source: issm/oecreview/Archive/24307-24683/ISSM-24327-24328.diff@ 24684

../trunk-jpl/externalpackages/lapack/install-3.8-Linux.sh

@@ +1 @@
+#!/bin/bash
+set -eu
+
+
+# NOTE: This installation script will build both BLAS and LAPACK libraries
+#
+
+## Constants
+#
+VER="3.8.0"
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/lapack-${VER}.tar.gz" "lapack-${VER}.tar.gz"
+
+# Unpack source
+tar -zxvf lapack-$VER.tar.gz
+
+# Cleanup
+rm -rf build install src
+mkdir build install install/lib src
+
+# Move source to 'src' directory
+mv lapack-$VER/* src
+rm -rf lapack-$VER
+
+# Configure
+#
+cd build
+cmake \
+        -DBUILD_SHARED_LIBS=ON \
+        ../src
+
+# Compile
+make
+
+# Install
+cd ..
+cp ./build/lib/* ./install/lib

../trunk-jpl/externalpackages/mpich/install-3.3-macOS_64.sh

@@ -1 @@
-#!/bin/bash
-set -eu
-
-
-## Constants
-#
-VER="3.3"
-
-# Cleanup
-rm -rf src install
-mkdir src install
-
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/mpich-${VER}.tar.gz" "mpich-${VER}.tar.gz"
-
-# Unpack source
-tar -zxvf  mpich-$VER.tar.gz
-
-# Move source into 'src' directory
-mv mpich-$VER/* src
-rm -rf mpich-$VER
-
-# Configure
-cd src
-./configure \
-        --prefix="${ISSM_DIR}/externalpackages/mpich/install" \
-        --enable-shared
-
-# Compile and install
-if [ $# -eq 0 ]; then
-        make
-        make install
-else
-        make -j $1
-        make -j $1 install
-fi
-
-# Return to initial directory
-cd ..

../trunk-jpl/externalpackages/petsc/install-3.11-linux64.sh

@@ -1 @@
-#!/bin/bash
-set -eu
-
-#Some cleanup
-rm -rf install petsc-3.11.0 src
-mkdir install src
-
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.sh 'http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.11.0.tar.gz' 'petsc-3.11.0.tar.gz'
-
-#Untar and move petsc to install directory
-tar -zxvf  petsc-3.11.0.tar.gz
-mv petsc-3.11.0/* src/
-rm -rf petsc-3.11.0
-
-#configure
-cd src
-./config/configure.py \
-        --prefix="$ISSM_DIR/externalpackages/petsc/install" \
-        --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \
-        --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
-        --with-debugging=1 \
-        --with-valgrind=0 \
-        --with-x=0 \
-        --with-ssl=0 \
-        --with-shared-libraries=1 \
-        --download-metis=1 \
-        --download-parmetis=1 \
-        --download-mumps=1 \
-        --download-scalapack=1 \
-        --download-fblaslapack=1 \
-        --with-pic=1
-
-#Compile and intall
-make
-make install

../trunk-jpl/externalpackages/petsc/install-3.11-macOS.sh

@@ +1 @@
+#!/bin/bash
+set -eu
+
+
+## Constants
+#
+VER="3.11.3"
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
+
+# Unpack source
+tar -zxvf  petsc-$VER.tar.gz
+
+# Cleanup
+rm -rf install src
+mkdir install src
+
+# Move source to 'src' directory
+mv petsc-$VER/* src/
+rm -rf petsc-$VER
+
+# Configure
+cd src
+./config/configure.py \
+        --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
+        --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
+        --with-mpi-dir="${ISSM_DIR}/externalpackages/mpich/install" \
+        --with-blas-lib="-L${ISSM_DIR}/externalpackages/lapack/install/lib -lblas" \
+        --with-lapack-lib="-L${ISSM_DIR}/externalpackages/lapack/install/lib -llapack" \
+        --with-debugging=0 \
+        --with-valgrind=0 \
+        --with-x=0 \
+        --with-ssl=0 \
+        --with-shared-libraries=1 \
+        --download-zlib=1\
+        --download-hdf5=1 \
+        --download-netcdf=1 \
+        --download-metis=1 \
+        --download-parmetis=1 \
+        --download-scalapack=1 \
+        --download-mumps=1
+
+# Compile and install
+if [ $# -eq 0 ]; then
+        make
+        make install
+else
+        make -j $1
+        make -j $1 install
+fi
+
+# Return to initial directory
+cd ..

../trunk-jpl/externalpackages/petsc/install-3.11-Linux.sh

@@ +1 @@
+#!/bin/bash
+set -eu
+
+
+## Constants
+#
+VER="3.11.3"
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
+
+# Unpack source
+tar -zxvf  petsc-$VER.tar.gz
+
+# Cleanup
+rm -rf install src
+mkdir install src
+
+# Move source to 'src' directory
+mv petsc-$VER/* src/
+rm -rf petsc-$VER
+
+# Configure
+cd src
+./config/configure.py \
+        --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
+        --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
+        --with-mpi-dir="${ISSM_DIR}/externalpackages/mpich/install" \
+        --with-blas-lib="-L${ISSM_DIR}/externalpackages/lapack/install/lib -lblas" \
+        --with-lapack-lib="-L${ISSM_DIR}/externalpackages/lapack/install/lib -llapack" \
+        --with-debugging=0 \
+        --with-valgrind=0 \
+        --with-x=0 \
+        --with-ssl=0 \
+        --with-shared-libraries=1 \
+        --download-zlib=1\
+        --download-hdf5=1 \
+        --download-netcdf=1 \
+        --download-metis=1 \
+        --download-parmetis=1 \
+        --download-scalapack=1 \
+        --download-mumps=1
+
+# Compile and install
+if [ $# -eq 0 ]; then
+        make
+        make install
+else
+        make -j $1
+        make -j $1 install
+fi
+
+# Return to initial directory
+cd ..

../trunk-jpl/m4/issm_options.m4

@@ -1491 +1491 @@
         dnl blas-lapack headers and libraries
         if test "x$HAVE_BLASLAPACK" == "xyes"; then
                 BLASLAPACKINCL=""
-                dnl: branch on whether we are running on windows or linux.
                 case "${host_os}" in
                 *cygwin*)
                   BLASLAPACKLIB="-L`cygpath -m $BLASLAPACK_ROOT` -Wl,libf2cblas.lib  -Wl,libf2clapack.lib"
                   ;;
                 *linux*)
-                                BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas "
-                #BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -llapack -lblas "
-                  ;;
+                        BLASLAPACKLIB="-L${BLASLAPACK_ROOT}/lib"
+                        if "x${BLASLAPACK_ROOT}" == "x${PETSC_ROOT}"; then
+                                BLASLAPACKLIB+=" -lflapack -lfblas"
+                        else
+                                BLASLAPACKLIB+=" -llapack -lblas"
+                        fi
+                ;;
                 *darwin*)
-                  BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas "
-                  ;;
+                        BLASLAPACKLIB="-L${BLASLAPACK_ROOT}/lib"
+                        if "x${BLASLAPACK_ROOT}" == "x${PETSC_ROOT}"; then
+                                BLASLAPACKLIB+=" -lflapack -lfblas"
+                        else
+                                BLASLAPACKLIB+=" -llapack -lblas"
+                        fi
+                ;;
                 esac
                 AC_DEFINE([_HAVE_BLASLAPACK_],[1],[with blas lapack in ISSM src])
                 AC_SUBST([BLASLAPACKLIB])

../trunk-jpl/externalpackages/gmt/configs/Linux/cmake/ConfigUser.cmake

@@ +1 @@
+#
+#
+# Copyright (c) 1991-2019 by the GMT Team (https://www.generic-mapping-tools.org/team.html)
+# See LICENSE.TXT file for copying and redistribution conditions.
+#
+# This program is free software; you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation; version 3 or 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 Lesser General Public License
+# for more details.
+#
+# Contact info: www.generic-mapping-tools.org
+# ----------------------------------------------------------------------------
+
+# Use this file to override variables in 'ConfigDefault.cmake' on a per-user
+# basis.  First copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake', then
+# edit 'ConfigUser.cmake'.  'ConfigUser.cmake' is not version controlled
+# (currently listed in .gitignore).
+#
+# Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string
+# ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so
+# "False", "off", "no", and "something-NotFound" are all false).  Other values
+# are true.  Thus it does not matter whether you use TRUE and FALSE, ON and
+# OFF, or YES and NO for your booleans.
+
+##
+## Section 1: Installation paths
+##
+
+# ============================================================================
+# Basic setup begins here.  All settings are optional.  In most cases, setting
+# CMAKE_INSTALL_PREFIX should be all you need to do in order to build GMT with
+# reasonable defaults enabled.  Note: If you need to specify directory names
+# with spaces (e.g., on Windows) then you must put them in quotes.
+# ============================================================================
+
+# Installation path (usually defaults to /usr/local) [auto]:
+set (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install")
+
+# Set install name suffix used for directories and gmt executables
+# [undefined]:
+#set (GMT_INSTALL_NAME_SUFFIX "suffix")
+
+# Install into traditional directory structure. Disable to install a
+# distribution type directory structure (doc and share separated) [on]:
+#set (GMT_INSTALL_TRADITIONAL_FOLDERNAMES OFF)
+
+# Install convenience links for GMT modules. Disable to install only the main
+# gmt program and access modules as "gmt modulename options" [TRUE]:
+#set (GMT_INSTALL_MODULE_LINKS FALSE)
+
+# Make executables relocatable on supported platforms (relative RPATH) [FALSE]:
+set (GMT_INSTALL_RELOCATABLE TRUE)
+
+# Exclude optional GDAL, PCRE, PCRE2, FFTW3, LAPACK, BLAS, ZLIB dependencies even if you have them installed [FALSE]
+#set (GMT_EXCLUDE_GDAL TRUE)
+#set (GMT_EXCLUDE_PCRE TRUE)
+#set (GMT_EXCLUDE_PCRE2 TRUE)
+#set (GMT_EXCLUDE_FFTW3 TRUE)
+#set (GMT_EXCLUDE_LAPACK TRUE)
+#set (GMT_EXCLUDE_BLAS TRUE)
+#set (GMT_EXCLUDE_ZLIB TRUE)
+
+# ============================================================================
+# Advanced configuration begins here.  Usually it is not necessary to edit any
+# settings below.  You should know what you are doing if you do though.  Note:
+# installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute
+# path is given.
+# ============================================================================
+
+# Set binary installation path [bin]:
+#set (GMT_BINDIR "bin")
+
+# Set library installation path [lib or lib64]:
+#set (GMT_LIBDIR "lib")
+
+# Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]:
+#set (GMT_INCLUDEDIR "include/gmt")
+
+# Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]:
+#set (GMT_DATADIR "share/gmt")
+
+# Set doc installation path [share/doc or
+# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]:
+#set (GMT_DOCDIR "share/doc/gmt")
+
+# Set manpage installation path [share/man or
+# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]:
+#set (GMT_MANDIR "share/doc/gmt/man")
+
+# Install documentation files from this external location instead of creating
+# new HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]:
+#set (GMT_INSTALL_EXTERNAL_DOC OFF)
+
+# Install manual pages from this external location instead of creating the
+# manpages from scratch [${GMT_SOURCE_DIR}/man_release]:
+#set (GMT_INSTALL_EXTERNAL_MAN OFF)
+
+##
+## Section 2: Build dependencies (should only be needed if CMake cannot
+## automatically detect the rights version or path.)
+##
+
+# Set URL to GMT Data server [auto]:
+#set (GMT_DATA_SERVER "data_server_url")
+
+# Set path to GSHHG Shoreline Database [auto]:
+set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install")
+
+# Copy GSHHG files to ${GMT_DATADIR}/coast [FALSE]:
+#set (COPY_GSHHG TRUE)
+
+# Set path to DCW Digital Chart of the World for GMT [auto]:
+#set (DCW_ROOT "dcw-gmt_path")
+
+# Copy DCW files to ${GMT_DATADIR}/dcw [FALSE]:
+#set (COPY_DCW TRUE)
+
+# Copy GDAL's 'data' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]:
+#set (GDAL_DATA_PATH C:/programs/compa_libs/gdal_GIT/compileds/VC14_64/data)
+
+# Copy PROJ4's 'share' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]:
+#set (PROJ_DATA_PATH C:/programs/compa_libs/proj5_GIT/compileds/VC14_64/share/proj)
+
+# FOR WINDOWS ONLY
+# Set path to location of Ghostscript binaries (optional install)
+#set (GHOST_DATA_PATH C:/programs/compa_libs/ghostscript/bin)
+
+# FOR WINDOWS ONLY
+# Set path to location where the gmtmex is located.
+#set (GMTMEX_PATH "C:/progs_cygw/GMTdev/gmtmex/${GMTver}")
+
+# Set location of NetCDF (can be root directory, path to header file or path
+# to nc-config) [auto]:
+set (NETCDF_ROOT "$ENV{ISSM_DIR}/externalpackages/petsc/install")
+
+# Set location of GDAL (can be root directory, path to header file or path to
+# gdal-config) [auto]:
+set (GDAL_ROOT "$ENV{ISSM_DIR}/externalpackages/gdal/install")
+
+# Set location of PCRE (can be root directory, path to header file or path to
+# pcre-config) [auto]:
+#set (PCRE_ROOT "pcre_install_prefix")
+# Alternatively, set location of PCRE2 (can be root directory, path to header file or path to
+# pcre2-config) [auto]:
+#set (PCRE2_ROOT "pcre2_install_prefix")
+
+# Set location of single precision FFTW (can be root directory or path to
+# header file) [auto]:
+#set (FFTW3_ROOT "fftw_install_prefix")
+
+# Set location of ZLIB (can be root directory or path to header file) [auto]:
+set (ZLIB_ROOT "$ENV{ISSM_DIR}/externalpackages/petsc/install")
+
+# Set location of CURL (can be root directory or path to header file) [auto]:
+#set (CURL_ROOT "curl_install_prefix")
+
+# Set location of GLIB component gthread [auto].  This is an optional (and
+# experimental) option which you need to enable:
+#set (GMT_USE_THREADS TRUE)
+# If pkg-config is not installed (e.g. on Windows) you need to specify these:
+#set (GLIB_INCLUDE_DIR c:/path/to/glib-dev/include/glib-2.0)
+#set (GLIB_LIBRARIES c:/path/to/glib-dev/lib/glib-2.0.lib)
+
+# Set LAPACK location. Use this when want to link with LAPACK and it's not found automatically
+set (LAPACK_LIBRARY "-L$ENV{ISSM_DIR}/externalpackages/lapack/install/lib -llapack")
+set (BLAS_LIBRARY "-L$ENV{ISSM_DIR}/externalpackages/lapack/install/lib -lblas")
+
+##
+## Section 3: GMT features
+##
+
+# Enforce GPL or LGPL conformity. Use this to disable routines that cannot be
+# redistributed under the terms of the GPL or LGPL such as Shewchuk's
+# triangulation (valid values are GPL, LGPL and off) [off]:
+#set (LICENSE_RESTRICTED GPL)
+
+# Allow building of OpenMP if compiler supports it
+# set (GMT_ENABLE_OPENMP TRUE)
+
+# Configure default units (possible values are SI and US) [SI]:
+#set (UNITS "US")
+
+# Enable building of shared libraries [TRUE] (disable to use static libraries;
+# not recommended; on non-x86 architectures uncomment the next option as well):
+#set (BUILD_SHARED_LIBS FALSE)
+
+# Create position independent code on all targets [auto] (needed for static
+# build on non-x86):
+#set (CMAKE_POSITION_INDEPENDENT_CODE TRUE)
+
+# Build GMT shared lib with supplemental modules [TRUE]:
+#set (BUILD_SUPPLEMENTS FALSE)
+
+# Build/Install GMT Developer include files [TRUE]:
+# This installs the extra include files and configured files needed by 3rd-party
+# developers.  Until we build a separate gmt-devel we include them in the main
+# Distribution.
+#set (BUILD_DEVELOPER FALSE)
+
+##
+## Section 4: Advanced tweaking
+##
+
+#
+# Testing and development
+#
+
+# Enable running examples/tests with "ctest" or "make check" (out-of-source).
+# Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following
+# line.
+#enable_testing()
+#set (DO_EXAMPLES TRUE)
+#set (DO_TESTS TRUE)
+#set (DO_ANIMATIONS TRUE)
+# Number of parallel test jobs with "make check":
+#set (N_TEST_JOBS 4)
+
+# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without
+# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required
+# for testing [OFF]:
+#set (SUPPORT_EXEC_IN_BINARY_DIR ON)
+
+# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes
+# that link against the full gmt libs (not just the API; for building codes
+# that only need the GMT API, see the gmt-custom project).
+#set (EXTRA_BUILD_DIRS apidemo)
+# Uncomment the following line to enable running low-level C tests of the API
+#set (DO_API_TESTS ON)
+
+# Directory in which to install the release sources per default
+# [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]:
+#set (GMT_RELEASE_PREFIX "release-src-prefix")
+
+# If set to false, image conversion from PS images to PNG and PDF does
+# not depend on the gmt binary target. Note: "make gmt" is then required
+# before docs_depends [TRUE].
+#set (GMT_DOCS_DEPEND_ON_GMT FALSE)
+
+#
+# Debugging
+#
+
+# Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel
+# [Release]:
+#set (CMAKE_BUILD_TYPE Debug)
+
+# Extra debugging for developers:
+#if ( CMAKE_GENERATOR STREQUAL "Xcode" )
+##      So Xcode can find the supplemental plug-ins during debug sessions
+#       add_definitions(-DXCODER)
+#   add_definitions(-DDEBUG_MODERN)                     # To set PPID == 0 during Xcode test
+#       message("Add Xcode definition for GMT")
+#endif()
+#add_definitions(-DDEBUG)
+#add_definitions(-DMEMDEBUG) # Turn on memory tracking see gmt_support.c for extra info
+#set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement") # recommended even for release build
+#set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}")            # extra warnings
+#set (CMAKE_C_FLAGS_DEBUG -ggdb3)                          # gdb debugging symbols
+#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE)                  # debug link dependencies
+if (HAVE_OPENMP)
+        set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized -flax-vector-conversions")  # check uninitialized variables
+else (HAVE_OPENMP)
+        set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized")  # check uninitialized variables
+endif (HAVE_OPENMP)
+
+#
+# System specific tweaks
+#
+
+# This is for GCC on Solaris to avoid "relocations remain against allocatable
+# but non-writable sections" problems:
+#set (USER_GMTLIB_LINK_FLAGS -mimpure-text)
+
+# This may be needed to enable strdup and extended math functions with GCC and
+# Suncc on Solaris:
+#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__")
+
+# Do not warn when building with Windows SDK or Visual Studio Express:
+#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON)
+
+# Manually select runtime library when compiling with Windows SDK or Visual
+# Studio Express:
+#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll)
+
+# If your NetCDF library is static (not recommended, applies to Windows only)
+#set (NETCDF_STATIC TRUE)
+
+# If want to rename the DLLs to something else than the default (e.g. to
+# append the bitness - Windows only)
+# WARNING: if using this option it is mandatory that the suffix starts with an underscore.
+#if (WIN32)
+# set (BITAGE 32)
+# # Detect if we are building a 32 or 64 bits version
+# if (CMAKE_SIZEOF_VOID_P EQUAL 8)
+#   set (BITAGE 64)
+# endif ()
+# set (GMT_DLL_RENAME gmt_w${BITAGE})
+# set (PSL_DLL_RENAME psl_w${BITAGE})
+#endif(WIN32)
+
+# On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build
+#if(MSVC11)
+#  add_definitions(/D_ALLOW_KEYWORD_MACROS)
+#endif(MSVC11)

../trunk-jpl/externalpackages/gmt/install-6.0-Linux.sh

@@ +1 @@
+#!/bin/bash
+set -eu
+
+
+## Constants
+#
+VER="6.0.0"
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz"
+
+# Unpack source
+tar -zxvf gmt-$VER.tar.gz
+
+# Cleanup
+rm -rf install src
+mkdir install src
+
+# Move source to 'src' directory
+mv gmt-$VER/* src
+rm -rf gmt-$VER
+
+# Copy custom configuration files
+cp ./configs/Linux/cmake/ConfigUser.cmake ./src/cmake
+
+# Configure
+cd src
+mkdir build
+cd build
+cmake ..
+
+# Compile and install
+if [ $# -eq 0 ]; then
+        make
+        make install
+else
+        make -j $1
+        make -j $1 install
+fi
+
+# Return to initial directory
+cd ../..

../trunk-jpl/externalpackages/mpich/install-3.3.sh

@@ +1 @@
+#!/bin/bash
+set -eu
+
+
+## Constants
+#
+VER="3.3"
+
+# Download source
+$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/mpich-${VER}.tar.gz" "mpich-${VER}.tar.gz"
+
+# Unpack source
+tar -zxvf  mpich-$VER.tar.gz
+
+# Cleanup
+rm -rf src install
+mkdir src install
+
+# Move source into 'src' directory
+mv mpich-$VER/* src
+rm -rf mpich-$VER
+
+# Configure
+cd src
+./configure \
+        --prefix="${ISSM_DIR}/externalpackages/mpich/install" \
+        --enable-shared
+
+# Compile and install
+if [ $# -eq 0 ]; then
+        make
+        make install
+else
+        make -j $1
+        make -j $1 install
+fi
+
+# Return to initial directory
+cd ..

../trunk-jpl/jenkins/linux64_ross_se

@@ -15 +15 @@
         --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9 -lgfortran" \
         --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \
         --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/mpich/install/lib -lmpi -lmpicxx -lmpifort" \
+        --with-blas-lapack-dir=$ISSM_DIR/externalpackages/lapack/install \
         --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
-        --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
-        --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
         --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
         --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
+        --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
         --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
         --with-boost-dir=$ISSM_DIR/externalpackages/boost/install \
         --with-numthreads=4 \
@@ -41 +41 @@
 EXTERNALPACKAGES="
         autotools       install.sh
         cmake           install.sh
-        mpich           install-3.2-linux64.sh
-        petsc           install-3.7-linux64.sh
+        mpich           install-3.3.sh
+        lapack          install-3.8.sh
+        petsc           install-3.11-Linux.sh
         triangle        install-linux64.sh
+        chaco           install.sh
+        m1qn3           install.sh
+        semic           install.sh
         boost           install-1.55-linux.sh
-        hdf5            install-1.10.sh
-        netcdf          install-4.7.sh
         proj            install-6.2.sh
         gdal            install-3.0-netcdf.sh
         gshhg           install.sh
-        gmt                     install.sh
+        gmt                     install-6.0-Linux.sh
         gmsh            install.sh
         shell2junit     install.sh
 "
@@ -64 +66 @@
 # NOTE: One is usually safer as some packages are very sensitive to parallel
 #       compilation.
 #
-NUMCPUS_INSTALL=10
+NUMCPUS_INSTALL=8
 
 #number of cpus used in the nightly runs. (pb of access to all_vertices.txt if more than 1)
-NUMCPUS_RUN=5
+NUMCPUS_RUN=8
 
 #Nightly run options. The matlab routine runme.m will be called
 #as follows: runme($MATLAB_NROPTIONS). The options must be understandable

../trunk-jpl/jenkins/linux64_ross

@@ -11 +11 @@
         --with-matlab-dir=$MATLAB_PATH \
         --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9 -lgfortran" \
         --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
-        --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/mpich/install/lib -lmpi" \
+        --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/mpich/install/lib -lmpi -lmpicxx -lmpifort" \
+        --with-blas-lapack-dir=$ISSM_DIR/externalpackages/lapack/install \
         --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
-        --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
         --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
         --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
         --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
@@ -40 +40 @@
 EXTERNALPACKAGES="
         autotools       install.sh
         cmake           install.sh
-        mpich           install-3.2-linux64.sh
-        petsc           install-3.7-linux64.sh
+        mpich           install-3.3.sh
+        lapack          install-3.8.sh
+        petsc           install-3.11-Linux.sh
         triangle        install-linux64.sh
         chaco           install.sh
         m1qn3           install.sh
-        hdf5            install-1.10.sh
-        netcdf          install-4.7.sh
         semic           install.sh
         shell2junit     install.sh
 "
@@ -55 +54 @@
 # 4: test options #
 #-----------------#
 
-# Number of CPUs used in ISSM compilation
-#
-# NOTE: One is usually safer as some packages are very sensitive to parallel
-#       compilation.
-#
-NUMCPUS_INSTALL=10
+#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=5
+NUMCPUS_RUN=8
 
 #Nightly run options. The matlab routine runme.m will be called
 #as follows: runme($MATLAB_NROPTIONS). The options must be understandable

../trunk-jpl/etc/environment.sh

@@ -191 +191 @@
         ld_library_path_prepend "$MPI_DIR/lib"
 fi
 
+LAPACK_DIR="${ISSM_DIR}/externalpackages/lapack/install"
+if [ -d "$LAPACK_DIR" ]; then
+        ld_library_path_append "$LAPACK_DIR/lib"
+fi
+
 PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/install"
 if [ -d "$PETSC_DIR" ]; then
         export PETSC_DIR