Changeset 24321


Ignore:
Timestamp:
11/11/19 10:25:50 (5 years ago)
Author:
jdquinn
Message:

CHG: Installation script changes and others, cleanup in support of macOS Examples build.

Location:
issm/trunk-jpl
Files:
16 added
8 edited

Legend:

Unmodified
Added
Removed

  • issm/trunk-jpl/etc/environment.sh

    r24085 r24321  
    1 # Modifies path-related envrionment variables based on which external packages 
     1# Modifies path-related envrionment variables based on which external packages
    22# have been installed.
    33#
    4 # ISSM_DIR and ISSM_ARCH should have been defined already in your shell 
     4# ISSM_DIR and ISSM_ARCH should have been defined already in your shell
    55# settings file (i.e. .bashrc, .cshrc).
    66
    77## Functions
    88#
    9 pathprepend(){ #{{{
    10         if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then
    11                 name=$1
    12                 if [[ "$ISSM_ARCH" == "cygwin-intel" ]]; then
    13                         #export path using the cygwin convention
    14                         name=`cygpath -u $1`
    15                 fi
    16                 export PATH="$name:$PATH"
    17         fi
    18 } #}}}
    19 pathappend(){ #{{{
    20         if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then
    21                 name=$1
    22                 if [[ "$ISSM_ARCH" == "cygwin-intel" ]]; then
    23                         #export path in cygwin convention
    24                         name=`cygpath -u $1`
    25                 fi
    26                 export PATH="$PATH:$name"
    27         fi
    28 } #}}}
    29 libpathprepend(){ #{{{
    30         if [ -d "$1" ]; then
    31                 if [ -z $LD_LIBRARY_PATH ]; then
    32                         export LD_LIBRARY_PATH="$1"
    33                 elif [[ ":$LD_LIBRARY_PATH:" != *":$1:"* ]]; then
    34                         export LD_LIBRARY_PATH="$1:$LD_LIBRARY_PATH"
    35                 fi
    36                 if [ -z $LD_RUN_PATH ]; then
    37                         export LD_RUN_PATH="$1"
    38                 elif [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
    39                         export LD_RUN_PATH="$1:$LD_RUN_PATH"
    40                 fi
    41         fi
    42 } #}}}
    43 libpathappend(){ #{{{
    44         if [ -d "$1" ]; then
    45                 if [ -z $LD_LIBRARY_PATH ]; then
    46                         export LD_LIBRARY_PATH=$1
    47                 elif [[ ":$LD_LIBRARY_PATH:" != *":$1:"* ]]; then
    48                         export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$1"
     9c_include_path_append(){ #{{{
     10        if [ -d "${1}" ]; then
     11                if [ -z $C_INCLUDE_PATH ]; then
     12                        export C_INCLUDE_PATH="${1}"
     13                elif [[ ":${C_INCLUDE_PATH}:" != *":${1}:"* ]]; then
     14                        export C_INCLUDE_PATH="${C_INCLUDE_PATH}:${1}"
     15                fi
     16        fi
     17} #}}}
     18c_include_path_prepend(){ #{{{
     19        if [ -d "${1}" ]; then
     20                if [ -z $C_INCLUDE_PATH ]; then
     21                        export C_INCLUDE_PATH="${1}"
     22                elif [[ ":${C_INCLUDE_PATH}:" != *":${1}:"* ]]; then
     23                        export C_INCLUDE_PATH="${1}:${C_INCLUDE_PATH}"
     24                fi
     25        fi
     26} #}}}
     27\
     28cpath_append(){ #{{{
     29        if [ -d "${1}" ]; then
     30                if [ -z $CPATH ]; then
     31                        export CPATH="${1}"
     32                elif [[ ":${CPATH}:" != *":${1}:"* ]]; then
     33                        export CPATH="${CPATH}:${1}"
     34                fi
     35        fi
     36} #}}}
     37cpath_prepend(){ #{{{
     38        if [ -d "${1}" ]; then
     39                if [ -z $CPATH ]; then
     40                        export CPATH="${1}"
     41                elif [[ ":${CPATH}:" != *":${1}:"* ]]; then
     42                        export CPATH="${1}:${CPATH}"
     43                fi
     44        fi
     45} #}}}
     46
     47cplus_include_path_append(){ #{{{
     48        if [ -d "${1}" ]; then
     49                if [ -z $CPLUS_INCLUDE_PATH ]; then
     50                        export CPLUS_INCLUDE_PATH="${1}"
     51                elif [[ ":${CPLUS_INCLUDE_PATH}:" != *":${1}:"* ]]; then
     52                        export CPLUS_INCLUDE_PATH="${CPLUS_INCLUDE_PATH}:${1}"
     53                fi
     54        fi
     55} #}}}
     56cplus_include_path_prepend(){ #{{{
     57        if [ -d "${1}" ]; then
     58                if [ -z $CPLUS_INCLUDE_PATH ]; then
     59                        export CPLUS_INCLUDE_PATH="${1}"
     60                elif [[ ":${CPLUS_INCLUDE_PATH}:" != *":${1}:"* ]]; then
     61                        export CPLUS_INCLUDE_PATH="${1}:${CPLUS_INCLUDE_PATH}"
     62                fi
     63        fi
     64} #}}}
     65
     66dyld_library_path_append(){ #{{{
     67        if [ -d "${1}" ]; then
     68                if [ -z $DYLD_LIBRARY_PATH ]; then
     69                        export DYLD_LIBRARY_PATH="${1}"
     70                elif [[ ":${DYLD_LIBRARY_PATH}:" != *":${1}:"* ]]; then
     71                        export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}:${1}"
    4972                fi
    5073                if [ -z $LD_RUN_PATH ]; then
    5174                        export LD_RUN_PATH=$1
    52                 elif [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
    53                         export LD_RUN_PATH="$LD_RUN_PATH:$1"
    54                 fi
    55         fi
    56 } #}}}
    57 dylibpathprepend(){ #{{{
    58         if [ -d "$1" ]; then
     75                elif [[ ":${LD_RUN_PATH}:" != *":${1}:"* ]]; then
     76                        export LD_RUN_PATH="${LD_RUN_PATH}:${1}"
     77                fi
     78        fi
     79} #}}}
     80dyld_library_path_prepend(){ #{{{
     81        if [ -d "${1}" ]; then
    5982                if [ -z $DYLD_LIBRARY_PATH ]; then
    60                         export DYLD_LIBRARY_PATH=$1
    61                 elif [[ ":$DYLD_LIBRARY_PATH:" != *":$1:"* ]]; then
    62                         export DYLD_LIBRARY_PATH="$1:$DYLD_LIBRARY_PATH"
     83                        export DYLD_LIBRARY_PATH="${1}"
     84                elif [[ ":${DYLD_LIBRARY_PATH}:" != *":${1}:"* ]]; then
     85                        export DYLD_LIBRARY_PATH="${1}:${DYLD_LIBRARY_PATH}"
    6386                fi
    6487                if [ -z $LD_RUN_PATH ]; then
    65                         export LD_RUN_PATH=$1
    66                 elif [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
    67                         export LD_RUN_PATH="$1:$LD_RUN_PATH"
    68                 fi
    69         fi
    70 } #}}}
    71 dylibpathappend(){ #{{{
    72         if [ -d "$1" ]; then
    73                 if [ -z $DYLD_LIBRARY_PATH ]; then
    74                         export DYLD_LIBRARY_PATH=$1
    75                 elif [[ ":$DYLD_LIBRARY_PATH:" != *":$1:"* ]]; then
    76                         export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$1"
     88                        export LD_RUN_PATH="${1}"
     89                elif [[ ":${LD_RUN_PATH}:" != *":${1}:"* ]]; then
     90                        export LD_RUN_PATH="${1}:${LD_RUN_PATH}"
     91                fi
     92        fi
     93} #}}}
     94
     95ld_library_path_append(){ #{{{
     96        if [ -d "${1}" ]; then
     97                if [ -z $LD_LIBRARY_PATH ]; then
     98                        export LD_LIBRARY_PATH="${1}"
     99                elif [[ ":${LD_LIBRARY_PATH}:" != *":${1}:"* ]]; then
     100                        export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${1}"
    77101                fi
    78102                if [ -z $LD_RUN_PATH ]; then
    79                         export LD_RUN_PATH=$1
    80                 elif [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
    81                         export LD_RUN_PATH="$LD_RUN_PATH:$1"
    82                 fi
    83         fi
    84 } #}}}
    85 
    86 # FIXME: during installation packages are installed one by one but
    87 # environment.sh was sourced before so new packages are NOT in the path. May
     103                        export LD_RUN_PATH="${1}"
     104                elif [[ ":${LD_RUN_PATH}:" != *":$1:"* ]]; then
     105                        export LD_RUN_PATH="${LD_RUN_PATH}:${1}"
     106                fi
     107        fi
     108} #}}}
     109ld_library_path_prepend(){ #{{{
     110        if [ -d "${1}" ]; then
     111                if [ -z $LD_LIBRARY_PATH ]; then
     112                        export LD_LIBRARY_PATH="${1}"
     113                elif [[ ":${LD_LIBRARY_PATH}:" != *":${1}:"* ]]; then
     114                        export LD_LIBRARY_PATH="${1}:${LD_LIBRARY_PATH}"
     115                fi
     116                if [ -z $LD_RUN_PATH ]; then
     117                        export LD_RUN_PATH="${1}"
     118                elif [[ ":${LD_RUN_PATH}:" != *":${1}:"* ]]; then
     119                        export LD_RUN_PATH="${1}:${LD_RUN_PATH}"
     120                fi
     121        fi
     122} #}}}
     123
     124library_path_append(){ #{{{
     125        if [ -d "${1}" ]; then
     126                if [ -z $LIBRARY_PATH ]; then
     127                        export LIBRARY_PATH="${1}"
     128                elif [[ ":${LIBRARY_PATH}:" != *":$1:"* ]]; then
     129                        export LIBRARY_PATH="${LIBRARY_PATH}:${1}"
     130                fi
     131        fi
     132} #}}}
     133library_path_prepend(){ #{{{
     134        if [ -d "${1}" ]; then
     135                if [ -z $LIBRARY_PATH ]; then
     136                        export LIBRARY_PATH="${1}"
     137                elif [[ ":${LIBRARY_PATH}:" != *":$1:"* ]]; then
     138                        export LIBRARY_PATH="${1}:${LIBRARY_PATH}"
     139                fi
     140        fi
     141} #}}}
     142
     143path_append(){ #{{{
     144        if [ -d "${1}" ] && [[ ":${PATH}:" != *":${1}:"* ]]; then
     145                path="${1}"
     146                if [[ "${ISSM_ARCH}" == "cygwin-intel" ]]; then
     147                        path=`cygpath -u "${1}"`
     148                fi
     149                export PATH="${PATH}:${path}"
     150        fi
     151} #}}}
     152path_prepend(){ #{{{
     153        if [ -d "${1}" ] && [[ ":${PATH}:" != *":${1}:"* ]]; then
     154                path="${1}"
     155                if [[ "${ISSM_ARCH}" == "cygwin-intel" ]]; then
     156                        path=`cygpath -u "${1}"`
     157                fi
     158                export PATH="${path}:${PATH}"
     159        fi
     160} #}}}
     161
     162# FIXME: during installation packages are installed one by one but
     163# environment.sh was sourced before so new packages are NOT in the path. May
    88164# source environment.sh again with:
    89165#       if [ -z $(echo "$PATH" | grep "$MATLAB_DIR") ]; then export $PATH...; fi
    … …  
    95171
    96172# Load ISSM scripts
    97 pathappend "$ISSM_DIR/scripts"
    98 
    99 GMT_DIR="$ISSM_DIR/externalpackages/gmt/install"
    100 if [ -d "$GMT_DIR" ]; then
    101         export GMT_DIR
    102         pathprepend   "$GMT_DIR/bin"
    103         libpathappend "$GMT_DIR/lib"
    104 fi
    105 
    106 MPI_DIR="$ISSM_DIR/externalpackages/mpich/install"
     173path_append "${ISSM_DIR}/scripts"
     174
     175SVN_DIR="${ISSM_DIR}/externalpackages/svn/install"
     176if [ -d "${SVN_DIR}" ]; then
     177        path_prepend   "${SVN_DIR}/bin"
     178        ld_library_path_append "${SVN_DIR}/lib"
     179fi
     180
     181GIT_DIR="${ISSM_DIR}/externalpackages/git/install"
     182if [ -d "${GIT_DIR}" ]; then
     183        path_prepend "${GIT_DIR}/bin"
     184fi
     185
     186MPI_DIR="${ISSM_DIR}/externalpackages/mpich/install"
    107187if [ -d "$MPI_DIR" ]; then
    108188        export MPI_DIR
    109189        export MPI_INC_DIR="$MPI_DIR/include"
    110         pathprepend    "$MPI_DIR/bin"
    111         libpathprepend "$MPI_DIR/lib"
    112 fi
    113 
    114 PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install"
     190        path_prepend    "$MPI_DIR/bin"
     191        ld_library_path_prepend "$MPI_DIR/lib"
     192fi
     193
     194PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/install"
    115195if [ -d "$PETSC_DIR" ]; then
    116196        export PETSC_DIR
    117         libpathappend "$PETSC_DIR/lib"
    118 fi
    119 
    120 SCOTCH_DIR="$ISSM_DIR/externalpackages/scotch/install"
    121 libpathappend "$SCOTCH_DIR/lib"
    122 
    123 SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install"
    124 libpathappend "$SLEPC_DIR/lib"
    125 
    126 TAO_DIR="$ISSM_DIR/externalpackages/tao/install"
    127 libpathappend "$TAO_DIR/lib"
    128 
    129 DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install"
    130 pathappend "$DAKOTA_DIR/bin"
    131 libpathappend "$DAKOTA_DIR/lib"
    132 dylibpathprepend "$DAKOTA_DIR/lib"
    133 
    134 DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install"
    135 pathprepend "$DOXYGEN_DIR/bin"
    136 
    137 AUTOTOOLS_DIR="$ISSM_DIR/externalpackages/autotools/install"
    138 pathprepend "$AUTOTOOLS_DIR/bin"
     197        ld_library_path_append "$PETSC_DIR/lib"
     198fi
     199
     200SCOTCH_DIR="${ISSM_DIR}/externalpackages/scotch/install"
     201ld_library_path_append "$SCOTCH_DIR/lib"
     202
     203SLEPC_DIR="${ISSM_DIR}/externalpackages/slepc/install"
     204ld_library_path_append "$SLEPC_DIR/lib"
     205
     206TAO_DIR="${ISSM_DIR}/externalpackages/tao/install"
     207ld_library_path_append "$TAO_DIR/lib"
     208
     209DAKOTA_DIR="${ISSM_DIR}/externalpackages/dakota/install"
     210path_append "$DAKOTA_DIR/bin"
     211ld_library_path_append "$DAKOTA_DIR/lib"
     212dyld_library_path_prepend "$DAKOTA_DIR/lib"
     213
     214DOXYGEN_DIR="${ISSM_DIR}/externalpackages/doxygen/install"
     215path_prepend "$DOXYGEN_DIR/bin"
     216
     217AUTOTOOLS_DIR="${ISSM_DIR}/externalpackages/autotools/install"
     218path_prepend "$AUTOTOOLS_DIR/bin"
    139219
    140220SDK_DIR="C:/MicrosoftVisualStudio 9.0/Microsoft Visual C++ 2008 Express Edition with SP1 - ENU"
    141 pathappend "$SDK_DIR"
    142 
    143 SSH_DIR="$ISSM_DIR/externalpackages/ssh"
    144 pathappend "$SSH_DIR"
    145 
    146 VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install"
    147 pathprepend "$VALGRIND_DIR/bin"
    148 
    149 NCO_DIR="$ISSM_DIR/externalpackages/nco/install/bin"
    150 pathprepend "$NCO_DIR/bin"
    151 
    152 CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install"
    153 pathappend "$CPPCHECK_DIR/bin"
    154 
    155 GDAL_DIR="$ISSM_DIR/externalpackages/gdal/install"
    156 pathprepend "$GDAL_DIR/bin"
    157 libpathappend "$GDAL_DIR/lib"
    158 
    159 PROJ4_DIR="$ISSM_DIR/externalpackages/proj.4/install"
    160 dylibpathprepend "$PROJ4_DIR/lib"
    161 libpathprepend "$PROJ4_DIR/lib"
    162 
    163 MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install"
     221path_append "$SDK_DIR"
     222
     223SSH_DIR="${ISSM_DIR}/externalpackages/ssh"
     224path_append "$SSH_DIR"
     225
     226VALGRIND_DIR="${ISSM_DIR}/externalpackages/valgrind/install"
     227path_prepend "$VALGRIND_DIR/bin"
     228
     229NCO_DIR="${ISSM_DIR}/externalpackages/nco/install/bin"
     230path_prepend "$NCO_DIR/bin"
     231
     232CPPCHECK_DIR="${ISSM_DIR}/externalpackages/cppcheck/install"
     233path_append "$CPPCHECK_DIR/bin"
     234
     235MERCURIAL_DIR="${ISSM_DIR}/externalpackages/mercurial/install"
    164236if [ -d "$MERCURIAL_DIR" ]; then
    165237        export PYTHONPATH="$PYTHONPATH:$MERCURIAL_DIR/mercurial/pure/"
    166         pathappend "$MERCURIAL_DIR"
    167 fi
    168 
    169 BOOST_DIR="$ISSM_DIR/externalpackages/boost/install"
    170 BOOSTROOT="$ISSM_DIR/externalpackages/boost/install"
     238        path_append "$MERCURIAL_DIR"
     239fi
     240
     241BOOST_DIR="${ISSM_DIR}/externalpackages/boost/install"
     242BOOSTROOT="${ISSM_DIR}/externalpackages/boost/install"
    171243if [ -d "$BOOST_DIR" ]; then
    172244        export BOOSTROOT
    173245        export BOOST_DIR
    174         libpathprepend   "$BOOST_DIR/lib"
    175         dylibpathprepend "$BOOST_DIR/lib"
    176         pathprepend      "$BOOST_DIR/bin"
    177 fi
    178 
    179 XERCESROOT="$ISSM_DIR/externalpackages/xerces/install"
    180 XERCESCROOT="$ISSM_DIR/externalpackages/xerces/src"
     246        ld_library_path_prepend   "$BOOST_DIR/lib"
     247        dyld_library_path_prepend "$BOOST_DIR/lib"
     248        path_prepend      "$BOOST_DIR/bin"
     249fi
     250
     251XERCESROOT="${ISSM_DIR}/externalpackages/xerces/install"
     252XERCESCROOT="${ISSM_DIR}/externalpackages/xerces/src"
    181253if [ -d "$XERCESROOT" ]; then
    182         export XERCESROOT 
     254        export XERCESROOT
    183255        export XERCESCROOT
    184256fi
    185257
    186 XAIF_DIR="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster"
    187 XAIFBOOSTERROOT="$ISSM_DIR/externalpackages/xaifbooster/"
    188 XAIFBOOSTER_HOME="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster"
     258XAIF_DIR="${ISSM_DIR}/externalpackages/xaifbooster/xaifBooster"
     259XAIFBOOSTERROOT="${ISSM_DIR}/externalpackages/xaifbooster/"
     260XAIFBOOSTER_HOME="${ISSM_DIR}/externalpackages/xaifbooster/xaifBooster"
    189261PLATFORM="x86-Linux"
    190262if [ -d "$XAIF_DIR" ]; then
    … …  
    195267fi
    196268
    197 ANGELROOT="$ISSM_DIR/externalpackages/angel/angel"
     269ANGELROOT="${ISSM_DIR}/externalpackages/angel/angel"
    198270if [ -d "$ANGELROOT" ]; then
    199271        export ANGELROOT
    200272fi
    201273
    202 OPENANALYSISROOT="$ISSM_DIR/externalpackages/openanalysis/install"
     274OPENANALYSISROOT="${ISSM_DIR}/externalpackages/openanalysis/install"
    203275if [ -d "$OPENANALYSISROOT" ]; then
    204276        export OPENANALYSISROOT
    205         libpathappend "$OPENANALYSISROOT/lib"
     277        ld_library_path_append "$OPENANALYSISROOT/lib"
    206278fi
    207279
    208280JVM_DIR="/usr/local/gcc/4.3.2/lib64/gcj-4.3.2-9/"
    209 libpathappend "$JVM_DIR"
    210 
    211 BBFTP_DIR="$ISSM_DIR/externalpackages/bbftp/install"
    212 pathappend "$BBFTP_DIR/bin"
    213 
    214 ADIC_DIR="$ISSM_DIR/externalpackages/adic/install"
    215 pathappend "$ADIC_DIR/bin"
    216 libpathappend "$ADIC_DIR/lib"
    217 
    218 COLPACK_DIR="$ISSM_DIR/externalpackages/colpack/install"
    219 libpathappend "$COLPACK_DIR/lib"
    220 
    221 ECLIPSE_DIR="$ISSM_DIR/externalpackages/eclipse/install"
    222 pathappend "$ECLIPSE_DIR"
    223 
    224 APPSCAN_DIR="$ISSM_DIR/externalpackages/appscan/install"
    225 pathappend "$APPSCAN_DIR/bin"
    226 
    227 RATS_DIR="$ISSM_DIR/externalpackages/rats/install"
    228 pathappend "$RATS_DIR/bin"
    229 
    230 DYSON_DIR="$ISSM_DIR/externalpackages/dyson/"
    231 pathappend "$DYSON_DIR"
    232 
    233 CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install"
    234 pathprepend "$CMAKE_DIR/bin"
    235 
    236 SHAPELIB_DIR="$ISSM_DIR/externalpackages/shapelib/install"
    237 pathappend "$SHAPELIB_DIR/exec"
    238 
    239 CCCL_DIR="$ISSM_DIR/externalpackages/cccl/install"
    240 pathappend "$CCCL_DIR/bin"
    241 
    242 PACKAGEMAKER_DIR="$ISSM_DIR/externalpackages/packagemaker/install"
    243 pathappend "$PACKAGEMAKER_DIR"
     281ld_library_path_append "$JVM_DIR"
     282
     283BBFTP_DIR="${ISSM_DIR}/externalpackages/bbftp/install"
     284path_append "$BBFTP_DIR/bin"
     285
     286ADIC_DIR="${ISSM_DIR}/externalpackages/adic/install"
     287path_append "$ADIC_DIR/bin"
     288ld_library_path_append "$ADIC_DIR/lib"
     289
     290COLPACK_DIR="${ISSM_DIR}/externalpackages/colpack/install"
     291ld_library_path_append "$COLPACK_DIR/lib"
     292
     293ECLIPSE_DIR="${ISSM_DIR}/externalpackages/eclipse/install"
     294path_append "$ECLIPSE_DIR"
     295
     296APPSCAN_DIR="${ISSM_DIR}/externalpackages/appscan/install"
     297path_append "$APPSCAN_DIR/bin"
     298
     299RATS_DIR="${ISSM_DIR}/externalpackages/rats/install"
     300path_append "$RATS_DIR/bin"
     301
     302DYSON_DIR="${ISSM_DIR}/externalpackages/dyson/"
     303path_append "$DYSON_DIR"
     304
     305CMAKE_DIR="${ISSM_DIR}/externalpackages/cmake/install"
     306path_prepend "$CMAKE_DIR/bin"
     307
     308SHAPELIB_DIR="${ISSM_DIR}/externalpackages/shapelib/install"
     309path_append "$SHAPELIB_DIR/exec"
     310
     311CCCL_DIR="${ISSM_DIR}/externalpackages/cccl/install"
     312path_append "$CCCL_DIR/bin"
     313
     314PACKAGEMAKER_DIR="${ISSM_DIR}/externalpackages/packagemaker/install"
     315path_append "$PACKAGEMAKER_DIR"
    244316
    245317#android-dev-dir
    246 export ANDROID_DIR="$ISSM_DIR/externalpackages/android"
     318export ANDROID_DIR="${ISSM_DIR}/externalpackages/android"
    247319
    248320export ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install"
    249 pathappend "$ANDROID_NDK_DIR/arm-linux-android-install/bin"
     321path_append "$ANDROID_NDK_DIR/arm-linux-android-install/bin"
    250322
    251323export ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install"
    252 pathappend "$ANDROID_SDK_DIR/"
    253 
    254 GSL_DIR="$ISSM_DIR/externalpackages/gsl/install"
    255 libpathappend "$GSL_DIR/lib"
    256 
    257 GMAKE_DIR="$ISSM_DIR/externalpackages/gmake/install"
    258 pathprepend "$GMAKE_DIR/bin"
    259 
    260 MODELE_DIR="$ISSM_DIR/externalpackages/modelE/install"
    261 pathappend "$MODELE_DIR/src/exec"
    262 
    263 GIT_DIR="$ISSM_DIR/externalpackages/git/install"
    264 pathprepend "$GIT_DIR/bin"
    265 
    266 NCVIEW_DIR="$ISSM_DIR/externalpackages/ncview/install"
    267 pathappend "$NCVIEW_DIR"
    268 
    269 TCLX_DIR="$ISSM_DIR/externalpackages/tclx/install/lib/tclx8.4"
    270 libpathappend "$TCLX_DIR"
    271 
    272 ASPELL_DIR="$ISSM_DIR/externalpackages/aspell/install"
    273 pathappend "$ASPELL_DIR/bin"
    274 
    275 HDF5_DIR="$ISSM_DIR/externalpackages/hdf5/install"
    276 dylibpathappend "$HDF5_DIR/lib"
    277 libpathappend "$HDF5_DIR/lib"
    278 if [ -d "$HDF5_DIR" ]; then
    279         export LIBRARY_PATH="$LIBRARY_PATH:$HDF5_DIR/lib"
    280         export C_INCLUDE_PATH="$C_INCLUDE_PATH:$HDF5_DIR/include"
    281 fi
    282 
    283 NETCDF_DIR="$ISSM_DIR/externalpackages/netcdf/install"
    284 pathappend "$NETCDF_DIR/bin"
    285 dylibpathappend "$NETCDF_DIR/lib"
    286 libpathappend "$NETCDF_DIR/lib"
    287 if [ -d "$NETCDF_DIR" ]; then
    288         export LIBRARY_PATH="$LIBRARY_PATH:$NETCDF_DIR/lib"
    289         dylibpathappend "$NETCDF_DIR/lib"
    290         libpathappend "$NETCDF_DIR/lib"
    291         export C_INCLUDE_PATH="$C_INCLUDE_PATH:$NETCDF_DIR/include"
    292 fi
    293 
    294 NETCDF_CXX_DIR="$ISSM_DIR/externalpackages/netcdf-cxx/install"
    295 libpathappend "$NETCDF_CXX_DIR/lib"
    296 
    297 SVN_DIR="$ISSM_DIR/externalpackages/svn/install"
    298 pathprepend   "$SVN_DIR/bin"
    299 libpathappend "$SVN_DIR/lib"
    300 
    301 CVS_DIR="$ISSM_DIR/externalpackages/cvs/install"
    302 pathprepend   "$CVS_DIR/bin"
    303 
    304 APR_DIR="$ISSM_DIR/externalpackages/apr/install"
    305 pathappend    "$APR_DIR/bin"
    306 libpathappend "$APR_DIR/lib"
    307 
    308 APR_UTIL_DIR="$ISSM_DIR/externalpackages/apr-util/install"
    309 pathappend   "$APR_UTIL_DIR/bin:$PATH"
    310 libpathappend "$APR_UTIL_DIR/lib"
    311 
    312 SQLITE_DIR="$ISSM_DIR/externalpackages/sqlite/install"
    313 pathappend   "$SQLITE_DIR/bin"
    314 libpathappend "$SQLITE_DIR/lib"
    315 
    316 YAMS_DIR="$ISSM_DIR/externalpackages/yams/install"
    317 pathappend   "$YAMS_DIR"
    318 
    319 SWIG_DIR="$ISSM_DIR/externalpackages/swig/install"
    320 pathappend   "$SWIG_DIR"
     324path_append "$ANDROID_SDK_DIR/"
     325
     326GSL_DIR="${ISSM_DIR}/externalpackages/gsl/install"
     327ld_library_path_append "$GSL_DIR/lib"
     328
     329GMAKE_DIR="${ISSM_DIR}/externalpackages/gmake/install"
     330path_prepend "$GMAKE_DIR/bin"
     331
     332MODELE_DIR="${ISSM_DIR}/externalpackages/modelE/install"
     333path_append "$MODELE_DIR/src/exec"
     334
     335NCVIEW_DIR="${ISSM_DIR}/externalpackages/ncview/install"
     336path_append "$NCVIEW_DIR"
     337
     338TCLX_DIR="${ISSM_DIR}/externalpackages/tclx/install/lib/tclx8.4"
     339ld_library_path_append "$TCLX_DIR"
     340
     341ASPELL_DIR="${ISSM_DIR}/externalpackages/aspell/install"
     342path_append "$ASPELL_DIR/bin"
     343
     344HDF5_DIR="${ISSM_DIR}/externalpackages/hdf5/install"
     345if [ -d "${HDF5_DIR}" ]; then
     346        c_include_path_append "${C_INCLUDE_PATH}:${HDF5_DIR}/include"
     347        library_path_append "${LIBRARY_PATH}:${HDF5_DIR}/lib"
     348        dyld_library_path_append "${HDF5_DIR}/lib"
     349        ld_library_path_append "${HDF5_DIR}/lib"
     350fi
     351
     352NETCDF_DIR="${ISSM_DIR}/externalpackages/netcdf/install"
     353if [ -d "${NETCDF_DIR}" ]; then
     354        c_include_path_append "${C_INCLUDE_PATH}:${NETCDF_DIR}/include"
     355        library_path_append "${LIBRARY_PATH}:${NETCDF_DIR}/lib"
     356        path_append "${NETCDF_DIR}/bin"
     357        dyld_library_path_append "${NETCDF_DIR}/lib"
     358        ld_library_path_append "${NETCDF_DIR}/lib"
     359fi
     360
     361NETCDF_CXX_DIR="${ISSM_DIR}/externalpackages/netcdf-cxx/install"
     362if [ -d "${NETCDF_CXX_DIR}" ]; then
     363        ld_library_path_append "${NETCDF_CXX_DIR}/lib"
     364fi
     365
     366SQLITE_DIR="${ISSM_DIR}/externalpackages/sqlite/install"
     367if [ -d "${SQLITE_DIR}" ]; then
     368        path_append   "${SQLITE_DIR}/bin"
     369        ld_library_path_append "${SQLITE_DIR}/lib"
     370fi
     371
     372PROJ4_DIR="${ISSM_DIR}/externalpackages/proj.4/install"
     373if [ -d "${PROJ4_DIR}" ]; then
     374        dyld_library_path_prepend "${PROJ4_DIR}/lib"
     375        ld_library_path_prepend "${PROJ4_DIR}/lib"
     376fi
     377
     378PROJ_DIR="${ISSM_DIR}/externalpackages/proj/install"
     379if [ -d "${PROJ_DIR}" ]; then
     380        dyld_library_path_prepend "${PROJ_DIR}/lib"
     381        ld_library_path_prepend "${PROJ_DIR}/lib"
     382fi
     383
     384GDAL_DIR="${ISSM_DIR}/externalpackages/gdal/install"
     385if [ -d "${GDAL_DIR}" ]; then
     386        path_prepend "${GDAL_DIR}/bin"
     387        ld_library_path_append "${GDAL_DIR}/lib"
     388fi
     389
     390GMT_DIR="${ISSM_DIR}/externalpackages/gmt/install"
     391if [ -d "${GMT_DIR}" ]; then
     392        export GMT_DIR
     393        path_prepend   "${GMT_DIR}/bin"
     394        ld_library_path_append "${GMT_DIR}/lib"
     395fi
     396
     397GMSH_DIR="${ISSM_DIR}/externalpackages/gmsh/install"
     398if [ -d "${GMSH_DIR}" ]; then
     399        path_append "${ISSM_DIR}/externalpackages/gmsh/install"
     400fi
     401
     402CVS_DIR="${ISSM_DIR}/externalpackages/cvs/install"
     403path_prepend   "$CVS_DIR/bin"
     404
     405APR_DIR="${ISSM_DIR}/externalpackages/apr/install"
     406path_append    "$APR_DIR/bin"
     407ld_library_path_append "$APR_DIR/lib"
     408
     409APR_UTIL_DIR="${ISSM_DIR}/externalpackages/apr-util/install"
     410path_append   "$APR_UTIL_DIR/bin:$PATH"
     411ld_library_path_append "$APR_UTIL_DIR/lib"
     412
     413YAMS_DIR="${ISSM_DIR}/externalpackages/yams/install"
     414path_append   "$YAMS_DIR"
     415
     416SWIG_DIR="${ISSM_DIR}/externalpackages/swig/install"
     417path_append   "$SWIG_DIR"
    321418
    322419#AUX-CONFIG
    323 pathappend   "$ISSM_DIR/aux-config"
     420path_append   "${ISSM_DIR}/aux-config"
    324421
    325422#INISHELL
    326 pathappend   "$ISSM_DIR/externalpackages/inishell/install"
     423path_append   "${ISSM_DIR}/externalpackages/inishell/install"
    327424
    328425#SHELL2JUNIT
    329 pathappend   "$ISSM_DIR/externalpackages/shell2junit/install"
     426path_append   "${ISSM_DIR}/externalpackages/shell2junit/install"
    330427
    331428#EXPAT
    332 libpathprepend   "$ISSM_DIR/externalpackages/expat/install"
    333 dylibpathprepend   "$ISSM_DIR/externalpackages/expat/install"
    334 
    335 #GMSH
    336 pathappend   "$ISSM_DIR/externalpackages/gmsh/install"
     429ld_library_path_prepend   "${ISSM_DIR}/externalpackages/expat/install"
     430dyld_library_path_prepend   "${ISSM_DIR}/externalpackages/expat/install"
    337431
    338432#CURL
    339 libpathprepend   "$ISSM_DIR/externalpackages/curl/install/lib"
    340 dylibpathprepend   "$ISSM_DIR/externalpackages/curl/install/lib"
    341 pathprepend "$ISSM_DIR/externalpackages/curl/install/bin"
    342 
    343 #GMT
    344 pathprepend "$ISSM_DIR/externalpackages/gmt/install/bin"
     433ld_library_path_prepend   "${ISSM_DIR}/externalpackages/curl/install/lib"
     434dyld_library_path_prepend   "${ISSM_DIR}/externalpackages/curl/install/lib"
     435path_prepend "${ISSM_DIR}/externalpackages/curl/install/bin"
    345436
    346437#NEOPZ
    347 NEOPZ_DIR="$ISSM_DIR/externalpackages/neopz/install"
     438NEOPZ_DIR="${ISSM_DIR}/externalpackages/neopz/install"
    348439if [ -d "$NEOPZ_DIR" ]; then
    349440        export REFPATTERNDIR="$NEOPZ_DIR/include/refpatterns"

  • issm/trunk-jpl/externalpackages/gmsh/install.sh

    r24283 r24321  
    22set -eu
    33
     4
     5## Constants
     6#
    47VER="3.0.5"
    58
    … …  
    2427        -DENABLE_MPI=1
    2528
    26 # Compile
     29# Compile and install
    2730if [ $# -eq 0 ]; then
    2831        make
     32        make install
    2933else
    3034        make -j $1
     35        make -j $1 install
    3136fi
    3237
    33 # Install
    34 make install
     38# Return to initial directory
     39cd ..
     40

  • issm/trunk-jpl/externalpackages/gmt/configs/ConfigUser.cmake

    r18900 r24321  
    103103
    104104# Set path to DCW Digital Chart of the World for GMT [auto]:
    105 #set (DCW_ROOT "dcw-gmt_path")
     105#set (DCW_ROOT "$ENV{ISSM_DIR}/externalpackages/dcw/install")
    106106
    107107# Copy DCW files to $/dcw [FALSE]:
    … …  
    141141# Enable building of shared libraries [TRUE] (disable to use static libraries;
    142142# not recommended):
    143 #set (BUILD_SHARED_LIBS FALSE)
     143#set (BUILD_SHARED_LIBS TRUE)
    144144
    145145# Build GMT shared lib with supplemental modules [TRUE]:
    146 #set (BUILD_SUPPLEMENTS FALSE)
     146#set (BUILD_SUPPLEMENTS TRUE)
    147147
    148148##

  • issm/trunk-jpl/externalpackages/gmt/install.sh

    r23435 r24321  
    22set -eu
    33
    4 #Erase install
    5 rm -rf install  src gmt
    64
    7 #Download from ISSM server
    8 $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gmt-5.1.1.tar.gz' 'gmt-5.1.1.tar.gz'
     5# Constants
     6#
     7VER="5.1.1"
    98
    10 #install directory
    11 mkdir src
    12 tar -zxvf gmt-5.1.1.tar.gz
    13 mv gmt-5.1.1/* src
    14 rm -rf gmt-5.1.1
     9# Download source
     10$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz"
    1511
    16 #configure:
    17 cp configs/ConfigUser.cmake ./src/cmake
     12# Unpack source
     13tar -zxvf gmt-$VER.tar.gz
    1814
     15# Cleanup
     16rm -rf install src
     17mkdir install src
     18
     19# Move source to 'src' directory
     20mv gmt-$VER/* src
     21rm -rf gmt-$VER
     22
     23# Copy source customizations
     24cp configs/ConfigUser.cmake src/cmake
     25
     26# Configure
    1927cd src
    2028mkdir build
    2129cd build
    22 cmake ../
     30cmake ..
    2331
    24 #compile
     32# Install
    2533if [ $# -eq 0 ]; then
    2634        make install
    … …  
    2937fi
    3038
    31 #come back:
    32 cd ../../
     39# Return to initial directory
     40cd ../..

  • issm/trunk-jpl/externalpackages/gshhg/install.sh

    r23435 r24321  
    22set -eu
    33
    4 rm -rf gssh-gmt-2.3.4.tar.gz  src install
    54
    6 #get gssh database from noaa's website:  http://www.ngdc.noaa.gov/mgg/shorelines/gshhs.html
    7 #curl http://www.ngdc.noaa.gov/mgg/shorelines/data/gshhg/latest/gshhg-gmt-2.3.4.tar.gz > gshhg-gmt-2.3.4.tar.gz
     5## Constants
     6#
     7VER="2.3.4"
    88
    9 #Download from ISSM server
    10 $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gshhg-gmt-2.3.4.tar.gz' 'gshhg-gmt-2.3.4.tar.gz'
     9# Cleanup
     10rm -rf install
    1111
    12 #untar:
    13 tar -zxvf gshhg-gmt-2.3.4.tar.gz
     12# Download source
     13$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gshhg-gmt-${VER}.tar.gz" "gshhg-gmt-${VER}.tar.gz"
    1414
    15 #move:
    16 mv gshhg-gmt-2.3.4 install
     15# Unpack source
     16tar -zxvf gshhg-gmt-${VER}.tar.gz
     17
     18# Install
     19mv gshhg-gmt-${VER} install

  • issm/trunk-jpl/externalpackages/sqlite/install.sh

    r23435 r24321  
    22set -eu
    33
    4 #Some cleanup
    5 rm -rf src
    6 rm -rf install
    7 rm -rf sqlite-autoconf-3071300
    8 mkdir src install
    94
    10 #Download from ISSM server
    11 $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/sqlite-autoconf-3071300.tar.gz' 'sqlite-autoconf-3071300.tar.gz'
     5VER="3300100"
    126
    13 #Untar
    14 tar -zxvf  sqlite-autoconf-3071300.tar.gz
     7# Cleanup
     8rm -rf install src
     9mkdir install src
    1510
    16 #Move sqlite-autoconf into src directory
    17 mv sqlite-autoconf-3071300/* src
    18 rm -rf sqlite-autoconf-3071300
     11# Download source
     12$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/sqlite-autoconf-${VER}.tar.gz" "sqlite-autoconf-${VER}.tar.gz"
    1913
    20 #Configure sqlite-autoconf
     14# Unpack source
     15tar -zxvf sqlite-autoconf-$VER.tar.gz
     16
     17# Move source into 'src' directory
     18mv sqlite-autoconf-$VER/* src
     19rm -rf sqlite-autoconf-$VER
     20
     21# Configure
    2122cd src
    22 ./configure  --prefix="$ISSM_DIR/externalpackages/sqlite/install"
     23./configure \
     24        --prefix="${ISSM_DIR}/externalpackages/sqlite/install"
    2325
    24 #Compile and install sqlite-autoconf
     26# Compile and install
    2527if [ $# -eq 0 ]; then
    2628        make
     29        make install
    2730else
    2831        make -j $1
     32        make -j $1 install
    2933fi
    30 make install

  • issm/trunk-jpl/jenkins/jenkins.sh

    r24317 r24321  
    3535fi
    3636
    37 #Defaults (to avoid -eq: unary operator expected)
    38 EXAMPLES_TEST=0
     37# Initialize test suite variables (to avoid "-eq: unary operator expected")
    3938MATLAB_TEST=0
    4039PYTHON_TEST=0
    4140JAVASCRIPT_TEST=0
     41EXAMPLES_TEST=0
    4242
    4343#source configuration script
    … …  
    432432                if [ -d "${dir}" ];
    433433                then
    434                 # Some of the examples are incomplete (on purpose). As such, we will have to populate the
    435                 # missing steps in order to make sure that everything is working.
     434                # Some of the examples are incomplete (on purpose). As such, we will
     435                # have to populate the missing steps in order to make sure that
     436                # everything is working.
    436437                        echo "Testing directory example: $(basename $dir)"
    437438
    438                         # Greenland is missing step 8
    439439                        if [ -z "$SED" ];
    440440                        then
    … …  
    446446                        if [ "${dir}" == "./Greenland" ];
    447447                        then
     448                                # Greenland is missing step 8
    448449                                STEP_EIGHT="\n  disp('   Step 8: Plotting exercise');\n md = loadmodel('.\/Models\/Greenland.HistoricTransient');\n     figure\n        surfmb=[]; for i=2:201; surfmb=[surfmb ...\n            md.results.TransientSolution(i).SmbMassBalance]; end\n  subplot(3,1,1); plot([1:200],mean(surfmb));\n   title('Mean Surface mass balance');\n   vel=[]; for i=2:201; vel=[vel md.results.TransientSolution(i).Vel]; end\n       subplot(3,1,2); plot([1:200],mean(vel));\n      title('Mean Velocity');\n       volume=[]; for i=2:201; volume=[volume md.results.TransientSolution(i).IceVolume]; end\n        subplot(3,1,3); plot([1:200],volume);\n title('Ice Volume'); xlabel('years');"
    449450
    450                                 $SED -i.bak 's/steps=\[1\];/steps=\[1:8\];\n\ntry\n/' $FILE
    451                                 $SED -i.bak "s/if any(steps==8)/&${STEP_EIGHT}/" $FILE
     451                                $SED -i .bak 's/steps=\[1\];/steps=\[1:8\];\n\ntry\n/' $FILE
     452                                $SED -i .bak "s/if any(steps==8)/&${STEP_EIGHT}/" $FILE
    452453                        elif [ "${dir}" == "./IceBridge" ];
    453454                        then
    454                                 $SED -i.bak 's/steps=\[1\];/steps=\[1:5\];\n\ntry\n/' $FILE
     455                                $SED -i .bak 's/steps=\[1\];/steps=\[1:5\];\n\ntry\n/' $FILE
    455456                        elif [ "${dir}" == "./IceflowModels" ];
    456457                        then
    457458                                # Almost nothing to this example
    458                                 $SED -i.bak '1 s/^.*$/try\n\n&/' $FILE
     459                                $SED -i .bak '1 s/^.*$/try\n\n&/' $FILE
    459460                        elif [ "${dir}" == "./ISMIP" ];
    460461                        then
    461462                                # Eight steps... none of which are implmented in the script...
    462                                 $SED -i.bak '1 s/^.*$/try\n\n&/' $FILE
     463                                $SED -i .bak '1 s/^.*$/try\n\n&/' $FILE
    463464                        elif [ "${dir}" == "./Inversion" ];
    464465                        then
    465                                 $SED -i.bak 's/steps=\[1\];/steps=\[1:4\];\n\ntry\n/' $FILE
     466                                $SED -i .bak 's/steps=\[1\];/steps=\[1:4\];\n\ntry\n/' $FILE
    466467                        elif [ "${dir}" == "./Jakobshavn" ];
    467468                        then
    468                                 $SED -i.bak 's/steps=\[1\];/steps=\[1:4\];\n\ntry\n/' $FILE
     469                                $SED -i .bak 's/steps=\[1\];/steps=\[1:4\];\n\ntry\n/' $FILE
    469470                        elif [ "${dir}" == "./Jakobshavn" ];
    470471                        then
    471                                 $SED -i.bak 's/steps=\[1\];/steps=\[1:4\];\n\ntry\n/' $FILE
     472                                $SED -i .bak 's/steps=\[1\];/steps=\[1:4\];\n\ntry\n/' $FILE
    472473                        elif [ "${dir}" == "./Pig" ];
    473474                        then
    474475                                # Step 6 is needed
    475476                                STEP_SIX="\n disp('Needs work!')"
    476                                 $SED -i.bak 's/steps=\[1\];/steps=\[1:7\];\n!mv DomainOutline.bkp DomainOutline.exp;\n\ntry\n/' $FILE
    477                                 $SED -i.bak "s/if any(steps==6)/&${STEP_SIX}/" $FILE
     477                                $SED -i .bak 's/steps=\[1\];/steps=\[1:7\];\n!mv DomainOutline.bkp DomainOutline.exp;\n\ntry\n/' $FILE
     478                                $SED -i .bak "s/if any(steps==6)/&${STEP_SIX}/" $FILE
    478479                        elif [ "${dir}" == "./PigSensitivity" ];
    479480                        then
    480481                                # Step 4 is needed
    481482                                STEP_FOUR="\n disp('Needs work!')"
    482                                 $SED -i.bak 's/steps=\[1\];/steps=\[1:4\];\n\ntry\n/' $FILE
    483                                 $SED -i.bak "s/if any(steps==6)/&${STEP_FOUR}/" $FILE
     483                                $SED -i .bak 's/steps=\[1\];/steps=\[1:4\];\n\ntry\n/' $FILE
     484                                $SED -i .bak "s/if any(steps==6)/&${STEP_FOUR}/" $FILE
    484485                        elif [ "${dir}" == "./SquareIceShelf" ];
    485486                        then
    486487                                # Almost nothing to this example
    487                                 $SED -i.bak '1 s/^.*$/try\n\n&/' $FILE
     488                                $SED -i .bak '1 s/^.*$/try\n\n&/' $FILE
    488489                        elif [ "${dir}" == "./UncertaintyQuantification" ];
    489490                        then
    490                                 $SED -i.bak 's/steps=\[1\];/steps=\[1:7\];\n\ntry\n/' $FILE
     491                                $SED -i .bak 's/steps=\[1\];/steps=\[1:7\];\n\ntry\n/' $FILE
    491492                        elif [ "${dir}" == "./Data" ];
    492493                        then
    … …  
    494495                        else
    495496                                echo "Not implemented yet!"
    496                                 $SED -i.bak '1 s/^.*$/try\n\n&/' $FILE
     497                                $SED -i .bak '1 s/^.*$/try\n\n&/' $FILE
    497498                        fi
    498499
    … …  
    573574then
    574575        # Inexplicably, there are backspace chars in the error output that are causing issues
    575         $SED -i.bak 's///g' matlab_log_examples.log
     576        $SED -i .bak 's///g' matlab_log_examples.log
    576577
    577578        numtests=`cat matlab_log_examples.log  | grep "starting: " | wc -l`

  • issm/trunk-jpl/jenkins/macosx_pine-island_examples

    r23275 r24321  
    1 
    21#-------------------------------#
    32# 1: ISSM general configuration #
    43#-------------------------------#
    54
    6 #MATLAB path
     5# MATLAB path
    76MATLAB_PATH="/Applications/MATLAB_R2015b.app"
    87
    9 #ISSM CONFIGURATION
    10 ISSM_CONFIG='--prefix=$ISSM_DIR \
     8# ISSM CONFIGURATION
     9ISSM_CONFIG='\
     10        --prefix=$ISSM_DIR \
    1111        --with-matlab-dir=$MATLAB_PATH \
     12        --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \
     13        --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \
     14        --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
     15        --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
     16        --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
     17        --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
     18        --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
    1219        --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
    13         --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
    14         --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \
    15         --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
    16         --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
    17         --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
    18         --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
    19         --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
    2020        --with-numthreads=4 \
    2121        --enable-debugging \
    22         --enable-development'
     22        --enable-development \
     23'
    2324
    24 #PYTHON and MATLAB testing
     25# Test suites
    2526MATLAB_TEST=0
    2627PYTHON_TEST=0
     28JAVASCRIPT_TEST=0
    2729EXAMPLES_TEST=1
    2830
    … …  
    3133#-----------------------------------#
    3234
    33 #List of external pakages to be installed and their installation scripts
    34 EXTERNALPACKAGES="autotools    install.sh
    35                                                 cmake        install.sh
    36                                                 mpich        install-3.2-macosx64.sh
    37                                                 m1qn3        install.sh
    38                                                 petsc        install-3.7-macosx64.sh
    39                                                 triangle     install-macosx64.sh
    40                                                 shell2junit  install.sh"
     35# List of external pakages to be installed and their installation scripts
     36EXTERNALPACKAGES="
     37        autotools       install.sh
     38        cmake           install.sh
     39        mpich           install-3.3-macOS_64.sh
     40        m1qn3           install.sh
     41        petsc           install-3.7-macosx64.sh
     42        triangle        install-macosx64.sh
     43        hdf5            install-1.10.sh
     44        netcdf          install-4.7.sh
     45        proj            install-6.2-macOS_64.sh
     46        gdal            install-3.0-macOS_64-netcdf.sh
     47        gshhg           install.sh
     48        gmt                     install.sh
     49        gmsh            install.sh
     50        shell2junit     install.sh
     51"
    4152
    4253#-----------------#
    … …  
    4455#-----------------#
    4556
    46 #number of cpus used in ISSM installation and compilation (one is usually
    47 #safer as some packages are very sensitive to parallel compilation)
    48 NUMCPUS_INSTALL=4
     57# Number of CPUs used in ISSM compilation
     58#
     59# NOTE: One is usually safer as some packages are very sensitive to parallel
     60#       compilation.
     61#
     62NUMCPUS_INSTALL=10
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