DP
On Thu, May 4, 2017 at 9:53 AM, Siddiqui, Shahzeb
<shahzeb.siddi...@pfizer.com <mailto:shahzeb.siddi...@pfizer.com>>
wrote:
Hello folks,____
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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?____
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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.____
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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.____
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-bash-4.2$ singularity shell /nfs/grid/software/testing.img __ __
Singularity: Invoking an interactive shell within container...____
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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____
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-----------------------------------------------------------
/usr/share/lmod/lmod/modulefiles/Core
------------------------------------------------------------____
lmod/6.5.1 settarg/6.5.1____
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----------------------------------------------------
/nfs/grid/software/RHEL7-BUILD/easybuild/modules/all
----------------------------------------------------____
EasyBuild/3.1.2____
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----------------------------------------------------
/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____
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Where:____
D: Default Module____
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Use "module spider" to find all possible modules.____
Use "module keyword key1 key2 ..." to search for all possible
modules matching any of the "keys".____
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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 <http://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. <http://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.____
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Singularity.testing.img> module use
$HOME/.local/easybuild/modules/all____
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Due to MODULEPATH changes the following have been reloaded:____
1) EasyBuild/3.1.2____
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Singularity.testing.img> module av____
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--------------------------------------------------------
/home/siddis14/.local/easybuild/modules/all
---------------------------------------------------------____
EasyBuild/3.1.2 (L,D) M4/1.4.17 (D) zlib/1.2.8 (D)____
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-----------------------------------------------------------
/usr/share/lmod/lmod/modulefiles/Core
------------------------------------------------------------____
lmod/6.5.1 settarg/6.5.1____
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----------------------------------------------------
/nfs/grid/software/RHEL7-BUILD/easybuild/modules/all
----------------------------------------------------____
EasyBuild/3.1.2____
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----------------------------------------------------
/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____
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Where:____
L: Module is loaded____
D: Default Module____
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Use "module spider" to find all possible modules.____
Use "module keyword key1 key2 ..." to search for all possible
modules matching any of the "keys".____
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Shahzeb Siddiqui____
HPC Linux Engineer____
B2220-447.2____
Groton, CT____
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