Changeset 24332

Timestamp:

11/14/19 19:57:23 (5 years ago)

Author:

jdquinn

Message:

CHG: Reverting installation of HDF5/NetCDF via PETSc (will reapply after updating Jenkins nodes to Ubuntu 18)

Location:

issm/trunk-jpl

Files:

• etc/environment.sh (modified) (6 diffs)
• externalpackages/petsc/install-3.7-linux64.sh (modified) (1 diff)
• jenkins/linux64_ross (modified) (3 diffs)
• jenkins/linux64_ross_python (modified) (1 diff)
• jenkins/linux64_ross_se (modified) (2 diffs)

issm/trunk-jpl/etc/environment.sh

@@ -25 +25 @@
         fi
 } #}}}
-\
+
 cpath_append(){ #{{{
         if [ -d "${1}" ]; then
@@ -349 +349 @@
 HDF5_DIR="${ISSM_DIR}/externalpackages/hdf5/install"
 if [ -d "${HDF5_DIR}" ]; then
-        c_include_path_append "${C_INCLUDE_PATH}:${HDF5_DIR}/include"
-        library_path_append "${LIBRARY_PATH}:${HDF5_DIR}/lib"
+        c_include_path_append "${HDF5_DIR}/include"
+        library_path_append "${HDF5_DIR}/lib"
         dyld_library_path_append "${HDF5_DIR}/lib"
         ld_library_path_append "${HDF5_DIR}/lib"
@@ -357 +357 @@
 NETCDF_DIR="${ISSM_DIR}/externalpackages/netcdf/install"
 if [ -d "${NETCDF_DIR}" ]; then
-        c_include_path_append "${C_INCLUDE_PATH}:${NETCDF_DIR}/include"
-        library_path_append "${LIBRARY_PATH}:${NETCDF_DIR}/lib"
         path_append "${NETCDF_DIR}/bin"
+        c_include_path_append "${NETCDF_DIR}/include"
+        library_path_append "${NETCDF_DIR}/lib"
         dyld_library_path_append "${NETCDF_DIR}/lib"
         ld_library_path_append "${NETCDF_DIR}/lib"
@@ -371 +371 @@
 SQLITE_DIR="${ISSM_DIR}/externalpackages/sqlite/install"
 if [ -d "${SQLITE_DIR}" ]; then
-        path_append   "${SQLITE_DIR}/bin"
+        path_append "${SQLITE_DIR}/bin"
         ld_library_path_append "${SQLITE_DIR}/lib"
 fi
@@ -396 +396 @@
 if [ -d "${GMT_DIR}" ]; then
         export GMT_DIR
-        path_prepend   "${GMT_DIR}/bin"
+        path_prepend "${GMT_DIR}/bin"
         ld_library_path_append "${GMT_DIR}/lib"
 fi
@@ -406 +406 @@
 
 CVS_DIR="${ISSM_DIR}/externalpackages/cvs/install"
-path_prepend   "$CVS_DIR/bin"
+path_prepend "$CVS_DIR/bin"
 
 APR_DIR="${ISSM_DIR}/externalpackages/apr/install"
-path_append    "$APR_DIR/bin"
+path_append "$APR_DIR/bin"
 ld_library_path_append "$APR_DIR/lib"
 
 APR_UTIL_DIR="${ISSM_DIR}/externalpackages/apr-util/install"
-path_append   "$APR_UTIL_DIR/bin:$PATH"
+path_prepend "$APR_UTIL_DIR/bin"
 ld_library_path_append "$APR_UTIL_DIR/lib"
 
 YAMS_DIR="${ISSM_DIR}/externalpackages/yams/install"
-path_append   "$YAMS_DIR"
+path_append "$YAMS_DIR"
 
 SWIG_DIR="${ISSM_DIR}/externalpackages/swig/install"
-path_append   "$SWIG_DIR"
+path_append "$SWIG_DIR"
 
 #AUX-CONFIG
-path_append   "${ISSM_DIR}/aux-config"
+path_append "${ISSM_DIR}/aux-config"
 
 #INISHELL
-path_append   "${ISSM_DIR}/externalpackages/inishell/install"
+path_append "${ISSM_DIR}/externalpackages/inishell/install"
 
 #SHELL2JUNIT
-path_append   "${ISSM_DIR}/externalpackages/shell2junit/install"
+path_append "${ISSM_DIR}/externalpackages/shell2junit/install"
 
 #EXPAT
-ld_library_path_prepend   "${ISSM_DIR}/externalpackages/expat/install"
-dyld_library_path_prepend   "${ISSM_DIR}/externalpackages/expat/install"
+ld_library_path_prepend "${ISSM_DIR}/externalpackages/expat/install"
+dyld_library_path_prepend "${ISSM_DIR}/externalpackages/expat/install"
 
 #CURL
-ld_library_path_prepend   "${ISSM_DIR}/externalpackages/curl/install/lib"
-dyld_library_path_prepend   "${ISSM_DIR}/externalpackages/curl/install/lib"
+ld_library_path_prepend "${ISSM_DIR}/externalpackages/curl/install/lib"
+dyld_library_path_prepend "${ISSM_DIR}/externalpackages/curl/install/lib"
 path_prepend "${ISSM_DIR}/externalpackages/curl/install/bin"
 

issm/trunk-jpl/externalpackages/petsc/install-3.7-linux64.sh

@@ -34 +34 @@
         --with-ssl=0 \
         --with-shared-libraries=1 \
-        --download-zlib=1\
-        --download-hdf5=1 \
-        --download-netcdf=1 \
         --download-metis=1 \
         --download-parmetis=1 \

issm/trunk-jpl/jenkins/linux64_ross

@@ -4 +4 @@
 
 # MATLAB path
-MATLAB_PATH="/usr/local/MATLAB/R2015a"
+MATLAB_PATH="/usr/local/MATLAB/R2019b"
 
 # ISSM CONFIGURATION
@@ -11 +11 @@
         --disable-static \
         --with-matlab-dir=$MATLAB_PATH \
-        --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9 -lgfortran" \
+        --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran" \
         --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \
         --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/mpich/install/lib -lmpi -lmpicxx -lmpifort" \
@@ -39 +39 @@
 
 # List of external packages to be installed and their installation scripts
+#
+# TODO:
+# - After upgrading Jenkins nodes to Ubuntu 18, use MPICH 3.3 and PETSc 3.11
+#       (which will install zlib, HDF5, and NetCDF).
+#
 EXTERNALPACKAGES="
         autotools       install.sh
         cmake           install.sh
         mpich           install-3.2-linux64.sh
+        hdf5            install-1.10.sh
+        netcdf          install-4.7.sh
         lapack          install-3.8-linux.sh
         petsc           install-3.7-linux64.sh

issm/trunk-jpl/jenkins/linux64_ross_python

@@ -36 +36 @@
 
 # List of external packages to be installed and their installation scripts
+#
+# TODO:
+# - After upgrading Jenkins nodes to Ubuntu 18, use MPICH 3.3 and PETSc 3.11
+#       (which will install zlib, HDF5, and NetCDF).
+#
 EXTERNALPACKAGES="
         autotools       install.sh
         cmake           install.sh
         mpich           install-3.2-linux64.sh
+        hdf5            install-1.10.sh
+        netcdf          install-4.7.sh
         lapack          install-3.8-linux.sh
         petsc           install-3.7-linux64.sh

issm/trunk-jpl/jenkins/linux64_ross_se

@@ -4 +4 @@
 
 #MATLAB path
-MATLAB_PATH="/usr/local/MATLAB/R2015a"
+MATLAB_PATH="/usr/local/MATLAB/R2019b"
 
 #ISSM CONFIGURATION
@@ -38 +38 @@
 #-----------------------------------#
 
-#List of external packages to be installed and their installation scripts
+# List of external packages to be installed and their installation scripts
+#
+# TODO:
+# - After upgrading Jenkins nodes to Ubuntu 18, use MPICH 3.3 and PETSc 3.11
+#       (which will install zlib, HDF5, and NetCDF).
+#
 EXTERNALPACKAGES="
         autotools       install.sh
         cmake           install.sh
         mpich           install-3.2-linux64.sh
+        hdf5            install-1.10.sh
+        netcdf          install-4.7.sh
         lapack          install-3.8-linux.sh
         petsc           install-3.7-linux64.sh