Feature/linux centos intel

build_stack.sh

@@ -140,6 +140,7 @@ build_lib libpng
 build_lib szip
 build_lib jasper
 build_lib sqlite
+build_lib libtiff
 build_lib proj
 build_lib geos
 

config/config_linux_centos_intel.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+
+# Compiler/MPI combination
+export HPC_PYTHON=${HPC_PYTHON:-"python/3.6.8"}
+export HPC_COMPILER=${HPC_COMPILER:-"intel/2020.0"}
+export HPC_MPI=${HPC_MPI:-"impi/2020u0"}
+
+# Build options
+export USE_SUDO=N
+export PKGDIR=pkg
+export LOGDIR=log
+export OVERWRITE=N
+export NTHREADS=4
+export   MAKE_CHECK=N
+export MAKE_VERBOSE=Y
+export   MAKE_CLEAN=N
+export DOWNLOAD_ONLY=N
+export STACK_EXIT_ON_FAIL=Y
+export WGET="wget -nv --no-check-certificate "
+
+module purge
+export BASH_ENV=$HOME/apps/lmod/lmod/init/bash # Point to the new definition of Lmod
+
+source $BASH_ENV                              # Redefine the module command to point
+                                              # to the new Lmod
+module use $HOME/modulefiles
+module load cmake
+module load intel/2020.0
+module load impi/2020u0
+#
+
+export CC=icc
+export FC=ifort
+export CXX=icpc
+
+export SERIAL_CC=icc
+export SERIAL_FC=ifort
+export SERIAL_CXX=icpc
+
+export MPI_CC=mpiicc
+export MPI_FC=mpiifort
+export MPI_CXX=mpiicpc
+
+#

libs/build_libtiff.sh

@@ -0,0 +1,61 @@
+#!/bin/bash
+
+set -eux
+
+name="libtiff"
+version=${1:-${STACK_libtiff_version}}
+
+[[ ${STACK_libtiff_shared:-} =~ [yYtT] ]] && enable_shared=YES || enable_shared=NO
+
+# Hyphenated version used for install prefix
+compiler=$(echo $HPC_COMPILER | sed 's/\//-/g')
+
+# manage package dependencies here
+if $MODULES; then
+    set +x
+    source $MODULESHOME/init/bash
+    module load hpc-$HPC_COMPILER
+    module try-load cmake
+    module load zlib
+    module list
+    set -x
+
+    prefix="${PREFIX:-"/opt/modules"}/$compiler/$name/$version"
+    if [[ -d $prefix ]]; then
+      if [[ $OVERWRITE =~ [yYtT] ]]; then
+          echo "WARNING: $prefix EXISTS: OVERWRITING!"
+          $SUDO rm -rf $prefix
+      else
+          echo "WARNING: $prefix EXISTS, SKIPPING"
+          exit 0
+      fi
+    fi
+
+else
+    prefix=${LIBTIFF_ROOT:-"/usr/local"}
+fi
+
+export CC=$SERIAL_CC
+export CFLAGS="${STACK_CFLAGS:-} ${STACK_libtiff_CFLAGS:-} -fPIC"
+
+cd ${HPC_STACK_ROOT}/${PKGDIR:-"pkg"}
+
+software=$name-$version
+URL="https://gitlab.com/${name}/${name}.git"
+[[ -d $software ]] || ( git clone $URL $software )
+[[ ${DOWNLOAD_ONLY} =~ [yYtT] ]] && exit 0
+[[ -d $software ]] && cd $software || ( echo "$software does not exist, ABORT!"; exit 1 )
+
+sourceDir=$PWD
+cd build
+cmake $sourceDir \
+  -DCMAKE_INSTALL_PREFIX=$prefix \
+  -DCMAKE_BUILD_TYPE=RELEASE \
+  -DZLIB_ROOT=${ZLIB_ROOT} 
+#
+make -j${NTHREADS:-4}
+$SUDO make install
+
+# generate modulefile from template
+$MODULES && update_modules compiler $name $version
+echo $name $version $URL >> ${HPC_STACK_ROOT}/hpc-stack-contents.log

libs/build_proj.sh

@@ -17,6 +17,7 @@ if $MODULES; then
   module load hpc-$HPC_COMPILER
   module try-load cmake
   module load sqlite
+  module try-load libtiff
   module list
   set -x
 
@@ -57,6 +58,16 @@ CMAKE_OPTS=${STACK_proj_cmake_opts:-""}
 
 [[ $MAKE_CHECK =~ [yYtT] ]] || CMAKE_OPTS+=" -DBUILD_TESTING=OFF"
 
+if [[ -n ${LIBTIFF_ROOT-} ]] ; then
+  CMAKE_OPTS+=" -DTIFF_INCLUDE_DIR=${LIBTIFF_ROOT}/include "
+  [[ -f ${LIBTIFF_ROOT}/lib64/libtiff.so ]] && CMAKE_OPTS+=" -DTIFF_LIBRARY=${LIBTIFF_ROOT}/lib64/libtiff.so " || CMAKE_OPTS+=" -DTIFF_LIBRARY=${LIBTIFF_ROOT}/lib/libtiff.so "
+fi
+
+if [[ -n ${SQLITE_ROOT-} ]] ; then
+  CMAKE_OPTS+=" -DSQLITE3_INCLUDE_DIR=${SQLITE_ROOT}/include "
+  CMAKE_OPTS+=" -DSQLITE3_LIBRARY=${SQLITE_ROOT}/lib/libsqlite3.so "
+fi
+
 LIB_DIR=${SQLITE_ROOT:-} cmake -H. -Bbuild -DCMAKE_INSTALL_PREFIX=$prefix $CMAKE_OPTS
 cd build
 VERBOSE=$MAKE_VERBOSE make -j${NTHREADS:-4}

modulefiles/compiler/compilerName/compilerVersion/libtiff/libtiff.lua

@@ -0,0 +1,32 @@
+help([[
+]])
+
+local pkgName    = myModuleName()
+local pkgVersion = myModuleVersion()
+local pkgNameVer = myModuleFullName()
+
+local hierA        = hierarchyA(pkgNameVer,1)
+local compNameVer  = hierA[1]
+local compNameVerD = compNameVer:gsub("/","-")
+
+conflict(pkgName)
+
+local opt = os.getenv("HPC_OPT") or os.getenv("OPT") or "/opt/modules"
+
+local base = pathJoin(opt,compNameVerD,pkgName,pkgVersion)
+
+prepend_path("PATH", pathJoin(base,"bin"))
+prepend_path("LD_LIBRARY_PATH", pathJoin(base,"${CMAKE_INSTALL_LIBDIR}"))
+prepend_path("DYLD_LIBRARY_PATH", pathJoin(base,"${CMAKE_INSTALL_LIBDIR}"))
+prepend_path("CPATH", pathJoin(base,"include"))
+prepend_path("MANPATH", pathJoin(base,"share","man"))
+
+setenv("LIBTIFF_ROOT", base)
+setenv("LIBTIFF_VERSION", pkgVersion)
+
+prepend_path("PKG_CONFIG_PATH", pathJoin(base,"${CMAKE_INSTALL_LIBDIR}","pkgconfig"))
+
+whatis("Name: ".. pkgName)
+whatis("Version: " .. pkgVersion)
+whatis("Category: library")
+whatis("Description: LIBTIFF (libtiff library) are Functions to read, write and display bitmap images stored in the LIBTIFF format. It can read and write both files and in-memory raw vectors, including native image representation")

stack/stack_custom.yaml

@@ -77,7 +77,7 @@ pio:
 
 esmf:
   build: YES
-  version: 8_1_1
+  version: 8_2_0
   shared: YES
   enable_pnetcdf: NO
   debug: NO
@@ -312,7 +312,7 @@ cmakemodules:
 gftl_shared:
   build: YES
   repo: Goddard-Fortran-Ecosystem
-  version: v1.3.0
+  version: v1.3.3
 
 yafyaml:
   build: YES
@@ -328,6 +328,10 @@ geos:
   build: YES
   version: 3.8.1
 
+libtiff:
+  build: YES
+  version: 4.0.3
+
 sqlite:
   build: YES
   version: 3.32.3

stack_helpers.sh

@@ -129,6 +129,11 @@ function no_modules {
       export MPI_CXX=${MPI_CXX:-"CC"}
       export MPI_FC=${MPI_FC:-"ftn"}
       ;;
+    mpt  )
+      export MPI_CC=${MPI_CC:-"mpicc"}
+      export MPI_CXX=${MPI_CXX:-"CC"}
+      export MPI_FC=${MPI_FC:-"mpif90"}
+      ;;
     * )
       echo "Unknown MPI option = $mpiName, ABORT!"
       local abort=Y