There is no documentation about these files.
My bad its hidden files in root, rename shell in .shell, it should work :
/.exec
/.shell
/.run
There is a /environment file too where you can put your own variables
Le 08/05/2017 à 20:56, Siddiqui, Shahzeb a écrit :
Cedric,
I would think this should be a feature with *singularity shell*
command rather than a configuration file inside a container. Also
after applying the change in /shell in the container, I was unable to
see the changes when shelling into container.
Could you please provide documentation where you found these files
/exec /run /shell. They don’t seem to be part of the container on a
centos image.
*From:*[email protected]
[mailto:[email protected]] *On Behalf Of *CEDRIC CLERGET
*Sent:* Thursday, May 4, 2017 2:21 PM
*To:* [email protected]
*Subject:* Re: [easybuild] eb in singularity
Hello Shahzeb,
If you want to load /etc/profile each time you launch image, you could
add -l to shebang (#!/bin/sh -l) in /exec /run /shell files located in
container, it will simulate a shell login and will load /etc/profile
Best regards,
Cédric Clerget
------------------------------------------------------------------------
*De: *"Siddiqui, Shahzeb" <[email protected]
<mailto:[email protected]>>
*À: *[email protected] <mailto:[email protected]>
*Cc: *"Gregory M. Kurtzer" <[email protected]
<mailto:[email protected]>>
*Envoyé: *Jeudi 4 Mai 2017 18:53:35
*Objet: *[easybuild] eb in singularity
Hello folks,
I would like to find out how Easybuild and Singularity are going to
work together. I am trying to design an eb environment in Singularity
as a container solution to host all of the eb apps in a prod
environment. Is there anyone in the HPC community that is working on this?
Currently, I have setup a container environment that can build
packages in container and also install RPMs from easybuild via
Artifactory that is done through the bootstrap process.
One of things that puzzles me is how to setup an isolated container
environment that runs /etc/profile for container. I’ve noticed I need
to do this inorder to get module command to work in container.
Currently, I have to do this manually after shelling in.
-bash-4.2$ singularity shell /nfs/grid/software/testing.img
Singularity: Invoking an interactive shell within container...
Singularity.testing.img> module --version
sh: module: command not found
Singularity.testing.img> env | grep MODULEPATH
MODULEPATH_ROOT=/usr/share/modulefiles
MODULEPATH=/modulefiles/Core/:/nfs/grid/software/RHEL7-BUILD/easybuild/modules/all/:/nfs/grid/software/RHEL7/non-easybuild/modules/all/:/nfs/grid/software/RHEL7/easybuild/modules/all/Core:/nfs/grid/software/moduledomains:/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core
Singularity.testing.img> unset MODULEPATH
Singularity.testing.img> . /etc/profile
Singularity.testing.img> . /nfs/grid/software/
module-setup.sh RHEL7/ RHEL7-BUILD/
Singularity.testing.img> . /nfs/grid/software/module-setup.sh
Singularity.testing.img> ml av
-----------------------------------------------------------
/usr/share/lmod/lmod/modulefiles/Core
------------------------------------------------------------
lmod/6.5.1 settarg/6.5.1
----------------------------------------------------
/nfs/grid/software/RHEL7-BUILD/easybuild/modules/all
----------------------------------------------------
EasyBuild/3.1.2
----------------------------------------------------
/nfs/grid/software/RHEL7/easybuild/modules/all/Core
-----------------------------------------------------
Advisor/2017_update1 IGV/2.3.80-Java-1.8.0_92 Java/1.8.0_92
gaussian/16-AVX iompi/2017.01 tbb/2017.2.132
GCC/5.4.0-2.27 Inspector/2017_update1 VTune/2017_update1
gaussian/16-SSE2 (D) ipp/2017.1.132
GCC/6.2.0-2.27 (D) IntelClusterChecker/2017.1.016
daal/2017.1.132 intel/2017.01 itac/2017.1.024
Where:
D: Default Module
Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules
matching any of the "keys".
Singularity.testing.img> ml EasyBuild
Singularity.testing.img> eb --version
This is EasyBuild 3.1.2 (framework: 3.1.2, easyblocks: 3.1.2) on host
amrndhl1157.pfizer.com.
Singularity.testing.img> eb --show-config
#
# Current EasyBuild configuration
# (C: command line argument, D: default value, E: environment
variable, F: configuration file)
#
buildpath (D) = /home/siddis14/.local/easybuild/build
installpath (D) = /home/siddis14/.local/easybuild
repositorypath (D) = /home/siddis14/.local/easybuild/ebfiles_repo
robot-paths (D) =
/nfs/grid/software/RHEL7-BUILD/easybuild/software/EasyBuild/3.1.2/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.2-py2.7.egg/easybuild/easyconfigs
sourcepath (D) = /home/siddis14/.local/easybuild/sources
Singularity.testing.img> eb zlib-1.2.8.eb
== temporary log file in case of crash /tmp/eb-BfnLvm/easybuild-ybJc4_.log
== zlib/1.2.8 is already installed (module found), skipping
== No easyconfigs left to be built.
== Build succeeded for 0 out of 0
== Temporary log file(s) /tmp/eb-BfnLvm/easybuild-ybJc4_.log* have
been removed.
== Temporary directory /tmp/eb-BfnLvm has been removed.
Singularity.testing.img> eb zlib-1.2.8.eb --rebuild
== temporary log file in case of crash /tmp/eb-IMN3vl/easybuild-lWCjI1.log
== processing EasyBuild easyconfig
/nfs/grid/software/RHEL7-BUILD/easybuild/software/EasyBuild/3.1.2/lib/python2.7/site-packages/easybuild_easyconfigs-3.1.2-py2.7.egg/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb
== building and installing zlib/1.2.8...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s)
/home/siddis14/.local/easybuild/software/zlib/1.2.8/easybuild/easybuild-zlib-1.2.8-20170504.163248.log
== Build succeeded for 1 out of 1
== Temporary log file(s) /tmp/eb-IMN3vl/easybuild-lWCjI1.log* have
been removed.
== Temporary directory /tmp/eb-IMN3vl has been removed.
Singularity.testing.img> module use $HOME/.local/easybuild/modules/all
Due to MODULEPATH changes the following have been reloaded:
1) EasyBuild/3.1.2
Singularity.testing.img> module av
--------------------------------------------------------
/home/siddis14/.local/easybuild/modules/all
---------------------------------------------------------
EasyBuild/3.1.2 (L,D) M4/1.4.17 (D) zlib/1.2.8 (D)
-----------------------------------------------------------
/usr/share/lmod/lmod/modulefiles/Core
------------------------------------------------------------
lmod/6.5.1 settarg/6.5.1
----------------------------------------------------
/nfs/grid/software/RHEL7-BUILD/easybuild/modules/all
----------------------------------------------------
EasyBuild/3.1.2
----------------------------------------------------
/nfs/grid/software/RHEL7/easybuild/modules/all/Core
-----------------------------------------------------
Advisor/2017_update1 IGV/2.3.80-Java-1.8.0_92 Java/1.8.0_92
gaussian/16-AVX iompi/2017.01 tbb/2017.2.132
GCC/5.4.0-2.27 Inspector/2017_update1 VTune/2017_update1
gaussian/16-SSE2 (D) ipp/2017.1.132
GCC/6.2.0-2.27 (D) IntelClusterChecker/2017.1.016
daal/2017.1.132 intel/2017.01 itac/2017.1.024
Where:
L: Module is loaded
D: Default Module
Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules
matching any of the "keys".
Shahzeb Siddiqui
HPC Linux Engineer
B2220-447.2
Groton, CT
--
Cédric Clerget
Mésocentre de calcul de Franche-Comté
16, Route de Gray - 25030 Besançon
Tél: 03 81 66 20 12
Mail: [email protected]
