExit (const SCOTCH_Graph * const, SCOTCH_Mapping * const); + int SCOTCH_graphMapLoad (const SCOTCH_Graph * const, const SCOTCH_Mapping * const, FILE * const); ++ #ifndef NOFILEIO + int SCOTCH_graphMapSave (const SCOTCH_Graph * const, const SCOTCH_Mapping * const, FILE * const); ++ #else /* NOFILEIO */ ++ int SCOTCH_graphMapSave (SCOTCH_Num *, SCOTCH_Num (**)[2], const SCOTCH_Graph * const, const SCOTCH_Mapping * const, FILE * const); ++ #endif /* NOFILEIO */ + int SCOTCH_graphMapView (const SCOTCH_Graph * const, const SCOTCH_Mapping * const, FILE * const); + int SCOTCH_graphMapCompute (const SCOTCH_Graph * const, SCOTCH_Mapping * const, const SCOTCH_Strat * const); + int SCOTCH_graphMap (const SCOTCH_Graph * const, const SCOTCH_Arch * const, const SCOTCH_Strat * const, SCOTCH_Num * const); +*************** +*** 278,280 **** +--- 292,296 ---- + #ifdef __cplusplus + } + #endif /* __cplusplus */ ++ ++ #endif //#ifndef _SCOTCH_H_ +diff -rc src/src/libscotch/Makefile new5/src/libscotch/Makefile +*** src/src/libscotch/Makefile 2009-05-09 16:08:04.000000000 -0700 +--- new5/src/libscotch/Makefile 2010-07-21 17:13:15.665257689 -0700 +*************** +*** 49,55 **** + ## Project rules. + ## + +! .PHONY : ptscotch scotch ptinstall install clean realclean + + scotch : clean + $(MAKE) CC="$(CCS)" CCD="$(CCS)" SCOTCHLIB=scotch \ +--- 49,55 ---- + ## Project rules. + ## + +! .PHONY : ptscotch scotch nfioscotch mexscotch ptinstall install nfioinstall mexinstall clean realclean + + scotch : clean + $(MAKE) CC="$(CCS)" CCD="$(CCS)" SCOTCHLIB=scotch \ +*************** +*** 68,73 **** +--- 68,93 ---- + libptscotcherr$(LIB) \ + libptscotcherrexit$(LIB) + ++ nfioscotch : clean ++ $(MAKE) CFLAGS="$(CFLAGS)" CC="$(CCS)" CCD="$(CCS)" LDFLAGS="$(LDFLAGS)" SCOTCHLIB=scotch \ ++ dummysizes$(EXE) ++ $(MAKE) CFLAGS="$(CFLAGS) -DNOFILEIO" CC="$(CCS)" CCD="$(CCS)" SCOTCHLIB=nfioscotch \ ++ scotch.h \ ++ scotchf.h \ ++ libnfioscotch$(LIB) \ ++ libnfioscotcherr$(LIB) \ ++ libnfioscotcherrexit$(LIB) ++ ++ mexscotch : clean ++ $(MAKE) CFLAGS="$(CFLAGS)" CC="$(CCS)" CCD="$(CCS)" LDFLAGS="$(LDFLAGS)" SCOTCHLIB=scotch \ ++ dummysizes$(EXE) ++ $(MAKE) CFLAGS="$(CFLAGS) -DNOFILEIO -DMATLAB -I${MATLAB_DIR}/extern/include" CC="$(CCS)" CCD="$(CCS)" LDFLAGS="$(LDFLAGS) -Wl,-rpath-link,${MATLAB_DIR}/bin/glnxa64 -L${MATLAB_DIR}/bin/glnxa64 -lmex -lmat" SCOTCHLIB=mexscotch \ ++ scotch.h \ ++ scotchf.h \ ++ libmexscotch$(LIB) \ ++ libmexscotcherr$(LIB) \ ++ libmexscotcherrexit$(LIB) ++ + install : + -$(CP) scotch.h scotchf.h $(includedir) + -$(CP) libscotch$(LIB) libscotcherr*$(LIB) $(libdir) +*************** +*** 77,82 **** +--- 97,110 ---- + -$(CP) scotchf.h $(includedir)/ptscotchf.h + -$(CP) libptscotch*$(LIB) $(libdir) + ++ nfioinstall : ++ -$(CP) scotch.h scotchf.h $(includedir) ++ -$(CP) libnfioscotch$(LIB) libnfioscotcherr*$(LIB) $(libdir) ++ ++ mexinstall : ++ -$(CP) scotch.h scotchf.h $(includedir) ++ -$(CP) libmexscotch$(LIB) libmexscotcherr*$(LIB) $(libdir) ++ + clean : + -$(RM) *~ *$(OBJ) lib*$(LIB) common2* parser_yy.c parser_ly.h parser_ll.c *scotch.h *scotchf.h y.output dummysizes$(EXE) + +*************** +*** 2452,2457 **** +--- 2480,2807 ---- + $(AR) $(ARFLAGS) lib$(SCOTCHLIB)$(LIB) $(?) + -$(RANLIB) lib$(SCOTCHLIB)$(LIB) + ++ libnfioscotch$(LIB) : arch$(OBJ) \ ++ arch_build$(OBJ) \ ++ arch_cmplt$(OBJ) \ ++ arch_cmpltw$(OBJ) \ ++ arch_deco$(OBJ) \ ++ arch_hcub$(OBJ) \ ++ arch_mesh$(OBJ) \ ++ arch_tleaf$(OBJ) \ ++ arch_torus$(OBJ) \ ++ arch_vcmplt$(OBJ) \ ++ arch_vhcub$(OBJ) \ ++ bgraph$(OBJ) \ ++ bgraph_bipart_bd$(OBJ) \ ++ bgraph_bipart_df$(OBJ) \ ++ bgraph_bipart_ex$(OBJ) \ ++ bgraph_bipart_fm$(OBJ) \ ++ bgraph_bipart_gg$(OBJ) \ ++ bgraph_bipart_gp$(OBJ) \ ++ bgraph_bipart_ml$(OBJ) \ ++ bgraph_bipart_st$(OBJ) \ ++ bgraph_bipart_zr$(OBJ) \ ++ bgraph_check$(OBJ) \ ++ bgraph_store$(OBJ) \ ++ common$(OBJ) \ ++ common_file$(OBJ) \ ++ common_file_compress$(OBJ) \ ++ common_file_uncompress$(OBJ) \ ++ common_integer$(OBJ) \ ++ common_memory$(OBJ) \ ++ common_stub$(OBJ) \ ++ gain$(OBJ) \ ++ geom$(OBJ) \ ++ graph$(OBJ) \ ++ graph_base$(OBJ) \ ++ graph_check$(OBJ) \ ++ graph_coarsen$(OBJ) \ ++ graph_induce$(OBJ) \ ++ graph_io$(OBJ) \ ++ graph_io_chac$(OBJ) \ ++ graph_io_habo$(OBJ) \ ++ graph_io_mmkt$(OBJ) \ ++ graph_io_scot$(OBJ) \ ++ graph_list$(OBJ) \ ++ hall_order_hd$(OBJ) \ ++ hall_order_hf$(OBJ) \ ++ hall_order_hx$(OBJ) \ ++ hgraph$(OBJ) \ ++ hgraph_check$(OBJ) \ ++ hgraph_induce$(OBJ) \ ++ hgraph_order_bl$(OBJ) \ ++ hgraph_order_cp$(OBJ) \ ++ hgraph_order_gp$(OBJ) \ ++ hgraph_order_hd$(OBJ) \ ++ hgraph_order_hf$(OBJ) \ ++ hgraph_order_hx$(OBJ) \ ++ hgraph_order_nd$(OBJ) \ ++ hgraph_order_si$(OBJ) \ ++ hgraph_order_st$(OBJ) \ ++ hmesh$(OBJ) \ ++ hmesh_check$(OBJ) \ ++ hmesh_hgraph$(OBJ) \ ++ hmesh_induce$(OBJ) \ ++ hmesh_mesh$(OBJ) \ ++ hmesh_order_bl$(OBJ) \ ++ hmesh_order_cp$(OBJ) \ ++ hmesh_order_gr$(OBJ) \ ++ hmesh_order_gp$(OBJ) \ ++ hmesh_order_hd$(OBJ) \ ++ hmesh_order_hf$(OBJ) \ ++ hmesh_order_hx$(OBJ) \ ++ hmesh_order_nd$(OBJ) \ ++ hmesh_order_si$(OBJ) \ ++ hmesh_order_st$(OBJ) \ ++ kgraph$(OBJ) \ ++ kgraph_map_rb$(OBJ) \ ++ kgraph_map_rb_map$(OBJ) \ ++ kgraph_map_rb_part$(OBJ) \ ++ kgraph_map_st$(OBJ) \ ++ library_arch$(OBJ) \ ++ library_arch_f$(OBJ) \ ++ library_arch_build$(OBJ) \ ++ library_arch_build_f$(OBJ) \ ++ library_arch_cmpltw$(OBJ) \ ++ library_arch_cmpltw_f$(OBJ) \ ++ library_geom$(OBJ) \ ++ library_geom_f$(OBJ) \ ++ library_graph$(OBJ) \ ++ library_graph_f$(OBJ) \ ++ library_graph_base$(OBJ) \ ++ library_graph_base_f$(OBJ) \ ++ library_graph_check$(OBJ) \ ++ library_graph_check_f$(OBJ) \ ++ library_graph_io_chac$(OBJ) \ ++ library_graph_io_chac_f$(OBJ) \ ++ library_graph_io_habo$(OBJ) \ ++ library_graph_io_habo_f$(OBJ) \ ++ library_graph_io_mmkt$(OBJ) \ ++ library_graph_io_mmkt_f$(OBJ) \ ++ library_graph_io_scot$(OBJ) \ ++ library_graph_io_scot_f$(OBJ) \ ++ library_graph_map$(OBJ) \ ++ library_graph_map_f$(OBJ) \ ++ library_graph_map_view$(OBJ) \ ++ library_graph_map_view_f$(OBJ) \ ++ library_graph_order$(OBJ) \ ++ library_graph_order_f$(OBJ) \ ++ library_mesh$(OBJ) \ ++ library_mesh_f$(OBJ) \ ++ library_mesh_graph$(OBJ) \ ++ library_mesh_graph_f$(OBJ) \ ++ library_mesh_io_habo$(OBJ) \ ++ library_mesh_io_habo_f$(OBJ) \ ++ library_mesh_io_scot$(OBJ) \ ++ library_mesh_io_scot_f$(OBJ) \ ++ library_mesh_order$(OBJ) \ ++ library_mesh_order_f$(OBJ) \ ++ library_parser$(OBJ) \ ++ library_parser_f$(OBJ) \ ++ library_random$(OBJ) \ ++ library_random_f$(OBJ) \ ++ mapping$(OBJ) \ ++ mapping_io$(OBJ) \ ++ mesh$(OBJ) \ ++ mesh_check$(OBJ) \ ++ mesh_coarsen$(OBJ) \ ++ mesh_graph$(OBJ) \ ++ mesh_induce_sepa$(OBJ) \ ++ mesh_io$(OBJ) \ ++ mesh_io_habo$(OBJ) \ ++ mesh_io_scot$(OBJ) \ ++ order$(OBJ) \ ++ order_check$(OBJ) \ ++ order_io$(OBJ) \ ++ parser$(OBJ) \ ++ parser_ll$(OBJ) \ ++ parser_yy$(OBJ) \ ++ vgraph$(OBJ) \ ++ vgraph_check$(OBJ) \ ++ vgraph_separate_bd$(OBJ) \ ++ vgraph_separate_es$(OBJ) \ ++ vgraph_separate_fm$(OBJ) \ ++ vgraph_separate_gg$(OBJ) \ ++ vgraph_separate_gp$(OBJ) \ ++ vgraph_separate_ml$(OBJ) \ ++ vgraph_separate_st$(OBJ) \ ++ vgraph_separate_th$(OBJ) \ ++ vgraph_separate_vw$(OBJ) \ ++ vgraph_separate_zr$(OBJ) \ ++ vgraph_store$(OBJ) \ ++ vmesh$(OBJ) \ ++ vmesh_check$(OBJ) \ ++ vmesh_separate_fm$(OBJ) \ ++ vmesh_separate_gg$(OBJ) \ ++ vmesh_separate_gr$(OBJ) \ ++ vmesh_separate_ml$(OBJ) \ ++ vmesh_separate_zr$(OBJ) \ ++ vmesh_separate_st$(OBJ) \ ++ vmesh_store$(OBJ) ++ $(AR) $(ARFLAGS) lib$(SCOTCHLIB)$(LIB) $(?) ++ -$(RANLIB) lib$(SCOTCHLIB)$(LIB) ++ ++ libmexscotch$(LIB) : arch$(OBJ) \ ++ arch_build$(OBJ) \ ++ arch_cmplt$(OBJ) \ ++ arch_cmpltw$(OBJ) \ ++ arch_deco$(OBJ) \ ++ arch_hcub$(OBJ) \ ++ arch_mesh$(OBJ) \ ++ arch_tleaf$(OBJ) \ ++ arch_torus$(OBJ) \ ++ arch_vcmplt$(OBJ) \ ++ arch_vhcub$(OBJ) \ ++ bgraph$(OBJ) \ ++ bgraph_bipart_bd$(OBJ) \ ++ bgraph_bipart_df$(OBJ) \ ++ bgraph_bipart_ex$(OBJ) \ ++ bgraph_bipart_fm$(OBJ) \ ++ bgraph_bipart_gg$(OBJ) \ ++ bgraph_bipart_gp$(OBJ) \ ++ bgraph_bipart_ml$(OBJ) \ ++ bgraph_bipart_st$(OBJ) \ ++ bgraph_bipart_zr$(OBJ) \ ++ bgraph_check$(OBJ) \ ++ bgraph_store$(OBJ) \ ++ common$(OBJ) \ ++ common_file$(OBJ) \ ++ common_file_compress$(OBJ) \ ++ common_file_uncompress$(OBJ) \ ++ common_integer$(OBJ) \ ++ common_memory$(OBJ) \ ++ common_stub$(OBJ) \ ++ gain$(OBJ) \ ++ geom$(OBJ) \ ++ graph$(OBJ) \ ++ graph_base$(OBJ) \ ++ graph_check$(OBJ) \ ++ graph_coarsen$(OBJ) \ ++ graph_induce$(OBJ) \ ++ graph_io$(OBJ) \ ++ graph_io_chac$(OBJ) \ ++ graph_io_habo$(OBJ) \ ++ graph_io_mmkt$(OBJ) \ ++ graph_io_scot$(OBJ) \ ++ graph_list$(OBJ) \ ++ hall_order_hd$(OBJ) \ ++ hall_order_hf$(OBJ) \ ++ hall_order_hx$(OBJ) \ ++ hgraph$(OBJ) \ ++ hgraph_check$(OBJ) \ ++ hgraph_induce$(OBJ) \ ++ hgraph_order_bl$(OBJ) \ ++ hgraph_order_cp$(OBJ) \ ++ hgraph_order_gp$(OBJ) \ ++ hgraph_order_hd$(OBJ) \ ++ hgraph_order_hf$(OBJ) \ ++ hgraph_order_hx$(OBJ) \ ++ hgraph_order_nd$(OBJ) \ ++ hgraph_order_si$(OBJ) \ ++ hgraph_order_st$(OBJ) \ ++ hmesh$(OBJ) \ ++ hmesh_check$(OBJ) \ ++ hmesh_hgraph$(OBJ) \ ++ hmesh_induce$(OBJ) \ ++ hmesh_mesh$(OBJ) \ ++ hmesh_order_bl$(OBJ) \ ++ hmesh_order_cp$(OBJ) \ ++ hmesh_order_gr$(OBJ) \ ++ hmesh_order_gp$(OBJ) \ ++ hmesh_order_hd$(OBJ) \ ++ hmesh_order_hf$(OBJ) \ ++ hmesh_order_hx$(OBJ) \ ++ hmesh_order_nd$(OBJ) \ ++ hmesh_order_si$(OBJ) \ ++ hmesh_order_st$(OBJ) \ ++ kgraph$(OBJ) \ ++ kgraph_map_rb$(OBJ) \ ++ kgraph_map_rb_map$(OBJ) \ ++ kgraph_map_rb_part$(OBJ) \ ++ kgraph_map_st$(OBJ) \ ++ library_arch$(OBJ) \ ++ library_arch_f$(OBJ) \ ++ library_arch_build$(OBJ) \ ++ library_arch_build_f$(OBJ) \ ++ library_arch_cmpltw$(OBJ) \ ++ library_arch_cmpltw_f$(OBJ) \ ++ library_geom$(OBJ) \ ++ library_geom_f$(OBJ) \ ++ library_graph$(OBJ) \ ++ library_graph_f$(OBJ) \ ++ library_graph_base$(OBJ) \ ++ library_graph_base_f$(OBJ) \ ++ library_graph_check$(OBJ) \ ++ library_graph_check_f$(OBJ) \ ++ library_graph_io_chac$(OBJ) \ ++ library_graph_io_chac_f$(OBJ) \ ++ library_graph_io_habo$(OBJ) \ ++ library_graph_io_habo_f$(OBJ) \ ++ library_graph_io_mmkt$(OBJ) \ ++ library_graph_io_mmkt_f$(OBJ) \ ++ library_graph_io_scot$(OBJ) \ ++ library_graph_io_scot_f$(OBJ) \ ++ library_graph_map$(OBJ) \ ++ library_graph_map_f$(OBJ) \ ++ library_graph_map_view$(OBJ) \ ++ library_graph_map_view_f$(OBJ) \ ++ library_graph_order$(OBJ) \ ++ library_graph_order_f$(OBJ) \ ++ library_mesh$(OBJ) \ ++ library_mesh_f$(OBJ) \ ++ library_mesh_graph$(OBJ) \ ++ library_mesh_graph_f$(OBJ) \ ++ library_mesh_io_habo$(OBJ) \ ++ library_mesh_io_habo_f$(OBJ) \ ++ library_mesh_io_scot$(OBJ) \ ++ library_mesh_io_scot_f$(OBJ) \ ++ library_mesh_order$(OBJ) \ ++ library_mesh_order_f$(OBJ) \ ++ library_parser$(OBJ) \ ++ library_parser_f$(OBJ) \ ++ library_random$(OBJ) \ ++ library_random_f$(OBJ) \ ++ mapping$(OBJ) \ ++ mapping_io$(OBJ) \ ++ mesh$(OBJ) \ ++ mesh_check$(OBJ) \ ++ mesh_coarsen$(OBJ) \ ++ mesh_graph$(OBJ) \ ++ mesh_induce_sepa$(OBJ) \ ++ mesh_io$(OBJ) \ ++ mesh_io_habo$(OBJ) \ ++ mesh_io_scot$(OBJ) \ ++ order$(OBJ) \ ++ order_check$(OBJ) \ ++ order_io$(OBJ) \ ++ parser$(OBJ) \ ++ parser_ll$(OBJ) \ ++ parser_yy$(OBJ) \ ++ vgraph$(OBJ) \ ++ vgraph_check$(OBJ) \ ++ vgraph_separate_bd$(OBJ) \ ++ vgraph_separate_es$(OBJ) \ ++ vgraph_separate_fm$(OBJ) \ ++ vgraph_separate_gg$(OBJ) \ ++ vgraph_separate_gp$(OBJ) \ ++ vgraph_separate_ml$(OBJ) \ ++ vgraph_separate_st$(OBJ) \ ++ vgraph_separate_th$(OBJ) \ ++ vgraph_separate_vw$(OBJ) \ ++ vgraph_separate_zr$(OBJ) \ ++ vgraph_store$(OBJ) \ ++ vmesh$(OBJ) \ ++ vmesh_check$(OBJ) \ ++ vmesh_separate_fm$(OBJ) \ ++ vmesh_separate_gg$(OBJ) \ ++ vmesh_separate_gr$(OBJ) \ ++ vmesh_separate_ml$(OBJ) \ ++ vmesh_separate_zr$(OBJ) \ ++ vmesh_separate_st$(OBJ) \ ++ vmesh_store$(OBJ) ++ $(AR) $(ARFLAGS) lib$(SCOTCHLIB)$(LIB) $(?) ++ -$(RANLIB) lib$(SCOTCHLIB)$(LIB) ++ + libptscotcherr$(LIB) : library_error$(OBJ) + $(AR) $(ARFLAGS) $(@) $(?) + -$(RANLIB) $(@) +*************** +*** 2467,2469 **** +--- 2817,2835 ---- + libscotcherrexit$(LIB) : library_error_exit$(OBJ) + $(AR) $(ARFLAGS) $(@) $(?) + -$(RANLIB) $(@) ++ ++ libnfioscotcherr$(LIB) : library_error$(OBJ) ++ $(AR) $(ARFLAGS) $(@) $(?) ++ -$(RANLIB) $(@) ++ ++ libnfioscotcherrexit$(LIB) : library_error_exit$(OBJ) ++ $(AR) $(ARFLAGS) $(@) $(?) ++ -$(RANLIB) $(@) ++ ++ libmexscotcherr$(LIB) : library_error$(OBJ) ++ $(AR) $(ARFLAGS) $(@) $(?) ++ -$(RANLIB) $(@) ++ ++ libmexscotcherrexit$(LIB) : library_error_exit$(OBJ) ++ $(AR) $(ARFLAGS) $(@) $(?) ++ -$(RANLIB) $(@) +diff -rc src/src/libscotch/mapping.h new5/src/libscotch/mapping.h +*** src/src/libscotch/mapping.h 2008-10-27 08:27:47.000000000 -0700 +--- new5/src/libscotch/mapping.h 2010-07-21 17:13:15.667257702 -0700 +*************** +*** 106,112 **** +--- 106,116 ---- + int mapInit2 (Mapping * restrict const, const Gnum, const Gnum, const Arch * restrict const, const ArchDom * restrict const); + void mapExit (Mapping * const); + int mapLoad (Mapping * restrict const, const Gnum * restrict const, FILE * restrict const); ++ #ifndef NOFILEIO + int mapSave (const Mapping * restrict const, const Gnum * restrict const, FILE * restrict const); ++ #else /* NOFILEIO */ ++ int mapSave (Gnum *, Gnum (**)[2], const Mapping * restrict const, const Gnum * restrict const, FILE * restrict const); ++ #endif /* NOFILEIO */ + int mapView (const Mapping * restrict const, const Graph * restrict const, FILE * const); + + #undef static +diff -rc src/src/libscotch/mapping_io.c new5/src/libscotch/mapping_io.c +*** src/src/libscotch/mapping_io.c 2008-05-22 06:44:43.000000000 -0700 +--- new5/src/libscotch/mapping_io.c 2010-07-21 17:13:15.670257723 -0700 +*************** +*** 199,204 **** +--- 199,208 ---- + + int + mapSave ( ++ #ifdef NOFILEIO ++ Gnum *pnvert, ++ Gnum (**pmaptab)[2], ++ #endif /* NOFILEIO */ + const Mapping * restrict const mappptr, + const Gnum * restrict const vlbltab, + FILE * restrict const stream) +*************** +*** 206,226 **** + const Gnum * restrict vlbltax; + Gnum vertnum; + + vlbltax = (vlbltab != NULL) ? (vlbltab - mappptr->baseval) : NULL; + + if (fprintf (stream, "%ld\n", (long) mappptr->vertnbr) == EOF) { + errorPrint ("mapSave: bad output (1)"); + return (1); + } + + for (vertnum = mappptr->baseval; vertnum < (mappptr->vertnbr + mappptr->baseval); vertnum ++) { + if (fprintf (stream, "%ld\t%ld\n", +! (long) ((vlbltax != NULL) ? vlbltax[vertnum] : vertnum), + (long) archDomNum (&mappptr->archdat, &mappptr->domntab[mappptr->parttax[vertnum]])) == EOF) { + errorPrint ("mapSave: bad output (2)"); + return (1); + } + } + + return (0); + } +--- 210,258 ---- + const Gnum * restrict vlbltax; + Gnum vertnum; + ++ #ifdef NOFILEIO ++ // printf("mapSave - stream=%p\n",stream); ++ #endif /* NOFILEIO */ + vlbltax = (vlbltab != NULL) ? (vlbltab - mappptr->baseval) : NULL; + ++ #ifndef NOFILEIO + if (fprintf (stream, "%ld\n", (long) mappptr->vertnbr) == EOF) { + errorPrint ("mapSave: bad output (1)"); + return (1); + } ++ #else /* NOFILEIO */ ++ if (pnvert) { ++ *pnvert=mappptr->vertnbr; ++ // printf("mapSave - nvert=%d\n",*pnvert); ++ } ++ if (pmaptab) { ++ *pmaptab = (Gnum (*)[2]) malloc(mappptr->vertnbr*2*sizeof(Gnum)); ++ // printf("mapSave - maptab=%p\n",*pmaptab); ++ } ++ #endif /* NOFILEIO */ + ++ #ifndef NOFILEIO + for (vertnum = mappptr->baseval; vertnum < (mappptr->vertnbr + mappptr->baseval); vertnum ++) { + if (fprintf (stream, "%ld\t%ld\n", +! /* not sure why, but need to offset vlbltax in other direction (jes, 12/11/09) */ +! // (long) ((vlbltax != NULL) ? vlbltax[vertnum] : vertnum), +! (long) ((vlbltax != NULL) ? vlbltax[vertnum+mappptr->baseval] : vertnum), + (long) archDomNum (&mappptr->archdat, &mappptr->domntab[mappptr->parttax[vertnum]])) == EOF) { + errorPrint ("mapSave: bad output (2)"); + return (1); + } + } ++ #else /* NOFILEIO */ ++ if (pmaptab && *pmaptab) ++ for (vertnum = mappptr->baseval; vertnum < (mappptr->vertnbr + mappptr->baseval); vertnum ++) { ++ /* not sure why, but need to offset vlbltax in other direction (jes, 12/11/09) */ ++ // (*pmaptab)[vertnum-mappptr->baseval][0]=((vlbltax != NULL) ? vlbltax[vertnum] : vertnum); ++ (*pmaptab)[vertnum-mappptr->baseval][0]=((vlbltax != NULL) ? vlbltax[vertnum+mappptr->baseval] : vertnum); ++ (*pmaptab)[vertnum-mappptr->baseval][1]=archDomNum (&mappptr->archdat, &mappptr->domntab[mappptr->parttax[vertnum]]); ++ // printf("mapSave - vertnum=%d; vlbltax=%d,archDomNum=%d\n", ++ // vertnum,((vlbltax != NULL) ? vlbltax[vertnum+mappptr->baseval] : -1),archDomNum (&mappptr->archdat, &mappptr->domntab[mappptr->parttax[vertnum]])); ++ } ++ #endif /* NOFILEIO */ + + return (0); + } +diff -rc src/src/libscotch/mesh_io_scot.c new5/src/libscotch/mesh_io_scot.c +*** src/src/libscotch/mesh_io_scot.c 2008-05-22 06:44:43.000000000 -0700 +--- new5/src/libscotch/mesh_io_scot.c 2010-07-21 17:13:15.672257737 -0700 +*************** +*** 85,91 **** +--- 85,95 ---- + int o; + + if (filesrcptr != NULL) { ++ #ifndef NOFILEIO + if (graphLoad (meshptr, filesrcptr, -1, 0) != 0) ++ #else /* NOFILEIO */ ++ if (graphLoad (meshptr, filesrcptr, -1, 0, 0, 0, NULL, NULL, NULL, NULL, NULL) != 0) ++ #endif /* NOFILEIO */ + return (1); + } + +diff -rc src/src/libscotch/module.h new5/src/libscotch/module.h +*** src/src/libscotch/module.h 2009-04-26 23:07:14.000000000 -0700 +--- new5/src/libscotch/module.h 2010-07-21 17:13:15.675257758 -0700 +*************** +*** 1,3 **** +--- 1,5 ---- ++ #ifndef _SCOTCH_MODULE_H_ ++ #define _SCOTCH_MODULE_H_ + /* Copyright 2004,2007-2009 ENSEIRB, INRIA & CNRS + ** + ** This file is part of the Scotch software package for static mapping, +*************** +*** 55,60 **** +--- 57,65 ---- + + #define MODULE_H + ++ /*Don't forget stdint.h:*/ ++ #include "stdint.h" ++ + /* + ** Collective communication handling. + */ +*************** +*** 156,161 **** +--- 161,167 ---- + #define intSave _SCOTCHintSave + #define intAscn _SCOTCHintAscn + #define intPerm _SCOTCHintPerm ++ #define intRandResetStatic _SCOTCHintRandResetStatic + #define intRandReset _SCOTCHintRandReset + #define intRandInit _SCOTCHintRandInit + /* #define intRandVal _SCOTCHintRandVal Already a macro */ +*************** +*** 681,683 **** +--- 687,691 ---- + #define vmeshStoreSave _SCOTCHvmeshStoreSave + #define vmeshStoreUpdt _SCOTCHvmeshStoreUpdt + #endif /* SCOTCH_RENAME */ ++ ++ #endif //#ifndef _SCOTCH_MODULE_H_ +diff -rc src/src/libscotch/parser_ll.l new5/src/libscotch/parser_ll.l +*** src/src/libscotch/parser_ll.l 2008-05-22 06:44:43.000000000 -0700 +--- new5/src/libscotch/parser_ll.l 2010-07-21 17:13:15.677257772 -0700 +*************** +*** 192,197 **** +--- 192,214 ---- + stratParserInit ( + const char * const string) /*+ Strategy string to parse +*/ + { ++ /* reset static variables from previous runs (jes, 4/29/10) */ ++ yy_current_buffer = 0; ++ yy_hold_char = (char) 0; ++ yy_n_chars=0; /* number of characters read into yy_ch_buf */ ++ yy_c_buf_p = (char *) 0; ++ yy_init = 1; /* whether we need to initialize */ ++ yy_start = 0; /* start state number */ ++ yy_did_buffer_switch_on_eof=0; ++ yy_last_accepting_state=0; ++ yy_last_accepting_cpos = (char *) 0; ++ stratparserstringptr = (char *) 0; /* Pointer to the string to parse */ ++ #if YY_STACK_USED ++ yy_start_stack_ptr = 0; ++ yy_start_stack_depth = 0; ++ yy_start_stack = 0; ++ #endif ++ + #ifdef FLEX_SCANNER + yyrestart (yyin); /* (Re-)initialize the parser */ + #endif /* FLEX_SCANNER */ +diff -rc src/src/libscotch/parser_yy.y new5/src/libscotch/parser_yy.y +*** src/src/libscotch/parser_yy.y 2008-10-22 15:12:48.000000000 -0700 +--- new5/src/libscotch/parser_yy.y 2010-07-21 17:13:15.679257786 -0700 +*************** +*** 774,779 **** +--- 774,780 ---- + stratParserInit (string); /* Initialize the lexical parser */ + parserstrattab = strattab; /* Point to the parsing tables */ + parserstratcurr = NULL; /* Clear up the temporary strategy pointer */ ++ parserparamcurr = NULL; /* reset the last static (jes, 4/29/10) */ + + if (stratParserParse2 () != 0) { /* Parse the strategy string */ + if (parserstratcurr != NULL) +diff -rc src/src/libscotch/vgraph_separate_vw.c new5/src/libscotch/vgraph_separate_vw.c +*** src/src/libscotch/vgraph_separate_vw.c 2008-05-22 06:44:43.000000000 -0700 +--- new5/src/libscotch/vgraph_separate_vw.c 2010-07-21 17:13:15.682257807 -0700 +*************** +*** 83,88 **** +--- 83,89 ---- + FILE * restrict fileptr; + Gnum vertnum; /* Vertex number */ + ++ printf("vgraphSeparateVw begin -- vgraphseparatevwfilenum=%d\n",vgraphseparatevwfilenum); + sprintf (nametab, "vgraphseparatevw_output_%08d.map", vgraphseparatevwfilenum ++); + if ((fileptr = fopen (nametab, "w+")) == NULL) { + errorPrint ("vgraphSeparateVw: cannot open partition file"); +*************** +*** 102,106 **** +--- 103,108 ---- + } + } + ++ printf("vgraphSeparateVw end -- vgraphseparatevwfilenum=%d\n",vgraphseparatevwfilenum); + return (0); + } +diff -rc src/src/Makefile new5/src/Makefile +*** src/src/Makefile 2008-09-15 05:50:51.000000000 -0700 +--- new5/src/Makefile 2010-07-21 17:13:15.684257821 -0700 +*************** +*** 97,102 **** +--- 97,109 ---- + (cd scotch ; $(MAKE) VERSION=\"$(VERSION)\" ptscotch && $(MAKE) ptinstall) + (cd libscotchmetis ; $(MAKE) ptscotch && $(MAKE) ptinstall) + ++ nfioscotch : required ++ (cd libscotch ; $(MAKE) VERSION=\"$(VERSION)\" nfioscotch && $(MAKE) nfioinstall) ++ ++ mexscotch : required ++ (cd libscotch ; $(MAKE) VERSION=\"$(VERSION)\" mexscotch && $(MAKE) mexinstall) ++ (cd scotch ; $(MAKE) VERSION=\"$(VERSION)\" mexscotch && $(MAKE) mexinstall) ++ + install : required $(bindir) $(includedir) $(libdir) $(mandir)/man1 + -$(CP) -f ../bin/[agm]*$(EXE) $(bindir) + -$(CP) -f ../include/*scotch*.h $(includedir) +Only in new5/src: Makefile.inc +diff -rc src/src/scotch/gmap.h new5/src/scotch/gmap.h +*** src/src/scotch/gmap.h 2008-06-18 11:05:17.000000000 -0700 +--- new5/src/scotch/gmap.h 2010-07-21 17:13:15.686257834 -0700 +*************** +*** 1,3 **** +--- 1,5 ---- ++ #ifndef _SCOTCH_GMAP_H_ ++ #define _SCOTCH_GMAP_H_ + /* Copyright 2004,2007,2008 ENSEIRB, INRIA & CNRS + ** + ** This file is part of the Scotch software package for static mapping, +*************** +*** 87,89 **** +--- 89,93 ---- + #define C_FLAGVERBSTR 0x0002 /* Verbose flags */ + #define C_FLAGVERBTIM 0x0004 + #define C_FLAGVERBMAP 0x0008 ++ ++ #endif //#ifndef _SCOTCH_GMAP_H_ +Only in new5/src/scotch: gmap_mex.c +Only in new5/src/scotch: gmapx.c +diff -rc src/src/scotch/Makefile new5/src/scotch/Makefile +*** src/src/scotch/Makefile 2009-04-27 02:19:43.000000000 -0700 +--- new5/src/scotch/Makefile 2010-07-21 17:13:15.689257855 -0700 +*************** +*** 49,59 **** + %$(EXE) : %.c + $(CC) $(CFLAGS) -I$(includedir) -I../libscotch -DSCOTCH_VERSION=\"$(VERSION)\" $(<) -o $(@) -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) + + ## + ## Project rules. + ## + +! .PHONY : ptscotch scotch ptinstall install clean realclean + + scotch : clean + $(MAKE) CC="$(CCS)" SCOTCHLIB=scotch \ +--- 49,62 ---- + %$(EXE) : %.c + $(CC) $(CFLAGS) -I$(includedir) -I../libscotch -DSCOTCH_VERSION=\"$(VERSION)\" $(<) -o $(@) -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) + ++ %$(MEX) : %.c ++ $(CCM) $(MFLAGS) -I$(includedir) -I../libscotch -DSCOTCH_VERSION=\"$(VERSION)\" $(<) -o $(@) -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) ++ + ## + ## Project rules. + ## + +! .PHONY : ptscotch scotch mexscotch ptinstall install mexinstall clean realclean + + scotch : clean + $(MAKE) CC="$(CCS)" SCOTCHLIB=scotch \ +*************** +*** 94,99 **** +--- 97,108 ---- + dgscat$(EXE) \ + dgtst$(EXE) + ++ mexscotch : clean ++ $(MAKE) CFLAGS="$(CFLAGS) -DNOFILEIO -DMATLAB -I${MATLAB_DIR}/extern/include" CC="$(CCS)" CCD="$(CCS)" LDFLAGS="$(LDFLAGS) -Wl,-rpath-link,${MATLAB_DIR}/bin/glnxa64 -L${MATLAB_DIR}/bin/glnxa64 -lmex -lmat" SCOTCHLIB=mexscotch \ ++ gmapx$(OBJ) ++ $(MAKE) CFLAGS="$(CFLAGS) -DNOFILEIO -DMATLAB -I${MATLAB_DIR}/extern/include" CC="$(CCS)" LDFLAGS="$(LDFLAGS) -Wl,-rpath-link,${MATLAB_DIR}/bin/glnxa64 -L${MATLAB_DIR}/bin/glnxa64 -lmex -lmat gmapx$(OBJ)" SCOTCHLIB=mexscotch \ ++ gmap_mex$(MEX) ++ + install : + -$(CP) acpl$(EXE) amk_ccc$(EXE) amk_fft2$(EXE) amk_grf$(EXE) amk_hy$(EXE) amk_m2$(EXE) amk_p2$(EXE) atst$(EXE) gbase$(EXE) gcv$(EXE) gmap$(EXE) gmk_hy$(EXE) gmk_m2$(EXE) gmk_m3$(EXE) gmk_msh$(EXE) gmk_ub2$(EXE) gmtst$(EXE) gord$(EXE) gotst$(EXE) gout$(EXE) *gtst$(EXE) gscat$(EXE) mcv$(EXE) mmk_m2$(EXE) mmk_m3$(EXE) mord$(EXE) mtst$(EXE) $(bindir) + -$(RM) $(bindir)/gpart$(EXE) +*************** +*** 104,111 **** +--- 113,126 ---- + -$(RM) $(bindir)/dgpart$(EXE) + -$(LN) $(bindir)/dgmap$(EXE) $(bindir)/dgpart$(EXE) + ++ mexinstall : ++ -$(CP) gmap_mex$(MEX) $(bindir) ++ -$(RM) $(bindir)/gpart_mex$(MEX) ++ -$(LN) $(bindir)/gmap_mex$(MEX) $(bindir)/gpart_mex$(MEX) ++ + clean : + -$(RM) *~ *$(OBJ) acpl$(EXE) amk_ccc$(EXE) amk_fft2$(EXE) amk_grf$(EXE) amk_hy$(EXE) amk_m2$(EXE) amk_p2$(EXE) atst$(EXE) gbase$(EXE) gcv$(EXE) *gmap$(EXE) gmk_hy$(EXE) gmk_m2$(EXE) gmk_m3$(EXE) gmk_msh$(EXE) gmk_ub2$(EXE) gmtst$(EXE) *gord$(EXE) gotst$(EXE) gout$(EXE) *gpart$(EXE) *gscat$(EXE) *gtst$(EXE) mcv$(EXE) mmk_m2$(EXE) mmk_m3$(EXE) mord$(EXE) mtst$(EXE) ++ -$(RM) gmap_mex$(MEX) + + realclean : clean + +*************** +*** 365,367 **** +--- 380,403 ---- + $(libdir)/libscotch$(LIB) \ + $(libdir)/libscotcherrexit$(LIB) \ + mtst.h ++ ++ gmapx$(OBJ) : gmapx.c \ ++ ../libscotch/module.h \ ++ ../libscotch/common.h \ ++ $(includedir)/scotch.h \ ++ $(libdir)/libmexscotch$(LIB) \ ++ $(libdir)/libmexscotcherrexit$(LIB) \ ++ gmap.h ++ ++ gmap_mex$(MEX) : gmap_mex.c \ ++ ../libscotch/module.h \ ++ ../libscotch/common.h \ ++ $(includedir)/scotch.h \ ++ $(libdir)/libmexscotch$(LIB) \ ++ $(libdir)/libmexscotcherrexit$(LIB) \ ++ gmap.h ++ ++ gpart_mex$(MEX) : gmap_mex$(MEX) ++ -$(RM) gpart_mex$(MEX) ++ -$(LN) gmap_mex$(MEX) gpart_mex$(MEX) ++ Index: /issm/trunk-jpl-damage/externalpackages/scotch/scotch_README.txt =================================================================== --- /issm/trunk-jpl-damage/externalpackages/scotch/scotch_README.txt (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/scotch/scotch_README.txt (revision 11330) @@ -0,0 +1,296 @@ +8/06/09: + +following INSTALL.txt: +- GNU Make 3.81, lex, yacc all present + + +[jschierm@astrid src]$ diff Makefile_old.inc Makefile.inc + +- started with Makefile.inc.i686_sun_solaris5 +- changed CCS from cc to gcc +- removed SCOTCH_PTHREAD, since MPICH2 1.0.2p1 is prior to 1.0.7 +- added -std=c99 to CFLAGS for "restrict" attribute (based on various internet pages) +- added -DCOMMON_TIMING_OLD to CFLAGS for undeclared CLOCK_REALTIME (based on common2.c) +- added MEX, CCM, and MFLAGS for Matlab mex modules (as well as Matlab libraries and -largeArrayDims) +- removed -DCOMMON_PTHREAD from CFLAGS and MFLAGS to eliminate fatal exception at pthread_exit in gmap_mex.c +- removed -DCOMMON_FILE_COMPRESS_GZ from CFLAGS and MFLAGS since gzip not used +- added -Wl,-rpath-link,/usr/local/pkgs/matlab-7.6/bin/glnxa64 to LDFLAGS to eliminate missing libhdf5.so.0 in Matlab directories (based on Cielo make) + +3a4 +> MEX = .mexa64 +12,13c13,16 +< CFLAGS = -m64 -O3 -std=c99 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DINTSIZE64 -Dintptr_t="long int" -DCOMMON_TIMING_OLD +< LDFLAGS = -lz -lm -lrt +--- +> CCM = mex +> CFLAGS = -m64 -O3 -std=c99 -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DCOMMON_TIMING_OLD -DMATLAB -fPIC -I/usr/local/pkgs/matlab-7.6/extern/include +> LDFLAGS = -lz -lm -lrt -Wl,-rpath-link,/usr/local/pkgs/matlab-7.6/bin/glnxa64 -L/usr/local/pkgs/matlab-7.6/bin/glnxa64 -lmex -lmat +> MFLAGS = -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DCOMMON_TIMING_OLD -DMATLAB -I/usr/local/pkgs/matlab-7.6/extern/include -largeArrayDims + + +[jschierm@astrid libscotch]$ diff common_old.c common.c + +- redirect usagePrint to within Matlab +102a103 +> #ifndef MATLAB +105a107,111 +> #else /* MATLAB */ +> mexPrintf ("Usage is:\n"); +> for (cptr = data; *cptr != NULL; cptr ++) +> mexPrintf (" %s\n", *cptr); +> #endif /* MATLAB */ + + +[jschierm@astrid libscotch]$ diff common_old.h common.h + +- fix undeclared type intptr_t +68a69 +> #include /* added for intptr_t */ + +- for running as a matlab mex function +- add macro for fprintf to capture missing output +- fix exits to exit within Matlab +90a92,105 +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> #define exit(status) mexErrMsgTxt("exit=" #status) +> #endif +> + + +[jschierm@astrid libscotch]$ diff dummysizes_old.c dummysizes.c + +- dummysizes must run by itself during compilation and exit cleanly +269a270 +> #ifndef MATLAB +270a272 +> #endif /* MATLAB */ + + +[jschierm@astrid libscotch]$ diff library_error_exit_old.c library_error_exit.c + +- redirect errorPrint and errorPrintW to within Matlab +116a117 +> #ifndef MATLAB +133a135,152 +> #else /* MATLAB */ +> mexPrintf ("%s", _SCOTCHerrorProgName); +> #ifdef SCOTCH_PTSCOTCH +> if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && +> (proclocnum != 0) && +> (MPI_Comm_rank (MPI_COMM_WORLD, &proclocnum) == MPI_SUCCESS)) +> mexPrintf ("(%d): ", proclocnum); +> #else /* SCOTCH_PTSCOTCH */ +> if (_SCOTCHerrorProgName[0] != '\0') +> mexPrintf (": "); +> #endif /* SCOTCH_PTSCOTCH */ +> mexPrintf ("ERROR: "); +> va_start (errlist, errstr); +> mexPrintf (errstr, errlist); /* Print arguments */ +> va_end (errlist); +> mexPrintf ("\n"); +> #endif /* MATLAB */ +> +157a177 +> #ifndef MATLAB +173a194,211 +> +> #else /* MATLAB */ +> mexPrintf ("%s", _SCOTCHerrorProgName); +> #ifdef SCOTCH_PTSCOTCH +> if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && +> (proclocnum != 0) && +> (MPI_Comm_rank (MPI_COMM_WORLD, &proclocnum) == MPI_SUCCESS)) +> mexPrintf ("(%d): ", proclocnum); +> #else /* SCOTCH_PTSCOTCH */ +> if (_SCOTCHerrorProgName[0] != '\0') +> mexPrintf (": "); +> #endif /* SCOTCH_PTSCOTCH */ +> mexPrintf ("WARNING: "); +> va_start (errlist, errstr); +> mexPrintf (errstr, errlist); /* Print arguments */ +> va_end (errlist); +> mexPrintf ("\n"); +> #endif /* MATLAB */ + + +[jschierm@astrid scotch]$ diff Makefile_old Makefile +- add MEX rule +- add gmap_mex into scotch, clean, and install rules +- add gmap_mex object +51a52,54 +> %$(MEX) : %.c +> $(CCM) $(MFLAGS) -I$(includedir) -I../libscotch -DSCOTCH_VERSION=\"$(VERSION)\" $(<) -o $(@) -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) +> +70a74 +> gmap_mex$(MEX) \ +98c102 +< -$(CP) acpl$(EXE) amk_ccc$(EXE) amk_fft2$(EXE) amk_grf$(EXE) amk_hy$(EXE) amk_m2$(EXE) amk_p2$(EXE) atst$(EXE) gbase$(EXE) gcv$(EXE) gmap$(EXE) gmk_hy$(EXE) gmk_m2$(EXE) gmk_m3$(EXE) gmk_msh$(EXE) gmk_ub2$(EXE) gmtst$(EXE) gord$(EXE) gotst$(EXE) gout$(EXE) *gtst$(EXE) gscat$(EXE) mcv$(EXE) mmk_m2$(EXE) mmk_m3$(EXE) mord$(EXE) mtst$(EXE) $(bindir) +--- +> -$(CP) acpl$(EXE) amk_ccc$(EXE) amk_fft2$(EXE) amk_grf$(EXE) amk_hy$(EXE) amk_m2$(EXE) amk_p2$(EXE) atst$(EXE) gbase$(EXE) gcv$(EXE) gmap$(EXE) gmap_mex$(MEX) gmk_hy$(EXE) gmk_m2$(EXE) gmk_m3$(EXE) gmk_msh$(EXE) gmk_ub2$(EXE) gmtst$(EXE) gord$(EXE) gotst$(EXE) gout$(EXE) *gtst$(EXE) gscat$(EXE) mcv$(EXE) mmk_m2$(EXE) mmk_m3$(EXE) mord$(EXE) mtst$(EXE) $(bindir) +108c112 +< -$(RM) *~ *$(OBJ) acpl$(EXE) amk_ccc$(EXE) amk_fft2$(EXE) amk_grf$(EXE) amk_hy$(EXE) amk_m2$(EXE) amk_p2$(EXE) atst$(EXE) gbase$(EXE) gcv$(EXE) *gmap$(EXE) gmk_hy$(EXE) gmk_m2$(EXE) gmk_m3$(EXE) gmk_msh$(EXE) gmk_ub2$(EXE) gmtst$(EXE) *gord$(EXE) gotst$(EXE) gout$(EXE) *gpart$(EXE) *gscat$(EXE) *gtst$(EXE) mcv$(EXE) mmk_m2$(EXE) mmk_m3$(EXE) mord$(EXE) mtst$(EXE) +--- +> -$(RM) *~ *$(OBJ) acpl$(EXE) amk_ccc$(EXE) amk_fft2$(EXE) amk_grf$(EXE) amk_hy$(EXE) amk_m2$(EXE) amk_p2$(EXE) atst$(EXE) gbase$(EXE) gcv$(EXE) *gmap$(EXE) gmap_mex$(MEX) gmk_hy$(EXE) gmk_m2$(EXE) gmk_m3$(EXE) gmk_msh$(EXE) gmk_ub2$(EXE) gmtst$(EXE) *gord$(EXE) gotst$(EXE) gout$(EXE) *gpart$(EXE) *gscat$(EXE) *gtst$(EXE) mcv$(EXE) mmk_m2$(EXE) mmk_m3$(EXE) mord$(EXE) mtst$(EXE) +239a244,251 +> gmap_mex$(MEX) : gmap_mex.c \ +> ../libscotch/module.h \ +> ../libscotch/common.h \ +> $(includedir)/scotch.h \ +> $(libdir)/libscotch$(LIB) \ +> $(libdir)/libscotcherrexit$(LIB) \ +> gmap.h +> + + +[jschierm@astrid scotch]$ diff gmap.c gmap_mex.c +- convert gmap to gmap_mex mex function with variable argument list +117,120c117,120 +< int +< main ( +< int argc, +< char * argv[]) +--- +> void mexFunction( int nlhs, +> mxArray *plhs[], +> int nrhs, +> const mxArray *prhs[] ) +121a122,123 +> int argcm; +> char argvm[21][257]; +130a133,152 +> /* check static variables from previous runs */ +> +> if (C_paraNum > 0 || C_fileNum > 0) +> mexErrMsgTxt("gmap_mex still in memory -- clear gmap_mex and try again.\n"); +> +> /* load matlab argument list */ +> +> argcm=nrhs+1; +> mexPrintf("argcm=%d\n",argcm); +> strcpy(argvm[0],"gmap"); +> for (i=0; i if (!mxIsChar(prhs[i])) { +> mexPrintf("%s -- prhs[%d] must be character.\n","gmap",i); +> mexErrMsgTxt(" "); +> } +> else +> mxGetString(prhs[i],argvm[i+1],256); +> for (i=0; i mexPrintf("argvm[%d]=%s\n",i,argvm[i]); +> +132,133c154,155 +< i = strlen (argv[0]); +< if ((i >= 5) && (strncmp (argv[0] + i - 5, "gpart", 5) == 0)) { +--- +> i = strlen (argvm[0]); +> if ((i >= 5) && (strncmp (argvm[0] + i - 5, "gpart", 5) == 0)) { +144c166 +< if ((argc >= 2) && (argv[1][0] == '?')) { /* If need for help */ +--- +> if ((argcm >= 2) && (argvm[1][0] == '?')) { /* If need for help */ +151a174,175 +> printf("point 0: C_FILENBR=%d, C_fileNbr=%d, C_paraNbr=%d\n", +> C_FILENBR,C_fileNbr,C_paraNbr); +154,155c178,183 +< for (i = 1; i < argc; i ++) { /* Loop for all option codes */ +< if ((argv[i][0] != '-') || (argv[i][1] == '\0') || (argv[i][1] == '.')) { /* If found a file name */ +--- +> for (i = 1; i < argcm; i ++) { /* Loop for all option codes */ +> printf("point 1: i=%d; C_fileNbr=%d, C_fileNum=%d, C_paraNbr=%d, C_paraNum=%d\n", +> i,C_fileNbr,C_fileNum,C_paraNbr,C_paraNum); +> if ((argvm[i][0] != '-') || (argvm[i][1] == '\0') || (argvm[i][1] == '.')) { /* If found a file name */ +> printf("point 2: i=%d; C_fileNbr=%d, C_fileNum=%d, C_paraNbr=%d, C_paraNum=%d\n", +> i,C_fileNbr,C_fileNum,C_paraNbr,C_paraNum); +157,158c185,186 +< if ((C_partNbr = atoi (argv[i])) < 1) /* Get the number of parts */ +< errorPrint ("main: invalid number of parts (\"%s\")", argv[i]); +--- +> if ((C_partNbr = atoi (argvm[i])) < 1) /* Get the number of parts */ +> errorPrint ("main: invalid number of parts (\"%s\")", argvm[i]); +161a190,191 +> printf("point 3: i=%d; C_fileNbr=%d, C_fileNum=%d, C_paraNbr=%d, C_paraNum=%d\n", +> i,C_fileNbr,C_fileNum,C_paraNbr,C_paraNum); +163c193 +< C_fileTab[C_fileNum ++].name = argv[i]; +--- +> C_fileTab[C_fileNum ++].name = argvm[i]; +165a196,197 +> printf("point 4: i=%d; C_fileNbr=%d, C_fileNum=%d, C_paraNbr=%d, C_paraNum=%d\n", +> i,C_fileNbr,C_fileNum,C_paraNbr,C_paraNum); +168c200 +< switch (argv[i][1]) { +--- +> switch (argvm[i][1]) { +177c209 +< SCOTCH_stratGraphMap (&stradat, &argv[i][2]); +--- +> SCOTCH_stratGraphMap (&stradat, &argvm[i][2]); +181,182c213,214 +< for (j = 2; argv[i][j] != '\0'; j ++) { +< switch (argv[i][j]) { +--- +> for (j = 2; argvm[i][j] != '\0'; j ++) { +> switch (argvm[i][j]) { +192c224 +< errorPrint ("main: invalid source graph option (\"%c\")", argv[i][j]); +--- +> errorPrint ("main: invalid source graph option (\"%c\")", argvm[i][j]); +202,203c234,235 +< for (j = 2; argv[i][j] != '\0'; j ++) { +< switch (argv[i][j]) { +--- +> for (j = 2; argvm[i][j] != '\0'; j ++) { +> switch (argvm[i][j]) { +217c249 +< errorPrint ("main: unprocessed parameter \"%c\" in \"%s\"", argv[i][j], argv[i]); +--- +> errorPrint ("main: unprocessed parameter \"%c\" in \"%s\"", argvm[i][j], argvm[i]); +222c254 +< errorPrint ("main: unprocessed option (\"%s\")", argv[i]); +--- +> errorPrint ("main: unprocessed option (\"%s\")", argvm[i]); +225a258 +> printf("point 5\n"); +230a264 +> printf("point 6\n"); +232a267 +> printf("point 7\n"); +235a271 +> printf("point 8\n"); +239a276 +> printf("point 9\n"); +244a282 +> printf("point 10\n"); +251a290 +> printf("point 11\n"); +256a296 +> printf("point 12\n"); +264a305 +> printf("point 13\n"); +271a313 +> printf("point 14\n"); +273a316 +> printf("point 15\n"); +276a320 +> printf("point 16\n"); +277a322 +> printf("point 16a\n"); +278a324 +> printf("point 16b\n"); +279a326 +> printf("point 16c\n"); +280a328 +> printf("point 17\n"); +284a333 +> printf("point 18\n"); + Index: /issm/trunk-jpl-damage/externalpackages/scotch/scotch_jes_notes.txt =================================================================== --- /issm/trunk-jpl-damage/externalpackages/scotch/scotch_jes_notes.txt (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/scotch/scotch_jes_notes.txt (revision 11330) @@ -0,0 +1,308 @@ +8/06/09: + +following INSTALL.txt: +- GNU Make 3.81, lex, yacc all present +- started with Makefile.inc.i686_sun_solaris5 +- changed CCS from cc to gcc +- removed SCOTCH_PTHREAD, since MPICH2 1.0.2p1 is prior to 1.0.7 + +graph.h:110: error: expected :, ,, ;, ) or __attribute__ before vnumtab +(and so on for "restrict" attribute in graph.h,geom.h,mesh.h,arch.h,mapping.h,order.h) +- added -std=c99 to CFLAGS (based on various internet pages) + +bgraph_bipart_gg.c:267: error: intptr_t undeclared +- according to various internet pages, should be included in c99 standard +- defined in /usr/include/stdint.h (also referenced in inttypes.h), so why not included? +- added -DINTSIZE64 to CFLAGS, still didn't work (based on INSTALL.txt) +- added -Dintptr_t="long int" (based on /usr/include/stdint.h) + +common2.c:764: error: storage size of tp isn't known +common2.c:766: error: CLOCK_REALTIME undeclared +- added -DCOMMON_TIMING_OLD to CFLAGS (based on source code) + +8/13/09: + +for running as a matlab mex function: +[jschierm@astrid libscotch]$ diff common_old.h common.h +90a91,102 +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> #endif +> + +[jschierm@astrid src]$ diff Makefile_old.inc Makefile.inc +12,13c12,13 +< CFLAGS = -m64 -O3 -std=c99 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DINTSIZE64 -Dintptr_t="long int" -DCOMMON_TIMING_OLD +< LDFLAGS = -lz -lm -lrt +--- +> CFLAGS = -m64 -O3 -std=c99 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Du_int32_t=uint32_t -Du_int64_t=uint64_t -DINTSIZE64 -Dintptr_t="long int" -DCOMMON_TIMING_OLD -DMATLAB -fPIC -I/usr/local/pkgs/matlab-7.6/extern/include +> LDFLAGS = -lz -lm -lrt -L/usr/local/pkgs/matlab-7.6/bin/glnxa64 -lmat -lmex + +8/19/09: + +- still having problems with intptr_t: +gcc: int: No such file or directory +In file included from ../libscotch/common.h:81, + from gmap_mex.c:75: +/usr/include/unistd.h:238: error: two or more data types in declaration specifiers +- removed -DINTSIZE64 and -Dintptr_t="long int" from CFLAGS above +[jschierm@astrid libscotch]$ diff common_old.h common.h +68a69 +> #include /* added for intptr_t */ + +8/20/09: + +- must fix exits to exit within Matlab: +[jschierm@astrid libscotch]$ diff common_old.h common.h +68a69 +> #include /* added for intptr_t */ +90a92,104 +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> #define exit(status) mexErrMsgTxt("exit=" #status) +> #endif +> + +- however, dummysizes must run by itself during compilation and exit cleanly: +[jschierm@astrid libscotch]$ diff dummysizes_old.c dummysizes.c +269a270 +> #ifndef MATLAB +270a272 +> #endif /* MATLAB */ + +- redirect errorPrint and errorPrintW to within Matlab: +[jschierm@astrid libscotch]$ diff library_error_exit_old.c +library_error_exit.c +116a117 +> #ifndef MATLAB +133a135,152 +> #else /* MATLAB */ +> mexPrintf ("%s", _SCOTCHerrorProgName); +> #ifdef SCOTCH_PTSCOTCH +> if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && +> (proclocnum != 0) && +> (MPI_Comm_rank (MPI_COMM_WORLD, &proclocnum) == MPI_SUCCESS)) +> mexPrintf ("(%d): ", proclocnum); +> #else /* SCOTCH_PTSCOTCH */ +> if (_SCOTCHerrorProgName[0] != '\0') +> mexPrintf (": "); +> #endif /* SCOTCH_PTSCOTCH */ +> mexPrintf ("ERROR: "); +> va_start (errlist, errstr); +> mexPrintf (errstr, errlist); /* Print arguments */ +> va_end (errlist); +> mexPrintf ("\n"); +> #endif /* MATLAB */ +> +157a177 +> #ifndef MATLAB +173a194,211 +> +> #else /* MATLAB */ +> mexPrintf ("%s", _SCOTCHerrorProgName); +> #ifdef SCOTCH_PTSCOTCH +> if ((MPI_Initialized (&proclocnum) == MPI_SUCCESS) && +> (proclocnum != 0) && +> (MPI_Comm_rank (MPI_COMM_WORLD, &proclocnum) == MPI_SUCCESS)) +> mexPrintf ("(%d): ", proclocnum); +> #else /* SCOTCH_PTSCOTCH */ +> if (_SCOTCHerrorProgName[0] != '\0') +> mexPrintf (": "); +> #endif /* SCOTCH_PTSCOTCH */ +> mexPrintf ("WARNING: "); +> va_start (errlist, errstr); +> mexPrintf (errstr, errlist); /* Print arguments */ +> va_end (errlist); +> mexPrintf ("\n"); +> #endif /* MATLAB */ + +- redirect usagePrint to within Matlab: +[jschierm@astrid libscotch]$ diff common_old.c common.c +102a103 +> #ifndef MATLAB +105a107,111 +> #else /* MATLAB */ +> mexPrintf ("Usage is:\n"); +> for (cptr = data; *cptr != NULL; cptr ++) +> mexPrintf (" %s\n", *cptr); +> #endif /* MATLAB */ + +8/21/09: + +- removed -DCOMMON_PTHREAD from CFLAGS and MFLAGS to eliminate fatal exception at pthread_exit in gmap_mex.c +- removed -DCOMMON_FILE_COMPRESS_GZ from CFLAGS and MFLAGS because unused + +8/25/09: + +added macro for fprintf to capture missing output: +[jschierm@astrid libscotch]$ diff common_old.h common.h +68a69 +> #include /* added for intptr_t */ +90a92,105 +> #ifdef MATLAB +> #include "mat.h" +> #include "mex.h" +> #include "matrix.h" +> +> #define printf mexPrintf +> #define fprintf(file,...) (file == stdout || file == stderr ? mexPrintf(__VA_ARGS__) : fprintf(file,__VA_ARGS__)) +> #define malloc mxMalloc +> #define calloc mxCalloc +> #define realloc mxRealloc +> #define free mxFree +> #define exit(status) mexErrMsgTxt("exit=" #status) +> #endif +> + +11/12/09: + +- added -Wl,-rpath-link,/usr/local/pkgs/matlab-7.6/bin/glnxa64 to LDFLAGS to eliminate missing libhdf5.so.0 in Matlab directories (based on Cielo make, but why did this not occur before?) + +11/18/09: + +- changed the following files to allow adjir,adjjc,vertlab,vertwgt,edgewgt rather than graph file + +libscotch/library.h +- argument list for SCOTCH_graphLoad +libscotch/library_graph.c +- SCOTCH_graphLoad changes and call to graphLoad +libscotch/graph.h +- argument list for graphLoad +libscotch/graph_io.c +- graphLoad changes +libscotch/graph_io_scot.c +- miscellaneous call to graphLoad +libscotch/mesh_io_scot.c +- miscellaneous call to graphLoad +libscotch/library_graph_f.c +- miscellaneous call to SCOTCH_graphLoad +scotch/gmap_mex.c +- input/processing of Matlab arguments and call to SCOTCH_graphLoad + +11/30/09: + +- changed the following files to allow nvert,maptab rather than map file + +libscotch/library.h +- argument list for SCOTCH_graphMapSave +libscotch/library_graph_map.c +- SCOTCH_graphMapSave changes and call to mapSave +libscotch/mapping.h +- argument list for mapSave +libscotch/mapping_io.c +- mapSave changes +libscotch/library_graph_map_f.c +- miscellaneous call to SCOTCH_graphMapSave +scotch/gmap_mex.c +- call to SCOTCH_graphMapSave and processing/output of Matlab arguments + +12/08/09: + +- changed the following files to allow archtyp,napar,archpar rather than target file + +libscotch/library.h +- argument list for SCOTCH_archLoad +libscotch/library_arch.c +- SCOTCH_archLoad changes and call to archLoad +libscotch/arch.h +- argument list for archLoad +libscotch/arch.c +- archLoad changes and call to class->archLoad +libscotch/arch_cmplt.h +libscotch/arch_cmpltw.h +libscotch/arch_deco.h +libscotch/arch_hcub.h +libscotch/arch_mesh.h +libscotch/arch_tleaf.h +libscotch/arch_torus.h +- argument lists for arch*ArchLoad +libscotch/arch_cmplt.c +libscotch/arch_cmpltw.c +libscotch/arch_deco.c +libscotch/arch_hcub.c +libscotch/arch_mesh.c +libscotch/arch_tleaf.c +libscotch/arch_torus.c +- arch*ArchLoad changes +libscotch/library_arch_f.c +- miscellaneous call to SCOTCH_archLoad +scotch/gmap_mex.c +- input/processing of Matlab arguments and call to SCOTCH_archLoad + +12/11/09: + +- fixed a couple bugs + +libscotch/graph.c -- caused crash when trying to free vertex labels +138c138,141 +< if (grafptr->vlbltax != NULL) +--- +> /* vlbltax must also check GRAPHVERTGROUP (jes, 12/11/09) */ +> // if (grafptr->vlbltax != NULL) +> if ((grafptr->vlbltax != NULL) && +> ((grafptr->flagval & GRAPHVERTGROUP) == 0)) + +libscotch/mapping_io.c -- caused first vertex label to be uninitialized +> /* not sure why, but need to offset vlbltax in other direction (jes, 12/11/09 +> // (long) ((vlbltax != NULL) ? vlbltax[vertnum] : vertnum), +> (long) ((vlbltax != NULL) ? vlbltax[vertnum+mappptr->baseva + +1/05/10: + +libscotch/graph_io.c -- if vertex labels are supplied, they must be referenced +263c265,268 +< edgeval=adjir[edgenum-grafptr->baseval]+1; +--- +> if (vertlab) +> edgeval=vertlab[adjir[edgenum-grafptr->baseval] ]; +> else +> edgeval= adjir[edgenum-grafptr->baseval]+1; + +2/08/10: + +- modified all source code changes to use the MATLAB compiler conditional, so that both mex and stand-alone modules could be built simultaneously + +2/10/10: + +- added mexscotch target to makefiles to separate mex from stand-alone modules +- removed Matlab-specific switches from CFLAGS and LDFLAGS and added them to mexscotch target + +3/03/10: + +- separated dummysizes within mexscotch target in libscotch/Makefile so that it is built without the matlab flag, includes, and libraries (matlab 7.8 would fail even though matlab 7.6 was okay). + +4/26/10: + +- separated gmap_mex.c driver into gmap_mex.c matlab-layer (independent of scotch) and gmapx.c x-layer (independent of matlab). + +4/29/10: + +- made changes to gmapx.c, parser_yy.y/stratParserParse, and parser_ll.l/stratParserInit to reset static variables from previous runs. +- inserted print statements into common_integer.c/intRand*, common_memory.c/mem*, and vgraph_separate_vw.c/vgraphSeparateVw to monitor static variables in case those have to be reset. + +5/03/10: + +- implemented gpart functionality in gmap_mex.c, gmapx.c, and new gpart.m. +- implemented common_integer.c/intRandResetStatic to reset static variables from previous runs. + +6/16/10: + +- renamed scotch x-layer and separated it from rest of build. +- set up scotch to build both stand-alone and mex libraries. + Index: /issm/trunk-jpl-damage/externalpackages/shapelib/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/shapelib/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/shapelib/install.sh (revision 11330) @@ -0,0 +1,50 @@ +#!/bin/bash + +# Some cleanup +rm -rf shapelib-1.2.10 +rm -rf src +rm -rf install +mkdir src install + +# Untar +tar -xvzf shapelib-1.2.10.tar.gz +unzip shape_eg_data.zip -d shapelib-1.2.10/eg_data + +# Move shapelib to src directory +mv shapelib-1.2.10/* src +rm -rf shapelib-1.2.10 + +# Apply patches (all at once) +# (written by diff -rc old_src new_src > shapelib.patch) +patch -p0 < shapelib.patch + +# Build shapelib and run self-tests +cd src +if [ -z $1 ]; then + make +else + make -j $1 +fi +make test + +# Clean up objects (but not library or executable) +#make clean +cd .. + +# Populate install directory +cp -p src/README install +cp -p src/*.html install +mkdir install/include +cp -p src/shapefil.h install/include +mkdir install/lib +mv src/libshape.a install/lib/libshape.a +mkdir install/exec +mv src/shpcreate install/exec +mv src/shpadd install/exec +mv src/shpdump install/exec +mv src/shprewind install/exec +mv src/dbfcreate install/exec +mv src/dbfadd install/exec +mv src/dbfdump install/exec +mv src/shputils install/exec +mv src/shptest install/exec Index: /issm/trunk-jpl-damage/externalpackages/shapelib/shapelib.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/shapelib/shapelib.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/shapelib/shapelib.patch (revision 11330) @@ -0,0 +1,139 @@ +diff -rc src/Makefile src_new/Makefile +*** src/Makefile 2003-04-07 06:03:22.000000000 -0700 +--- src_new/Makefile 2011-10-19 11:58:13.993411828 -0700 +*************** +*** 1,20 **** + + #LINKOPT = /usr/local/lib/libdbmalloc.a +! CFLAGS = -g + + default: all + +! all: shpcreate shpadd shpdump shprewind dbfcreate dbfadd dbfdump shptest + + shpopen.o: shpopen.c shapefil.h + $(CC) $(CFLAGS) -c shpopen.c + +- shptree.o: shptree.c shapefil.h +- $(CC) $(CFLAGS) -c shptree.c +- + dbfopen.o: dbfopen.c shapefil.h + $(CC) $(CFLAGS) -c dbfopen.c + + shpcreate: shpcreate.c shpopen.o + $(CC) $(CFLAGS) shpcreate.c shpopen.o $(LINKOPT) -o shpcreate + +--- 1,24 ---- + + #LINKOPT = /usr/local/lib/libdbmalloc.a +! CC = gcc +! #CFLAGS = -g +! CFLAGS = -fPIC -fno-omit-frame-pointer -pthread -fexceptions -g +! AR = /usr/bin/ar rcv +! RANLIB = /usr/bin/ranlib + + default: all + +! all: libshape.a shpcreate shpadd shpdump shprewind dbfcreate dbfadd dbfdump shputils shptest + + shpopen.o: shpopen.c shapefil.h + $(CC) $(CFLAGS) -c shpopen.c + + dbfopen.o: dbfopen.c shapefil.h + $(CC) $(CFLAGS) -c dbfopen.c + ++ libshape.a: shpopen.o dbfopen.o ++ ${AR} libshape.a shpopen.o dbfopen.o ; ${RANLIB} libshape.a ++ + shpcreate: shpcreate.c shpopen.o + $(CC) $(CFLAGS) shpcreate.c shpopen.o $(LINKOPT) -o shpcreate + +*************** +*** 36,58 **** + dbfdump: dbfdump.c dbfopen.o + $(CC) $(CFLAGS) dbfdump.c dbfopen.o $(LINKOPT) -o dbfdump + + shptest: shptest.c shpopen.o + $(CC) $(CFLAGS) shptest.c shpopen.o $(LINKOPT) -o shptest + +! shputils: shputils.c shpopen.o dbfopen.o +! $(CC) $(CFLAGS) shputils.c shpopen.o dbfopen.o $(LINKOPT) -o shputils + + shptreedump: shptreedump.c shptree.o shpopen.o + $(CC) $(CFLAGS) shptreedump.c shptree.o shpopen.o $(LINKOPT) \ + -o shptreedump + + clean: +! rm -f *.o dbfdump dbfcreate dbfadd shpdump shpcreate shpadd shputils + rm -f shptreedump + rm -rf *.lo *.la .libs +- rm -f shptest + +! test: test2 test3 + + # + # Note this stream only works if example data is accessable. +--- 40,64 ---- + dbfdump: dbfdump.c dbfopen.o + $(CC) $(CFLAGS) dbfdump.c dbfopen.o $(LINKOPT) -o dbfdump + ++ shputils: shputils.c shpopen.o dbfopen.o ++ $(CC) $(CFLAGS) shputils.c shpopen.o dbfopen.o $(LINKOPT) -o shputils ++ + shptest: shptest.c shpopen.o + $(CC) $(CFLAGS) shptest.c shpopen.o $(LINKOPT) -o shptest + +! shptree.o: shptree.c shapefil.h +! $(CC) $(CFLAGS) -c shptree.c + + shptreedump: shptreedump.c shptree.o shpopen.o + $(CC) $(CFLAGS) shptreedump.c shptree.o shpopen.o $(LINKOPT) \ + -o shptreedump + + clean: +! rm -f *.o *.a shpcreate shpadd shpdump shprewind dbfcreate dbfadd dbfdump shputils shptest + rm -f shptreedump + rm -rf *.lo *.la .libs + +! test: test1 test2 test3 + + # + # Note this stream only works if example data is accessable. +diff -rc src/shputils.c src_new/shputils.c +*** src/shputils.c 2003-04-07 06:03:22.000000000 -0700 +--- src_new/shputils.c 2011-10-14 14:52:32.179022813 -0700 +*************** +*** 274,280 **** + if (factor == 0) + { + if (infactor ==0) +! { puts("ERROR: Input unit must be defined before output unit"); exit(); } + factor=infactor/outfactor; + } + printf("Output file coordinate values will be factored by %lg\n",factor); +--- 274,280 ---- + if (factor == 0) + { + if (infactor ==0) +! { puts("ERROR: Input unit must be defined before output unit"); exit( 1 ); } + factor=infactor/outfactor; + } + printf("Output file coordinate values will be factored by %lg\n",factor); +diff -rc src/stream1.sh src_new/stream1.sh +*** src/stream1.sh 2003-04-07 06:03:22.000000000 -0700 +--- src_new/stream1.sh 2011-10-19 11:45:08.192964291 -0700 +*************** +*** 1,6 **** + #!/bin/sh + +! EG_DATA=/u/www/projects/shapelib/eg_data + + echo ------------------------------------------------------------------------- + echo Test 1: dump anno.shp +--- 1,6 ---- + #!/bin/sh + +! EG_DATA=./eg_data + + echo ------------------------------------------------------------------------- + echo Test 1: dump anno.shp Index: /issm/trunk-jpl-damage/externalpackages/slepc/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/slepc/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/slepc/install.sh (revision 11330) @@ -0,0 +1,21 @@ +#!/bin/bash + +#Some cleanup +rm -rf install slepc-2.3.2 +mkdir install + +#Untar +tar -zxvf slepc-2.3.2.tgz + +#Move slepc to install directory +mv slepc-2.3.2/* install/ +rm -rf slepc-2.3.2 + +#Make slepc +cd install +./config/configure.py +if [ -z $1 ]; then + make +else + make -j $1 +fi Index: /issm/trunk-jpl-damage/externalpackages/ssh/README =================================================================== --- /issm/trunk-jpl-damage/externalpackages/ssh/README (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/ssh/README (revision 11330) @@ -0,0 +1,6 @@ +These two command line tools are taken from the Putty web page: +http://www.chiark.greenend.org.uk/~sgtatham/putty + +These two tools are used instead of ssh and scp (the ones that ship with cygwin), +because ssh and scp do not work when called directly from matlab using the 'system' +command. Index: /issm/trunk-jpl-damage/externalpackages/swig/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/swig/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/swig/install.sh (revision 11330) @@ -0,0 +1,26 @@ +#!/bin/bash + +#Some cleanup +rm -rf install +rm -rf swig-2.0.4 +mkdir install + +#Untar and move python into install directory +tar -zxvf swig-2.0.4.tar.gz +mv swig-2.0.4/* install +rm -rf swig-2.0.4 + +#Copy pcre prototype in include directory +cd install +#cp $ISSM_TIER/externalpackages/pcre/install/pcre.h ./Source/Include/ +#cp $ISSM_TIER/externalpackages/pcre/install/.libs/* ./Source/Include/ +export CFLAGS="$CFLAGS -I$ISSM_TIER/externalpackages/pcre/install" +export LDFLAGS="-L$ISSM_TIER/externalpackages/pcre/install/.libs/" +export LIBS="-lpcre" +#Configure doxygen +./configure \ + --prefix="$ISSM_TIER/externalpackages/python/install" \ + --with-pcre-prefix="$ISSM_TIER/externalpackages/pcre/install" \ + --with-pcre-exec-prefix="$ISSM_TIER/externalpackages/pcre/install" +make +make install Index: /issm/trunk-jpl-damage/externalpackages/tao/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/tao/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/tao/install.sh (revision 11330) @@ -0,0 +1,18 @@ +#!/bin/bash +#wget http://www.mcs.anl.gov/research/projects/tao/download/tao-2.0.tar.gz + +#Some cleanup +rm -rf install tao-2.0 +mkdir install + +#Untar +tar -zxvf tao-2.0.tar.gz + +#move into place +mv tao-2.0/* install/ +rm -rf tao-2.0 +cd install +export TAO_DIR="$ISSM_TIER/externalpackages/tao/install/" + +#petsc needs to be compiled with --with-clanguage=C++ +make Index: /issm/trunk-jpl-damage/externalpackages/tex2im/install.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/tex2im/install.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/tex2im/install.sh (revision 11330) @@ -0,0 +1,12 @@ +#!/bin/bash + +#Some cleanup +rm -rf install +mkdir install + +#Untar +tar -zxvf tex2im-1.8.tar.gz + +#Move tex2im into src directory +mv tex2im-1.8/tex2im install/ +rm -rf tex2im-1.8 Index: /issm/trunk-jpl-damage/externalpackages/triangle/README =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/README (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/README (revision 11330) @@ -0,0 +1,2 @@ +Go pick up the correct configure.make file in the config directory (according to your platform), +copy it to the top triangle directory, and run install.sh Index: /issm/trunk-jpl-damage/externalpackages/triangle/configs/altix64/configure.make =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/configs/altix64/configure.make (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/configs/altix64/configure.make (revision 11330) @@ -0,0 +1,4 @@ +CC=gcc +CSWITCHES = $(CFLAGS) -I$(MATLAB_DIR)/extern/include -I$(MATLAB_DIR)/include -DLIN64 -fPIC +OBJ_EXT=o +LIB_EXT=a Index: /issm/trunk-jpl-damage/externalpackages/triangle/configs/linux64/configure.make =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/configs/linux64/configure.make (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/configs/linux64/configure.make (revision 11330) @@ -0,0 +1,4 @@ +CC=gcc +CSWITCHES = $(CFLAGS) -I$(MATLAB_DIR)/extern/include -I$(MATLAB_DIR)/include -DLIN64 -fPIC +OBJ_EXT=o +LIB_EXT=a Index: /issm/trunk-jpl-damage/externalpackages/triangle/configs/macosx32/configure.make =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/configs/macosx32/configure.make (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/configs/macosx32/configure.make (revision 11330) @@ -0,0 +1,5 @@ +CC=gcc -arch i386 +CSWITCHES = $(CFLAGS) -I/usr/X11R6/include -L/usr/X11R6/lib -I$(MATLAB_DIR)/extern/include -fPIC -I$(MATLAB_DIR)/include +TRILIBDEFS = -DTRILIBRARY +OBJ_EXT=o +LIB_EXT=a Index: /issm/trunk-jpl-damage/externalpackages/triangle/configs/macosx64/configure.make =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/configs/macosx64/configure.make (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/configs/macosx64/configure.make (revision 11330) @@ -0,0 +1,5 @@ +CC=gcc -arch x86_64 +CSWITCHES = $(CFLAGS) -I/usr/X11R6/include -L/usr/X11R6/lib -I$(MATLAB_DIR)/extern/include -fPIC -I$(MATLAB_DIR)/include +TRILIBDEFS = -DTRILIBRARY +OBJ_EXT=o +LIB_EXT=a Index: /issm/trunk-jpl-damage/externalpackages/triangle/configs/pleiades/configure.make =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/configs/pleiades/configure.make (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/configs/pleiades/configure.make (revision 11330) @@ -0,0 +1,4 @@ +CC=gcc +CSWITCHES = $(CFLAGS) -I$(MATLAB_DIR)/extern/include -I$(MATLAB_DIR)/include -DLIN64 -fPIC +OBJ_EXT=o +LIB_EXT=a Index: /issm/trunk-jpl-damage/externalpackages/triangle/configs/win32/configure.make =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/configs/win32/configure.make (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/configs/win32/configure.make (revision 11330) @@ -0,0 +1,4 @@ +CC=icl +CSWITCHES = $(CFLAGS) -I$(MATLAB_DIR)/extern/include -I$(MATLAB_DIR)/include -DWIN32 +OBJ_EXT=obj +LIB_EXT=a Index: /issm/trunk-jpl-damage/externalpackages/triangle/install-altix64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/install-altix64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/install-altix64.sh (revision 11330) @@ -0,0 +1,23 @@ +#!/bin/bash + +#Some cleanup +rm -rf install triangle +mkdir install + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/altix64/configure.make ./ +cp ../makefile ./ + +#Patch triangle.c +patch triangle.c ../triangle.c.patch + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/trunk-jpl-damage/externalpackages/triangle/install-linux64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/install-linux64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/install-linux64.sh (revision 11330) @@ -0,0 +1,23 @@ +#!/bin/bash + +#Some cleanup +rm -rf install triangle +mkdir install + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/linux64/configure.make ./ +cp ../makefile ./ + +#Patch triangle.c +patch triangle.c ../triangle.c.patch + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/trunk-jpl-damage/externalpackages/triangle/install-macosx32.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/install-macosx32.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/install-macosx32.sh (revision 11330) @@ -0,0 +1,23 @@ +#!/bin/bash + +#Some cleanup +rm -rf install triangle +mkdir install + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/macosx32/configure.make ./ +cp ../makefile ./ + +#Patch triangle.c +patch triangle.c ../triangle.c.patch + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/trunk-jpl-damage/externalpackages/triangle/install-macosx64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/install-macosx64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/install-macosx64.sh (revision 11330) @@ -0,0 +1,23 @@ +#!/bin/bash + +#Some cleanup +rm -rf install triangle +mkdir install + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/macosx64/configure.make ./ +cp ../makefile ./ + +#Patch triangle.c +patch triangle.c ../triangle.c.patch + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/trunk-jpl-damage/externalpackages/triangle/install-pleiades.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/install-pleiades.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/install-pleiades.sh (revision 11330) @@ -0,0 +1,23 @@ +#!/bin/bash + +#Some cleanup +rm -rf install triangle +mkdir install + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/pleiades/configure.make ./ +cp ../makefile ./ + +#Patch triangle.c +patch triangle.c ../triangle.c.patch + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/trunk-jpl-damage/externalpackages/triangle/install-win32.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/install-win32.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/install-win32.sh (revision 11330) @@ -0,0 +1,23 @@ +#!/bin/bash + +#Some cleanup +rm -rf install triangle +mkdir install + +#Untar +cd install +cp ../triangle.zip ./ +unzip triangle.zip + +#copy new makefile +cp ../configs/win32/configure.make ./ +cp ../makefile ./ + +#Patch triangle.c +patch triangle.c ../triangle.c.patch + +#Compile triangle +make + +#Patch triangle.h +patch triangle.h ../triangle.h.patch Index: /issm/trunk-jpl-damage/externalpackages/triangle/makefile =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/makefile (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/makefile (revision 11330) @@ -0,0 +1,22 @@ +#Adaptation of Triangle makefile to compile only the triangle.c file, +#into a standalone library that can then be used to compile mex modules + +include ./configure.make + +AR = ar + +TRILIBDEFS = -DTRILIBRARY + +all: triangle.$(LIB_EXT) + +OBJECTS=triangle.$(OBJ_EXT) + +triangle.$(LIB_EXT): $(OBJECTS) + ar cr triangle.$(LIB_EXT) $(OBJECTS) + ranlib triangle.$(LIB_EXT) + +triangle.$(OBJ_EXT): triangle.c triangle.h + $(CC) $(CSWITCHES) $(TRILIBDEFS) -c triangle.c + +clean: + rm -rf *.$(LIB_EXT) *.$(OBJ_EXT) *.LIB *.LST *.$(OBJ_EXT)bj *.BAK Index: /issm/trunk-jpl-damage/externalpackages/triangle/triangle.c.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/triangle.c.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/triangle.c.patch (revision 11330) @@ -0,0 +1,164 @@ +0a1,10 +> /*Notes for the Ice code: +> * to be able to compile Triangle within a mex function that can run within +> * matlab, we had to change the allocation routine trimalloc, as well as the +> * double precision activation in exactinit(); The rest is not changed. +> * We also created the ice_makefile to compile Triangle into a library. */ +> #include +> #include +> #define ANSI_DECLARATORS +> #define NO_TIMER +> +347a358 +> #ifndef _WIN_ +348a360 +> #endif +641d652 +< +817a829,922 +> /*Some missing prototypes: */ +> int scale_expansion_zeroelim(int elen, REAL *e, REAL b, REAL *h); +> int fast_expansion_sum_zeroelim(int elen, REAL *e, int flen, REAL *f, REAL *h); +> void poolzero(struct memorypool *pool); +> int triunsuitable(vertex triorg, vertex tridest, vertex triapex, REAL area); +> triangle *triangletraverse(struct mesh *m); +> void pooldeinit(struct memorypool *pool); +> void printtriangle(struct mesh *m, struct behavior *b, struct otri *t); +> VOID *poolalloc(struct memorypool *pool); +> void enqueuebadtriang(struct mesh *m, struct behavior *b, +> struct badtriang *badtri); +> void triangulatepolygon(struct mesh *m, struct behavior *b, +> struct otri *firstedge, struct otri *lastedge, +> int edgecount, int doflip, int triflaws); +> void triangledealloc(struct mesh *m, triangle *dyingtriangle); +> void unflip(struct mesh *m, struct behavior *b, struct otri *flipedge); +> void vertexmedian(vertex *sortarray, int arraysize, int median, int axis); +> REAL counterclockwiseadapt(vertex pa, vertex pb, vertex pc, REAL detsum); +> REAL incircleadapt(vertex pa, vertex pb, vertex pc, vertex pd, REAL permanent); +> void enqueuebadtri(struct mesh *m, struct behavior *b, struct otri *enqtri, +> REAL minedge, vertex enqapex, vertex enqorg, vertex enqdest); +> void alternateaxes(vertex *sortarray, int arraysize, int axis); +> REAL incircleadapt(vertex pa, vertex pb, vertex pc, vertex pd, REAL permanent); +> void maketriangle(struct mesh *m, struct behavior *b, struct otri *newotri); +> REAL counterclockwise(struct mesh *m, struct behavior *b, +> vertex pa, vertex pb, vertex pc); +> vertex vertextraverse(struct mesh *m); +> void mergehulls(struct mesh *m, struct behavior *b, struct otri *farleft, +> struct otri *innerleft, struct otri *innerright, +> struct otri *farright, int axis); +> REAL incircle(struct mesh *m, struct behavior *b, +> vertex pa, vertex pb, vertex pc, vertex pd); +> void poolrestart(struct memorypool *pool); +> void trifree(VOID *memptr); +> struct splaynode *splay(struct mesh *m, struct splaynode *splaytree, +> vertex searchpoint, struct otri *searchtri); +> void eventheapdelete(struct event **heap, int heapsize, int eventnum); +> void eventheapdelete(struct event **heap, int heapsize, int eventnum); +> void flip(struct mesh *m, struct behavior *b, struct otri *flipedge); +> void check4deadevent(struct otri *checktri, struct event **freeevents, +> struct event **eventheap, int *heapsize); +> REAL orient3d(struct mesh *m, struct behavior *b, +> vertex pa, vertex pb, vertex pc, vertex pd, +> REAL aheight, REAL bheight, REAL cheight, REAL dheight); +> REAL circletop(struct mesh *m, vertex pa, vertex pb, vertex pc, REAL ccwabc); +> void poolinit(struct memorypool *pool, int bytecount, int itemcount, +> int firstitemcount, int alignment); +> void eventheapinsert(struct event **heap, int heapsize, struct event *newevent); +> int rightofhyperbola(struct mesh *m, struct otri *fronttri, vertex newsite); +> void insertsubseg(struct mesh *m, struct behavior *b, struct otri *tri, +> int subsegmark); +> int scoutsegment(struct mesh *m, struct behavior *b, struct otri *searchtri, +> vertex endpoint2, int newmark); +> vertex getvertex(struct mesh *m, struct behavior *b, int number); +> void internalerror(); +> unsigned long randomnation(unsigned int choices); +> struct splaynode *splayinsert(struct mesh *m, struct splaynode *splayroot, +> struct otri *newkey, vertex searchpoint); +> void delaunayfixup(struct mesh *m, struct behavior *b, +> struct otri *fixuptri, int leftside); +> void traversalinit(struct memorypool *pool); +> enum insertvertexresult insertvertex(struct mesh *m, struct behavior *b, +> vertex newvertex, struct otri *searchtri, +> struct osub *splitseg, +> int segmentflaws, int triflaws); +> void conformingedge(struct mesh *m, struct behavior *b, +> vertex endpoint1, vertex endpoint2, int newmark); +> enum finddirectionresult finddirection(struct mesh *m, struct behavior *b, +> struct otri *searchtri, +> vertex searchpoint); +> VOID *traverse(struct memorypool *pool); +> void deletevertex(struct mesh *m, struct behavior *b, struct otri *deltri); +> void pooldealloc(struct memorypool *pool, VOID *dyingitem); +> int checkseg4encroach(struct mesh *m, struct behavior *b, +> struct osub *testsubseg); +> void badsubsegdealloc(struct mesh *m, struct badsubseg *dyingseg); +> void vertexdealloc(struct mesh *m, vertex dyingvertex); +> void vertexsort(vertex *sortarray, int arraysize); +> void tallyencs(struct mesh *m, struct behavior *b); +> void splittriangle(struct mesh *m, struct behavior *b, +> struct badtriang *badtri); +> subseg *subsegtraverse(struct mesh *m); +> enum locateresult locate(struct mesh *m, struct behavior *b, +> vertex searchpoint, struct otri *searchtri); +> void writenodes(struct mesh *m, struct behavior *b, REAL **pointlist, +> REAL **pointattriblist, int **pointmarkerlist); +> void writevoronoi(struct mesh *m, struct behavior *b, REAL **vpointlist, +> REAL **vpointattriblist, int **vpointmarkerlist, +> int **vedgelist, int **vedgemarkerlist, REAL **vnormlist); +> void writeneighbors(struct mesh *m, struct behavior *b, int **neighborlist); +> void testtriangle(struct mesh *m, struct behavior *b, struct otri *testtri); +> void triangleinit(struct mesh *m); +> +> +1408a1514 +> void triexit(int status); +1410d1515 +< #ifdef ANSI_DECLARATORS +1412,1416d1516 +< #else /* not ANSI_DECLARATORS */ +< void triexit(status) +< int status; +< #endif /* not ANSI_DECLARATORS */ +< +1421c1521 +< #ifdef ANSI_DECLARATORS +--- +> VOID *trimalloc(int size); +1423,1427d1522 +< #else /* not ANSI_DECLARATORS */ +< VOID *trimalloc(size) +< int size; +< #endif /* not ANSI_DECLARATORS */ +< +1431c1526,1527 +< memptr = (VOID *) malloc((unsigned int) size); +--- +> memptr = (VOID *) mxMalloc((unsigned int) size); +> //memptr = (VOID *) malloc((unsigned int) size); +1447c1543,1544 +< free(memptr); +--- +> //free(memptr); +> mxFree(memptr); +3665,3670c3762,3767 +< void printtriangle(struct mesh *m, struct behavior *b, struct otri *t) +< #else /* not ANSI_DECLARATORS */ +< void printtriangle(m, b, t) +< struct mesh *m; +< struct behavior *b; +< struct otri *t; +--- +> void printtriangle(struct mesh *m, struct behavior *b, struct otri *t){ +> //#else /* not ANSI_DECLARATORS */ +> //void printtriangle(m, b, t) +> //struct mesh *m; +> //struct behavior *b; +> //struct otri *t; +3673c3770 +< { +--- +> //{ +4910c5007 +< _FPU_SETCW(cword); +--- +> //_FPU_SETCW(cword); //taken care of by Matlab Index: /issm/trunk-jpl-damage/externalpackages/triangle/triangle.h =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/triangle.h (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/triangle.h (revision 11330) @@ -0,0 +1,291 @@ +/*****************************************************************************/ +/* */ +/* (triangle.h) */ +/* */ +/* Include file for programs that call Triangle. */ +/* */ +/* Accompanies Triangle Version 1.6 */ +/* July 28, 2005 */ +/* */ +/* Copyright 1996, 2005 */ +/* Jonathan Richard Shewchuk */ +/* 2360 Woolsey #H */ +/* Berkeley, California 94705-1927 */ +/* jrs@cs.berkeley.edu */ +/* */ +/*****************************************************************************/ + +/*****************************************************************************/ +/* */ +/* How to call Triangle from another program */ +/* */ +/* */ +/* If you haven't read Triangle's instructions (run "triangle -h" to read */ +/* them), you won't understand what follows. */ +/* */ +/* Triangle must be compiled into an object file (triangle.o) with the */ +/* TRILIBRARY symbol defined (generally by using the -DTRILIBRARY compiler */ +/* switch). The makefile included with Triangle will do this for you if */ +/* you run "make trilibrary". The resulting object file can be called via */ +/* the procedure triangulate(). */ +/* */ +/* If the size of the object file is important to you, you may wish to */ +/* generate a reduced version of triangle.o. The REDUCED symbol gets rid */ +/* of all features that are primarily of research interest. Specifically, */ +/* the -DREDUCED switch eliminates Triangle's -i, -F, -s, and -C switches. */ +/* The CDT_ONLY symbol gets rid of all meshing algorithms above and beyond */ +/* constrained Delaunay triangulation. Specifically, the -DCDT_ONLY switch */ +/* eliminates Triangle's -r, -q, -a, -u, -D, -Y, -S, and -s switches. */ +/* */ +/* IMPORTANT: These definitions (TRILIBRARY, REDUCED, CDT_ONLY) must be */ +/* made in the makefile or in triangle.c itself. Putting these definitions */ +/* in this file (triangle.h) will not create the desired effect. */ +/* */ +/* */ +/* The calling convention for triangulate() follows. */ +/* */ +/* void triangulate(triswitches, in, out, vorout) */ +/* char *triswitches; */ +/* struct triangulateio *in; */ +/* struct triangulateio *out; */ +/* struct triangulateio *vorout; */ +/* */ +/* `triswitches' is a string containing the command line switches you wish */ +/* to invoke. No initial dash is required. Some suggestions: */ +/* */ +/* - You'll probably find it convenient to use the `z' switch so that */ +/* points (and other items) are numbered from zero. This simplifies */ +/* indexing, because the first item of any type always starts at index */ +/* [0] of the corresponding array, whether that item's number is zero or */ +/* one. */ +/* - You'll probably want to use the `Q' (quiet) switch in your final code, */ +/* but you can take advantage of Triangle's printed output (including the */ +/* `V' switch) while debugging. */ +/* - If you are not using the `q', `a', `u', `D', `j', or `s' switches, */ +/* then the output points will be identical to the input points, except */ +/* possibly for the boundary markers. If you don't need the boundary */ +/* markers, you should use the `N' (no nodes output) switch to save */ +/* memory. (If you do need boundary markers, but need to save memory, a */ +/* good nasty trick is to set out->pointlist equal to in->pointlist */ +/* before calling triangulate(), so that Triangle overwrites the input */ +/* points with identical copies.) */ +/* - The `I' (no iteration numbers) and `g' (.off file output) switches */ +/* have no effect when Triangle is compiled with TRILIBRARY defined. */ +/* */ +/* `in', `out', and `vorout' are descriptions of the input, the output, */ +/* and the Voronoi output. If the `v' (Voronoi output) switch is not used, */ +/* `vorout' may be NULL. `in' and `out' may never be NULL. */ +/* */ +/* Certain fields of the input and output structures must be initialized, */ +/* as described below. */ +/* */ +/*****************************************************************************/ + +/*****************************************************************************/ +/* */ +/* The `triangulateio' structure. */ +/* */ +/* Used to pass data into and out of the triangulate() procedure. */ +/* */ +/* */ +/* Arrays are used to store points, triangles, markers, and so forth. In */ +/* all cases, the first item in any array is stored starting at index [0]. */ +/* However, that item is item number `1' unless the `z' switch is used, in */ +/* which case it is item number `0'. Hence, you may find it easier to */ +/* index points (and triangles in the neighbor list) if you use the `z' */ +/* switch. Unless, of course, you're calling Triangle from a Fortran */ +/* program. */ +/* */ +/* Description of fields (except the `numberof' fields, which are obvious): */ +/* */ +/* `pointlist': An array of point coordinates. The first point's x */ +/* coordinate is at index [0] and its y coordinate at index [1], followed */ +/* by the coordinates of the remaining points. Each point occupies two */ +/* REALs. */ +/* `pointattributelist': An array of point attributes. Each point's */ +/* attributes occupy `numberofpointattributes' REALs. */ +/* `pointmarkerlist': An array of point markers; one int per point. */ +/* */ +/* `trianglelist': An array of triangle corners. The first triangle's */ +/* first corner is at index [0], followed by its other two corners in */ +/* counterclockwise order, followed by any other nodes if the triangle */ +/* represents a nonlinear element. Each triangle occupies */ +/* `numberofcorners' ints. */ +/* `triangleattributelist': An array of triangle attributes. Each */ +/* triangle's attributes occupy `numberoftriangleattributes' REALs. */ +/* `trianglearealist': An array of triangle area constraints; one REAL per */ +/* triangle. Input only. */ +/* `neighborlist': An array of triangle neighbors; three ints per */ +/* triangle. Output only. */ +/* */ +/* `segmentlist': An array of segment endpoints. The first segment's */ +/* endpoints are at indices [0] and [1], followed by the remaining */ +/* segments. Two ints per segment. */ +/* `segmentmarkerlist': An array of segment markers; one int per segment. */ +/* */ +/* `holelist': An array of holes. The first hole's x and y coordinates */ +/* are at indices [0] and [1], followed by the remaining holes. Two */ +/* REALs per hole. Input only, although the pointer is copied to the */ +/* output structure for your convenience. */ +/* */ +/* `regionlist': An array of regional attributes and area constraints. */ +/* The first constraint's x and y coordinates are at indices [0] and [1], */ +/* followed by the regional attribute at index [2], followed by the */ +/* maximum area at index [3], followed by the remaining area constraints. */ +/* Four REALs per area constraint. Note that each regional attribute is */ +/* used only if you select the `A' switch, and each area constraint is */ +/* used only if you select the `a' switch (with no number following), but */ +/* omitting one of these switches does not change the memory layout. */ +/* Input only, although the pointer is copied to the output structure for */ +/* your convenience. */ +/* */ +/* `edgelist': An array of edge endpoints. The first edge's endpoints are */ +/* at indices [0] and [1], followed by the remaining edges. Two ints per */ +/* edge. Output only. */ +/* `edgemarkerlist': An array of edge markers; one int per edge. Output */ +/* only. */ +/* `normlist': An array of normal vectors, used for infinite rays in */ +/* Voronoi diagrams. The first normal vector's x and y magnitudes are */ +/* at indices [0] and [1], followed by the remaining vectors. For each */ +/* finite edge in a Voronoi diagram, the normal vector written is the */ +/* zero vector. Two REALs per edge. Output only. */ +/* */ +/* */ +/* Any input fields that Triangle will examine must be initialized. */ +/* Furthermore, for each output array that Triangle will write to, you */ +/* must either provide space by setting the appropriate pointer to point */ +/* to the space you want the data written to, or you must initialize the */ +/* pointer to NULL, which tells Triangle to allocate space for the results. */ +/* The latter option is preferable, because Triangle always knows exactly */ +/* how much space to allocate. The former option is provided mainly for */ +/* people who need to call Triangle from Fortran code, though it also makes */ +/* possible some nasty space-saving tricks, like writing the output to the */ +/* same arrays as the input. */ +/* */ +/* Triangle will not free() any input or output arrays, including those it */ +/* allocates itself; that's up to you. You should free arrays allocated by */ +/* Triangle by calling the trifree() procedure defined below. (By default, */ +/* trifree() just calls the standard free() library procedure, but */ +/* applications that call triangulate() may replace trimalloc() and */ +/* trifree() in triangle.c to use specialized memory allocators.) */ +/* */ +/* Here's a guide to help you decide which fields you must initialize */ +/* before you call triangulate(). */ +/* */ +/* `in': */ +/* */ +/* - `pointlist' must always point to a list of points; `numberofpoints' */ +/* and `numberofpointattributes' must be properly set. */ +/* `pointmarkerlist' must either be set to NULL (in which case all */ +/* markers default to zero), or must point to a list of markers. If */ +/* `numberofpointattributes' is not zero, `pointattributelist' must */ +/* point to a list of point attributes. */ +/* - If the `r' switch is used, `trianglelist' must point to a list of */ +/* triangles, and `numberoftriangles', `numberofcorners', and */ +/* `numberoftriangleattributes' must be properly set. If */ +/* `numberoftriangleattributes' is not zero, `triangleattributelist' */ +/* must point to a list of triangle attributes. If the `a' switch is */ +/* used (with no number following), `trianglearealist' must point to a */ +/* list of triangle area constraints. `neighborlist' may be ignored. */ +/* - If the `p' switch is used, `segmentlist' must point to a list of */ +/* segments, `numberofsegments' must be properly set, and */ +/* `segmentmarkerlist' must either be set to NULL (in which case all */ +/* markers default to zero), or must point to a list of markers. */ +/* - If the `p' switch is used without the `r' switch, then */ +/* `numberofholes' and `numberofregions' must be properly set. If */ +/* `numberofholes' is not zero, `holelist' must point to a list of */ +/* holes. If `numberofregions' is not zero, `regionlist' must point to */ +/* a list of region constraints. */ +/* - If the `p' switch is used, `holelist', `numberofholes', */ +/* `regionlist', and `numberofregions' is copied to `out'. (You can */ +/* nonetheless get away with not initializing them if the `r' switch is */ +/* used.) */ +/* - `edgelist', `edgemarkerlist', `normlist', and `numberofedges' may be */ +/* ignored. */ +/* */ +/* `out': */ +/* */ +/* - `pointlist' must be initialized (NULL or pointing to memory) unless */ +/* the `N' switch is used. `pointmarkerlist' must be initialized */ +/* unless the `N' or `B' switch is used. If `N' is not used and */ +/* `in->numberofpointattributes' is not zero, `pointattributelist' must */ +/* be initialized. */ +/* - `trianglelist' must be initialized unless the `E' switch is used. */ +/* `neighborlist' must be initialized if the `n' switch is used. If */ +/* the `E' switch is not used and (`in->numberofelementattributes' is */ +/* not zero or the `A' switch is used), `elementattributelist' must be */ +/* initialized. `trianglearealist' may be ignored. */ +/* - `segmentlist' must be initialized if the `p' or `c' switch is used, */ +/* and the `P' switch is not used. `segmentmarkerlist' must also be */ +/* initialized under these circumstances unless the `B' switch is used. */ +/* - `edgelist' must be initialized if the `e' switch is used. */ +/* `edgemarkerlist' must be initialized if the `e' switch is used and */ +/* the `B' switch is not. */ +/* - `holelist', `regionlist', `normlist', and all scalars may be ignored.*/ +/* */ +/* `vorout' (only needed if `v' switch is used): */ +/* */ +/* - `pointlist' must be initialized. If `in->numberofpointattributes' */ +/* is not zero, `pointattributelist' must be initialized. */ +/* `pointmarkerlist' may be ignored. */ +/* - `edgelist' and `normlist' must both be initialized. */ +/* `edgemarkerlist' may be ignored. */ +/* - Everything else may be ignored. */ +/* */ +/* After a call to triangulate(), the valid fields of `out' and `vorout' */ +/* will depend, in an obvious way, on the choice of switches used. Note */ +/* that when the `p' switch is used, the pointers `holelist' and */ +/* `regionlist' are copied from `in' to `out', but no new space is */ +/* allocated; be careful that you don't free() the same array twice. On */ +/* the other hand, Triangle will never copy the `pointlist' pointer (or any */ +/* others); new space is allocated for `out->pointlist', or if the `N' */ +/* switch is used, `out->pointlist' remains uninitialized. */ +/* */ +/* All of the meaningful `numberof' fields will be properly set; for */ +/* instance, `numberofedges' will represent the number of edges in the */ +/* triangulation whether or not the edges were written. If segments are */ +/* not used, `numberofsegments' will indicate the number of boundary edges. */ +/* */ +/*****************************************************************************/ +typedef double REAL; +typedef void VOID; + +extern "C" struct triangulateio { + REAL *pointlist; /* In / out */ + REAL *pointattributelist; /* In / out */ + int *pointmarkerlist; /* In / out */ + int numberofpoints; /* In / out */ + int numberofpointattributes; /* In / out */ + + int *trianglelist; /* In / out */ + REAL *triangleattributelist; /* In / out */ + REAL *trianglearealist; /* In only */ + int *neighborlist; /* Out only */ + int numberoftriangles; /* In / out */ + int numberofcorners; /* In / out */ + int numberoftriangleattributes; /* In / out */ + + int *segmentlist; /* In / out */ + int *segmentmarkerlist; /* In / out */ + int numberofsegments; /* In / out */ + + REAL *holelist; /* In / pointer to array copied out */ + int numberofholes; /* In / copied out */ + + REAL *regionlist; /* In / pointer to array copied out */ + int numberofregions; /* In / copied out */ + + int *edgelist; /* Out only */ + int *edgemarkerlist; /* Not used with Voronoi diagram; out only */ + REAL *normlist; /* Used only with Voronoi diagram; out only */ + int numberofedges; /* Out only */ +}; + +#ifdef ANSI_DECLARATORS +extern "C" void triangulate(char *, struct triangulateio *, struct triangulateio *, + struct triangulateio *); +extern "C" void trifree(VOID *memptr); +#else /* not ANSI_DECLARATORS */ +void triangulate(); +void trifree(); +#endif /* not ANSI_DECLARATORS */ Index: /issm/trunk-jpl-damage/externalpackages/triangle/triangle.h.patch =================================================================== --- /issm/trunk-jpl-damage/externalpackages/triangle/triangle.h.patch (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/triangle/triangle.h.patch (revision 11330) @@ -0,0 +1,17 @@ +249a250,253 +> #ifndef REAL +> typedef double REAL; +> typedef void VOID; +> #endif +251c255 +< struct triangulateio { +--- +> extern "C" struct triangulateio { +283c287 +< void triangulate(char *, struct triangulateio *, struct triangulateio *, +--- +> extern "C" void triangulate(char *, struct triangulateio *, struct triangulateio *, +285c289 +< void trifree(VOID *memptr); +--- +> extern "C" void trifree(VOID *memptr); Index: /issm/trunk-jpl-damage/externalpackages/valgrind/README =================================================================== --- /issm/trunk-jpl-damage/externalpackages/valgrind/README (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/valgrind/README (revision 11330) @@ -0,0 +1,5 @@ +How to use valgrind to debug memory leaks. +Install valgrind (jut type valgrind.sh). +Compile the parallel code using -g -O0 as optoins (edit src/c/Makefile if necessary). +Then set md.mem_debug=1, and run in parallel. Voila! +The errlog will contain all the info spit out by valgrind. Index: /issm/trunk-jpl-damage/externalpackages/valgrind/install-altix64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/valgrind/install-altix64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/valgrind/install-altix64.sh (revision 11330) @@ -0,0 +1,24 @@ +#!/bin/bash + +#Some cleanup +rm -rf install valgrind-3.7.0 +mkdir install + +#Untar +tar -jxvf valgrind-3.7.0.tar.bz2 + +#Move valgrind into install directory +mv valgrind-3.7.0/* install +rm -rf valgrind-3.7.0 + +#configure +cd install +./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" + +#Compile valgrind +make -j 4 +make install + +#final thing: if mpi is compiled in, soft link its target to a simpler name +cd lib +ln -s valgrind/libmpi* ./libmpidebug.so Index: /issm/trunk-jpl-damage/externalpackages/valgrind/install-linux64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/valgrind/install-linux64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/valgrind/install-linux64.sh (revision 11330) @@ -0,0 +1,24 @@ +#!/bin/bash + +#Some cleanup +rm -rf install valgrind-3.7.0 +mkdir install + +#Untar +tar -jxvf valgrind-3.7.0.tar.bz2 + +#Move valgrind into install directory +mv valgrind-3.7.0/* install +rm -rf valgrind-3.7.0 + +#configure +cd install +./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" + +#Compile valgrind +make -j 4 +make install + +#final thing: if mpi is compiled in, soft link its target to a simpler name +cd lib +ln -s valgrind/libmpi* ./libmpidebug.so Index: /issm/trunk-jpl-damage/externalpackages/valgrind/install-macosx32.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/valgrind/install-macosx32.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/valgrind/install-macosx32.sh (revision 11330) @@ -0,0 +1,20 @@ +#!/bin/bash + +#Some cleanup +rm -rf install valgrind-3.7.0 +mkdir install + +#Untar +tar -jxvf valgrind-3.7.0.tar.bz2 + +#Move valgrind into install directory +mv valgrind-3.7.0/* install +rm -rf valgrind-3.7.0 + +#configure +cd install +./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" --enable-only32bit + +#Compile valgrind +make -j 4 +make install Index: /issm/trunk-jpl-damage/externalpackages/valgrind/install-macosx64.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/valgrind/install-macosx64.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/valgrind/install-macosx64.sh (revision 11330) @@ -0,0 +1,20 @@ +#!/bin/bash + +#Some cleanup +rm -rf install valgrind-3.7.0 +mkdir install + +#Untar +tar -jxvf valgrind-3.7.0.tar.bz2 + +#Move valgrind into install directory +mv valgrind-3.7.0/* install +rm -rf valgrind-3.7.0 + +#configure +cd install +./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" --enable-only64bit + +#Compile valgrind +make -j 4 +make install Index: /issm/trunk-jpl-damage/externalpackages/valgrind/install-win32.sh =================================================================== --- /issm/trunk-jpl-damage/externalpackages/valgrind/install-win32.sh (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/valgrind/install-win32.sh (revision 11330) @@ -0,0 +1,24 @@ +#!/bin/bash + +#Some cleanup +rm -rf install valgrind-3.7.0 +mkdir install + +#Untar +tar -jxvf valgrind-3.7.0.tar.bz2 + +#Move valgrind into install directory +mv valgrind-3.7.0/* install +rm -rf valgrind-3.7.0 + +#configure +cd install +./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install" + +#Compile valgrind +make -j 4 +make install + +#final thing: if mpi is compiled in, soft link its target to a simpler name +cd lib +ln -s valgrind/libmpi* ./libmpidebug.so Index: /issm/trunk-jpl-damage/externalpackages/valgrind/issm.supp =================================================================== --- /issm/trunk-jpl-damage/externalpackages/valgrind/issm.supp (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/valgrind/issm.supp (revision 11330) @@ -0,0 +1,142 @@ +# This holds the errors to be suppressed from valgrind report for ISSM. +# See: http://valgrind.org/docs/manual/manual-core.html#manual-core.suppress +# +# to add errors: +# 1. in m/public/queue/ClusterScript.m, +# add: --gen-suppressions=all +# 2. in the errlog, copy and paste the suppression log +# in this file. + +#General errors from MPI, Petsc +#PETSC General {{{1 +{ + petsc1general + Memcheck:User + fun:check_mem_is_defined_untyped + fun:PMPI_Allreduce + fun:MPI_ALLREDUCE + fun:dmumps_276_ + fun:dmumps_ + fun:dmumps_f77_ + fun:dmumps_c + fun:MatFactorNumeric_AIJMUMPS + fun:MatLUFactorNumeric + fun:PCSetUp_LU + fun:PCSetUp + fun:KSPSetUp +} +{ + petsc2general + Memcheck:User + fun:check_mem_is_defined_untyped + fun:PMPI_Bcast + fun:PMPI_BCAST + fun:dmumps_300_ + fun:dmumps_ + fun:dmumps_f77_ + fun:dmumps_c + fun:MatFactorNumeric_AIJMUMPS + fun:MatLUFactorNumeric + fun:PCSetUp_LU + fun:PCSetUp + fun:KSPSetUp +} +{ + petsc3general + Memcheck:User + fun:check_mem_is_defined_untyped + fun:PMPI_Bcast + fun:PMPI_BCAST + fun:dmumps_ + fun:dmumps_f77_ + fun:dmumps_c + fun:MatFactorNumeric_AIJMUMPS + fun:MatLUFactorNumeric + fun:PCSetUp_LU + fun:PCSetUp + fun:KSPSetUp + fun:KSPSolve +} +{ + petsc4firstcall + Memcheck:User + fun:check_mem_is_defined_untyped + fun:walk_type + fun:PMPI_Allreduce + fun:MPIR_Get_contextid + fun:MPIR_Comm_copy + fun:PMPI_Comm_dup + fun:PMPI_Comm_dup + fun:PetscCommDuplicate + fun:PetscHeaderCreate_Private +} +#}}}1 +#Dakota {{{1 +{ + dakota1 + Memcheck:Leak + fun:_Znwm + fun:_ZNSs4_Rep9_S_createEmmRKSaIcE + fun:_ZNSs12_S_constructIPKcEEPcT_S3_RKSaIcESt20forward_iterator_tag + fun:_ZNSsC1EPKcRKSaIcE + fun:_ZN4JEGA10Algorithms17SOGAOperatorGroup4NameEv + fun:_Z41__static_initialization_and_destruction_0ii +} +{ + dakota2 + Memcheck:Leak + fun:_Znwm + fun:_ZNSs4_Rep9_S_createEmmRKSaIcE + fun:_ZNSs12_S_constructIPKcEEPcT_S3_RKSaIcESt20forward_iterator_tag + fun:_ZNSsC1EPKcRKSaIcE + fun:_ZN4JEGA10Algorithms26FavorFeasibleOperatorGroup4NameEv + fun:_Z41__static_initialization_and_destruction_0ii +} +{ + dakota3 + Memcheck:Leak + fun:_Znwm + fun:_ZNSs4_Rep9_S_createEmmRKSaIcE + fun:_ZNSs12_S_constructIPKcEEPcT_S3_RKSaIcESt20forward_iterator_tag + fun:_ZNSsC1EPKcRKSaIcE + fun:_ZN4JEGA10Algorithms17MOGAOperatorGroup4NameEv + fun:_Z41__static_initialization_and_destruction_0ii +} +{ + dakota4 + Memcheck:Leak + fun:_Znwm + fun:_ZNSs4_Rep9_S_createEmmRKSaIcE + fun:_ZNSs12_S_constructIPKcEEPcT_S3_RKSaIcESt20forward_iterator_tag + fun:_ZNSsC1EPKcRKSaIcE + fun:_ZN4JEGA10Algorithms28DominationCountOperatorGroup4NameEv + fun:_Z41__static_initialization_and_destruction_0ii +} +#}}} +#Miscellaneous {{{1 +{ + miscellaneous1 + Memcheck:Free + fun:free + obj:/lib64/libc-2.5.so + obj:/lib64/libc-2.5.so + fun:_vgnU_freeres + fun:exit + fun:(below main) +} +#}}} +#Solution specific errors to ignore +#solver_diagnostic_nonlinear{{{1 +{ + petsc1diagnosticcore + Memcheck:Cond + fun:dmumps_ + fun:dmumps_f77_ + fun:dmumps_c + fun:MatFactorNumeric_AIJMUMPS + fun:MatLUFactorNumeric + fun:PCSetUp_LU + fun:PCSetUp + fun:KSPSetUp + fun:KSPSolve +} Index: /issm/trunk-jpl-damage/externalpackages/vim/addons/README =================================================================== --- /issm/trunk-jpl-damage/externalpackages/vim/addons/README (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/vim/addons/README (revision 11330) @@ -0,0 +1,5 @@ +To use ISSM's settings for vim: + +1. Add the settings from vimrc to your .vimrc file + +2. Add softlinks from vim to your .vim directory Index: /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/autoload/Align.vim =================================================================== --- /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/autoload/Align.vim (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/autoload/Align.vim (revision 11330) @@ -0,0 +1,1029 @@ +" Align: tool to align multiple fields based on one or more separators +" Author: Charles E. Campbell, Jr. +" Date: Mar 03, 2009 +" Version: 35 +" GetLatestVimScripts: 294 1 :AutoInstall: Align.vim +" GetLatestVimScripts: 1066 1 :AutoInstall: cecutil.vim +" Copyright: Copyright (C) 1999-2007 Charles E. Campbell, Jr. {{{1 +" Permission is hereby granted to use and distribute this code, +" with or without modifications, provided that this copyright +" notice is copied with it. Like anything else that's free, +" Align.vim is provided *as is* and comes with no warranty +" of any kind, either expressed or implied. By using this +" plugin, you agree that in no event will the copyright +" holder be liable for any damages resulting from the use +" of this software. +" +" Romans 1:16,17a : For I am not ashamed of the gospel of Christ, for it is {{{1 +" the power of God for salvation for everyone who believes; for the Jew first, +" and also for the Greek. For in it is revealed God's righteousness from +" faith to faith. + +" --------------------------------------------------------------------- +" Load Once: {{{1 +if exists("g:loaded_Align") || &cp + finish +endif +let g:loaded_Align = "v35" +if v:version < 700 + echohl WarningMsg + echo "***warning*** this version of Align needs vim 7.0" + echohl Normal + finish +endif +let s:keepcpo= &cpo +set cpo&vim +"DechoTabOn + +" --------------------------------------------------------------------- +" Debugging Support: {{{1 +"if !exists("g:loaded_Decho") | runtime plugin/Decho.vim | endif + +" --------------------------------------------------------------------- +" Options: {{{1 +if !exists("g:Align_xstrlen") + if &enc == "latin1" || $LANG == "en_US.UTF-8" || !has("multi_byte") + let g:Align_xstrlen= 0 + else + let g:Align_xstrlen= 1 + endif +endif + +" --------------------------------------------------------------------- +" Align#AlignCtrl: enter alignment patterns here {{{1 +" +" Styles = all alignment-break patterns are equivalent +" C cycle through alignment-break pattern(s) +" l left-justified alignment +" r right-justified alignment +" c center alignment +" - skip separator, treat as part of field +" : treat rest of line as field +" + repeat previous [lrc] style +" < left justify separators +" > right justify separators +" | center separators +" +" Builds = s:AlignPat s:AlignCtrl s:AlignPatQty +" C s:AlignPat s:AlignCtrl s:AlignPatQty +" p s:AlignPrePad +" P s:AlignPostPad +" w s:AlignLeadKeep +" W s:AlignLeadKeep +" I s:AlignLeadKeep +" l s:AlignStyle +" r s:AlignStyle +" - s:AlignStyle +" + s:AlignStyle +" : s:AlignStyle +" c s:AlignStyle +" g s:AlignGPat +" v s:AlignVPat +" < s:AlignSep +" > s:AlignSep +" | s:AlignSep +fun! Align#AlignCtrl(...) + +" call Dfunc("AlignCtrl(...) a:0=".a:0) + + " save options that will be changed + let keep_search = @/ + let keep_ic = &ic + + " turn ignorecase off + set noic + + " clear visual mode so that old visual-mode selections don't + " get applied to new invocations of Align(). + if v:version < 602 + if !exists("s:Align_gavemsg") + let s:Align_gavemsg= 1 + echomsg "Align needs at least Vim version 6.2 to clear visual-mode selection" + endif + elseif exists("s:dovisclear") +" call Decho("clearing visual mode a:0=".a:0." a:1<".a:1.">") + let clearvmode= visualmode(1) + endif + + " set up a list akin to an argument list + if a:0 > 0 + let A= s:QArgSplitter(a:1) + else + let A=[0] + endif + + if A[0] > 0 + let style = A[1] + + " Check for bad separator patterns (zero-length matches) + " (but zero-length patterns for g/v is ok) + if style !~# '[gv]' + let ipat= 2 + while ipat <= A[0] + if "" =~ A[ipat] + echoerr "AlignCtrl: separator<".A[ipat]."> matches zero-length string" + let &ic= keep_ic +" call Dret("AlignCtrl") + return + endif + let ipat= ipat + 1 + endwhile + endif + endif + +" call Decho("AlignCtrl() A[0]=".A[0]) + if !exists("s:AlignStyle") + let s:AlignStyle= "l" + endif + if !exists("s:AlignPrePad") + let s:AlignPrePad= 0 + endif + if !exists("s:AlignPostPad") + let s:AlignPostPad= 0 + endif + if !exists("s:AlignLeadKeep") + let s:AlignLeadKeep= 'w' + endif + + if A[0] == 0 + " ---------------------- + " List current selection + " ---------------------- + if !exists("s:AlignPatQty") + let s:AlignPatQty= 0 + endif + echo "AlignCtrl<".s:AlignCtrl."> qty=".s:AlignPatQty." AlignStyle<".s:AlignStyle."> Padding<".s:AlignPrePad."|".s:AlignPostPad."> LeadingWS=".s:AlignLeadKeep." AlignSep=".s:AlignSep +" call Decho("AlignCtrl<".s:AlignCtrl."> qty=".s:AlignPatQty." AlignStyle<".s:AlignStyle."> Padding<".s:AlignPrePad."|".s:AlignPostPad."> LeadingWS=".s:AlignLeadKeep." AlignSep=".s:AlignSep) + if exists("s:AlignGPat") && !exists("s:AlignVPat") + echo "AlignGPat<".s:AlignGPat.">" + elseif !exists("s:AlignGPat") && exists("s:AlignVPat") + echo "AlignVPat<".s:AlignVPat.">" + elseif exists("s:AlignGPat") && exists("s:AlignVPat") + echo "AlignGPat<".s:AlignGPat."> AlignVPat<".s:AlignVPat.">" + endif + let ipat= 1 + while ipat <= s:AlignPatQty + echo "Pat".ipat."<".s:AlignPat_{ipat}.">" +" call Decho("Pat".ipat."<".s:AlignPat_{ipat}.">") + let ipat= ipat + 1 + endwhile + + else + " ---------------------------------- + " Process alignment control settings + " ---------------------------------- +" call Decho("process the alignctrl settings") +" call Decho("style<".style.">") + + if style ==? "default" + " Default: preserve initial leading whitespace, left-justified, + " alignment on '=', one space padding on both sides + if exists("s:AlignCtrlStackQty") + " clear AlignCtrl stack + while s:AlignCtrlStackQty > 0 + call Align#AlignPop() + endwhile + unlet s:AlignCtrlStackQty + endif + " Set AlignCtrl to its default value + call Align#AlignCtrl("Ilp1P1=<",'=') + call Align#AlignCtrl("g") + call Align#AlignCtrl("v") + let s:dovisclear = 1 + let &ic = keep_ic + let @/ = keep_search +" call Dret("AlignCtrl") + return + endif + + if style =~# 'm' + " map support: Do an AlignPush now and the next call to Align() + " will do an AlignPop at exit +" call Decho("style case m: do AlignPush") + call Align#AlignPush() + let s:DoAlignPop= 1 + endif + + " = : record a list of alignment patterns that are equivalent + if style =~# "=" +" call Decho("style case =: record list of equiv alignment patterns") + let s:AlignCtrl = '=' + if A[0] >= 2 + let s:AlignPatQty= 1 + let s:AlignPat_1 = A[2] + let ipat = 3 + while ipat <= A[0] + let s:AlignPat_1 = s:AlignPat_1.'\|'.A[ipat] + let ipat = ipat + 1 + endwhile + let s:AlignPat_1= '\('.s:AlignPat_1.'\)' +" call Decho("AlignCtrl<".s:AlignCtrl."> AlignPat<".s:AlignPat_1.">") + endif + + "c : cycle through alignment pattern(s) + elseif style =~# 'C' +" call Decho("style case C: cycle through alignment pattern(s)") + let s:AlignCtrl = 'C' + if A[0] >= 2 + let s:AlignPatQty= A[0] - 1 + let ipat = 1 + while ipat < A[0] + let s:AlignPat_{ipat}= A[ipat+1] +" call Decho("AlignCtrl<".s:AlignCtrl."> AlignQty=".s:AlignPatQty." AlignPat_".ipat."<".s:AlignPat_{ipat}.">") + let ipat= ipat + 1 + endwhile + endif + endif + + if style =~# 'p' + let s:AlignPrePad= substitute(style,'^.*p\(\d\+\).*$','\1','') +" call Decho("style case p".s:AlignPrePad.": pre-separator padding") + if s:AlignPrePad == "" + echoerr "AlignCtrl: 'p' needs to be followed by a numeric argument' + let @/ = keep_search + let &ic= keep_ic +" call Dret("AlignCtrl") + return + endif + endif + + if style =~# 'P' + let s:AlignPostPad= substitute(style,'^.*P\(\d\+\).*$','\1','') +" call Decho("style case P".s:AlignPostPad.": post-separator padding") + if s:AlignPostPad == "" + echoerr "AlignCtrl: 'P' needs to be followed by a numeric argument' + let @/ = keep_search + let &ic= keep_ic +" call Dret("AlignCtrl") + return + endif + endif + + if style =~# 'w' +" call Decho("style case w: ignore leading whitespace") + let s:AlignLeadKeep= 'w' + elseif style =~# 'W' +" call Decho("style case w: keep leading whitespace") + let s:AlignLeadKeep= 'W' + elseif style =~# 'I' +" call Decho("style case w: retain initial leading whitespace") + let s:AlignLeadKeep= 'I' + endif + + if style =~# 'g' + " first list item is a "g" selector pattern +" call Decho("style case g: global selector pattern") + if A[0] < 2 + if exists("s:AlignGPat") + unlet s:AlignGPat +" call Decho("unlet s:AlignGPat") + endif + else + let s:AlignGPat= A[2] +" call Decho("s:AlignGPat<".s:AlignGPat.">") + endif + elseif style =~# 'v' + " first list item is a "v" selector pattern +" call Decho("style case v: global selector anti-pattern") + if A[0] < 2 + if exists("s:AlignVPat") + unlet s:AlignVPat +" call Decho("unlet s:AlignVPat") + endif + else + let s:AlignVPat= A[2] +" call Decho("s:AlignVPat<".s:AlignVPat.">") + endif + endif + + "[-lrc+:] : set up s:AlignStyle + if style =~# '[-lrc+:]' +" call Decho("style case [-lrc+:]: field justification") + let s:AlignStyle= substitute(style,'[^-lrc:+]','','g') +" call Decho("AlignStyle<".s:AlignStyle.">") + endif + + "[<>|] : set up s:AlignSep + if style =~# '[<>|]' +" call Decho("style case [-lrc+:]: separator justification") + let s:AlignSep= substitute(style,'[^<>|]','','g') +" call Decho("AlignSep ".s:AlignSep) + endif + endif + + " sanity + if !exists("s:AlignCtrl") + let s:AlignCtrl= '=' + endif + + " restore search and options + let @/ = keep_search + let &ic= keep_ic + +" call Dret("AlignCtrl ".s:AlignCtrl.'p'.s:AlignPrePad.'P'.s:AlignPostPad.s:AlignLeadKeep.s:AlignStyle) + return s:AlignCtrl.'p'.s:AlignPrePad.'P'.s:AlignPostPad.s:AlignLeadKeep.s:AlignStyle +endfun + +" --------------------------------------------------------------------- +" s:MakeSpace: returns a string with spacecnt blanks {{{1 +fun! s:MakeSpace(spacecnt) +" call Dfunc("MakeSpace(spacecnt=".a:spacecnt.")") + let str = "" + let spacecnt = a:spacecnt + while spacecnt > 0 + let str = str . " " + let spacecnt = spacecnt - 1 + endwhile +" call Dret("MakeSpace <".str.">") + return str +endfun + +" --------------------------------------------------------------------- +" Align#Align: align selected text based on alignment pattern(s) {{{1 +fun! Align#Align(hasctrl,...) range +" call Dfunc("Align#Align(hasctrl=".a:hasctrl.",...) a:0=".a:0) + + " sanity checks + if string(a:hasctrl) != "0" && string(a:hasctrl) != "1" + echohl Error|echo 'usage: Align#Align(hasctrl<'.a:hasctrl.'> (should be 0 or 1),"separator(s)" (you have '.a:0.') )'|echohl None +" call Dret("Align#Align") + return + endif + if exists("s:AlignStyle") && s:AlignStyle == ":" + echohl Error |echo '(Align#Align) your AlignStyle is ":", which implies "do-no-alignment"!'|echohl None +" call Dret("Align#Align") + return + endif + + " set up a list akin to an argument list + if a:0 > 0 + let A= s:QArgSplitter(a:1) + else + let A=[0] + endif + + " if :Align! was used, then the first argument is (should be!) an AlignCtrl string + " Note that any alignment control set this way will be temporary. + let hasctrl= a:hasctrl +" call Decho("hasctrl=".hasctrl) + if a:hasctrl && A[0] >= 1 +" call Decho("Align! : using A[1]<".A[1]."> for AlignCtrl") + if A[1] =~ '[gv]' + let hasctrl= hasctrl + 1 + call Align#AlignCtrl('m') + call Align#AlignCtrl(A[1],A[2]) +" call Decho("Align! : also using A[2]<".A[2]."> for AlignCtrl") + elseif A[1] !~ 'm' + call Align#AlignCtrl(A[1]."m") + else + call Align#AlignCtrl(A[1]) + endif + endif + + " Check for bad separator patterns (zero-length matches) + let ipat= 1 + hasctrl + while ipat <= A[0] + if "" =~ A[ipat] + echoerr "Align: separator<".A[ipat]."> matches zero-length string" +" call Dret("Align#Align") + return + endif + let ipat= ipat + 1 + endwhile + + " record current search pattern for subsequent restoration + let keep_search= @/ + let keep_ic = &ic + let keep_report= &report + set noic report=10000 + + if A[0] > hasctrl + " Align will accept a list of separator regexps +" call Decho("A[0]=".A[0].": accepting list of separator regexp") + + if s:AlignCtrl =~# "=" + "= : consider all separators to be equivalent +" call Decho("AlignCtrl: record list of equivalent alignment patterns") + let s:AlignCtrl = '=' + let s:AlignPat_1 = A[1 + hasctrl] + let s:AlignPatQty= 1 + let ipat = 2 + hasctrl + while ipat <= A[0] + let s:AlignPat_1 = s:AlignPat_1.'\|'.A[ipat] + let ipat = ipat + 1 + endwhile + let s:AlignPat_1= '\('.s:AlignPat_1.'\)' +" call Decho("AlignCtrl<".s:AlignCtrl."> AlignPat<".s:AlignPat_1.">") + + elseif s:AlignCtrl =~# 'C' + "c : cycle through alignment pattern(s) +" call Decho("AlignCtrl: cycle through alignment pattern(s)") + let s:AlignCtrl = 'C' + let s:AlignPatQty= A[0] - hasctrl + let ipat = 1 + while ipat <= s:AlignPatQty + let s:AlignPat_{ipat}= A[(ipat + hasctrl)] +" call Decho("AlignCtrl<".s:AlignCtrl."> AlignQty=".s:AlignPatQty." AlignPat_".ipat."<".s:AlignPat_{ipat}.">") + let ipat= ipat + 1 + endwhile + endif + endif + + " Initialize so that begline + " is greater than the line's string length -> ragged right. + " Have to be careful about visualmode() -- it returns the last visual + " mode used whether or not it was used currently. + let begcol = virtcol("'<")-1 + let endcol = virtcol("'>")-1 + if begcol > endcol + let begcol = virtcol("'>")-1 + let endcol = virtcol("'<")-1 + endif +" call Decho("begcol=".begcol." endcol=".endcol) + let begline = a:firstline + let endline = a:lastline + if begline > endline + let begline = a:lastline + let endline = a:firstline + endif +" call Decho("begline=".begline." endline=".endline) + let fieldcnt = 0 + if (begline == line("'>") && endline == line("'<")) || (begline == line("'<") && endline == line("'>")) + let vmode= visualmode() +" call Decho("vmode=".vmode) + if vmode == "\" + if exists("g:Align_xstrlen") && g:Align_xstrlen + let ragged = ( col("'>") > s:Strlen(getline("'>")) || col("'<") > s:Strlen(getline("'<")) ) + else + let ragged = ( col("'>") > strlen(getline("'>")) || col("'<") > strlen(getline("'<")) ) + endif + else + let ragged= 1 + endif + else + let ragged= 1 + endif + if ragged + let begcol= 0 + endif +" call Decho("lines[".begline.",".endline."] col[".begcol.",".endcol."] ragged=".ragged." AlignCtrl<".s:AlignCtrl.">") + + " Keep user options + let etkeep = &l:et + let pastekeep= &l:paste + setlocal et paste + + " convert selected range of lines to use spaces instead of tabs + " but if first line's initial white spaces are to be retained + " then use 'em + if begcol <= 0 && s:AlignLeadKeep == 'I' + " retain first leading whitespace for all subsequent lines + let bgntxt= substitute(getline(begline),'^\(\s*\).\{-}$','\1','') +" call Decho("retaining 1st leading whitespace: bgntxt<".bgntxt.">") + set noet + endif + exe begline.",".endline."ret" + + " Execute two passes + " First pass: collect alignment data (max field sizes) + " Second pass: perform alignment + let pass= 1 + while pass <= 2 +" call Decho(" ") +" call Decho("---- Pass ".pass.": ----") + + let line= begline + while line <= endline + " Process each line + let txt = getline(line) +" call Decho(" ") +" call Decho("Pass".pass.": Line ".line." <".txt.">") + + " AlignGPat support: allows a selector pattern (akin to g/selector/cmd ) + if exists("s:AlignGPat") +" call Decho("Pass".pass.": AlignGPat<".s:AlignGPat.">") + if match(txt,s:AlignGPat) == -1 +" call Decho("Pass".pass.": skipping") + let line= line + 1 + continue + endif + endif + + " AlignVPat support: allows a selector pattern (akin to v/selector/cmd ) + if exists("s:AlignVPat") +" call Decho("Pass".pass.": AlignVPat<".s:AlignVPat.">") + if match(txt,s:AlignVPat) != -1 +" call Decho("Pass".pass.": skipping") + let line= line + 1 + continue + endif + endif + + " Always skip blank lines + if match(txt,'^\s*$') != -1 +" call Decho("Pass".pass.": skipping") + let line= line + 1 + continue + endif + + " Extract visual-block selected text (init bgntxt, endtxt) + if exists("g:Align_xstrlen") && g:Align_xstrlen + let txtlen= s:Strlen(txt) + else + let txtlen= strlen(txt) + endif + if begcol > 0 + " Record text to left of selected area + let bgntxt= strpart(txt,0,begcol) +" call Decho("Pass".pass.": record text to left: bgntxt<".bgntxt.">") + elseif s:AlignLeadKeep == 'W' + let bgntxt= substitute(txt,'^\(\s*\).\{-}$','\1','') +" call Decho("Pass".pass.": retaining all leading ws: bgntxt<".bgntxt.">") + elseif s:AlignLeadKeep == 'w' || !exists("bgntxt") + " No beginning text + let bgntxt= "" +" call Decho("Pass".pass.": no beginning text") + endif + if ragged + let endtxt= "" + else + " Elide any text lying outside selected columnar region + let endtxt= strpart(txt,endcol+1,txtlen-endcol) + let txt = strpart(txt,begcol,endcol-begcol+1) + endif +" call Decho(" ") +" call Decho("Pass".pass.": bgntxt<".bgntxt.">") +" call Decho("Pass".pass.": txt<". txt .">") +" call Decho("Pass".pass.": endtxt<".endtxt.">") + if !exists("s:AlignPat_{1}") + echohl Error|echo "no separators specified!"|echohl None +" call Dret("Align#Align") + return + endif + + " Initialize for both passes + let seppat = s:AlignPat_{1} + let ifield = 1 + let ipat = 1 + let bgnfield = 0 + let endfield = 0 + let alignstyle = s:AlignStyle + let doend = 1 + let newtxt = "" + let alignprepad = s:AlignPrePad + let alignpostpad= s:AlignPostPad + let alignsep = s:AlignSep + let alignophold = " " + let alignop = "l" +" call Decho("Pass".pass.": initial alignstyle<".alignstyle."> seppat<".seppat.">") + + " Process each field on the line + while doend > 0 + + " C-style: cycle through pattern(s) + if s:AlignCtrl == 'C' && doend == 1 + let seppat = s:AlignPat_{ipat} +" call Decho("Pass".pass.": processing field: AlignCtrl=".s:AlignCtrl." ipat=".ipat." seppat<".seppat.">") + let ipat = ipat + 1 + if ipat > s:AlignPatQty + let ipat = 1 + endif + endif + + " cyclic alignment/justification operator handling + let alignophold = alignop + let alignop = strpart(alignstyle,0,1) + if alignop == '+' || doend == 2 + let alignop= alignophold + else + let alignstyle = strpart(alignstyle,1).strpart(alignstyle,0,1) + let alignopnxt = strpart(alignstyle,0,1) + if alignop == ':' + let seppat = '$' + let doend = 2 +" call Decho("Pass".pass.": alignop<:> case: setting seppat<$> doend==2") + endif + endif + + " cylic separator alignment specification handling + let alignsepop= strpart(alignsep,0,1) + let alignsep = strpart(alignsep,1).alignsepop + + " mark end-of-field and the subsequent end-of-separator. + " Extend field if alignop is '-' + let endfield = match(txt,seppat,bgnfield) + let sepfield = matchend(txt,seppat,bgnfield) + let skipfield= sepfield +" call Decho("Pass".pass.": endfield=match(txt<".txt.">,seppat<".seppat.">,bgnfield=".bgnfield.")=".endfield) + while alignop == '-' && endfield != -1 + let endfield = match(txt,seppat,skipfield) + let sepfield = matchend(txt,seppat,skipfield) + let skipfield = sepfield + let alignop = strpart(alignstyle,0,1) + let alignstyle= strpart(alignstyle,1).strpart(alignstyle,0,1) +" call Decho("Pass".pass.": extend field: endfield<".strpart(txt,bgnfield,endfield-bgnfield)."> alignop<".alignop."> alignstyle<".alignstyle.">") + endwhile + let seplen= sepfield - endfield +" call Decho("Pass".pass.": seplen=[sepfield=".sepfield."] - [endfield=".endfield."]=".seplen) + + if endfield != -1 + if pass == 1 + " --------------------------------------------------------------------- + " Pass 1: Update FieldSize to max +" call Decho("Pass".pass.": before lead/trail remove: field<".strpart(txt,bgnfield,endfield-bgnfield).">") + let field = substitute(strpart(txt,bgnfield,endfield-bgnfield),'^\s*\(.\{-}\)\s*$','\1','') + if s:AlignLeadKeep == 'W' + let field = bgntxt.field + let bgntxt= "" + endif + if exists("g:Align_xstrlen") && g:Align_xstrlen + let fieldlen = s:Strlen(field) + else + let fieldlen = strlen(field) + endif + let sFieldSize = "FieldSize_".ifield + if !exists(sFieldSize) + let FieldSize_{ifield}= fieldlen +" call Decho("Pass".pass.": set FieldSize_{".ifield."}=".FieldSize_{ifield}." <".field.">") + elseif fieldlen > FieldSize_{ifield} + let FieldSize_{ifield}= fieldlen +" call Decho("Pass".pass.": oset FieldSize_{".ifield."}=".FieldSize_{ifield}." <".field.">") + endif + let sSepSize= "SepSize_".ifield + if !exists(sSepSize) + let SepSize_{ifield}= seplen +" call Decho(" set SepSize_{".ifield."}=".SepSize_{ifield}." <".field.">") + elseif seplen > SepSize_{ifield} + let SepSize_{ifield}= seplen +" call Decho("Pass".pass.": oset SepSize_{".ifield."}=".SepSize_{ifield}." <".field.">") + endif + + else + " --------------------------------------------------------------------- + " Pass 2: Perform Alignment + let prepad = strpart(alignprepad,0,1) + let postpad = strpart(alignpostpad,0,1) + let alignprepad = strpart(alignprepad,1).strpart(alignprepad,0,1) + let alignpostpad = strpart(alignpostpad,1).strpart(alignpostpad,0,1) + let field = substitute(strpart(txt,bgnfield,endfield-bgnfield),'^\s*\(.\{-}\)\s*$','\1','') + if s:AlignLeadKeep == 'W' + let field = bgntxt.field + let bgntxt= "" + endif + if doend == 2 + let prepad = 0 + let postpad= 0 + endif + if exists("g:Align_xstrlen") && g:Align_xstrlen + let fieldlen = s:Strlen(field) + else + let fieldlen = strlen(field) + endif + let sep = s:MakeSpace(prepad).strpart(txt,endfield,sepfield-endfield).s:MakeSpace(postpad) + if seplen < SepSize_{ifield} + if alignsepop == "<" + " left-justify separators + let sep = sep.s:MakeSpace(SepSize_{ifield}-seplen) + elseif alignsepop == ">" + " right-justify separators + let sep = s:MakeSpace(SepSize_{ifield}-seplen).sep + else + " center-justify separators + let sepleft = (SepSize_{ifield} - seplen)/2 + let sepright = SepSize_{ifield} - seplen - sepleft + let sep = s:MakeSpace(sepleft).sep.s:MakeSpace(sepright) + endif + endif + let spaces = FieldSize_{ifield} - fieldlen +" call Decho("Pass".pass.": Field #".ifield."<".field."> spaces=".spaces." be[".bgnfield.",".endfield."] pad=".prepad.','.postpad." FS_".ifield."<".FieldSize_{ifield}."> sep<".sep."> ragged=".ragged." doend=".doend." alignop<".alignop.">") + + " Perform alignment according to alignment style justification + if spaces > 0 + if alignop == 'c' + " center the field + let spaceleft = spaces/2 + let spaceright= FieldSize_{ifield} - spaceleft - fieldlen + let newtxt = newtxt.s:MakeSpace(spaceleft).field.s:MakeSpace(spaceright).sep + elseif alignop == 'r' + " right justify the field + let newtxt= newtxt.s:MakeSpace(spaces).field.sep + elseif ragged && doend == 2 + " left justify rightmost field (no trailing blanks needed) + let newtxt= newtxt.field + else + " left justfiy the field + let newtxt= newtxt.field.s:MakeSpace(spaces).sep + endif + elseif ragged && doend == 2 + " field at maximum field size and no trailing blanks needed + let newtxt= newtxt.field + else + " field is at maximum field size already + let newtxt= newtxt.field.sep + endif +" call Decho("Pass".pass.": newtxt<".newtxt.">") + endif " pass 1/2 + + " bgnfield indexes to end of separator at right of current field + " Update field counter + let bgnfield= sepfield + let ifield = ifield + 1 + if doend == 2 + let doend= 0 + endif + " handle end-of-text as end-of-field + elseif doend == 1 + let seppat = '$' + let doend = 2 + else + let doend = 0 + endif " endfield != -1 + endwhile " doend loop (as well as regularly separated fields) + + if pass == 2 + " Write altered line to buffer +" call Decho("Pass".pass.": bgntxt<".bgntxt."> line=".line) +" call Decho("Pass".pass.": newtxt<".newtxt.">") +" call Decho("Pass".pass.": endtxt<".endtxt.">") + call setline(line,bgntxt.newtxt.endtxt) + endif + + let line = line + 1 + endwhile " line loop + + let pass= pass + 1 + endwhile " pass loop +" call Decho("end of two pass loop") + + " Restore user options + let &l:et = etkeep + let &l:paste = pastekeep + + if exists("s:DoAlignPop") + " AlignCtrl Map support + call Align#AlignPop() + unlet s:DoAlignPop + endif + + " restore current search pattern + let @/ = keep_search + let &ic = keep_ic + let &report = keep_report + +" call Dret("Align#Align") + return +endfun + +" --------------------------------------------------------------------- +" Align#AlignPush: this command/function pushes an alignment control string onto a stack {{{1 +fun! Align#AlignPush() +" call Dfunc("AlignPush()") + + " initialize the stack + if !exists("s:AlignCtrlStackQty") + let s:AlignCtrlStackQty= 1 + else + let s:AlignCtrlStackQty= s:AlignCtrlStackQty + 1 + endif + + " construct an AlignCtrlStack entry + if !exists("s:AlignSep") + let s:AlignSep= '' + endif + let s:AlignCtrlStack_{s:AlignCtrlStackQty}= s:AlignCtrl.'p'.s:AlignPrePad.'P'.s:AlignPostPad.s:AlignLeadKeep.s:AlignStyle.s:AlignSep +" call Decho("AlignPush: AlignCtrlStack_".s:AlignCtrlStackQty."<".s:AlignCtrlStack_{s:AlignCtrlStackQty}.">") + + " push [GV] patterns onto their own stack + if exists("s:AlignGPat") + let s:AlignGPat_{s:AlignCtrlStackQty}= s:AlignGPat + else + let s:AlignGPat_{s:AlignCtrlStackQty}= "" + endif + if exists("s:AlignVPat") + let s:AlignVPat_{s:AlignCtrlStackQty}= s:AlignVPat + else + let s:AlignVPat_{s:AlignCtrlStackQty}= "" + endif + +" call Dret("AlignPush") +endfun + +" --------------------------------------------------------------------- +" Align#AlignPop: this command/function pops an alignment pattern from a stack {{{1 +" and into the AlignCtrl variables. +fun! Align#AlignPop() +" call Dfunc("Align#AlignPop()") + + " sanity checks + if !exists("s:AlignCtrlStackQty") + echoerr "AlignPush needs to be used prior to AlignPop" +" call Dret("Align#AlignPop <> : AlignPush needs to have been called first") + return "" + endif + if s:AlignCtrlStackQty <= 0 + unlet s:AlignCtrlStackQty + echoerr "AlignPush needs to be used prior to AlignPop" +" call Dret("Align#AlignPop <> : AlignPop needs to have been called first") + return "" + endif + + " pop top of AlignCtrlStack and pass value to AlignCtrl + let retval=s:AlignCtrlStack_{s:AlignCtrlStackQty} + unlet s:AlignCtrlStack_{s:AlignCtrlStackQty} + call Align#AlignCtrl(retval) + + " pop G pattern stack + if s:AlignGPat_{s:AlignCtrlStackQty} != "" + call Align#AlignCtrl('g',s:AlignGPat_{s:AlignCtrlStackQty}) + else + call Align#AlignCtrl('g') + endif + unlet s:AlignGPat_{s:AlignCtrlStackQty} + + " pop V pattern stack + if s:AlignVPat_{s:AlignCtrlStackQty} != "" + call Align#AlignCtrl('v',s:AlignVPat_{s:AlignCtrlStackQty}) + else + call Align#AlignCtrl('v') + endif + + unlet s:AlignVPat_{s:AlignCtrlStackQty} + let s:AlignCtrlStackQty= s:AlignCtrlStackQty - 1 + +" call Dret("Align#AlignPop <".retval."> : AlignCtrlStackQty=".s:AlignCtrlStackQty) + return retval +endfun + +" --------------------------------------------------------------------- +" Align#AlignReplaceQuotedSpaces: {{{1 +fun! Align#AlignReplaceQuotedSpaces() +" call Dfunc("AlignReplaceQuotedSpaces()") + + let l:line = getline(line(".")) + if exists("g:Align_xstrlen") && g:Align_xstrlen + let l:linelen = s:Strlen(l:line) + else + let l:linelen = strlen(l:line) + endif + let l:startingPos = 0 + let l:startQuotePos = 0 + let l:endQuotePos = 0 + let l:spacePos = 0 + let l:quoteRe = '\\\@, is needed. {{{1 +" However, doesn't split at all, so this function returns a list +" of arguments which has been: +" * split at whitespace +" * unless inside "..."s. One may escape characters with a backslash inside double quotes. +" along with a leading length-of-list. +" +" Examples: %Align "\"" will align on "s +" %Align " " will align on spaces +" +" The resulting list: qarglist[0] corresponds to a:0 +" qarglist[i] corresponds to a:{i} +fun! s:QArgSplitter(qarg) +" call Dfunc("s:QArgSplitter(qarg<".a:qarg.">)") + + if a:qarg =~ '".*"' + " handle "..." args, which may include whitespace + let qarglist = [] + let args = a:qarg +" call Decho("handle quoted arguments: args<".args.">") + while args != "" + let iarg = 0 + let arglen = strlen(args) +" call Decho("args[".iarg."]<".args[iarg]."> arglen=".arglen) + " find index to first not-escaped '"' + while args[iarg] != '"' && iarg < arglen + if args[iarg] == '\' + let args= strpart(args,1) + endif + let iarg= iarg + 1 + endwhile +" call Decho("args<".args."> iarg=".iarg." arglen=".arglen) + + if iarg > 0 + " handle left of quote or remaining section +" call Decho("handle left of quote or remaining section") + if args[iarg] == '"' + let qarglist= qarglist + split(strpart(args,0,iarg-1)) + else + let qarglist= qarglist + split(strpart(args,0,iarg)) + endif + let args = strpart(args,iarg) + let arglen = strlen(args) + + elseif iarg < arglen && args[0] == '"' + " handle "quoted" section +" call Decho("handle quoted section") + let iarg= 1 + while args[iarg] != '"' && iarg < arglen + if args[iarg] == '\' + let args= strpart(args,1) + endif + let iarg= iarg + 1 + endwhile +" call Decho("args<".args."> iarg=".iarg." arglen=".arglen) + if args[iarg] == '"' + call add(qarglist,strpart(args,1,iarg-1)) + let args= strpart(args,iarg+1) + else + let qarglist = qarglist + split(args) + let args = "" + endif + endif +" call Decho("qarglist".string(qarglist)." iarg=".iarg." args<".args.">") + endwhile + + else + " split at all whitespace + let qarglist= split(a:qarg) + endif + + let qarglistlen= len(qarglist) + let qarglist = insert(qarglist,qarglistlen) +" call Dret("s:QArgSplitter ".string(qarglist)) + return qarglist +endfun + +" --------------------------------------------------------------------- +" s:Strlen: this function returns the length of a string, even if its {{{1 +" using two-byte etc characters. +" Currently, its only used if g:Align_xstrlen is set to a +" nonzero value. Solution from Nicolai Weibull, vim docs +" (:help strlen()), Tony Mechelynck, and my own invention. +fun! s:Strlen(x) +" call Dfunc("s:Strlen(x<".a:x.">") + if g:Align_xstrlen == 1 + " number of codepoints (Latin a + combining circumflex is two codepoints) + " (comment from TM, solution from NW) + let ret= strlen(substitute(a:x,'.','c','g')) + + elseif g:Align_xstrlen == 2 + " number of spacing codepoints (Latin a + combining circumflex is one spacing + " codepoint; a hard tab is one; wide and narrow CJK are one each; etc.) + " (comment from TM, solution from TM) + let ret=strlen(substitute(a:x, '.\Z', 'x', 'g')) + + elseif g:Align_xstrlen == 3 + " virtual length (counting, for instance, tabs as anything between 1 and + " 'tabstop', wide CJK as 2 rather than 1, Arabic alif as zero when immediately + " preceded by lam, one otherwise, etc.) + " (comment from TM, solution from me) + let modkeep= &l:mod + exe "norm! o\" + call setline(line("."),a:x) + let ret= virtcol("$") - 1 + d + let &l:mod= modkeep + + else + " at least give a decent default + ret= strlen(a:x) + endif +" call Dret("s:Strlen ".ret) + return ret +endfun + +" --------------------------------------------------------------------- +" Set up default values: {{{1 +"call Decho("-- Begin AlignCtrl Initialization --") +call Align#AlignCtrl("default") +"call Decho("-- End AlignCtrl Initialization --") + +" --------------------------------------------------------------------- +" Restore: {{{1 +let &cpo= s:keepcpo +unlet s:keepcpo +" vim: ts=4 fdm=marker Index: /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/autoload/AlignMaps.vim =================================================================== --- /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/autoload/AlignMaps.vim (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/autoload/AlignMaps.vim (revision 11330) @@ -0,0 +1,330 @@ +" AlignMaps.vim : support functions for AlignMaps +" Author: Charles E. Campbell, Jr. +" Date: Mar 03, 2009 +" Version: 41 +" --------------------------------------------------------------------- +" Load Once: {{{1 +if &cp || exists("g:loaded_AlignMaps") + finish +endif +let g:loaded_AlignMaps= "v41" +let s:keepcpo = &cpo +set cpo&vim + +" ===================================================================== +" Functions: {{{1 + +" --------------------------------------------------------------------- +" AlignMaps#WrapperStart: {{{2 +fun! AlignMaps#WrapperStart(vis) range +" call Dfunc("AlignMaps#WrapperStart(vis=".a:vis.")") + + if a:vis + norm! ' + endif + + if line("'y") == 0 || line("'z") == 0 || !exists("s:alignmaps_wrapcnt") || s:alignmaps_wrapcnt <= 0 +" call Decho("wrapper initialization") + let s:alignmaps_wrapcnt = 1 + let s:alignmaps_keepgd = &gdefault + let s:alignmaps_keepsearch = @/ + let s:alignmaps_keepch = &ch + let s:alignmaps_keepmy = SaveMark("'y") + let s:alignmaps_keepmz = SaveMark("'z") + let s:alignmaps_posn = SaveWinPosn(0) + " set up fencepost blank lines + put ='' + norm! mz'a + put! ='' + ky + let s:alignmaps_zline = line("'z") + exe "'y,'zs/@/\177/ge" + else +" call Decho("embedded wrapper") + let s:alignmaps_wrapcnt = s:alignmaps_wrapcnt + 1 + norm! 'yjma'zk + endif + + " change some settings to align-standard values + set nogd + set ch=2 + AlignPush + norm! 'zk +" call Dret("AlignMaps#WrapperStart : alignmaps_wrapcnt=".s:alignmaps_wrapcnt." my=".line("'y")." mz=".line("'z")) +endfun + +" --------------------------------------------------------------------- +" AlignMaps#WrapperEnd: {{{2 +fun! AlignMaps#WrapperEnd() range +" call Dfunc("AlignMaps#WrapperEnd() alignmaps_wrapcnt=".s:alignmaps_wrapcnt." my=".line("'y")." mz=".line("'z")) + + " remove trailing white space introduced by whatever in the modification zone + 'y,'zs/ \+$//e + + " restore AlignCtrl settings + AlignPop + + let s:alignmaps_wrapcnt= s:alignmaps_wrapcnt - 1 + if s:alignmaps_wrapcnt <= 0 + " initial wrapper ending + exe "'y,'zs/\177/@/ge" + + " if the 'z line hasn't moved, then go ahead and restore window position + let zstationary= s:alignmaps_zline == line("'z") + + " remove fencepost blank lines. + " restore 'a + norm! 'yjmakdd'zdd + + " restore original 'y, 'z, and window positioning + call RestoreMark(s:alignmaps_keepmy) + call RestoreMark(s:alignmaps_keepmz) + if zstationary > 0 + call RestoreWinPosn(s:alignmaps_posn) +" call Decho("restored window positioning") + endif + + " restoration of options + let &gd= s:alignmaps_keepgd + let &ch= s:alignmaps_keepch + let @/ = s:alignmaps_keepsearch + + " remove script variables + unlet s:alignmaps_keepch + unlet s:alignmaps_keepsearch + unlet s:alignmaps_keepmy + unlet s:alignmaps_keepmz + unlet s:alignmaps_keepgd + unlet s:alignmaps_posn + endif + +" call Dret("AlignMaps#WrapperEnd : alignmaps_wrapcnt=".s:alignmaps_wrapcnt." my=".line("'y")." mz=".line("'z")) +endfun + +" --------------------------------------------------------------------- +" AlignMaps#StdAlign: some semi-standard align calls {{{2 +fun! AlignMaps#StdAlign(mode) range +" call Dfunc("AlignMaps#StdAlign(mode=".a:mode.")") + if a:mode == 1 + " align on @ +" call Decho("align on @") + AlignCtrl mIp1P1=l @ + 'a,.Align + elseif a:mode == 2 + " align on @, retaining all initial white space on each line +" call Decho("align on @, retaining all initial white space on each line") + AlignCtrl mWp1P1=l @ + 'a,.Align + elseif a:mode == 3 + " like mode 2, but ignore /* */-style comments +" call Decho("like mode 2, but ignore /* */-style comments") + AlignCtrl v ^\s*/[/*] + AlignCtrl mWp1P1=l @ + 'a,.Align + else + echoerr "(AlignMaps) AlignMaps#StdAlign doesn't support mode#".a:mode + endif +" call Dret("AlignMaps#StdAlign") +endfun + +" --------------------------------------------------------------------- +" AlignMaps#CharJoiner: joins lines which end in the given character (spaces {{{2 +" at end are ignored) +fun! AlignMaps#CharJoiner(chr) +" call Dfunc("AlignMaps#CharJoiner(chr=".a:chr.")") + let aline = line("'a") + let rep = line(".") - aline + while rep > 0 + norm! 'a + while match(getline(aline),a:chr . "\s*$") != -1 && rep >= 0 + " while = at end-of-line, delete it and join with next + norm! 'a$ + j! + let rep = rep - 1 + endwhile + " update rep(eat) count + let rep = rep - 1 + if rep <= 0 + " terminate loop if at end-of-block + break + endif + " prepare for next line + norm! jma + let aline = line("'a") + endwhile +" call Dret("AlignMaps#CharJoiner") +endfun + +" --------------------------------------------------------------------- +" AlignMaps#Equals: supports \t= and \T= {{{2 +fun! AlignMaps#Equals() range +" call Dfunc("AlignMaps#Equals()") + 'a,'zs/\s\+\([*/+\-%|&\~^]\==\)/ \1/e + 'a,'zs@ \+\([*/+\-%|&\~^]\)=@\1=@ge + 'a,'zs/==/\="\\"/ge + 'a,'zs/\([!<>:]\)=/\=submatch(1)."\"/ge + norm g'zk + AlignCtrl mIp1P1=l = + AlignCtrl g = + 'a,'z-1Align + 'a,'z-1s@\([*/+\-%|&\~^!=]\)\( \+\)=@\2\1=@ge + 'a,'z-1s/\( \+\);/;\1/ge + if &ft == "c" || &ft == "cpp" +" call Decho("exception for ".&ft) + 'a,'z-1v/^\s*\/[*/]/s/\/[*/]/@&@/e + 'a,'z-1v/^\s*\/[*/]/s/\*\//@&/e + if exists("g:mapleader") + exe "norm 'zk" + call AlignMaps#StdAlign(1) + else + exe "norm 'zk" + call AlignMaps#StdAlign(1) + endif + 'y,'zs/^\(\s*\) @/\1/e + endif + 'a,'z-1s/\%x0f/=/ge + 'y,'zs/ @//eg +" call Dret("AlignMaps#Equals") +endfun + +" --------------------------------------------------------------------- +" AlignMaps#Afnc: useful for splitting one-line function beginnings {{{2 +" into one line per argument format +fun! AlignMaps#Afnc() +" call Dfunc("AlignMaps#Afnc()") + + " keep display quiet + let chkeep = &ch + let gdkeep = &gd + let vekeep = &ve + set ch=2 nogd ve= + + " will use marks y,z ; save current values + let mykeep = SaveMark("'y") + let mzkeep = SaveMark("'z") + + " Find beginning of function -- be careful to skip over comments + let cmmntid = synIDtrans(hlID("Comment")) + let stringid = synIDtrans(hlID("String")) + exe "norm! ]]" + while search(")","bW") != 0 +" call Decho("line=".line(".")." col=".col(".")) + let parenid= synIDtrans(synID(line("."),col("."),1)) + if parenid != cmmntid && parenid != stringid + break + endif + endwhile + norm! %my + s/(\s*\(\S\)/(\r \1/e + exe "norm! `y%" + s/)\s*\(\/[*/]\)/)\r\1/e + exe "norm! `y%mz" + 'y,'zs/\s\+$//e + 'y,'zs/^\s\+//e + 'y+1,'zs/^/ / + + " insert newline after every comma only one parenthesis deep + sil! exe "norm! `y\h" + let parens = 1 + let cmmnt = 0 + let cmmntline= -1 + while parens >= 1 +" call Decho("parens=".parens." @a=".@a) + exe 'norm! ma "ay`a ' + if @a == "(" + let parens= parens + 1 + elseif @a == ")" + let parens= parens - 1 + + " comment bypass: /* ... */ or //... + elseif cmmnt == 0 && @a == '/' + let cmmnt= 1 + elseif cmmnt == 1 + if @a == '/' + let cmmnt = 2 " //... + let cmmntline= line(".") + elseif @a == '*' + let cmmnt= 3 " /*... + else + let cmmnt= 0 + endif + elseif cmmnt == 2 && line(".") != cmmntline + let cmmnt = 0 + let cmmntline= -1 + elseif cmmnt == 3 && @a == '*' + let cmmnt= 4 + elseif cmmnt == 4 + if @a == '/' + let cmmnt= 0 " ...*/ + elseif @a != '*' + let cmmnt= 3 + endif + + elseif @a == "," && parens == 1 && cmmnt == 0 + exe "norm! i\\" + endif + endwhile + norm! `y%mz% + sil! 'y,'zg/^\s*$/d + + " perform substitutes to mark fields for Align + sil! 'y+1,'zv/^\//s/^\s\+\(\S\)/ \1/e + sil! 'y+1,'zv/^\//s/\(\S\)\s\+/\1 /eg + sil! 'y+1,'zv/^\//s/\* \+/*/ge + sil! 'y+1,'zv/^\//s/\w\zs\s*\*/ */ge + " func + " ws <- declaration -> <-ptr -> <-var-> <-[array][] -> <-glop-> <-end-> + sil! 'y+1,'zv/^\//s/^\s*\(\(\K\k*\s*\)\+\)\s\+\([(*]*\)\s*\(\K\k*\)\s*\(\(\[.\{-}]\)*\)\s*\(.\{-}\)\=\s*\([,)]\)\s*$/ \1@#\3@\4\5@\7\8/e + sil! 'y+1,'z+1g/^\s*\/[*/]/norm! kJ + sil! 'y+1,'z+1s%/[*/]%@&@%ge + sil! 'y+1,'z+1s%*/%@&%ge + AlignCtrl mIp0P0=l @ + sil! 'y+1,'zAlign + sil! 'y,'zs%@\(/[*/]\)@%\t\1 %e + sil! 'y,'zs%@\*/% */%e + sil! 'y,'zs/@\([,)]\)/\1/ + sil! 'y,'zs/@/ / + AlignCtrl mIlrp0P0= # @ + sil! 'y+1,'zAlign + sil! 'y+1,'zs/#/ / + sil! 'y+1,'zs/@// + sil! 'y+1,'zs/\(\s\+\)\([,)]\)/\2\1/e + + " Restore + call RestoreMark(mykeep) + call RestoreMark(mzkeep) + let &ch= chkeep + let &gd= gdkeep + let &ve= vekeep + +" call Dret("AlignMaps#Afnc") +endfun + +" --------------------------------------------------------------------- +" AlignMaps#FixMultiDec: converts a type arg,arg,arg; line to multiple lines {{{2 +fun! AlignMaps#FixMultiDec() +" call Dfunc("AlignMaps#FixMultiDec()") + + " save register x + let xkeep = @x + let curline = getline(".") +" call Decho("curline<".curline.">") + + " Get the type. I'm assuming one type per line (ie. int x; double y; on one line will not be handled properly) + let @x=substitute(curline,'^\(\s*[a-zA-Z_ \t][a-zA-Z0-9_ \t]*\)\s\+[(*]*\h.*$','\1','') +" call Decho("@x<".@x.">") + + " transform line + exe 's/,/;\r'.@x.' /ge' + + "restore register x + let @x= xkeep + +" call Dret("AlignMaps#FixMultiDec : my=".line("'y")." mz=".line("'z")) +endfun + +" --------------------------------------------------------------------- +" Restore: {{{1 +let &cpo= s:keepcpo +unlet s:keepcpo +" vim: ts=4 fdm=marker Index: /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/colors/issm_black.vim =================================================================== --- /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/colors/issm_black.vim (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/colors/issm_black.vim (revision 11330) @@ -0,0 +1,227 @@ +" ir_black color scheme +" More at: http://blog.infinitered.com/entries/show/8 + + +" ******************************************************************************** +" Standard colors used in all ir_black themes: +" Note, x:x:x are RGB values +" +" normal: #f6f3e8 +" +" string: #A8FF60 168:255:96 +" string inner (punc, code, etc): #00A0A0 0:160:160 +" number: #FF73FD 255:115:253 +" comments: #7C7C7C 124:124:124 +" keywords: #96CBFE 150:203:254 +" operators: white +" class: #FFFFB6 255:255:182 +" method declaration name: #FFD2A7 255:210:167 +" regular expression: #E9C062 233:192:98 +" regexp alternate: #FF8000 255:128:0 +" regexp alternate 2: #B18A3D 177:138:61 +" variable: #C6C5FE 198:197:254 +" +" Misc colors: +" red color (used for whatever): #FF6C60 255:108:96 +" light red: #FFB6B0 255:182:176 +" +" brown: #E18964 good for special +" +" lightpurpleish: #FFCCFF +" +" Interface colors: +" background color: black +" cursor (where underscore is used): #FFA560 255:165:96 +" cursor (where block is used): white +" visual selection: #1D1E2C +" current line: #151515 21:21:21 +" search selection: #07281C 7:40:28 +" line number: #3D3D3D 61:61:61 + + +" ******************************************************************************** +" The following are the preferred 16 colors for your terminal +" Colors Bright Colors +" Black #4E4E4E #7C7C7C +" Red #FF6C60 #FFB6B0 +" Green #A8FF60 #CEFFAB +" Yellow #FFFFB6 #FFFFCB +" Blue #96CBFE #FFFFCB +" Magenta #FF73FD #FF9CFE +" Cyan #C6C5FE #DFDFFE +" White #EEEEEE #FFFFFF + + +" ******************************************************************************** +hi clear + +if exists("syntax_on") + syntax reset +endif +syntax on + +let colors_name = "issm_black" + +" GUI not used in terminal mode forground background style (reverse,bold,..) +"hi Example guifg=NONE guibg=NONE gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE + +" General colors +hi Normal guifg=#f6f3e8 guibg=black gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE +hi NonText guifg=#070707 guibg=black gui=NONE ctermfg=129 ctermbg=NONE cterm=NONE "214 =orange + +hi Cursor guifg=black guibg=white gui=NONE ctermfg=NONE ctermbg=NONE cterm=reverse "cursor (mouse) +hi LineNr guifg=#3D3D3D guibg=black gui=NONE ctermfg=249 ctermbg=232 cterm=NONE "line numbering gray/blak + +hi VertSplit guifg=#202020 guibg=#202020 gui=NONE ctermfg=241 ctermbg=241 cterm=NONE "vertical split +hi StatusLine guifg=#CCCCCC guibg=#202020 gui=italic ctermfg=241 ctermbg=87 cterm=NONE "87 = cyan +hi StatusLineNC guifg=black guibg=#202020 gui=NONE ctermfg=87 ctermbg=241 cterm=NONE "241 = dark gray + +hi Folded guifg=#a0a8b0 guibg=#384048 gui=NONE ctermfg=135 ctermbg=234 cterm=NONE "folded 129 = violet ,234 Gray +hi Title guifg=#f6f3e8 guibg=NONE gui=bold ctermfg=NONE ctermbg=NONE cterm=NONE +hi Visual guifg=NONE guibg=#262D51 gui=NONE ctermfg=NONE ctermbg=NONE cterm=reverse "visual 255 = white + +hi SpecialKey guifg=#808080 guibg=#343434 gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE + +hi WildMenu guifg=green guibg=yellow gui=NONE ctermfg=black ctermbg=yellow cterm=NONE "????? +hi PmenuSbar guifg=black guibg=white gui=NONE ctermfg=black ctermbg=magenta cterm=NONE "???? +"hi Ignore guifg=gray guibg=black gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE + +hi Error guifg=white guibg=NONE gui=none ctermfg=255 ctermbg=129 cterm=NONE +hi ErrorMsg guifg=white guibg=#FF6C60 gui=BOLD ctermfg=255 ctermbg=129 cterm=NONE " 196 = red +hi WarningMsg guifg=white guibg=#FF6C60 gui=BOLD ctermfg=255 ctermbg=201 cterm=NONE "201 = magenta + +" Message displayed in lower left, such as --INSERT-- +hi ModeMsg guifg=black guibg=#C6C5FE gui=BOLD ctermfg=241 ctermbg=87 cterm=BOLD + +if version >= 700 " Vim 7.x specific colors + hi CursorLine guifg=NONE guibg=#121212 gui=NONE ctermfg=NONE ctermbg=NONE cterm=BOLD + hi CursorColumn guifg=NONE guibg=#121212 gui=NONE ctermfg=NONE ctermbg=NONE cterm=BOLD + hi MatchParen guifg=#f6f3e8 guibg=#857b6f gui=BOLD ctermfg=87 ctermbg=241 cterm=BOLD,reverse "matching parenthesis + hi Pmenu guifg=#f6f3e8 guibg=#444444 gui=NONE ctermfg=black ctermbg=white cterm=NONE "auto completion panel + hi PmenuSel guifg=#000000 guibg=#cae682 gui=NONE ctermfg=255 ctermbg=darkgray cterm=NONE + hi Search guifg=NONE guibg=NONE gui=underline ctermfg=black ctermbg=220 cterm=NONE "227 = yellow +endif + +" Syntax highlighting +hi Comment guifg=#7C7C7C guibg=NONE gui=NONE ctermfg=243 ctermbg=NONE cterm=NONE +hi String guifg=#A8FF60 guibg=NONE gui=NONE ctermfg=120 ctermbg=NONE cterm=NONE +hi Number guifg=#FF73FD guibg=NONE gui=NONE ctermfg=201 ctermbg=NONE cterm=NONE + +hi Keyword guifg=#96CBFE guibg=NONE gui=NONE ctermfg=red ctermbg=NONE cterm=NONE " matlab function +hi PreProc guifg=#96CBFE guibg=NONE gui=NONE ctermfg=red ctermbg=NONE cterm=NONE " def undef include +hi Conditional guifg=#6699CC guibg=NONE gui=NONE ctermfg=220 ctermbg=NONE cterm=NONE " if else end + +hi Todo guifg=#8f8f8f guibg=NONE gui=NONE ctermfg=214 ctermbg=NONE cterm=NONE +hi Constant guifg=#99CC99 guibg=NONE gui=NONE ctermfg=196 ctermbg=NONE cterm=NONE + +hi Identifier guifg=#C6C5FE guibg=NONE gui=NONE ctermfg=red ctermbg=NONE cterm=NONE +hi Function guifg=#FFD2A7 guibg=NONE gui=NONE ctermfg=69 ctermbg=NONE cterm=NONE "functions 69 = pastel blue +hi Type guifg=#FFFFB6 guibg=NONE gui=NONE ctermfg=87 ctermbg=NONE cterm=NONE "cterm matlab global +hi Statement guifg=#6699CC guibg=NONE gui=NONE ctermfg=69 ctermbg=NONE cterm=NONE " cd ls sed mv + +hi Special guifg=#E18964 guibg=NONE gui=NONE ctermfg=202 ctermbg=NONE cterm=NONE " ; 202 = orange +hi Delimiter guifg=#00A0A0 guibg=NONE gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE " [ ] +hi Operator guifg=white guibg=NONE gui=NONE ctermfg=202 ctermbg=NONE cterm=NONE " == & 178 = darkyellow + +hi Directory guifg=white guibg=NONE gui=NONE ctermfg=87 ctermbg=NONE cterm=NONE " == & 178 = darkyellow + + "Specific for diff + hi DiffAdd guifg=#ffff33 guibg=#404010 gui=bold term=none cterm=none ctermfg=black ctermbg=119 + hi DiffChange guibg=#202020 gui=bold term=none cterm=none ctermfg=black ctermbg=228 + hi DiffText guifg=#3333ff guibg=#100040 gui=bold term=none cterm=none ctermfg=black ctermbg=178 + hi DiffDelete guifg=#ff0000 guibg=#401010 gui=bold term=none cterm=none ctermfg=black ctermbg=197 + hi diffLine guifg=#444444 guibg=bg gui=bold term=none cterm=bold ctermfg=darkgrey + hi diffOldLine guifg=#444444 guibg=bg gui=none term=none cterm=none ctermfg=darkgrey + hi diffOldFile guifg=#444444 guibg=bg gui=none term=none cterm=none ctermfg=darkgrey + hi diffNewFile guifg=#444444 guibg=bg gui=none term=none cterm=none ctermfg=darkgrey + hi diffAdded guifg=#80ff80 guibg=bg gui=none term=none cterm=none + hi diffRemoved guifg=#ff0000 guibg=bg gui=none term=none cterm=none ctermfg=red + hi diffChanged guifg=#0000ff guibg=bg gui=none term=none cterm=none ctermfg=blue + +hi link Character Constant +hi link Boolean Constant +hi link Float Number +hi link Repeat Statement +hi link Label Statement +hi link Exception Statement +hi link Include PreProc +hi link Define PreProc +hi link Macro PreProc +hi link PreCondit PreProc +hi link StorageClass Type +hi link Structure Type +hi link Typedef Type +hi link Tag Special +hi link SpecialChar Special +hi link SpecialComment Special +hi link Debug Special + + +" Special for Ruby +hi rubyRegexp guifg=#B18A3D guibg=NONE gui=NONE ctermfg=brown ctermbg=NONE cterm=NONE +hi rubyRegexpDelimiter guifg=#FF8000 guibg=NONE gui=NONE ctermfg=brown ctermbg=NONE cterm=NONE +hi rubyEscape guifg=white guibg=NONE gui=NONE ctermfg=cyan ctermbg=NONE cterm=NONE +hi rubyInterpolationDelimiter guifg=#00A0A0 guibg=NONE gui=NONE ctermfg=blue ctermbg=NONE cterm=NONE +hi rubyControl guifg=#6699CC guibg=NONE gui=NONE ctermfg=blue ctermbg=NONE cterm=NONE "and break, etc +"hi rubyGlobalVariable guifg=#FFCCFF guibg=NONE gui=NONE ctermfg=lightblue ctermbg=NONE cterm=NONE "yield +hi rubyStringDelimiter guifg=#336633 guibg=NONE gui=NONE ctermfg=lightgreen ctermbg=NONE cterm=NONE +"rubyInclude +"rubySharpBang +"rubyAccess +"rubyPredefinedVariable +"rubyBoolean +"rubyClassVariable +"rubyBeginEnd +"rubyRepeatModifier +"hi link rubyArrayDelimiter Special " [ , , ] +"rubyCurlyBlock { , , } + +hi link rubyClass Keyword +hi link rubyModule Keyword +hi link rubyKeyword Keyword +hi link rubyOperator Operator +hi link rubyIdentifier Identifier +hi link rubyInstanceVariable Identifier +hi link rubyGlobalVariable Identifier +hi link rubyClassVariable Identifier +hi link rubyConstant Type + + +" Special for Java +" hi link javaClassDecl Type +hi link javaScopeDecl Identifier +hi link javaCommentTitle javaDocSeeTag +hi link javaDocTags javaDocSeeTag +hi link javaDocParam javaDocSeeTag +hi link javaDocSeeTagParam javaDocSeeTag + +hi javaDocSeeTag guifg=#CCCCCC guibg=NONE gui=NONE ctermfg=darkgray ctermbg=NONE cterm=NONE +hi javaDocSeeTag guifg=#CCCCCC guibg=NONE gui=NONE ctermfg=darkgray ctermbg=NONE cterm=NONE +"hi javaClassDecl guifg=#CCFFCC guibg=NONE gui=NONE ctermfg=white ctermbg=NONE cterm=NONE + + +" Special for XML +hi link xmlTag Keyword +hi link xmlTagName Conditional +hi link xmlEndTag Identifier + + +" Special for HTML +hi link htmlTag Keyword +hi link htmlTagName Conditional +hi link htmlEndTag Identifier + + +" Special for Javascript +hi link javaScriptNumber Number + + +" Special for Python +"hi link pythonEscape Keyword + + +" Special for CSharp +hi link csXmlTag Keyword + + +" Special for PHP Index: /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/colors/issm_white.vim =================================================================== --- /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/colors/issm_white.vim (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/colors/issm_white.vim (revision 11330) @@ -0,0 +1,212 @@ +" ir_black color scheme +" More at: http://blog.infinitered.com/entries/show/8 + + +" ******************************************************************************** +" Standard colors used in all ir_black themes: +" Note, x:x:x are RGB values +" +" normal: #f6f3e8 +" +" string: #A8FF60 168:255:96 +" string inner (punc, code, etc): #00A0A0 0:160:160 +" number: #FF73FD 255:115:253 +" comments: #7C7C7C 124:124:124 +" keywords: #96CBFE 150:203:254 +" operators: white +" class: #FFFFB6 255:255:182 +" method declaration name: #FFD2A7 255:210:167 +" regular expression: #E9C062 233:192:98 +" regexp alternate: #FF8000 255:128:0 +" regexp alternate 2: #B18A3D 177:138:61 +" variable: #C6C5FE 198:197:254 +" +" Misc colors: +" red color (used for whatever): #FF6C60 255:108:96 +" light red: #FFB6B0 255:182:176 +" +" brown: #E18964 good for special +" +" lightpurpleish: #FFCCFF +" +" Interface colors: +" background color: black +" cursor (where underscore is used): #FFA560 255:165:96 +" cursor (where block is used): white +" visual selection: #1D1E2C +" current line: #151515 21:21:21 +" search selection: #07281C 7:40:28 +" line number: #3D3D3D 61:61:61 + + +" ******************************************************************************** +" The following are the preferred 16 colors for your terminal +" Colors Bright Colors +" Black #4E4E4E #7C7C7C +" Red #FF6C60 #FFB6B0 +" Green #A8FF60 #CEFFAB +" Yellow #FFFFB6 #FFFFCB +" Blue #96CBFE #FFFFCB +" Magenta #FF73FD #FF9CFE +" Cyan #C6C5FE #DFDFFE +" White #EEEEEE #FFFFFF + + +" ******************************************************************************** +hi clear + +if exists("syntax_on") + syntax reset +endif +syntax on + +let colors_name = "issm_white" + +" GUI not used in terminal mode forground background style (reverse,bold,..) +"hi Example guifg=NONE guibg=NONE gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE + +" General colors +hi Normal guifg=#f6f3e8 guibg=black gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE +hi NonText guifg=#070707 guibg=black gui=NONE ctermfg=129 ctermbg=NONE cterm=NONE "214 =orange + +hi Cursor guifg=black guibg=white gui=NONE ctermfg=NONE ctermbg=NONE cterm=reverse "cursor (mouse) +hi LineNr guifg=#3D3D3D guibg=black gui=NONE ctermfg=249 ctermbg=232 cterm=NONE "line numbering gray/blak + +hi VertSplit guifg=#202020 guibg=#202020 gui=NONE ctermfg=241 ctermbg=241 cterm=NONE "vertical split +hi StatusLine guifg=#CCCCCC guibg=#202020 gui=italic ctermfg=241 ctermbg=87 cterm=NONE "87 = cyan +hi StatusLineNC guifg=black guibg=#202020 gui=NONE ctermfg=87 ctermbg=241 cterm=NONE "241 = dark gray + +hi Folded guifg=#a0a8b0 guibg=#384048 gui=NONE ctermfg=NONE ctermbg=129 cterm=NONE "folded 129 = violet +hi Title guifg=#f6f3e8 guibg=NONE gui=bold ctermfg=NONE ctermbg=NONE cterm=NONE +hi Visual guifg=NONE guibg=#262D51 gui=NONE ctermbg=255 cterm=bold,reverse "visual 255 = white + +hi SpecialKey guifg=#808080 guibg=#343434 gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE + +hi WildMenu guifg=green guibg=yellow gui=NONE ctermfg=black ctermbg=yellow cterm=NONE "????? +hi PmenuSbar guifg=black guibg=white gui=NONE ctermfg=black ctermbg=magenta cterm=NONE "???? +"hi Ignore guifg=gray guibg=black gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE + +hi Error guifg=NONE guibg=black gui=NONE ctermfg=255 ctermbg=129 cterm=NONE +hi ErrorMsg guifg=white guibg=#FF6C60 gui=BOLD ctermfg=255 ctermbg=129 cterm=NONE " 196 = red +hi WarningMsg guifg=white guibg=#FF6C60 gui=BOLD ctermfg=255 ctermbg=201 cterm=NONE "201 = magenta + +" Message displayed in lower left, such as --INSERT-- +hi ModeMsg guifg=black guibg=#C6C5FE gui=BOLD ctermfg=241 ctermbg=87 cterm=BOLD + +if version >= 700 " Vim 7.x specific colors + hi CursorLine guifg=NONE guibg=#121212 gui=NONE ctermfg=NONE ctermbg=NONE cterm=BOLD + hi CursorColumn guifg=NONE guibg=#121212 gui=NONE ctermfg=NONE ctermbg=NONE cterm=BOLD + hi MatchParen guifg=#f6f3e8 guibg=#857b6f gui=BOLD ctermfg=87 ctermbg=241 cterm=BOLD,reverse "matching parenthesis + hi Pmenu guifg=#f6f3e8 guibg=#444444 gui=NONE ctermfg=232 ctermbg=254 cterm=NONE "auto completion panel + hi PmenuSel guifg=#000000 guibg=#cae682 gui=NONE ctermfg=255 ctermbg=201 cterm=NONE + hi Search guifg=NONE guibg=NONE gui=underline ctermfg=NONE ctermbg=227 cterm=NONE "227 = yellow +endif + +" Syntax highlighting +hi Comment guifg=#7C7C7C guibg=NONE gui=NONE ctermfg=243 ctermbg=NONE cterm=NONE +hi String guifg=#A8FF60 guibg=NONE gui=NONE ctermfg=40 ctermbg=NONE cterm=NONE +hi Number guifg=#FF73FD guibg=NONE gui=NONE ctermfg=201 ctermbg=NONE cterm=NONE + +hi Keyword guifg=#96CBFE guibg=NONE gui=NONE ctermfg=196 ctermbg=NONE cterm=NONE " matlab function +hi PreProc guifg=#96CBFE guibg=NONE gui=NONE ctermfg=196 ctermbg=NONE cterm=NONE " def undef include +hi Conditional guifg=#6699CC guibg=NONE gui=NONE ctermfg=93 ctermbg=NONE cterm=NONE " if else end + +hi Todo guifg=#8f8f8f guibg=NONE gui=NONE ctermfg=18 ctermbg=NONE cterm=NONE +hi Constant guifg=#99CC99 guibg=NONE gui=NONE ctermfg=21 ctermbg=NONE cterm=NONE + +hi Identifier guifg=#C6C5FE guibg=NONE gui=NONE ctermfg=21 ctermbg=NONE cterm=NONE +hi Function guifg=#FFD2A7 guibg=NONE gui=NONE ctermfg=69 ctermbg=NONE cterm=NONE "functions 69 = pastel blue +hi Type guifg=#FFFFB6 guibg=NONE gui=NONE ctermfg=165 ctermbg=NONE cterm=NONE +hi Statement guifg=#6699CC guibg=NONE gui=NONE ctermfg=69 ctermbg=NONE cterm=NONE " cd ls sed mv + +hi Special guifg=#E18964 guibg=NONE gui=NONE ctermfg=43 ctermbg=NONE cterm=NONE " ; 202 = orange +hi Delimiter guifg=#00A0A0 guibg=NONE gui=NONE ctermfg=NONE ctermbg=NONE cterm=NONE " [ ] +hi Operator guifg=white guibg=NONE gui=NONE ctermfg=43 ctermbg=NONE cterm=NONE " == & 178 = darkyellow + +hi link Character Constant +hi link Boolean Constant +hi link Float Number +hi link Repeat Statement +hi link Label Statement +hi link Exception Statement +hi link Include PreProc +hi link Define PreProc +hi link Macro PreProc +hi link PreCondit PreProc +hi link StorageClass Type +hi link Structure Type +hi link Typedef Type +hi link Tag Special +hi link SpecialChar Special +hi link SpecialComment Special +hi link Debug Special + + +" Special for Ruby +hi rubyRegexp guifg=#B18A3D guibg=NONE gui=NONE ctermfg=brown ctermbg=NONE cterm=NONE +hi rubyRegexpDelimiter guifg=#FF8000 guibg=NONE gui=NONE ctermfg=brown ctermbg=NONE cterm=NONE +hi rubyEscape guifg=white guibg=NONE gui=NONE ctermfg=cyan ctermbg=NONE cterm=NONE +hi rubyInterpolationDelimiter guifg=#00A0A0 guibg=NONE gui=NONE ctermfg=blue ctermbg=NONE cterm=NONE +hi rubyControl guifg=#6699CC guibg=NONE gui=NONE ctermfg=blue ctermbg=NONE cterm=NONE "and break, etc +"hi rubyGlobalVariable guifg=#FFCCFF guibg=NONE gui=NONE ctermfg=lightblue ctermbg=NONE cterm=NONE "yield +hi rubyStringDelimiter guifg=#336633 guibg=NONE gui=NONE ctermfg=lightgreen ctermbg=NONE cterm=NONE +"rubyInclude +"rubySharpBang +"rubyAccess +"rubyPredefinedVariable +"rubyBoolean +"rubyClassVariable +"rubyBeginEnd +"rubyRepeatModifier +"hi link rubyArrayDelimiter Special " [ , , ] +"rubyCurlyBlock { , , } + +hi link rubyClass Keyword +hi link rubyModule Keyword +hi link rubyKeyword Keyword +hi link rubyOperator Operator +hi link rubyIdentifier Identifier +hi link rubyInstanceVariable Identifier +hi link rubyGlobalVariable Identifier +hi link rubyClassVariable Identifier +hi link rubyConstant Type + + +" Special for Java +" hi link javaClassDecl Type +hi link javaScopeDecl Identifier +hi link javaCommentTitle javaDocSeeTag +hi link javaDocTags javaDocSeeTag +hi link javaDocParam javaDocSeeTag +hi link javaDocSeeTagParam javaDocSeeTag + +hi javaDocSeeTag guifg=#CCCCCC guibg=NONE gui=NONE ctermfg=darkgray ctermbg=NONE cterm=NONE +hi javaDocSeeTag guifg=#CCCCCC guibg=NONE gui=NONE ctermfg=darkgray ctermbg=NONE cterm=NONE +"hi javaClassDecl guifg=#CCFFCC guibg=NONE gui=NONE ctermfg=white ctermbg=NONE cterm=NONE + + +" Special for XML +hi link xmlTag Keyword +hi link xmlTagName Conditional +hi link xmlEndTag Identifier + + +" Special for HTML +hi link htmlTag Keyword +hi link htmlTagName Conditional +hi link htmlEndTag Identifier + + +" Special for Javascript +hi link javaScriptNumber Number + + +" Special for Python +"hi link pythonEscape Keyword + + +" Special for CSharp +hi link csXmlTag Keyword + + +" Special for PHP Index: /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/doc/Align.txt =================================================================== --- /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/doc/Align.txt (revision 11330) +++ /issm/trunk-jpl-damage/externalpackages/vim/addons/vim/doc/Align.txt (revision 11330) @@ -0,0 +1,1469 @@ +*align.txt* The Alignment Tool Mar 04, 2009 + +Author: Charles E. Campbell, Jr. + (remove NOSPAM from Campbell's email first) +Copyright: (c) 2004-2008 by Charles E. Campbell, Jr. *Align-copyright* + The VIM LICENSE applies to Align.vim, AlignMaps.vim, and Align.txt + (see |copyright|) except use "Align and AlignMaps" instead of "Vim" + NO WARRANTY, EXPRESS OR IMPLIED. USE AT-YOUR-OWN-RISK. + +============================================================================== +1. Contents *align* *align-contents* {{{1 + + 1. Contents.................: |align-contents| + 2. Alignment Manual.........: |align-manual| + 3. Alignment Usage..........: |align-usage| + Alignment Concepts.......: |align-concepts| + Alignment Commands.......: |align-commands| + Alignment Control........: |align-control| + Separators.............: |alignctrl-separators| + Initial Whitespace.....: |alignctrl-w| |alignctrl-W| |alignctrl-I| + Justification..........: |alignctrl-l| |alignctrl-r| |alignctrl-c| + Justification Control..: |alignctrl--| |alignctrl-+| |alignctrl-:| + Cyclic/Sequential......: |alignctrl-=| |alignctrl-C| + Separator Justification: |alignctrl-<| |alignctrl->| |alignctrl-|| + Line (de)Selection.....: |alignctrl-g| |alignctrl-v| + Temporary Settings.....: |alignctrl-m| + Padding................: |alignctrl-p| |alignctrl-P| + Current Options........: |alignctrl-settings| |alignctrl-| + Alignment................: |align-align| + 4. Alignment Maps...........: |align-maps| + \a,....................: |alignmap-a,| + \a?....................: |alignmap-a?| + \a<....................: |alignmap-a<| + \abox..................: |alignmap-abox| + \acom..................: |alignmap-acom| + \anum..................: |alignmap-anum| + \ascom.................: |alignmap-ascom| + \adec..................: |alignmap-adec| + \adef..................: |alignmap-adef| + \afnc..................: |alignmap-afnc| + \adcom.................: |alignmap-adcom| + \aocom.................: |alignmap-aocom| + \tsp...................: |alignmap-tsp| + \tsq...................: |alignmap-tsq| + \tt....................: |alignmap-tt| + \t=....................: |alignmap-t=| + \T=....................: |alignmap-T=| + \Htd...................: |alignmap-Htd| + 5. Alignment Tool History...: |align-history| + +============================================================================== +2. Align Manual *alignman* *alignmanual* *align-manual* {{{1 + + Align comes as a vimball; simply typing > + vim Align.vba.gz + :so % +< should put its components where they belong. The components are: > + .vim/plugin/AlignPlugin.vim + .vim/plugin/AlignMapsPlugin.vim + .vim/plugin/cecutil.vim + .vim/autoload/Align.vim + .vim/autoload/AlignMaps.vim + .vim/doc/Align.txt +< To see a user's guide, see |align-userguide| + To see examples, see |alignctrl| and |alignmaps| +> +/=============+=========+=====================================================\ +|| \ Default/ || +|| Commands \ Value/ Explanation || +|| | | || +++==============+====+=======================================================++ +|| AlignCtrl | | =Clrc-+:pPIWw [..list-of-separator-patterns..] || +|| | +-------------------------------------------------------+| +|| | | may be called as a command or as a function: || +|| | | :AlignCtrl =lp0P0W & \\ || +|| | | :call Align#AlignCtrl('=lp0P0W','&','\\') || +|| | | || +|| | +-------------------------------------------------------++ +|| 1st arg | = | = all separator patterns are equivalent and are || +|| | | simultaneously active. Patterns are |regexp|. || +|| | | C cycle through separator patterns. Patterns are || +|| | | |regexp| and are active sequentially. || +|| | | || +|| | < | < left justify separator Separators are justified, || +|| | | > right justify separator too. Separator styles || +|| | | | center separator are cyclic. || +|| | | || +|| | l | l left justify Justification styles are always || +|| | | r right justify cyclic (ie. lrc would mean left j., || +|| | | c center then right j., then center, repeat. || +|| | | - skip this separator || +|| | | + re-use last justification method || +|| | | : treat rest of text as a field || +|| | | || +|| | p1 | p### pad separator on left by # blanks || +|| | P1 | P### pad separator on right by # blanks || +|| | | || +|| | I | I preserve and apply first line's leading white || +|| | | space to all lines || +|| | | W preserve leading white space on every line, even || +|| | | if it varies from line to line || +|| | | w don't preserve leading white space || +|| | | || +|| | | g second argument is a selection pattern -- only || +|| | | align on lines that have a match (inspired by || +|| | | :g/selection pattern/command) || +|| | | v second argument is a selection pattern -- only || +|| | | align on lines that _don't_ have a match (inspired || +|| | | by :v/selection pattern/command) || +|| | | || +|| | | m Map support: AlignCtrl will immediately do an || +|| | | AlignPush() and the next call to Align() will do || +|| | | an AlignPop at the end. This feature allows maps || +|| | | to preserve user settings. || +|| | | || +|| | | default || +|| | | AlignCtrl default || +|| | | will clear the AlignCtrl || +|| | | stack & set the default: AlignCtrl "Ilp1P1=" '=' || +|| | | || +|| +----+-------------------------------------------------------+| +|| More args | More arguments are interpreted as describing separators || +|| +------------------------------------------------------------+| +|| No args | AlignCtrl will display its current settings || +||==============+============================================================+| +||[range]Align | [..list-of-separators..] || +||[range]Align! | [AlignCtrl settings] [..list-of-separators..] || +|| +------------------------------------------------------------+| +|| | Aligns text over the given range. The range may be || +|| | selected via visual mode (v, V, or ctrl-v) or via || +|| | the command line. The Align operation may be invoked || +|| | as a command or as a function; as a function, the first || +|| | argument is 0=separators only, 1=AlignCtrl option string || +|| | followed by a list of separators. || +|| | :[range]Align || +|| | :[range]Align [list of separators] || +|| | :[range]call Align#Align(0) || +|| | :[range]call Align#Align(0,"list","of","separators",...) || +\=============================================================================/ + +============================================================================== +3. Alignment Usage *alignusage* *align-usage* *align-userguide* {{{1 + + +ALIGNMENT CONCEPTS *align-concept* *align-concepts* {{{2 + + The typical text to be aligned is considered to be: + + * composed of two or more fields + * separated by one or more separator pattern(s): + * two or more lines +> + ws field ws separator ws field ws separator ... + ws field ws separator ws field ws separator ... +< + where "ws" stands for "white space" such as blanks and/or tabs, + and "fields" are arbitrary text. For example, consider > + + x= y= z= 3; + xx= yy= zz= 4; + zzz= yyy= zzz= 5; + a= b= c= 3; +< + Assume that it is desired to line up all the "=" signs; these, + then, are the separators. The fields are composed of all the + alphameric text. Assuming they lie on lines 1-4, one may align + those "=" signs with: > + :AlignCtrl l + :1,4Align = +< The result is: > + x = y = z = 3; + xx = yy = zz = 4; + zzz = yyy = zzz = 5; + a = b = c = 3; + +< Note how each "=" sign is surrounded by a single space; the + default padding is p1P1 (p1 means one space before the separator, + and P1 means one space after it). If you wish to change the + padding, say to no padding, use (see |alignctrl-p|) > + :AlignCtrl lp0P0 + +< Next, note how each field is left justified; that's what the "l" + (a small letter "ell") does. If right-justification of the fields + had been desired, an "r" could've been used: > + :AlignCtrl r +< yielding > + x = y = z = 3; + xx = yy = zz = 4; + zzz = yyy = zzz = 5; + a = b = c = 3; +< There are many more options available for field justification: see + |alignctrl-c| and |alignctrl--|. + + Separators, although commonly only one character long, are actually + specified by regular expressions (see |regexp|), and one may left + justify, right justify, or center them, too (see |alignctrl-<|). + + Assume that for some reason a left-right-left-right-... justification + sequence was wished. This wish is simply achieved with > + :AlignCtrl lr + :1,4Align = +< because the justification commands are considered to be "cylic"; ie. + lr is the same as lrlrlrlrlrlrlr... + + There's a lot more discussed under |alignctrl|; hopefully the examples + there will help, too. + + +ALIGNMENT COMMANDS *align-command* *align-commands* {{{2 + + The script includes two primary commands and two + minor commands: + + AlignCtrl : this command/function sets up alignment options + which persist until changed for later Align calls. + It controls such things as: how to specify field + separators, initial white space, padding about + separators, left/right/center justification, etc. > + ex. AlignCtrl wp0P1 + Interpretation: during subsequent alignment + operations, preserve each line's initial + whitespace. Use no padding before separators + but provide one padding space after separators. +< + Align : this command/function operates on the range given it to + align text based on one or more separator patterns. The + patterns may be provided via AlignCtrl or via Align + itself. > + + ex. :%Align , + Interpretation: align all commas over the entire + file. +< The :Align! format permits alignment control commands + to precede the alignment patterns. > + ex. :%Align! p2P2 = +< This will align all "=" in the file with two padding + spaces on both sides of each "=" sign. + + NOTE ON USING PATTERNS WITH ALIGN:~ + Align and AlignCtrl use || to obtain their + input patterns and they use an internal function to + split arguments at whitespace unless inside "..."s. + One may escape characters inside a double-quote string + by preceding such characters with a backslash. + + AlignPush : this command/function pushes the current AlignCtrl + state onto an internal stack. > + ex. :AlignPush + Interpretation: save the current AlignCtrl + settings, whatever they may be. They'll + also remain as the current settings until + AlignCtrl is used to change them. +< + AlignPop : this command/function pops the current AlignCtrl + state from an internal stack. > + ex. :AlignPop + Interpretation: presumably AlignPush was + used (at least once) previously; this command + restores the AlignCtrl settings when AlignPush + was last used. +< Also see |alignctrl-m| for a way to automatically do + an AlignPop after an Align (primarily this is for maps). + +ALIGNMENT OPTIONS *align-option* *align-options* {{{2 + *align-utf8* *align-utf* *align-codepoint* *align-strlen* *align-multibyte* + + For those of you who are using 2-byte (or more) characters such as are + available with utf-8, Align now provides a special option which you + may choose based upon your needs: + + Use Built-in strlen() ~ +> + let g:Align_xstrlen= 0 + +< This is the fastest method, but it doesn't handle multibyte characters + well. It is the default for: + + enc=latin1 + vim compiled without multi-byte support + $LANG is en_US.UTF-8 (assuming USA english) + + Number of codepoints (Latin a + combining circumflex is two codepoints)~ +> + let g:Align_xstrlen= 1 (default) +< + Number of spacing codepoints (Latin a + combining circumflex is one~ + spacing codepoint; a hard tab is one; wide and narrow CJK are one~ + each; etc.)~ +> + let g:Align_xstrlen= 2 +< + Virtual length (counting, for instance, tabs as anything between 1 and~ + 'tabstop', wide CJK as 2 rather than 1, Arabic alif as zero when~ + immediately preceded by lam, one otherwise, etc.)~ +> + let g:Align_xstrlen= 3 +< + By putting one of these settings into your <.vimrc>, Align will use an + internal (interpreted) function to determine a string's length instead + of the Vim's built-in |strlen()| function. Since the function is + interpreted, Align will run a bit slower but will handle such strings + correctly. The last setting (g:Align_xstrlen= 3) probably will run + the slowest but be the most accurate. (thanks to Tony Mechelynck for + these) + + +ALIGNMENT CONTROL *alignctrl* *align-control* {{{2 + + This command doesn't do the alignment operation itself; instead, it + controls subsequent alignment operation(s). + + The first argument to AlignCtrl is a string which may contain one or + more alignment control settings. Most of the settings are specified + by single letters; the exceptions are the p# and P# commands which + interpret a digit following the p or P as specifying padding about the + separator. + + The typical text line is considered to be composed of two or more + fields separated by one or more separator pattern(s): > + + ws field ws separator ws field ws separator ... +< + where "ws" stands for "white space" such as blanks and/or tabs. + + + SEPARATORS *alignctrl-separators* {{{3 + + As a result, separators may not have white space (tabs or blanks) on + their outsides (ie. ": :" is fine as a separator, but " :: " is + not). Usually such separators are not needed, although a map has been + provided which works around this limitation and aligns on whitespace + (see |alignmap-tsp|). + + However, if you really need to have separators with leading or + trailing whitespace, consider handling them by performing a substitute + first (ie. s/ :: /@/g), do the alignment on the temporary pattern + (ie. @), and then perform a substitute to revert the separators back + to their desired condition (ie. s/@/ :: /g). + + The Align#Align() function will first convert tabs over the region into + spaces and then apply alignment control. Except for initial white + space, white space surrounding the fields is ignored. One has three + options just for handling initial white space: + + + --- *alignctrl-w* + wWI INITIAL WHITE SPACE *alignctrl-W* {{{3 + --- *alignctrl-I* + w : ignore all selected lines' initial white space + W : retain all selected lines' initial white space + I : retain only the first line's initial white space and + re-use it for subsequent lines + + Example: Leading white space options: > + +---------------+-------------------+-----------------+ + |AlignCtrl w= :=| AlignCtrl W= := | AlignCtrl I= := | + +------------------+---------------+-------------------+-----------------+ + | Original | w option | W option | I option | + +------------------+---------------+-------------------+-----------------+ + | a := baaa |a := baaa | a : = baaa | a := baaa | + | caaaa := deeee |caaaa := deeee | caaaa : = deeee| caaaa := deeee| + | ee := f |ee := f | ee : = f | ee := f | + +------------------+---------------+-------------------+-----------------+ +< + The original has at least one leading white space on every line. + Using Align with w eliminated each line's leading white space. + Using Align with W preserved each line's leading white space. + Using Align with I applied the first line's leading white space + (three spaces) to each line. + + + ------ *alignctrl-l* + lrc-+: FIELD JUSTIFICATION *alignctrl-r* {{{3 + ------ *alignctrl-c* + + With "lrc", the fields will be left-justified, right-justified, or + centered as indicated by the justification specifiers (lrc). The + "lrc" options are re-used by cycling through them as needed: + + l means llllll.... + r means rrrrrr.... + lr means lrlrlr.... + llr means llrllr.... + + Example: Justification options: Align = > + +------------+-------------------+-------------------+-------------------+ + | Original | AlignCtrl l | AlignCtrl r | AlignCtrl lr | + +------------+-------------------+-------------------+-------------------+ + | a=bb=ccc=1 |a = bb = ccc = 1| a = bb = ccc = 1|a = bb = ccc = 1| + | ccc=a=bb=2 |ccc = a = bb = 2|ccc = a = bb = 2|ccc = a = bb = 2| + | dd=eee=f=3 |dd = eee = f = 3| dd = eee = f = 3|dd = eee = f = 3| + +------------+-------------------+-------------------+-------------------+ + | Alignment |l l l l| r r r r|l r l r| + +------------+-------------------+-------------------+-------------------+ +< + AlignCtrl l : The = separator is repeatedly re-used, as the + cycle only consists of one character (the "l"). + Every time left-justification is used for fields. + AlignCtrl r : The = separator is repeatedly re-used, as the + cycle only consists of one character (the "l"). + Every time right-justification is used for fields + AlignCtrl lr: Again, the "=" separator is repeatedly re-used, + but the fields are justified alternately between + left and right. + + Even more separator control is available. With "-+:": + + - : skip treating the separator as a separator. *alignctrl--* + + : repeat use of the last "lrc" justification *alignctrl-+* + : : treat the rest of the line as a single field *alignctrl-:* + + Example: More justification options: Align = > + +------------+---------------+--------------------+---------------+ + | Original | AlignCtrl -l | AlignCtrl rl+ | AlignCtrl l: | + +------------+---------------+--------------------+---------------+ + | a=bb=ccc=1 |a=bb = ccc=1 | a = bb = ccc = 1 |a = bb=ccc=1 | + | ccc=a=bb=2 |ccc=a = bb=2 |ccc = a = bb = 2 |ccc = a=bb=2 | + | dd=eee=f=3 |dd=eee = f=3 | dd = eee = f = 3 |dd = eee=f=3 | + +------------+---------------+--------------------+---------------+ + | Alignment |l l | r l l l |l l | + +------------+---------------+--------------------+---------------+ +< + In the first example in "More justification options": + + The first "=" separator is skipped by the "-" specification, + and so "a=bb", "ccc=a", and "dd=eee" are considered as single fields. + + The next "=" separator has its (left side) field left-justified. + Due to the cyclic nature of separator patterns, the "-l" + specification is equivalent to "-l-l-l ...". + + Hence the next specification is a "skip", so "ccc=1", etc are fields. + + In the second example in "More justification options": + + The first field is right-justified, the second field is left + justified, and all remaining fields repeat the last justification + command (ie. they are left justified, too). + + Hence rl+ is equivalent to rlllllllll ... + (whereas plain rl is equivalent to rlrlrlrlrl ... ). + + In the third example in "More justification options": + + The text following the first separator is treated as a single field. + + Thus using the - and : operators one can apply justification to a + single separator. + + ex. 1st separator only: AlignCtrl l: + 2nd separator only: AlignCtrl -l: + 3rd separator only: AlignCtrl --l: + etc. + + + --- *alignctrl-=* + =C CYCLIC VS ALL-ACTIVE SEPARATORS *alignctrl-C* {{{3 + --- + + The separators themselves may be considered as equivalent and + simultaneously active ("=") or sequentially cycled through ("C"). + Separators are regular expressions (|regexp|) and are specified as the + second, third, etc arguments. When the separator patterns are + equivalent and simultaneously active, there will be one pattern + constructed: > + + AlignCtrl ... pat1 pat2 pat3 + \(pat1\|pat2\|pat3\) +< + Each separator pattern is thus equivalent and simultaneously active. + The cyclic separator AlignCtrl option stores a list of patterns, only + one of which is active for each field at a time. + + Example: Equivalent/Simultaneously-Active vs Cyclic Separators > + +-------------+------------------+---------------------+----------------------+ + | Original | AlignCtrl = = + -| AlignCtrl = = | AlignCtrl C = + - | + +-------------+------------------+---------------------+----------------------+ + |a = b + c - d|a = b + c - d |a = b + c - d |a = b + c - d | + |x = y = z + 2|x = y = z + 2 |x = y = z + 2|x = y = z + 2 | + |w = s - t = 0|w = s - t = 0 |w = s - t = 0 |w = s - t = 0 | + +-------------+------------------+---------------------+----------------------+ +< + The original is initially aligned with all operators (=+-) being + considered as equivalent and simultaneously active field separators. + Thus the "AlignCtrl = = + -" example shows no change. + + The second example only accepts the '=' as a field separator; + consequently "b + c - d" is now a single field. + + The third example illustrates cyclic field separators and is analyzed + in the following illustration: > + + field1 separator field2 separator field3 separator field4 + a = b + c - d + x = y = z + 2 + w = s - t = 0 +< + The word "cyclic" is used because the patterns form a cycle of use; in + the above case, its = + - = + - = + - = + -... + + Example: Cyclic separators > + Label : this is some text discussing ":"s | ex. abc:def:ghi + Label : this is some text with a ":" in it | ex. abc:def +< + apply AlignCtrl lWC : | | + (select lines)Align > + Label : this is some text discussing ":"s | ex. abc:def:ghi + Label : this is some text with a ":" in it | ex. abcd:efg +< + In the current example, + : is the first separator So the first ":"s are aligned + | is the second separator but subsequent ":"s are not. + | is the third separator The "|"s are aligned, too. + : is the fourth separator Since there aren't two bars, + | is the fifth separator the subsequent potential cycles + | is the sixth separator don't appear. + ... + + In this case it would probably have been a better idea to have used > + AlignCtrl WCl: : | +< as that alignment control would guarantee that no more cycling + would be used after the vertical bar. + + Example: Cyclic separators + + Original: > + a| b&c | (d|e) & f-g-h + aa| bb&cc | (dd|ee) & ff-gg-hh + aaa| bbb&ccc | (ddd|eee) & fff-ggg-hhh +< + AlignCtrl C | | & - > + a | b&c | (d|e) & f - g-h + aa | bb&cc | (dd|ee) & ff - gg-hh + aaa | bbb&ccc | (ddd|eee) & fff - ggg-hhh +< + In this example, + the first and second separators are "|", + the third separator is "&", and + the fourth separator is "-", + + (cycling) + the fifth and sixth separators are "|", + the seventh separator is "&", and + the eighth separator is "-", etc. + + Thus the first "&"s are (not yet) separators, and hence are treated as + part of the field. Ignoring white space for the moment, the AlignCtrl + shown here means that Align will work with > + + field | field | field & field - field | field | field & field - ... +< + + --- *alignctrl-<* + <>| SEPARATOR JUSTIFICATION *alignctrl->* {{{3 + --- *alignctrl-|* + + Separators may be of differing lengths as shown in the example below. + Hence they too may be justified left, right, or centered. + Furthermore, separator justification specifications are cyclic: + + < means <<<<<... justify separator(s) to the left + > means >>>>>... justify separator(s) to the right + | means |||||... center separator(s) + + Example: Separator Justification: Align -\+ > + +-----------------+ + | Original | + +-----------------+ + | a - bbb - c | + | aa -- bb -- ccc | + | aaa --- b --- cc| + +---------------------+-+-----------------+-+---------------------+ + | AlignCtrl < | AlignCtrl > | AlignCtrl | | + +---------------------+---------------------+---------------------+ + | a - bbb - c | a - bbb - c | a - bbb - c | + | aa -- bb -- ccc | aa -- bb -- ccc | aa -- bb -- ccc | + | aaa --- b --- cc | aaa --- b --- cc | aaa --- b --- cc | + +---------------------+---------------------+---------------------+ +< + + --- *alignctrl-g* + gv SELECTIVE APPLICATION *alignctrl-v* {{{3 + --- + + + These two options provide a way to select (g) or to deselect (v) lines + based on a pattern. Ideally :g/pat/Align would work; unfortunately + it results in Align#Align() being called on each line satisfying the + pattern separately. > + + AlignCtrl g pattern +< + Align will only consider those lines which have the given pattern. > + + AlignCtrl v pattern +< + Align will only consider those lines without the given pattern. As an + example of use, consider the following example: > + + :AlignCtrl v ^\s*/\* + Original :Align = :Align = + +----------------+------------------+----------------+ + |one= 2; |one = 2; |one = 2; | + |three= 4; |three = 4; |three = 4; | + |/* skip=this */ |/* skip = this */ |/* skip=this */ | + |five= 6; |five = 6; |five = 6; | + +----------------+------------------+----------------+ +< + The first "Align =" aligned with all "="s, including that one in the + "skip=this" comment. + + The second "Align =" had a AlignCtrl v-pattern which caused it to skip + (ignore) the "skip=this" line when aligning. + + To remove AlignCtrl's g and v patterns, use (as appropriate) > + + AlignCtrl g + AlignCtrl v +< + To see what g/v patterns are currently active, just use the reporting + capability of an unadorned call to AlignCtrl: > + + AlignCtrl +< + + --- + m MAP SUPPORT *alignctrl-m* {{{3 + --- + + This option primarily supports the development of maps. The + Align#AlignCtrl() call will first do an Align#AlignPush() (ie. retain + current alignment control settings). The next Align#Align() will, in + addition to its alignment job, finish up with an Align#AlignPop(). + Thus the Align#AlignCtrl settings that follow the "m" are only + temporarily in effect for just the next Align#Align(). + + + --- + p### *alignctrl-p* + P### PADDING *alignctrl-P* {{{3 + --- + + These two options control pre-padding and post-padding with blanks + about the separator. One may pad separators with zero to nine spaces; + the padding number(s) is/are treated as a cyclic parameter. Thus one + may specify padding separately for each field or re-use a padding + pattern. > + + Example: AlignCtrl p102P0 + +---------+----------------------------------+ + | Original| a=b=c=d=e=f=g=h=1 | + | Align = | a =b=c =d =e=f =g =h=1 | + +---------+----------------------------------+ + | prepad | 1 0 2 1 0 2 1 0 | + +---------+----------------------------------+ +< + This example will cause Align to: + + pre-pad the first "=" with a single blank, + pre-pad the second "=" with no blanks, + pre-pad the third "=" with two blanks, + pre-pad the fourth "=" with a single blank, + pre-pad the fifth "=" with no blanks, + pre-pad the sixth "=" with two blanks, + etc. + + --------------- *alignctrl-settings* + No option given DISPLAY STATUS *alignctrl-* {{{3 + --------------- *alignctrl-no-option* + + AlignCtrl, when called with no arguments, will display the current + alignment control settings. A typical display is shown below: > + + AlignCtrl<=> qty=1 AlignStyle Padding<1|1> + Pat1<\(=\)> +< + Interpreting, this means that the separator patterns are all + equivalent; in this case, there's only one (qty=1). Fields will be + padded on the right with spaces (left justification), and separators + will be padded on each side with a single space. + + To change one of these items, see: + + AlignCtrl......|alignctrl| + qty............|align-concept| + AlignStyle.....|alignctrl--| |alignctrl-+| |alignctrl-:||alignctrl-c| + Padding........|alignctrl-p| |alignctrl-P| + + One may get a string which can be fed back into AlignCtrl: > + + :let alignctrl= Align#AlignCtrl() +< + This form will put a string describing the current AlignCtrl options, + except for the "g" and "v" patterns, into a variable. The + Align#AlignCtrl() function will still echo its settings, however. One + can feed any non-supported "option" to AlignCtrl() to prevent this, + however: > + + :let alignctrl= Align#AlignCtrl("d") +< + +ALIGNMENT *align-align* {{{2 + + Once the alignment control has been determined, the user specifies a + range of lines for the Align command/function to do its thing. + Alignment is often done on a line-range basis, but one may also + restrict alignment to a visual block using ctrl-v. For any visual + mode, one types the colon (:) and then "Align". One may, of course, + specify a range of lines: > + + :[range]Align [list-of-separators] +< + where the |:range| is the usual Vim-powered set of possibilities; the + list of separators is the same as the AlignCtrl capability. There is + only one list of separators, but either AlignCtrl or Align can be used + to specify that list. + + An alternative form of the Align command can handle both alignment + control and the separator list: > + + :[range]Align! [alignment-control-string] [list-of-separators] +< + The alignment control string will be applied only for this particular + application of Align (it uses |alignctrl-m|). The "g pattern" and + "v pattern" alignment controls (see |alignctrl-g| and |alignctrl-v|) + are also available via this form of the Align command. + + Align makes two passes over the text to be aligned. The first pass + determines how many fields there are and determines the maximum sizes + of each field; these sizes are then stored in a vector. The second + pass pads the field (left/right/centered as specified) to bring its + length up to the maximum size of the field. Then the separator and + its AlignCtrl-specified padding is appended. + + Pseudo-Code:~ + During pass 1 + | For all fields in the current line + || Determine current separator + || Examine field specified by current separator + || Determine length of field and save if largest thus far + Initialize newline based on initial whitespace option (wWI) + During pass 2 + | For all fields in current line + || Determine current separator + || Extract field specified by current separator + || Prepend/append padding as specified by AlignCtrl + || (right/left/center)-justify to fit field into max-size field + || Append separator with AlignCtrl-specified separator padding + || Delete current line, install newly aligned line + + The g and v AlignCtrl patterns cause the passes not to consider lines + for alignment, either by requiring that the g-pattern be present or + that the v-pattern not be present. + + The whitespace on either side of a separator is ignored. + + +============================================================================== +4. Alignment Maps *alignmaps* *align-maps* {{{1 + + There are a number of maps using Align#AlignCtrl() and Align#Align() + in the file. This file may also be put into the + plugins subdirectory. Since AlignCtrl and Align supercede textab and + its file, the maps either have a leading "t" (for + "textab") or the more complicated ones an "a" (for "alignment") for + backwards compatibility. + + The maps are shown below with a leading backslash (\). Actually, the + construct is used (see |mapleader|), so the maps' leading + kick-off character is easily customized. + + Furthermore, all AlignMapsPlugin.vim maps use the construct (see + ||and |usr_41.txt|). Hence, if one wishes to override the + mapping entirely, one may do that, too. As an example: > + map ACOM AM_acom +< would have \ACOM do what \acom previously did (assuming that the + mapleader has been left at its default value of a backslash). + + \a, : useful for breaking up comma-separated + declarations prior to \adec |alignmap-a,| + \a( : aligns ( and , (useful for prototypes) *alignmap-a(* + \a? : aligns (...)? ...:... expressions on ? and : |alignmap-a?| + \a< : aligns << and >> for c++ |alignmap-a<| + \a= : aligns := assignments |alignmap-a=| + \abox : draw a C-style comment box around text lines |alignmap-abox| + \acom : useful for aligning comments |alignmap-acom| + \adcom: useful for aligning comments in declarations |alignmap-adcom| + \anum : useful for aligning numbers |alignmap-anum| + NOTE: For the visual-mode use of \anum, is needed! + See http://mysite.verizon.net/astronaut/vim/index.html#VIS + \aenum: align a European-style number |alignmap-anum| + \aunum: align a USA-style number |alignmap-anum| + \adec : useful for aligning declarations |alignmap-adec| + \adef : useful for aligning definitions |alignmap-adef| + \afnc : useful for aligning ansi-c style functions' + argument lists |alignmap-afnc| + \adcom: a variant of \acom, restricted to comment |alignmap-adcom| + containing lines only, but also only for + those which don't begin with a comment. + Good for certain declaration styles. + \aocom: a variant of \acom, restricted to comment |alignmap-aocom| + containing lines only + \tab : align a table based on tabs *alignmap-tab* + (converts to spaces) + \tml : useful for aligning the trailing backslashes |alignmap-tml| + used to continue lines (shell programming, etc) + \tsp : use Align to make a table separated by blanks |alignmap-tsp| + (left justified) + \ts, : like \t, but swaps whitespace on the right of *alignmap-ts,* + the commas to their left + \ts: : like \t: but swaps whitespace on the right of *alignmap-ts:* + the colons to their left + \ts< : like \t< but swaps whitespace on the right of *alignmap-ts<* + the less-than signs to their left + \ts= : like \t= but swaps whitespace on the right of *alignmap-ts=* + the equals signs to their left + \Tsp : use Align to make a table separated by blanks |alignmap-Tsp| + (right justified) + \tsq : use Align to make a table separated by blanks |alignmap-tsq| + (left justified) -- "strings" are not split up + \tt : useful for aligning LaTeX tabular tables |alignmap-tt| + \Htd : tabularizes html tables: |alignmap-Htd| + ...field... ...field... + + *alignmap-t|* *alignmap-t#* *alignmap-t,* *alignmap-t:* + *alignmap-t;* *alignmap-t<* *alignmap-t?* *alignmap-t~* + *alignmap-m=* + \tx : make a left-justified alignment on + character "x" where "x" is: ,:<=@|# |alignmap-t=| + \Tx : make a right-justified alignment on + character "x" where "x" is: ,:<=@# |alignmap-T=| + \m= : like \t= but aligns with %... style comments + + The leading backslash is actually (see |mapleader| for how to + customize the leader to be whatever you like). These maps use the + package and are defined in the file. + Although the maps use AlignCtrl options, they typically use the "m" + option which pushes the options (AlignPush). The associated Align + call which follows will then AlignPop the user's original options + back. + + ALIGNMENT MAP USE WITH MARK AND MOVE~ + In the examples below, one may select the text with a "ma" at the + first line, move to the last line, then execute the map. + + ALIGNMENT MAP USE WITH VISUAL MODE~ + Alternatively, one may select the text with the "V" visual mode + command. + + ALIGNMENT MAP USE WITH MENUS~ + One may use the mark-and-move style (ma, move, use the menu) or + the visual mode style (use the V visual mode, move, then select + the alignment map with menu selection). The alignment map menu + items are under DrChip.AlignMaps . + + One may even change the top level menu name to whatever is wished; by + default, its > + let g:DrChipTopLvlMenu= "DrChip." +< If you set the variable to the empty string (""), then no menu items + will be produced. Of course, one must have a vim with +menu, the gui + must be running, and |'go'| must have the menu bar suboption (ie. m + must be included). + + COMPLEX ALIGNMENT MAP METHOD~ + + For those complex alignment maps which do alignment on constructs + (e.g. \acom, \adec, etc), a series of substitutes is used to insert + "@" symbols in appropriate locations. Align#Align() is then used to + do alignment directly on "@"s; then it is followed by further + substitutes to do clean-up. However, the maps \WS and \WE, used by + every map supported by AlignMaps, protect any original embedded "@" + symbols by first converting them to characters, doing the + requested job, and then converting them back. > + + \WS calls AlignMaps#WrapperStart() + \WE calls AlignMaps#WrapperEnd() +< + + --------------------------- + Alignment Map Examples: \a, *alignmap-a,* {{{3 + --------------------------- + + Original: illustrates comma-separated declaration splitting: > + int a,b,c; + struct ABC_str abc,def; +< + Becomes: > + int a; + int b; + int c; + struct ABC_str abc; + struct ABC_str def; +< + + --------------------------- + Alignment Map Examples: \a? *alignmap-a?* {{{3 + --------------------------- + + Original: illustrates ()?: aligning > + printf("<%s>\n", + (x == ABC)? "abc" : + (x == DEFG)? "defg" : + (x == HIJKL)? "hijkl" : "???"); +< + Becomes: select "(x == ..." lines, then \a? > + printf("<%s>\n", + (x == ABC)? "abc" : + (x == DEFG)? "defg" : + (x == HIJKL)? "hijkl" : "???"); +< + + --------------------------- + Alignment Map Examples: \a< *alignmap-a<* {{{3 + --------------------------- + + Original: illustrating aligning of << and >> > + cin << x; + cin << y; + cout << "this is x=" << x; + cout << "but y=" << y << "is not"; +< + Becomes: select "(x == ..." lines, then \a< > + cin << x; + cin << y; + cout << "this is x=" << x; + cout << "but y=" << y << "is not"; +< + + --------------------------- + Alignment Map Examples: \a= *alignmap-a=* {{{3 + --------------------------- + + Original: illustrates how to align := assignments > + aa:=bb:=cc:=1; + a:=b:=c:=1; + aaa:=bbb:=ccc:=1; +< + Bcomes: select the three assignment lines, then \a:= > + aa := bb := cc := 1; + a := b := c := 1; + aaa := bbb := ccc := 1; +< + + --------------------------- + Alignment Map Examples: \abox *alignmap-abox* {{{3 + --------------------------- + + Original: illustrates how to comment-box some text > + This is some plain text + which will + soon be surrounded by a + comment box. +< + Becomes: Select "This..box." with ctrl-v, press \abox > + /*************************** + * This is some plain text * + * which will * + * soon be surrounded by a * + * comment box. * + ***************************/ +< + + --------------------------- + Alignment Map Examples: \acom *alignmap-acom* {{{3 + --------------------------- + + Original: illustrates aligning C-style comments (works for //, too) > + if(itworks) { /* this */ + then= dothis; /* is a */ + } /* set of three comments */ +< + Becomes: Select the three lines, press \acom > + if(itworks) { /* this */ + then= dothis; /* is a */ + } /* set of three comments */ +< + Also see |alignmap-aocom| + + + --------------------------- + Alignment Map Examples: \anum *alignmap-anum* {{{3 + --------------------------- + + Original: illustrates how to get numbers lined up > + -1.234 .5678 -.901e-4 + 1.234 5.678 9.01e-4 + 12.34 56.78 90.1e-4 + 123.4 567.8 901.e-4 +< + Becomes: Go to first line, ma. Go to last line, press \anum > + -1.234 .5678 -.901e-4 + 1.234 5.678 9.01e-4 + 12.34 56.78 90.1e-4 + 123.4 567.8 901.e-4 +< + Original: > + | -1.234 .5678 -.901e-4 | + | 1.234 5.678 9.01e-4 | + | 12.34 56.78 90.1e-4 | + | 123.4 567.8 901.e-4 | +< + Becomes: Select the numbers with ctrl-v (visual-block mode), > + press \anum + | -1.234 .5678 -.901e-4 | + | 1.234 5.678 9.01e-4 | + | 12.34 56.78 90.1e-4 | + | 123.4 567.8 901.e-4 | +< + Original: > + -1,234 ,5678 -,901e-4 + 1,234 5,678 9,01e-4 + 12,34 56,78 90,1e-4 + 123,4 567,8 901,e-4 +< + Becomes: Go to first line, ma. Go to last line, press \anum > + -1,234 ,5678 -,901e-4 + 1,234 5,678 9,01e-4 + 12,34 56,78 90,1e-4 + 123,4 567,8 901,e-4 +< + In addition: + \aenum is provided to support European-style numbers + \aunum is provided to support USA-style numbers + + One may get \aenum behavior for \anum > + let g:alignmaps_euronumber= 1 +< or \aunum behavior for \anum if one puts > + let g:alignmaps_usanumber= 1 +< in one's <.vimrc>. + + + --------------------------- + Alignment Map Examples: \ascom *alignmap-ascom* {{{3 + --------------------------- + + Original: > + /* A Title */ + int x; /* this is a comment */ + int yzw; /* this is another comment*/ +< + Becomes: Select the three lines, press \ascom > + /* A Title */ + int x; /* this is a comment */ + int yzw; /* this is another comment */ +< + + --------------------------- + Alignment Map Examples: \adec *alignmap-adec* {{{3 + --------------------------- + + Original: illustrates how to clean up C/C++ declarations > + int a; + float b; + double *c=NULL; + char x[5]; + struct abc_str abc; + struct abc_str *pabc; + int a; /* a */ + float b; /* b */ + double *c=NULL; /* b */ + char x[5]; /* x[5] */ + struct abc_str abc; /* abc */ + struct abc_str *pabc; /* pabc */ + static int a; /* a */ + static float b; /* b */ + static double *c=NULL; /* b */ + static char x[5]; /* x[5] */ + static struct abc_str abc; /* abc */ + static struct abc_str *pabc; /* pabc */ +< + Becomes: Select the declarations text, then \adec > + int a; + float b; + double *c = NULL; + char x[5]; + struct abc_str abc; + struct abc_str *pabc; + int a; /* a */ + float b; /* b */ + double *c = NULL; /* b */ + char x[5]; /* x[5] */ + struct abc_str abc; /* abc */ + struct abc_str *pabc; /* pabc */ + static int a; /* a */ + static float b; /* b */ + static double *c = NULL; /* b */ + static char x[5]; /* x[5] */ + static struct abc_str abc; /* abc */ + static struct abc_str *pabc; /* pabc */ +< + + --------------------------- + Alignment Map Examples: \adef *alignmap-adef* {{{3 + --------------------------- + + Original: illustrates how to line up #def'initions > + #define ONE 1 + #define TWO 22 + #define THREE 333 + #define FOUR 4444 +< + Becomes: Select four definition lines, apply \adef > + # define ONE 1 + # define TWO 22 + # define THREE 333 + # define FOUR 4444 +< + + --------------------------- + Alignment Map Examples: \afnc *alignmap-afnc* {{{3 + --------------------------- + + This map is an exception to the usual selection rules. + It uses "]]" to find the function body's leading "{". + Just put the cursor anywhere in the function arguments and + the entire function declaration should be processed. + + Because "]]" looks for that "{" in the first column, the + "original" and "becomes" examples are in the first column, + too. + + Original: illustrates lining up ansi-c style function definitions > + int f( + struct abc_str ***a, /* one */ + long *b, /* two */ + int c) /* three */ + { + } +< + Becomes: put cursor anywhere before the '{', press \afnc > + int f( + struct abc_str ***a, /* one */ + long *b, /* two */ + int c) /* three */ + { + } +< + + --------------------------- + Alignment Map Examples: \adcom *alignmap-adcom* {{{3 + --------------------------- + + Original: illustrates aligning comments that don't begin + lines (optionally after some whitespace). > + struct { + /* this is a test */ + int x; /* of how */ + double y; /* to use adcom */ + }; +< + Becomes: Select the inside lines of the structure, + then press \adcom. The comment-only + line is ignored but the other two comments + get aligned. > + struct { + /* this is a test */ + int x; /* of how */ + double y; /* to use adcom */ + }; +< + + --------------------------- + Alignment Map Examples: \aocom *alignmap-aocom* {{{3 + --------------------------- + + Original: illustrates how to align C-style comments (works for //, too) + but restricted only to aligning with those lines containing + comments. See the difference from \acom (|alignmap-acom|). > + if(itworks) { /* this comment */ + then= dothis; + } /* only appears on two lines */ +< + Becomes: Select the three lines, press \aocom > + if(itworks) { /* this comment */ + then= dothis; + } /* only appears on two lines */ +< + Also see |alignmap-acom| + + + --------------------------- *alignmap-Tsp* + Alignment Map Examples: \tsp *alignmap-tsp* {{{3 + --------------------------- + + Normally Align can't use white spaces for field separators as such + characters are ignored surrounding field separators. The \tsp and + \Tsp maps get around this limitation. + + Original: > + one two three four five + six seven eight nine ten + eleven twelve thirteen fourteen fifteen +< + Becomes: Select the lines, \tsp > + one two three four five + six seven eight nine ten + eleven twelve thirteen fourteen fifteen +< + Becomes: Select the lines, \Tsp > + one two three four five + six seven eight nine ten + eleven twelve thirteen fourteen fifteen +< + + --------------------------- + Alignment Map Examples: \tsq *alignmap-tsq* {{{3 + --------------------------- + + The \tsp map is useful for aligning tables based on white space, + but sometimes one wants double-quoted strings to act as a single + object in spite of embedded spaces. The \tsq map was invented + to support this. (thanks to Leif Wickland) + + Original: > + "one two" three + four "five six" +< + Becomes: Select the lines, \tsq > + "one two" three + four "five six" +< + + --------------------------- + Alignment Map Examples: \tt *alignmap-tt* {{{3 + --------------------------- + + Original: illustrates aligning a LaTex Table > + \begin{tabular}{||c|l|r||} + \hline\hline + one&two&three\\ \hline + four&five&six\\ + seven&eight&nine\\ + \hline\hline + \end{tabular} +< + Becomes: Select the three lines inside the table > + (ie. one..,four..,seven..) and press \tt + \begin{tabular}{||c|l|r||} + \hline\hline + one & two & three \\ \hline + four & five & six \\ + seven & eight & nine \\ + \hline\hline + \end{tabular} +< + + ---------------------------- + Alignment Map Examples: \tml *alignmap-tml* {{{3 + ---------------------------- + + Original: illustrates aligning multi-line continuation marks > + one \ + two three \ + four five six \ + seven \\ \ + eight \nine \ + ten \ +< + Becomes: > + one \ + two three \ + four five six \ + seven \\ \ + eight \nine \ + ten \ +< + + --------------------------- + Alignment Map Examples: \t= *alignmap-t=* {{{3 + --------------------------- + + Original: illustrates left-justified aligning of = > + aa=bb=cc=1;/*one*/ + a=b=c=1;/*two*/ + aaa=bbb=ccc=1;/*three*/ +< + Becomes: Select the three equations, press \t= > + aa = bb = cc = 1; /* one */ + a = b = c = 1; /* two */ + aaa = bbb = ccc = 1; /* three */ +< + + --------------------------- + Alignment Map Examples: \T= *alignmap-T=* {{{3 + --------------------------- + + Original: illustrates right-justified aligning of = > + aa=bb=cc=1; /* one */ + a=b=c=1; /* two */ + aaa=bbb=ccc=1; /* three */ +< + Becomes: Select the three equations, press \T= > + aa = bb = cc = 1; /* one */ + a = b = c = 1; /* two */ + aaa = bbb = ccc = 1; /* three */ +< + + --------------------------- + Alignment Map Examples: \Htd *alignmap-Htd* {{{3 + --------------------------- + + Original: for aligning tables with html > + ...field one......field two... + ...field three......field four... +< + Becomes: Select ... lines, press \Htd > + ...field one... ...field two... + ...field three... ...field four... +< +============================================================================== +4. Alignment Tools' History *align-history* {{{1 + +ALIGN HISTORY {{{2 + 35 : Nov 02, 2008 * g:loaded_AlignPlugin testing to prevent re-loading + installed + Nov 19, 2008 * new sanity check for an AlignStyle of just ":" + Jan 08, 2009 * save&restore of |'mod'| now done with local + variant + 34 : Jul 08, 2008 * using :AlignCtrl before entering any alignment + control commands was causing an error. + 33 : Sep 20, 2007 * s:Strlen() introduced to support various ways + used to represent characters and their effects + on string lengths. See |align-strlen|. + * Align now accepts "..." -- so it can accept + whitespace as separators. + 32 : Aug 18, 2007 * uses || instead of || plus a + custom argument splitter to allow patterns with + backslashes to slide in unaltered. + 31 : Aug 06, 2007 * :[range]Align! [AlignCtrl settings] pattern(s) + implemented. + 30 : Feb 12, 2007 * now uses |setline()| + 29 : Jan 18, 2006 * cecutil updated to use keepjumps + Feb 23, 2006 * Align now converted to vim 7.0 style using + auto-loading functions. + 28 : Aug 17, 2005 * report option workaround + Oct 24, 2005 * AlignCtrl l: wasn't behaving as expected; fixed + 27 : Apr 15, 2005 : cpo workaround + ignorecase workaround + 26 : Aug 20, 2004 : loaded_align now also indicates version number + GetLatestVimScripts :AutoInstall: now supported + 25 : Jul 27, 2004 : For debugging, uses Dfunc(), Dret(), and Decho() + 24 : Mar 03, 2004 : (should've done this earlier!) visualmode(1) + not supported until v6.2, now Align will avoid + calling it for earlier versions. Visualmode + clearing won't take place then, of course. + 23 : Oct 07, 2003 : Included Leif Wickland's ReplaceQuotedSpaces() + function which supports \tsq + 22 : Jan 29, 2003 : Now requires 6.1.308 or later to clear visualmode() + 21 : Jan 10, 2003 : BugFix: similar problem to #19; new code + bypasses "norm! v\" until initialization + is over. + 20 : Dec 30, 2002 : BugFix: more on "unable to highlight" fixed + 19 : Nov 21, 2002 : BugFix: some terminals gave an "unable to highlight" + message at startup; Hari Krishna Dara tracked it + down; a silent! now included to prevent noise. + 18 : Nov 04, 2002 : BugFix: re-enabled anti-repeated-loading + 17 : Nov 04, 2002 : BugFix: forgot to have AlignPush() push s:AlignSep + AlignCtrl now clears visual-block mode when used so + that Align won't try to use old visual-block + selection marks '< '> + 16 : Sep 18, 2002 : AlignCtrl <>| options implemented (separator + justification) + 15 : Aug 22, 2002 : bug fix: AlignCtrl's ":" now acts as a modifier of + the preceding alignment operator (lrc) + 14 : Aug 20, 2002 : bug fix: AlignCtrl default now keeps &ic unchanged + bug fix: Align, on end-field, wasn't using correct + alignop bug fix: Align, on end-field, was appending + padding + 13 : Aug 19, 2002 : bug fix: zero-length g/v patterns are accepted + bug fix: always skip blank lines + bug fix: AlignCtrl default now also clears g and v + patterns + 12 : Aug 16, 2002 : moved keep_ic above zero-length pattern checks + added "AlignCtrl default" + fixed bug with last field getting separator spaces + at end line + 11 : Jul 08, 2002 : prevent separator patterns which match zero length + -+: included as additional alignment/justification + styles + 10 : Jun 26, 2002 : =~# used instead of =~ (for matching case) + ignorecase option handled + 9 : Jun 25, 2002 : implemented cyclic padding + +ALIGNMENT MAP HISTORY *alignmap-history* {{{2 + v41 Nov 02, 2008 * g:loaded_AlignMapsPlugin testing to prevent + re-loading installed + * AlignMaps now use 0x0f (ctrl-p) for special + character substitutions (instead of 0xff). + Seems to avoid some problems with having to + use Strlen(). + * bug fixed with \ts, + * new maps: \ts; \ts, \ts: \ts< \ts= \a( + v40 Oct 21, 2008 * Modified AlignMaps so that its maps use s + and