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lammps/tools/singularity/centos7.def

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Singularity definition files for compiling LAMMPS
2019-10-15 22:22:08 +08:00
BootStrap: library
From: centos:7
%post
update container definitions for building documentation
2020-04-03 05:48:17 +08:00
yum -y install epel-release
Singularity definition files for compiling LAMMPS
2019-10-15 22:22:08 +08:00
yum -y update
update container definitions for building documentation
2020-04-03 05:48:17 +08:00
yum -y install vim-enhanced \
ccache gcc-c++ gcc-gfortran clang gdb valgrind-openmpi \
update singularity definition files
2020-04-12 09:36:08 +08:00
make cmake cmake3 ninja-build patch which file git Lmod \
Add missing python36 and hdf5-devel to CentOS containers
2020-04-30 04:46:22 +08:00
libpng-devel libjpeg-devel openmpi-devel mpich-devel python-devel python36-devel \
hdf5-devel python36-virtualenv python36-pip python-pip \
update container definitions for building documentation
2020-04-03 05:48:17 +08:00
python-virtualenv fftw-devel voro++-devel eigen3-devel gsl-devel openblas-devel enchant
Add valgrind, gdb to containers and clean caches
2020-04-30 05:32:19 +08:00
yum clean all
update container definitions for building documentation
2020-04-03 05:48:17 +08:00
%environment
LC_ALL=C
export LC_ALL
Avoid errors due to host Lmod in containers These changes ensure that environment variables that are automatically passed to the container don't interfere with Lmod inside of the container. The previous implementation would not take care of sticky packages from the outside and Lmod would try to reload them. Note that Lmod defines the 'module' bash function, which doesn't propagate to the final shell when using 'singularity shell'. If the 'module' command is needed a login shell needs to be launched: $ singularity exec <CONTAINER> bash -l
2020-04-30 04:48:25 +08:00
# we need to reset any module variables
# inherited from the host.
unset __LMOD_REF_COUNT__LMFILES_
unset __LMOD_REF_COUNT_PATH
unset __LMOD_REF_COUNT_LD_LIBRARY_PATH
unset __LMOD_REF_COUNT_MANPATH
unset __LMOD_REF_COUNT_MODULEPATH
unset __LMOD_REF_COUNT_LOADEDMODULES
unset _LMFILES_
unset MODULEPATH
unset MODULESHOME
unset MODULEPATH_ROOT
update singularity definition files
2020-04-12 09:36:08 +08:00
unset LOADEDMODULES
Avoid errors due to host Lmod in containers These changes ensure that environment variables that are automatically passed to the container don't interfere with Lmod inside of the container. The previous implementation would not take care of sticky packages from the outside and Lmod would try to reload them. Note that Lmod defines the 'module' bash function, which doesn't propagate to the final shell when using 'singularity shell'. If the 'module' command is needed a login shell needs to be launched: $ singularity exec <CONTAINER> bash -l
2020-04-30 04:48:25 +08:00
unset LMOD_SYSTEM_DEFAULT_MODULES
# load MPI by default
. /etc/profile
update singularity definition files
2020-04-12 09:36:08 +08:00
module load mpi
Singularity definition files for compiling LAMMPS
2019-10-15 22:22:08 +08:00
%labels
Add missing python36 and hdf5-devel to CentOS containers
2020-04-30 04:46:22 +08:00
Author akohlmey, rbberger