Index: /issm/trunk-jpl/etc/environment.sh =================================================================== --- /issm/trunk-jpl/etc/environment.sh (revision 21656) +++ /issm/trunk-jpl/etc/environment.sh (revision 21657) @@ -124,5 +124,5 @@ pathappend "$SSH_DIR" -VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install" +VALGRIND_DIR="/usr/bin/valgrind" pathprepend "$VALGRIND_DIR/bin" Index: /issm/trunk-jpl/externalpackages/valgrind/install-linux64.sh =================================================================== --- /issm/trunk-jpl/externalpackages/valgrind/install-linux64.sh (revision 21656) +++ /issm/trunk-jpl/externalpackages/valgrind/install-linux64.sh (revision 21657) @@ -2,27 +2,47 @@ set -eu +#old version (Kernel issue) +# #Some cleanup +# rm -rf install valgrind-3.10.0 +# mkdir install + + +# #Download from ISSM server +# # $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.10.0.tar.bz2' 'valgrind-3.10.0.tar.bz2' + +# #Untar +# tar -jxvf valgrind-3.10.0.tar.bz2 + +# #Move valgrind into install directory +# mv valgrind-3.10.0/* install +# rm -rf valgrind-3.10.0 + +# #configure +# cd install +# ./configure --prefix="$ISSM_DIR/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/libmpiwrap-* ./libmpidebug.so + +#New way cloned on mac + #Some cleanup -rm -rf install valgrind-3.10.0 -mkdir install +rm -rf install -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.10.0.tar.bz2' 'valgrind-3.10.0.tar.bz2' - -#Untar -tar -jxvf valgrind-3.10.0.tar.bz2 - -#Move valgrind into install directory -mv valgrind-3.10.0/* install -rm -rf valgrind-3.10.0 +#Download development version, the current release never supports the latest OS X releases +svn co svn://svn.valgrind.org/valgrind/trunk install #configure cd install -./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" +./autogen.sh +./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install" --enable-only64bit #Compile valgrind -make -j 4 + +make -j 8 make install - -#final thing: if mpi is compiled in, soft link its target to a simpler name -cd lib -ln -s valgrind/libmpiwrap-* ./libmpidebug.so Index: /issm/trunk-jpl/m4/analyses.m4 =================================================================== --- /issm/trunk-jpl/m4/analyses.m4 (revision 21656) +++ /issm/trunk-jpl/m4/analyses.m4 (revision 21657) @@ -11,912 +11,492 @@ dnl with-Smb{{{ - AC_ARG_WITH([Smb], - AS_HELP_STRING([--with-Smb = YES], [compile with Smb capabilities (default is yes)]), - [SMB=$withval],[SMB=yes]) - AC_MSG_CHECKING(for Smb capability compilation) - HAVE_SMB=no - if test "x$SMB" = "xyes"; then - HAVE_SMB=yes - AC_DEFINE([_HAVE_SMB_],[1],[with Smb capability]) - -fi - +fi AM_CONDITIONAL([SMB], [test x$HAVE_SMB = xyes]) - AC_MSG_RESULT($HAVE_SMB) - dnl }}} dnl with-AdjointBalancethickness{{{ - AC_ARG_WITH([AdjointBalancethickness], - AS_HELP_STRING([--with-AdjointBalancethickness = YES], [compile with AdjointBalancethickness capabilities (default is yes)]), - [ADJOINTBALANCETHICKNESS=$withval],[ADJOINTBALANCETHICKNESS=yes]) - AC_MSG_CHECKING(for AdjointBalancethickness capability compilation) - HAVE_ADJOINTBALANCETHICKNESS=no - if test "x$ADJOINTBALANCETHICKNESS" = "xyes"; then - HAVE_ADJOINTBALANCETHICKNESS=yes - AC_DEFINE([_HAVE_ADJOINTBALANCETHICKNESS_],[1],[with AdjointBalancethickness capability]) - -fi - +fi AM_CONDITIONAL([ADJOINTBALANCETHICKNESS], [test x$HAVE_ADJOINTBALANCETHICKNESS = xyes]) - AC_MSG_RESULT($HAVE_ADJOINTBALANCETHICKNESS) - dnl }}} dnl with-AdjointBalancethickness2{{{ - AC_ARG_WITH([AdjointBalancethickness2], - AS_HELP_STRING([--with-AdjointBalancethickness2 = YES], [compile with AdjointBalancethickness2 capabilities (default is yes)]), - [ADJOINTBALANCETHICKNESS2=$withval],[ADJOINTBALANCETHICKNESS2=yes]) - AC_MSG_CHECKING(for AdjointBalancethickness2 capability compilation) - HAVE_ADJOINTBALANCETHICKNESS2=no - if test "x$ADJOINTBALANCETHICKNESS2" = "xyes"; then - HAVE_ADJOINTBALANCETHICKNESS2=yes - AC_DEFINE([_HAVE_ADJOINTBALANCETHICKNESS2_],[1],[with AdjointBalancethickness2 capability]) - -fi - +fi AM_CONDITIONAL([ADJOINTBALANCETHICKNESS2], [test x$HAVE_ADJOINTBALANCETHICKNESS2 = xyes]) - AC_MSG_RESULT($HAVE_ADJOINTBALANCETHICKNESS2) - dnl }}} dnl with-AdjointHoriz{{{ - AC_ARG_WITH([AdjointHoriz], - AS_HELP_STRING([--with-AdjointHoriz = YES], [compile with AdjointHoriz capabilities (default is yes)]), - [ADJOINTHORIZ=$withval],[ADJOINTHORIZ=yes]) - AC_MSG_CHECKING(for AdjointHoriz capability compilation) - HAVE_ADJOINTHORIZ=no - if test "x$ADJOINTHORIZ" = "xyes"; then - HAVE_ADJOINTHORIZ=yes - AC_DEFINE([_HAVE_ADJOINTHORIZ_],[1],[with AdjointHoriz capability]) - -fi - +fi AM_CONDITIONAL([ADJOINTHORIZ], [test x$HAVE_ADJOINTHORIZ = xyes]) - AC_MSG_RESULT($HAVE_ADJOINTHORIZ) - dnl }}} dnl with-Balancethickness{{{ - AC_ARG_WITH([Balancethickness], - AS_HELP_STRING([--with-Balancethickness = YES], [compile with Balancethickness capabilities (default is yes)]), - [BALANCETHICKNESS=$withval],[BALANCETHICKNESS=yes]) - AC_MSG_CHECKING(for Balancethickness capability compilation) - HAVE_BALANCETHICKNESS=no - if test "x$BALANCETHICKNESS" = "xyes"; then - HAVE_BALANCETHICKNESS=yes - AC_DEFINE([_HAVE_BALANCETHICKNESS_],[1],[with Balancethickness capability]) - -fi - +fi AM_CONDITIONAL([BALANCETHICKNESS], [test x$HAVE_BALANCETHICKNESS = xyes]) - AC_MSG_RESULT($HAVE_BALANCETHICKNESS) - dnl }}} dnl with-Balancethickness2{{{ - AC_ARG_WITH([Balancethickness2], - AS_HELP_STRING([--with-Balancethickness2 = YES], [compile with Balancethickness2 capabilities (default is yes)]), - [BALANCETHICKNESS2=$withval],[BALANCETHICKNESS2=yes]) - AC_MSG_CHECKING(for Balancethickness2 capability compilation) - HAVE_BALANCETHICKNESS2=no - if test "x$BALANCETHICKNESS2" = "xyes"; then - HAVE_BALANCETHICKNESS2=yes - AC_DEFINE([_HAVE_BALANCETHICKNESS2_],[1],[with Balancethickness2 capability]) - -fi - +fi AM_CONDITIONAL([BALANCETHICKNESS2], [test x$HAVE_BALANCETHICKNESS2 = xyes]) - AC_MSG_RESULT($HAVE_BALANCETHICKNESS2) - dnl }}} dnl with-BalancethicknessSoft{{{ - AC_ARG_WITH([BalancethicknessSoft], - AS_HELP_STRING([--with-BalancethicknessSoft = YES], [compile with BalancethicknessSoft capabilities (default is yes)]), - [BALANCETHICKNESSSOFT=$withval],[BALANCETHICKNESSSOFT=yes]) - AC_MSG_CHECKING(for BalancethicknessSoft capability compilation) - HAVE_BALANCETHICKNESSSOFT=no - if test "x$BALANCETHICKNESSSOFT" = "xyes"; then - HAVE_BALANCETHICKNESSSOFT=yes - AC_DEFINE([_HAVE_BALANCETHICKNESSSOFT_],[1],[with BalancethicknessSoft capability]) - -fi - +fi AM_CONDITIONAL([BALANCETHICKNESSSOFT], [test x$HAVE_BALANCETHICKNESSSOFT = xyes]) - AC_MSG_RESULT($HAVE_BALANCETHICKNESSSOFT) - dnl }}} dnl with-Balancevelocity{{{ - AC_ARG_WITH([Balancevelocity], - AS_HELP_STRING([--with-Balancevelocity = YES], [compile with Balancevelocity capabilities (default is yes)]), - [BALANCEVELOCITY=$withval],[BALANCEVELOCITY=yes]) - AC_MSG_CHECKING(for Balancevelocity capability compilation) - HAVE_BALANCEVELOCITY=no - if test "x$BALANCEVELOCITY" = "xyes"; then - HAVE_BALANCEVELOCITY=yes - AC_DEFINE([_HAVE_BALANCEVELOCITY_],[1],[with Balancevelocity capability]) - -fi - +fi AM_CONDITIONAL([BALANCEVELOCITY], [test x$HAVE_BALANCEVELOCITY = xyes]) - AC_MSG_RESULT($HAVE_BALANCEVELOCITY) - dnl }}} dnl with-L2ProjectionEPL{{{ - AC_ARG_WITH([L2ProjectionEPL], - AS_HELP_STRING([--with-L2ProjectionEPL = YES], [compile with L2ProjectionEPL capabilities (default is yes)]), - [L2PROJECTIONEPL=$withval],[L2PROJECTIONEPL=yes]) - AC_MSG_CHECKING(for L2ProjectionEPL capability compilation) - HAVE_L2PROJECTIONEPL=no - if test "x$L2PROJECTIONEPL" = "xyes"; then - HAVE_L2PROJECTIONEPL=yes - AC_DEFINE([_HAVE_L2PROJECTIONEPL_],[1],[with L2ProjectionEPL capability]) - -fi - +fi AM_CONDITIONAL([L2PROJECTIONEPL], [test x$HAVE_L2PROJECTIONEPL = xyes]) - AC_MSG_RESULT($HAVE_L2PROJECTIONEPL) - dnl }}} dnl with-L2ProjectionBase{{{ - AC_ARG_WITH([L2ProjectionBase], - AS_HELP_STRING([--with-L2ProjectionBase = YES], [compile with L2ProjectionBase capabilities (default is yes)]), - [L2PROJECTIONBASE=$withval],[L2PROJECTIONBASE=yes]) - AC_MSG_CHECKING(for L2ProjectionBase capability compilation) - HAVE_L2PROJECTIONBASE=no - if test "x$L2PROJECTIONBASE" = "xyes"; then - HAVE_L2PROJECTIONBASE=yes - AC_DEFINE([_HAVE_L2PROJECTIONBASE_],[1],[with L2ProjectionBase capability]) - -fi - +fi AM_CONDITIONAL([L2PROJECTIONBASE], [test x$HAVE_L2PROJECTIONBASE = xyes]) - AC_MSG_RESULT($HAVE_L2PROJECTIONBASE) - dnl }}} dnl with-DamageEvolution{{{ - AC_ARG_WITH([DamageEvolution], - AS_HELP_STRING([--with-DamageEvolution = YES], [compile with DamageEvolution capabilities (default is yes)]), - [DAMAGEEVOLUTION=$withval],[DAMAGEEVOLUTION=yes]) - AC_MSG_CHECKING(for DamageEvolution capability compilation) - HAVE_DAMAGEEVOLUTION=no - if test "x$DAMAGEEVOLUTION" = "xyes"; then - HAVE_DAMAGEEVOLUTION=yes - AC_DEFINE([_HAVE_DAMAGEEVOLUTION_],[1],[with DamageEvolution capability]) - -fi - +fi AM_CONDITIONAL([DAMAGEEVOLUTION], [test x$HAVE_DAMAGEEVOLUTION = xyes]) - AC_MSG_RESULT($HAVE_DAMAGEEVOLUTION) - dnl }}} dnl with-Stressbalance{{{ - AC_ARG_WITH([Stressbalance], - AS_HELP_STRING([--with-Stressbalance = YES], [compile with Stressbalance capabilities (default is yes)]), - [STRESSBALANCE=$withval],[STRESSBALANCE=yes]) - AC_MSG_CHECKING(for Stressbalance capability compilation) - HAVE_STRESSBALANCE=no - if test "x$STRESSBALANCE" = "xyes"; then - HAVE_STRESSBALANCE=yes - AC_DEFINE([_HAVE_STRESSBALANCE_],[1],[with Stressbalance capability]) - -fi - +fi AM_CONDITIONAL([STRESSBALANCE], [test x$HAVE_STRESSBALANCE = xyes]) - AC_MSG_RESULT($HAVE_STRESSBALANCE) - dnl }}} dnl with-StressbalanceSIA{{{ - AC_ARG_WITH([StressbalanceSIA], - AS_HELP_STRING([--with-StressbalanceSIA = YES], [compile with StressbalanceSIA capabilities (default is yes)]), - [STRESSBALANCESIA=$withval],[STRESSBALANCESIA=yes]) - AC_MSG_CHECKING(for StressbalanceSIA capability compilation) - HAVE_STRESSBALANCESIA=no - if test "x$STRESSBALANCESIA" = "xyes"; then - HAVE_STRESSBALANCESIA=yes - AC_DEFINE([_HAVE_STRESSBALANCESIA_],[1],[with StressbalanceSIA capability]) - -fi - +fi AM_CONDITIONAL([STRESSBALANCESIA], [test x$HAVE_STRESSBALANCESIA = xyes]) - AC_MSG_RESULT($HAVE_STRESSBALANCESIA) - dnl }}} dnl with-StressbalanceVertical{{{ - AC_ARG_WITH([StressbalanceVertical], - AS_HELP_STRING([--with-StressbalanceVertical = YES], [compile with StressbalanceVertical capabilities (default is yes)]), - [STRESSBALANCEVERTICAL=$withval],[STRESSBALANCEVERTICAL=yes]) - AC_MSG_CHECKING(for StressbalanceVertical capability compilation) - HAVE_STRESSBALANCEVERTICAL=no - if test "x$STRESSBALANCEVERTICAL" = "xyes"; then - HAVE_STRESSBALANCEVERTICAL=yes - AC_DEFINE([_HAVE_STRESSBALANCEVERTICAL_],[1],[with StressbalanceVertical capability]) - -fi - +fi AM_CONDITIONAL([STRESSBALANCEVERTICAL], [test x$HAVE_STRESSBALANCEVERTICAL = xyes]) - AC_MSG_RESULT($HAVE_STRESSBALANCEVERTICAL) - dnl }}} dnl with-Enthalpy{{{ - AC_ARG_WITH([Enthalpy], - AS_HELP_STRING([--with-Enthalpy = YES], [compile with Enthalpy capabilities (default is yes)]), - [ENTHALPY=$withval],[ENTHALPY=yes]) - AC_MSG_CHECKING(for Enthalpy capability compilation) - HAVE_ENTHALPY=no - if test "x$ENTHALPY" = "xyes"; then - HAVE_ENTHALPY=yes - AC_DEFINE([_HAVE_ENTHALPY_],[1],[with Enthalpy capability]) - -fi - +fi AM_CONDITIONAL([ENTHALPY], [test x$HAVE_ENTHALPY = xyes]) - AC_MSG_RESULT($HAVE_ENTHALPY) - dnl }}} dnl with-HydrologyShreve{{{ - AC_ARG_WITH([HydrologyShreve], - AS_HELP_STRING([--with-HydrologyShreve = YES], [compile with HydrologyShreve capabilities (default is yes)]), - [HYDROLOGYSHREVE=$withval],[HYDROLOGYSHREVE=yes]) - AC_MSG_CHECKING(for HydrologyShreve capability compilation) - HAVE_HYDROLOGYSHREVE=no - if test "x$HYDROLOGYSHREVE" = "xyes"; then - HAVE_HYDROLOGYSHREVE=yes - AC_DEFINE([_HAVE_HYDROLOGYSHREVE_],[1],[with HydrologyShreve capability]) - -fi - +fi AM_CONDITIONAL([HYDROLOGYSHREVE], [test x$HAVE_HYDROLOGYSHREVE = xyes]) - AC_MSG_RESULT($HAVE_HYDROLOGYSHREVE) - dnl }}} dnl with-HydrologyDCInefficient{{{ - AC_ARG_WITH([HydrologyDCInefficient], - AS_HELP_STRING([--with-HydrologyDCInefficient = YES], [compile with HydrologyDCInefficient capabilities (default is yes)]), - [HYDROLOGYDCINEFFICIENT=$withval],[HYDROLOGYDCINEFFICIENT=yes]) - AC_MSG_CHECKING(for HydrologyDCInefficient capability compilation) - HAVE_HYDROLOGYDCINEFFICIENT=no - if test "x$HYDROLOGYDCINEFFICIENT" = "xyes"; then - HAVE_HYDROLOGYDCINEFFICIENT=yes - AC_DEFINE([_HAVE_HYDROLOGYDCINEFFICIENT_],[1],[with HydrologyDCInefficient capability]) - -fi - +fi AM_CONDITIONAL([HYDROLOGYDCINEFFICIENT], [test x$HAVE_HYDROLOGYDCINEFFICIENT = xyes]) - AC_MSG_RESULT($HAVE_HYDROLOGYDCINEFFICIENT) - dnl }}} dnl with-HydrologyDCEfficient{{{ - AC_ARG_WITH([HydrologyDCEfficient], - AS_HELP_STRING([--with-HydrologyDCEfficient = YES], [compile with HydrologyDCEfficient capabilities (default is yes)]), - [HYDROLOGYDCEFFICIENT=$withval],[HYDROLOGYDCEFFICIENT=yes]) - AC_MSG_CHECKING(for HydrologyDCEfficient capability compilation) - HAVE_HYDROLOGYDCEFFICIENT=no - if test "x$HYDROLOGYDCEFFICIENT" = "xyes"; then - HAVE_HYDROLOGYDCEFFICIENT=yes - AC_DEFINE([_HAVE_HYDROLOGYDCEFFICIENT_],[1],[with HydrologyDCEfficient capability]) - -fi - +fi AM_CONDITIONAL([HYDROLOGYDCEFFICIENT], [test x$HAVE_HYDROLOGYDCEFFICIENT = xyes]) - AC_MSG_RESULT($HAVE_HYDROLOGYDCEFFICIENT) - dnl }}} dnl with-HydrologySommers{{{ - AC_ARG_WITH([HydrologySommers], - AS_HELP_STRING([--with-HydrologySommers = YES], [compile with HydrologySommers capabilities (default is yes)]), - [HYDROLOGYSOMMERS=$withval],[HYDROLOGYSOMMERS=yes]) - AC_MSG_CHECKING(for HydrologySommers capability compilation) - HAVE_HYDROLOGYSOMMERS=no - if test "x$HYDROLOGYSOMMERS" = "xyes"; then - HAVE_HYDROLOGYSOMMERS=yes - AC_DEFINE([_HAVE_HYDROLOGYSOMMERS_],[1],[with HydrologySommers capability]) - -fi - +fi AM_CONDITIONAL([HYDROLOGYSOMMERS], [test x$HAVE_HYDROLOGYSOMMERS = xyes]) - AC_MSG_RESULT($HAVE_HYDROLOGYSOMMERS) - dnl }}} dnl with-Melting{{{ - AC_ARG_WITH([Melting], - AS_HELP_STRING([--with-Melting = YES], [compile with Melting capabilities (default is yes)]), - [MELTING=$withval],[MELTING=yes]) - AC_MSG_CHECKING(for Melting capability compilation) - HAVE_MELTING=no - if test "x$MELTING" = "xyes"; then - HAVE_MELTING=yes - AC_DEFINE([_HAVE_MELTING_],[1],[with Melting capability]) - -fi - +fi AM_CONDITIONAL([MELTING], [test x$HAVE_MELTING = xyes]) - AC_MSG_RESULT($HAVE_MELTING) - dnl }}} dnl with-Masstransport{{{ - AC_ARG_WITH([Masstransport], - AS_HELP_STRING([--with-Masstransport = YES], [compile with Masstransport capabilities (default is yes)]), - [MASSTRANSPORT=$withval],[MASSTRANSPORT=yes]) - AC_MSG_CHECKING(for Masstransport capability compilation) - HAVE_MASSTRANSPORT=no - if test "x$MASSTRANSPORT" = "xyes"; then - HAVE_MASSTRANSPORT=yes - AC_DEFINE([_HAVE_MASSTRANSPORT_],[1],[with Masstransport capability]) - -fi - +fi AM_CONDITIONAL([MASSTRANSPORT], [test x$HAVE_MASSTRANSPORT = xyes]) - AC_MSG_RESULT($HAVE_MASSTRANSPORT) - dnl }}} dnl with-FreeSurfaceBase{{{ - AC_ARG_WITH([FreeSurfaceBase], - AS_HELP_STRING([--with-FreeSurfaceBase = YES], [compile with FreeSurfaceBase capabilities (default is yes)]), - [FREESURFACEBASE=$withval],[FREESURFACEBASE=yes]) - AC_MSG_CHECKING(for FreeSurfaceBase capability compilation) - HAVE_FREESURFACEBASE=no - if test "x$FREESURFACEBASE" = "xyes"; then - HAVE_FREESURFACEBASE=yes - AC_DEFINE([_HAVE_FREESURFACEBASE_],[1],[with FreeSurfaceBase capability]) - -fi - +fi AM_CONDITIONAL([FREESURFACEBASE], [test x$HAVE_FREESURFACEBASE = xyes]) - AC_MSG_RESULT($HAVE_FREESURFACEBASE) - dnl }}} dnl with-FreeSurfaceTop{{{ - AC_ARG_WITH([FreeSurfaceTop], - AS_HELP_STRING([--with-FreeSurfaceTop = YES], [compile with FreeSurfaceTop capabilities (default is yes)]), - [FREESURFACETOP=$withval],[FREESURFACETOP=yes]) - AC_MSG_CHECKING(for FreeSurfaceTop capability compilation) - HAVE_FREESURFACETOP=no - if test "x$FREESURFACETOP" = "xyes"; then - HAVE_FREESURFACETOP=yes - AC_DEFINE([_HAVE_FREESURFACETOP_],[1],[with FreeSurfaceTop capability]) - -fi - +fi AM_CONDITIONAL([FREESURFACETOP], [test x$HAVE_FREESURFACETOP = xyes]) - AC_MSG_RESULT($HAVE_FREESURFACETOP) - dnl }}} dnl with-ExtrudeFromBase{{{ - AC_ARG_WITH([ExtrudeFromBase], - AS_HELP_STRING([--with-ExtrudeFromBase = YES], [compile with ExtrudeFromBase capabilities (default is yes)]), - [EXTRUDEFROMBASE=$withval],[EXTRUDEFROMBASE=yes]) - AC_MSG_CHECKING(for ExtrudeFromBase capability compilation) - HAVE_EXTRUDEFROMBASE=no - if test "x$EXTRUDEFROMBASE" = "xyes"; then - HAVE_EXTRUDEFROMBASE=yes - AC_DEFINE([_HAVE_EXTRUDEFROMBASE_],[1],[with ExtrudeFromBase capability]) - -fi - +fi AM_CONDITIONAL([EXTRUDEFROMBASE], [test x$HAVE_EXTRUDEFROMBASE = xyes]) - AC_MSG_RESULT($HAVE_EXTRUDEFROMBASE) - dnl }}} dnl with-ExtrudeFromTop{{{ - AC_ARG_WITH([ExtrudeFromTop], - AS_HELP_STRING([--with-ExtrudeFromTop = YES], [compile with ExtrudeFromTop capabilities (default is yes)]), - [EXTRUDEFROMTOP=$withval],[EXTRUDEFROMTOP=yes]) - AC_MSG_CHECKING(for ExtrudeFromTop capability compilation) - HAVE_EXTRUDEFROMTOP=no - if test "x$EXTRUDEFROMTOP" = "xyes"; then - HAVE_EXTRUDEFROMTOP=yes - AC_DEFINE([_HAVE_EXTRUDEFROMTOP_],[1],[with ExtrudeFromTop capability]) - -fi - +fi AM_CONDITIONAL([EXTRUDEFROMTOP], [test x$HAVE_EXTRUDEFROMTOP = xyes]) - AC_MSG_RESULT($HAVE_EXTRUDEFROMTOP) - dnl }}} dnl with-DepthAverage{{{ - AC_ARG_WITH([DepthAverage], - AS_HELP_STRING([--with-DepthAverage = YES], [compile with DepthAverage capabilities (default is yes)]), - [DEPTHAVERAGE=$withval],[DEPTHAVERAGE=yes]) - AC_MSG_CHECKING(for DepthAverage capability compilation) - HAVE_DEPTHAVERAGE=no - if test "x$DEPTHAVERAGE" = "xyes"; then - HAVE_DEPTHAVERAGE=yes - AC_DEFINE([_HAVE_DEPTHAVERAGE_],[1],[with DepthAverage capability]) - -fi - +fi AM_CONDITIONAL([DEPTHAVERAGE], [test x$HAVE_DEPTHAVERAGE = xyes]) - AC_MSG_RESULT($HAVE_DEPTHAVERAGE) - dnl }}} dnl with-Sealevelrise{{{ - AC_ARG_WITH([Sealevelrise], - AS_HELP_STRING([--with-Sealevelrise = YES], [compile with Sealevelrise capabilities (default is yes)]), - [SEALEVELRISE=$withval],[SEALEVELRISE=yes]) - AC_MSG_CHECKING(for Sealevelrise capability compilation) - HAVE_SEALEVELRISE=no - if test "x$SEALEVELRISE" = "xyes"; then - HAVE_SEALEVELRISE=yes - AC_DEFINE([_HAVE_SEALEVELRISE_],[1],[with Sealevelrise capability]) - -fi - +fi AM_CONDITIONAL([SEALEVELRISE], [test x$HAVE_SEALEVELRISE = xyes]) - AC_MSG_RESULT($HAVE_SEALEVELRISE) - dnl }}} dnl with-Smooth{{{ - AC_ARG_WITH([Smooth], - AS_HELP_STRING([--with-Smooth = YES], [compile with Smooth capabilities (default is yes)]), - [SMOOTH=$withval],[SMOOTH=yes]) - AC_MSG_CHECKING(for Smooth capability compilation) - HAVE_SMOOTH=no - if test "x$SMOOTH" = "xyes"; then - HAVE_SMOOTH=yes - AC_DEFINE([_HAVE_SMOOTH_],[1],[with Smooth capability]) - -fi - +fi AM_CONDITIONAL([SMOOTH], [test x$HAVE_SMOOTH = xyes]) - AC_MSG_RESULT($HAVE_SMOOTH) - dnl }}} dnl with-Thermal{{{ - AC_ARG_WITH([Thermal], - AS_HELP_STRING([--with-Thermal = YES], [compile with Thermal capabilities (default is yes)]), - [THERMAL=$withval],[THERMAL=yes]) - AC_MSG_CHECKING(for Thermal capability compilation) - HAVE_THERMAL=no - if test "x$THERMAL" = "xyes"; then - HAVE_THERMAL=yes - AC_DEFINE([_HAVE_THERMAL_],[1],[with Thermal capability]) - -fi - +fi AM_CONDITIONAL([THERMAL], [test x$HAVE_THERMAL = xyes]) - AC_MSG_RESULT($HAVE_THERMAL) - dnl }}} dnl with-UzawaPressure{{{ - AC_ARG_WITH([UzawaPressure], - AS_HELP_STRING([--with-UzawaPressure = YES], [compile with UzawaPressure capabilities (default is yes)]), - [UZAWAPRESSURE=$withval],[UZAWAPRESSURE=yes]) - AC_MSG_CHECKING(for UzawaPressure capability compilation) - HAVE_UZAWAPRESSURE=no - if test "x$UZAWAPRESSURE" = "xyes"; then - HAVE_UZAWAPRESSURE=yes - AC_DEFINE([_HAVE_UZAWAPRESSURE_],[1],[with UzawaPressure capability]) - -fi - +fi AM_CONDITIONAL([UZAWAPRESSURE], [test x$HAVE_UZAWAPRESSURE = xyes]) - AC_MSG_RESULT($HAVE_UZAWAPRESSURE) - dnl }}} dnl with-GiaIvins{{{ - AC_ARG_WITH([GiaIvins], - AS_HELP_STRING([--with-GiaIvins = YES], [compile with GiaIvins capabilities (default is yes)]), - [GIAIVINS=$withval],[GIAIVINS=yes]) - AC_MSG_CHECKING(for GiaIvins capability compilation) - HAVE_GIAIVINS=no - if test "x$GIAIVINS" = "xyes"; then - HAVE_GIAIVINS=yes - AC_DEFINE([_HAVE_GIAIVINS_],[1],[with GiaIvins capability]) - -fi - +fi AM_CONDITIONAL([GIAIVINS], [test x$HAVE_GIAIVINS = xyes]) - AC_MSG_RESULT($HAVE_GIAIVINS) - dnl }}} dnl with-Esa{{{ - AC_ARG_WITH([Esa], - AS_HELP_STRING([--with-Esa = YES], [compile with Esa capabilities (default is yes)]), - [ESA=$withval],[ESA=yes]) - AC_MSG_CHECKING(for Esa capability compilation) - HAVE_ESA=no - if test "x$ESA" = "xyes"; then - HAVE_ESA=yes - AC_DEFINE([_HAVE_ESA_],[1],[with Esa capability]) - -fi - +fi AM_CONDITIONAL([ESA], [test x$HAVE_ESA = xyes]) - AC_MSG_RESULT($HAVE_ESA) - dnl }}} dnl with-Meshdeformation{{{ - AC_ARG_WITH([Meshdeformation], - AS_HELP_STRING([--with-Meshdeformation = YES], [compile with Meshdeformation capabilities (default is yes)]), - [MESHDEFORMATION=$withval],[MESHDEFORMATION=yes]) - AC_MSG_CHECKING(for Meshdeformation capability compilation) - HAVE_MESHDEFORMATION=no - if test "x$MESHDEFORMATION" = "xyes"; then - HAVE_MESHDEFORMATION=yes - AC_DEFINE([_HAVE_MESHDEFORMATION_],[1],[with Meshdeformation capability]) - -fi - +fi AM_CONDITIONAL([MESHDEFORMATION], [test x$HAVE_MESHDEFORMATION = xyes]) - AC_MSG_RESULT($HAVE_MESHDEFORMATION) - dnl }}} dnl with-Levelset{{{ - AC_ARG_WITH([Levelset], - AS_HELP_STRING([--with-Levelset = YES], [compile with Levelset capabilities (default is yes)]), - [LEVELSET=$withval],[LEVELSET=yes]) - AC_MSG_CHECKING(for Levelset capability compilation) - HAVE_LEVELSET=no - if test "x$LEVELSET" = "xyes"; then - HAVE_LEVELSET=yes - AC_DEFINE([_HAVE_LEVELSET_],[1],[with Levelset capability]) - -fi - +fi AM_CONDITIONAL([LEVELSET], [test x$HAVE_LEVELSET = xyes]) - AC_MSG_RESULT($HAVE_LEVELSET) - dnl }}} dnl with-Extrapolation{{{ - AC_ARG_WITH([Extrapolation], - AS_HELP_STRING([--with-Extrapolation = YES], [compile with Extrapolation capabilities (default is yes)]), - [EXTRAPOLATION=$withval],[EXTRAPOLATION=yes]) - AC_MSG_CHECKING(for Extrapolation capability compilation) - HAVE_EXTRAPOLATION=no - if test "x$EXTRAPOLATION" = "xyes"; then - HAVE_EXTRAPOLATION=yes - AC_DEFINE([_HAVE_EXTRAPOLATION_],[1],[with Extrapolation capability]) - -fi - +fi AM_CONDITIONAL([EXTRAPOLATION], [test x$HAVE_EXTRAPOLATION = xyes]) - AC_MSG_RESULT($HAVE_EXTRAPOLATION) - dnl }}} Index: /issm/trunk-jpl/src/m/io/loadvars.py =================================================================== --- /issm/trunk-jpl/src/m/io/loadvars.py (revision 21656) +++ /issm/trunk-jpl/src/m/io/loadvars.py (revision 21657) @@ -228,5 +228,5 @@ classe=str(group)+'.'+str(subgroup) class_dict[classe]=[str(getattr(NCData.groups[group].groups[subgroup],'classtype')),] - if class_dict[classe][0] not in ['dict','list']: + if class_dict[classe][0] not in ['dict','list','cell']: class_dict[classe].append(__import__(class_dict[classe][0])) class_tree[classe]=[group,subgroup] @@ -235,5 +235,5 @@ try: class_dict[classe]=[str(getattr(NCData.groups[group],'classtype')),] - if class_dict[classe][0] not in ['dict','list']: + if class_dict[classe][0] not in ['dict','list','cell']: class_dict[classe].append(__import__(class_dict[classe][0])) class_tree[classe]=[group,] Index: /issm/trunk-jpl/test/Par/SquareSheetConstrained.py =================================================================== --- /issm/trunk-jpl/test/Par/SquareSheetConstrained.py (revision 21656) +++ /issm/trunk-jpl/test/Par/SquareSheetConstrained.py (revision 21657) @@ -1,4 +1,4 @@ import os.path -import numpy +import numpy as np import inspect from verbose import verbose @@ -13,8 +13,8 @@ hmin=300. hmax=1000. -ymin=numpy.min(md.mesh.y) -ymax=numpy.max(md.mesh.y) -xmin=min(md.mesh.x) -xmax=max(md.mesh.x) +ymin=np.min(md.mesh.y) +ymax=np.max(md.mesh.y) +xmin=np.min(md.mesh.x) +xmax=np.max(md.mesh.x) md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin)+0.1*(hmin-hmax)*(md.mesh.x-xmin)/(xmax-xmin) md.geometry.base=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness+20. @@ -22,29 +22,29 @@ #Initial velocity -x = numpy.array(archread('../Data/SquareSheetConstrained.arch','x')) -y = numpy.array(archread('../Data/SquareSheetConstrained.arch','y')) -vx = numpy.array(archread('../Data/SquareSheetConstrained.arch','vx')); -vy = numpy.array(archread('../Data/SquareSheetConstrained.arch','vy')); +x = np.array(archread('../Data/SquareSheetConstrained.arch','x')) +y = np.array(archread('../Data/SquareSheetConstrained.arch','y')) +vx = np.array(archread('../Data/SquareSheetConstrained.arch','vx')); +vy = np.array(archread('../Data/SquareSheetConstrained.arch','vy')); index = archread('../Data/SquareSheetConstrained.arch','index').astype(int); -[md.initialization.vx]=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y) -[md.initialization.vy]=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y) -md.initialization.vz=numpy.zeros((md.mesh.numberofvertices)) -md.initialization.pressure=numpy.zeros((md.mesh.numberofvertices)) +md.initialization.vx=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y)[0] +md.initialization.vy=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y)[0] +md.initialization.vz=np.zeros((md.mesh.numberofvertices)) +md.initialization.pressure=np.zeros((md.mesh.numberofvertices)) #Materials -md.initialization.temperature=(273.-20.)*numpy.ones((md.mesh.numberofvertices)) +md.initialization.temperature=(273.-20.)*np.ones((md.mesh.numberofvertices)) md.materials.rheology_B=paterson(md.initialization.temperature) -md.materials.rheology_n=3.*numpy.ones((md.mesh.numberofelements)) +md.materials.rheology_n=3.*np.ones((md.mesh.numberofelements)) #Calving -md.calving.calvingrate=0.*numpy.ones((md.mesh.numberofvertices)) -md.levelset.spclevelset=float('NaN')*numpy.ones((md.mesh.numberofvertices)) +md.calving.calvingrate=np.zeros((md.mesh.numberofvertices)) +md.levelset.spclevelset=np.nan*np.ones((md.mesh.numberofvertices)) #Friction -md.friction.coefficient=20.*numpy.ones((md.mesh.numberofvertices)) -md.friction.coefficient[numpy.nonzero(md.mask.groundedice_levelset<0.)[0]]=0. -md.friction.p=numpy.ones((md.mesh.numberofelements)) -md.friction.q=numpy.ones((md.mesh.numberofelements)) +md.friction.coefficient=20.*np.ones((md.mesh.numberofvertices)) +md.friction.coefficient[np.where(md.mask.groundedice_levelset<0.)[0]]=0. +md.friction.p=np.ones((md.mesh.numberofelements)) +md.friction.q=np.ones((md.mesh.numberofelements)) #Numerical parameters @@ -57,11 +57,11 @@ md.steadystate.reltol=0.05 md.stressbalance.reltol=0.05 -md.stressbalance.abstol=float('NaN') +md.stressbalance.abstol=np.nan md.timestepping.time_step=1. md.timestepping.final_time=3. #GIA: -md.gia.lithosphere_thickness=100.*numpy.ones((md.mesh.numberofvertices)); # in km -md.gia.mantle_viscosity=1.*10**21*numpy.ones((md.mesh.numberofvertices)); # in Pa.s +md.gia.lithosphere_thickness=100.*np.ones((md.mesh.numberofvertices)); # in km +md.gia.mantle_viscosity=1.*10**21*np.ones((md.mesh.numberofvertices)); # in Pa.s md.materials.lithosphere_shear_modulus=6.7*10**10; # in Pa md.materials.lithosphere_density=3.32; # in g/cm^-3