Changeset 705

Timestamp:

06/20/18 15:31:05 (6 years ago)

Author:

dubos

Message:

devel : fixes build for CICLAD

Location:

codes/icosagcm/devel

Files:

• Python/env/ifort_CICLAD.env (moved) (moved from codes/icosagcm/devel/Python/env/CICLAD.env) (4 diffs)
• arch/arch-ifort_CICLAD.fcm (modified) (2 diffs)
• arch/arch-ifort_CICLAD.path (modified) (3 diffs)
• make_python (modified) (2 diffs)

codes/icosagcm/devel/Python/env/ifort_CICLAD.env

@@ -1 @@
-module purge
-module load intel/15.0.6.233
-module load openmpi/1.6.5-ifort
-module load hdf5/1.8.18-parallel-ifort
-module load netcdf4/4.4.1.1-parallel-ifort
+# arch.env and arch.path should be sourced before sourcing this script
 module load python/2.7-anaconda
 
-# If not done yet, certain python packages must be installed in a dynamico-only conda environment :
+# If not done yet, certain python packages must be installed in a dynamico-only conda environment of yours :
 #   conda create -n dynamico python
 #   source activate dynamico
@@ -12 +8 @@
 
 # netCDF4 must be installed manually in order to use the netCDF library from the modules (requires Cython, see above)
-# for this download and unpack 
-#   https://pypi.python.org/packages/6a/37/49fd7cc21af0fb173e40de5e15f7fdd48d521429922a90347219c77b0c36/netCDF4-1.2.9.tar.gz#md5=e320491d52c42e937e6df47b56a2579c
-# then
-#   python setup.py build
-#   python setup.py install
+# for unpack Python/extern/netCDF4-1.2.9.tar.gz then
+#   LDFLAGS='-lirc' python setup.py build
+#   cp -pr build/lib.linux-x86_64-2.7/net* ~/.conda/envs/dynamico/lib/python2.7/site-packages/
+# NOTE : libirc.so is the intel runtime library and is needed at runtime.
+# FIXME : python setup.py install does not seem to install anything, hence 'cp -pr ...'. There must be a better way.
 
 # CICLAD does not have a parmetis module
 # compiling parmetis uses cmake, installed above using pip because the system-wide cmake might not work with the modules
-# then download parmetis from 
-#   http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz
-# unpack, follow workaround given in 
-#   https://stackoverflow.com/questions/35058709/building-shared-parmetis-4-0-3
-# then
+# for this unpack Python/extern/parmetis-4.0.3.tar.gz then
 #   make config shared=1 prefix=$HOME/.conda/envs/dynamico
 #   make install
@@ -30 +22 @@
 #   cp $(find . -name 'libmetis.so') $HOME/.conda/envs/dynamico/lib/
 #   cp $(find . -name 'metis.h') $HOME/.conda/envs/dynamico/include/
+# NOTE : the tar.gz is derived from http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz 
+#        with modifications along the lines of
+#        https://stackoverflow.com/questions/35058709/building-shared-parmetis-4-0-3
 
 source activate dynamico
 PARMETIS_CFLAGS="-I$HOME/.conda/envs/dynamico/include"
-PARMETIS_LDFLAGS="-L$HOME/.conda/envs/dynamico/lib"
+PARMETIS_LDFLAGS="-L$HOME/.conda/envs/dynamico/lib -liomp5"
 
 export NETCDF_LDFLAGS="$(nf-config --flibs) -lhdf5 -lz -ldl -lm"
@@ -43 +38 @@
 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/.conda/envs/dynamico/lib
 
-BASEDIR=$(dirname ${BASH_SOURCE[0]})
-. $BASEDIR/linux.env
+. linux.env

codes/icosagcm/devel/arch/arch-ifort_CICLAD.fcm

@@ -6 +6 @@
 %FPP_FLAGS           -P
 %FPP_DEF             KEY_NONE CPP_NETCDF4
-%BASE_FFLAGS         -i4 -r8 -auto -align all -I${MKLROOT}/include
+%BASE_FFLAGS         -fPIC -i4 -r8 -auto -align all -I${MKLROOT}/include
 %PROD_FFLAGS         -g -traceback -O3
 %DEV_FFLAGS          -g -O1 -traceback
@@ -12 +12 @@
 %MPI_FFLAGS
 %OMP_FFLAGS          -openmp -openmp-threadprivate compat
-%BASE_LD             -i4 -r8 -auto -L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lm
+%BASE_LD             -fPIC -i4 -r8 -auto -L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lm
 %MPI_LD
 %OMP_LD              -openmp

codes/icosagcm/devel/arch/arch-ifort_CICLAD.path

@@ -2 +2 @@
 NETCDF_LIBDIR=$(nf-config --flibs)
 NETCDF_LIB=""
+
 MPI_INCDIR=""
 MPI_LIBDIR=""
@@ -9 +10 @@
 HDF5_LIB=""
 
-XIOS_INCDIR="-I$PWD/../XIOS/inc"
-XIOS_LIBDIR="-L$PWD/../XIOS/lib"
+XIOS_ROOTDIR=$(cd -P ../XIOS ; pwd)
+XIOS_INCDIR="-I$XIOS_ROOTDIR/inc"
+XIOS_LIBDIR="-L$XIOS_ROOTDIR/lib"
 XIOS_LIB="-lxios -lstdc++"
 
@@ -16 +18 @@
 IOIPSL_LIBDIR="-L $PWD/../IOIPSL/lib"
 IOIPSL_LIB="-lioipsl"
+
+MKL_LIBDIR="-L $MKLROOT/lib"
+MKL_LIBDIR="-I $MKLROOT/include"
+MKL_LIB=""
+CURRENT_ARCH=ifort_CICLAD

codes/icosagcm/devel/make_python

@@ -83 +83 @@
 
     log mpicc -c -std=c99 -fPIC $PARMETIS_CFLAGS Python/src/partition.c -o obj/partition.o
-    make_so $XIOS_ROOTDIR/lib/libxios.a $LIBDIR/libxios.so "$NETCDF_LDFLAGS"
+    make_so $XIOS_ROOTDIR/lib/libxios.a $LIBDIR/libxios.so "$NETCDF_LDFLAGS -lstdc++"
     make_so $LIBDIR/libicosa.a $LIBDIR/libicosa.so "-L$LIBDIR -lxios $KERNELS_LDFLAGS" "physics_external_mod.o physics_mod.o timeloop_gcm_mod.o icosa_init_mod.o" obj/partition.o
 
@@ -115 +115 @@
 if [[ "$CURRENT_ARCH" == "" ]] ; then echo "Current architecture undefined or unsupported" ; exit ; fi
 
-. Python/env/${CURRENT_ARCH}.env
+cd Python/env ;  . ${CURRENT_ARCH}.env ; cd $DYNAMICO_ROOT
 
 cmd_$1