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BrianThank you for the response. The purpose of a significant part of our software package is to decide what jobs are necessary and submit them. I imagine this is not such an unusual potential use case.Cheers,
On Sun, Jul 16, 2017 at 6:46 PM, Paolo Di Tommaso <paolo.d...@gmail.com> wrote:
A better approach is to separate the application logic from the scheduling logic, by doing that you will be able to isole your job executions with singularity and submit them to SLURM or any other cluster.Hope it helps.pOn Sun, Jul 16, 2017 at 8:44 PM, Brian Puchala <bpuc...@umich.edu> wrote:Hi,--
I'm trying to familiarize myself with how Singularity might work for our application. We have components that submit additional jobs through the host job manager (TORQUE or SLURM). Is it possible to run these within their own container? Is there an example that shows how?
Thanks!
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singularity pull docker://centos:7
# create a place for the host programs I need and copy them over
# because our home directories are always bound no additional
# bind commands are needed when starting the container
mkdir -p ~/.local/host/bin
cp /usr/local/bin/qstat ~/.local/host/bin
# etc.
# ends up with:
$ tree /home/bpuchala/.local/host/bin
/home/bpuchala/.local/host/bin
├── qalter
├── qdel
├── qhold
├── qrls
├── qselect
├── qstat
└── qsub
# create a place for the host libs I need:
mkdir -p ~/.local/host/lib
# use ldd on the programs inside and outside the container to
# find which libraries need to be copied.
# inside container
singularity shell centos-7.img
> ldd /home/bpuchala/.local/host/bin/qstat
> ldd /home/bpuchala/.local/host/bin/qstat
linux-vdso.so.1 => (0x00007ffc5cf42000)
libtorque.so.2 => not found
libtcl8.5.so => not found
...
$ ldd /usr/local/bin/qstat
linux-vdso.so.1 => (0x00007fff90391000)
libtorque.so.2 => /usr/local/lib/libtorque.so.2 (0x00002b2567edb000)
libtcl8.5.so => /lib64/libtcl8.5.so (0x00002b2568808000)
...
# Ends up with:
$ tree /home/bpuchala/.local/host/lib
/home/bpuchala/.local/host/lib
├── libhwloc.so.5
├── libltdl.so.7
├── libnuma.so.1
├── libtcl8.5.so
└── libtorque.so.2
# test job submission and management from inside container:
singularity shell centos-7.img
# set PATH inside the container to find host programs we copied
export PATH=$HOME/.local/host/bin:$PATH
# set LD_LIBRARY_PATH inside the container find host libs we copied
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/.local/host/lib
# test
qstatqsub ~/submit_scripts/hello_world.sh
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