c1t4r/multinode_sshwrapper:latest
$ singularity pull shub://c1t4r/multinode_sshwrapper:latest
Singularity Recipe
BootStrap: debootstrap
OSVersion: stable
MirrorURL: http://ftp.us.debian.org/debian/
%runscript
source /.singularity.d/env/90-environment.sh
cd /tmp
if [[ $# -eq 0 ]]; then
echo "Single node run on 4 cores, should take ~40 secs real, ~2mins30 user..."
time mpirun -n 4 mdrun_mpi.openmpi -s /data/ion_channel.tpr -maxh 0.50 -noconfout -nsteps 500 -g logfile -v
else
echo "Multi node run on 2 nodes, 2 cores should take ~40 secs real, ~2mins30 user..."
time mpirun --oversubscribe -H "$1" -np 4 mdrun_mpi.openmpi -s /data/ion_channel.tpr -maxh 0.50 -noconfout -nsteps 500 -g logfile -v
fi
%environment
echo "### Setting up shell environment ..."
echo
unset LANG; export LC_ALL="C"; export MKL_NUM_THREADS=1; export OMP_NUM_THREADS=1
%setup
mkdir -p ${SINGULARITY_ROOTFS}/data
%post
echo "Hello from inside the container"
apt-get update
apt-get -y --force-yes install vim gromacs gromacs-openmpi libipathverbs1 ssh
mv /usr/bin/ssh /usr/bin/ssh_orig
mv /usr/bin/ssh_wrapper.sh /usr/bin/ssh
ln -sf bash /bin/sh
%files
README.md /README.md
ssh_wrapper.sh /usr/bin/ssh_wrapper.sh
ion_channel.tpr /data/
Collection
- Name: c1t4r/multinode_sshwrapper
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/c1t4r-multinode_sshwrapper-latest |
collection name | c1t4r/multinode_sshwrapper |
branch | master |
tag | latest |
commit | a4a27c5b27bbf9a7b667a6118aa047c374680982 |
version (container hash) | ce9915c1ff22399fe5dc876355e61026 |
build date | 2017-10-24T12:17:43.712Z |
size (MB) | 588 |
size (bytes) | 319291423 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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