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configure Lmod w.r.t. spider cache in generated Singularity container recipes + also install OS pkgs for OpenSSL & IB libs #2910

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merged 4 commits into from
Jun 5, 2019
Merged

configure Lmod w.r.t. spider cache in generated Singularity container recipes + also install OS pkgs for OpenSSL & IB libs #2910

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4f24cb8
also include libibverbs/rdma-core + openssl in set of default OS pack…
boegel Jun 5, 2019
8781e63
unuse $MODULEPATH in container environment section to avoid picking u…
boegel Jun 5, 2019
29c53a6
configure Lmod and update Lmod cache in generated container recipes
boegel Jun 5, 2019
08676b8
forcibly purge loaded modules in environment section of generated con…
boegel Jun 5, 2019
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29 changes: 29 additions & 0 deletions easybuild/tools/containers/singularity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,11 +83,29 @@

%(post_commands)s

# install Lmod RC file
cat > /etc/lmodrc.lua << EOF
scDescriptT = {
{
["dir"] = "/app/lmodcache",
["timestamp"] = "/app/lmodcache/timestamp",
},
}
EOF

# change to 'easybuild' user
su - easybuild

# verbose commands
set -v

# use EasyBuild to install specified software
eb %(easyconfigs)s --robot --installpath=/app/ --prefix=/scratch --tmpdir=/scratch/tmp

# update Lmod cache
mkdir -p /app/lmodcache
$LMOD_DIR/update_lmod_system_cache_files -d /app/lmodcache -t /app/lmodcache/timestamp /app/modules/all

# exit from 'easybuild' user
exit

Expand All @@ -98,8 +116,17 @@
eval "$@"

%%environment
# make sure that 'module' and 'ml' commands are defined
source /etc/profile
# increase threshold time for Lmod to write cache in $HOME (which we don't want to do)
export LMOD_SHORT_TIME=86400
# purge any modules that may be loaded outside container
module --force purge
# avoid picking up modules from outside of container
module unuse $MODULEPATH
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# pick up modules installed in /app
module use /app/modules/all
# load module(s) corresponding to installed software
module load %(mod_names)s

%%labels
Expand Down Expand Up @@ -235,6 +262,8 @@ def resolve_template_data(self):
'python-pip',
# additional packages that EasyBuild relies on (for now)
'gcc-c++', # C/C++ components of GCC (gcc, g++)
('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel'), # for OpenMPI
('openssl-devel', 'libssl-dev', 'libopenssl-devel'), # for CMake, Python, ...
'perl-Data-Dumper', # required for GCC build
# required for Automake build, see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822
'perl-Thread-Queue',
Expand Down