Compiling Code_Saturne 4.0.3 on ARCHER (Cray XC30)

Source Modification

A call to getpwuid() was removed in the supplied source package. This is to work around the crash issue with this function when used on ARCHER compute nodes due to the unavailability of the nscd daemon (see https://sourceware.org/bugzilla/show_bug.cgi?id=12491).

File diff follows:

$ diff code_saturne-4.0.3/src/base/cs_system_info.c code_saturne-4.0.3-ARCHER/src/base/cs_system_info.c
275c275
<   pwd_user = getpwuid(geteuid());
---
>   pwd_user = NULL; /* getpwuid(geteuid()); */

Following install, change file lib/python2.7/site-packages/code_saturne/cs_exec_environment.py to allow running on MOM/compute nodes:

$ diff cs_exec_environment.py.bak cs_exec_environment.py
1251a1252,1254
>         # DSM EPCC Edit 12-11-2015 (broken mpiexec on ARCHER mom nodes workaround)
>         self.type = 'MPICH2'
>
1439,1442c1442,1447
<             launcher_names = ['mpiexec.mpich', 'mpiexec.mpich2', 'mpiexec',
<                               'mpiexec.hydra', 'mpiexec.smpd',
<                               'mpiexec.gforker', 'mpiexec.remshell',
<                               'mpirun.mpich2', 'mpirun.mpich', 'mpirun']
---
>             # DSM EPCC Edit 12-11-2015: ARCHER mom mpiexec issue
>             #launcher_names = ['mpiexec.mpich', 'mpiexec.mpich2', 'mpiexec',
>             #                  'mpiexec.hydra', 'mpiexec.smpd',
>             #                  'mpiexec.gforker', 'mpiexec.remshell',
>             #                  'mpirun.mpich2', 'mpirun.mpich', 'mpirun']
>             launcher_names = []
1468a1474,1477
>         # DSM EPCC Edit 12-11-2015: ARCHER mom mpiexec issue
>         self.mpiexec = 'aprun'
>         basename = 'aprun'
>
1512,1522c1521,1535
<         if not self.mpiexec_n:
<             if launcher_base[:7] == 'mpiexec':
<                 self.mpiexec_n = ' -n '
<             elif launcher_base[:6] == 'mpirun':
<                 self.mpiexec_n = ' -np '
<
<         if not self.mpmd:
<             if launcher_base[:7] == 'mpiexec':
<                 self.mpmd = MPI_MPMD_mpiexec | MPI_MPMD_configfile | MPI_MPMD_script
<             elif launcher_base[:6] == 'mpirun':
<                 self.mpmd = MPI_MPMD_script
---
>
>         # DSM EPCC Edit 12-11-2015: ARCHER mom mpiexec issue
>         self.mpiexec_n = ' -n '
>         self.mpmd = MPI_MPMD_mpiexec | MPI_MPMD_configfile | MPI_MPMD_script
> #        if not self.mpiexec_n:
> #            if launcher_base[:7] == 'mpiexec':
> #                self.mpiexec_n = ' -n '
> #            elif launcher_base[:6] == 'mpirun':
> #                self.mpiexec_n = ' -np '
> #
> #        if not self.mpmd:
> #            if launcher_base[:7] == 'mpiexec':
> #                self.mpmd = MPI_MPMD_mpiexec | MPI_MPMD_configfile | MPI_MPMD_script
> #            elif launcher_base[:6] == 'mpirun':
> #                self.mpmd = MPI_MPMD_script

Environment

A dynamically linked build is recommended to enable use of user subroutines.

module swap PrgEnv-cray PrgEnv-gnu
module load cray-tpsl
module load python-compute
module load cray-hdf5-parallel
module load cmake
module load qt # Can be skipped if building without GUI 
export CXX=CC
export CC=cc
export FC=ftn
export F77=ftn
export F90=ftn
export CRAYPE_LINK_TYPE=dynamic

export PREFIX_DIR=/path/to/install/dir

Compilation

Assuming prerequisites are installed in $PREFIX_DIR:

export METISPATH=$CRAY_TPSL_PREFIX_DIR
export SCOTCHPATH=$CRAY_TPSL_PREFIX_DIR
export CGNSPATH=$PREFIX_DIR
export LIBXML2=$PREFIX_DIR
export BLASPATH=$CRAY_LIBSCI_PREFIX_DIR

./configure --host=x86_64-unknown-linux-gnu --without-modules --disable-rpath --disable-sockets --without-salome --with-mpi --disable-dlloader --enable-long-gnum --disable-mei --with-libxml2=$LIBXML2 --with-libxml2-lib=$LIBXML2/lib --with-libxml2-include=$LIBXML2/include --with-metis=$METISPATH --with-metis-include=$METISPATH/include --with-metis-lib=$METISPATH/lib --with-scotch=$SCOTCHPATH --with-scotch-include=$SCOTCHPATH/include --with-scotch-lib=$SCOTCHPATH/lib --with-cgns=$CGNSPATH --with-cgns-include=$CGNSPATH/include --with-cgns-lib=$CGNSPATH/lib --with-blas=$BLASPATH --with-blas-include=$BLASPATH/include --with-blas-lib=$BLASPATH/lib --with-blas-libs=-lsci_gnu --prefix=$PREFIX_DIR
make
make install

Testing

After making, from the source directory:

make check

To rerun tests against installed version:

make installcheck

Prerequisites

libxml2-2.9.2

mkdir -p $PREFIX_DIR/lib/python2.7/site-packages
LDFLAGS=-L/work/y07/y07/cse/python/2.7.6/lib ./configure --prefix=$PREFIX_DIR --with-python-install-dir=$PREFIX_DIR/lib/python2.7/site-packages
make
make install

cgns-3.2.1

cd CGNS-3.2.1
mkdir build
cd build
cmake .. \
  -DCGNS_ENABLE_FORTRAN=ON -DFORTRAN_NAMING=LOWERCASE_ \ 
  -DCMAKE_BUILD_TYPE=Release -DCMAKE_SKIP_RPATH=YES -DBUILD_SHARED_LIBS=ON \
  -DCGNS_ENABLE_HDF5=ON -DHDF5_NEED_MPI=ON \
  -DHDF5_LIBRARY=$HDF5_DIR/lib/libhdf5.so -DHDF5_INCLUDE_PATH=$HDF5_DIR/include \
  -DCMAKE_INSTALL_PREFIX=$PREFIX_DIR
make
make install

sip-4.1.7 and PyQt4-4.11.4

Can be skipped if building without GUI.

sip-4.1.7:

cd sip-4.17
python configure.py --bindir=$PREFIX_DIR/bin --destdir=$PREFIX_DIR/lib/python2.7/site-packages --incdir=$PREFIX_DIR/include/python2.7 --sipdir=$PREFIX_DIR/share/sip
make
make install

PyQt4-4.11.4:

export PYTHONPATH=$PREFIX_DIR/lib/python2.7/site-packages:$PYTHONPATH
export PATH=$PREFIX_DIR/bin:$PATH
cd PyQt-x11-gpl-4.11.4
python configure-ng.py --sip-incdir=$PREFIX_DIR/include/python2.7 --bindir=$PREFIX_DIR/bin --destdir=$PREFIX_DIR/lib/python2.7/site-packages --sipdir=$PREFIX_DIR/share/sip
make
make install