Hi Di,
Your first link doesn’t work it is referencing your gmail. Please provide
another link.
Right now eb shares easyconfig files that can be used by any HPC sites to build
the packages on their own environment. If we decide to go in a containerized
software stack, we are looking at sharing binaries instead of easyconfig files.
A singularity container is just a binary that can be executed as any normal
program.
If EB decides to with containerization then I foresee all the builds to happen
inside a container that can produce a new container with only the application
that was built along with dependencies. There would be a container naming
format similar to RPM naming convention to allow for multiple software &
toolchain version to coexist in a repository. This would be extremely useful
for deploying apps like R, Python, perl, ruby in a container so that you can
make your runscript like the following
%runscript
echo "Arguments received: $*"
exec /usr/bin/python "$@"
Currently EB installs packages in non-standard paths, we would need to
translate module file environment in runscript to allow the user to access the
binaries inside the container in their PATH environment. If there was only a
way to redirect container output into your host shell environment, we might be
able to do module loads inside the container runscript and redirect output to
host shell.
From: easybuild-requ...@lists.ugent.be
[mailto:easybuild-requ...@lists.ugent.be] On Behalf Of Di Pe
Sent: Monday, May 8, 2017 1:43 PM
To: easybuild@lists.ugent.be
Subject: Re: [easybuild] eb in singularity
Interesting discussion about Singularity, there was an older thread here
https://mail.google.com/mail/u/0/#search/singularity/159045c3913ad572<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.google.com_mail_u_0_-23search_singularity_159045c3913ad572&d=DwMFaQ&c=UE1eNsedaKncO0Yl_u8bfw&r=RMJdCm7m5fiPWhajwKUnEW5yn4eK2YdUWW-MLVShghg&m=U1Ye_dBtCfKKvzdeYTPD9IUfYLhVCCQYcTW04W3jMFI&s=5Y8Aj2dkooBU_izF82b21XY7ckGP_7CRyAjXFR29TUA&e=>
and it would be great to learn what EB leadership thinks about integration of
containers in EB?
To look a little bit into our requirements we would like to make it easy to
share the software stacks we build using EB with
1) other researchers outside our organization who are also running things on
HPC systems
2) other software platforms in the same organization (outside HPC clusters)
In both cases we want to support a certain version of a containerized software
stack for a certain period of time. Take for example a data science stack. We
would bundle a certain version of R with a certain version of Python and some
other ancillary tools. We would build a container that has one version of
Python2 and one version of R and another container that has Python3 with R.
I would not need or even want any Lmod environment inside the container because
we may need to tie R and python together. For example R argparse is linked to a
specific version of Python and Python rpy2 is linked to a specific version or
R. This cannot be handled well with lmod.
Another issue that plays into this is size of the container. We want to keep
the container relatively small to facilitate sharing but the easybuild
environment is actually pretty large with sources and everything. if there was
a good way to remove all the unnecessary things including compiler after the
container is created that would be great.
Yet another issue is that non-HPC people are not used to lmod. So if I have
hadoop or devops folks they need to know a little bit of lmod to be able to
troubleshoot the software stack and because that is not the case (at least
here) they are building stuff by hand or are using crappy Ubuntu debs even
through the HPC person one floor down has already done the (better) job using
EB. In that sense it would be great if we could use EB to create a container
stack that support only one version of each software and wherethe software
inside the container simply installs to /usr/local to they can use it as a base
and then fuzz with it further if they need to.
Another interesting discussion was Singularity vs Docker. After reading this
https://www.nextplatform.com/2017/04/10/singularity-containers-hpc-reproducibility-mobility/<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nextplatform.com_2017_04_10_singularity-2Dcontainers-2Dhpc-2Dreproducibility-2Dmobility_&d=DwMFaQ&c=UE1eNsedaKncO0Yl_u8bfw&r=RMJdCm7m5fiPWhajwKUnEW5yn4eK2YdUWW-MLVShghg&m=U1Ye_dBtCfKKvzdeYTPD9IUfYLhVCCQYcTW04W3jMFI&s=vQBRkyNKZ0AuhN1k27RTgwrznsvOcwJfGydKEpPx5y4&e=>
and trying out singularity I think the answer is that we want to use both.
Docker plain will probably never be usable on HPC systems (See the story about
rejected pull requests) so you have to take a detour and use Shifter (Shifter
needs to be integrated by a HPC sysadmin requiring root access and a test plan.
It is optimized towards and tested with Slurm.) Singularity works out of the
box on HPC and standalone systems. The benefit of Shifter seems to be that it
can use Docker images natively while singularity requires you to either build
singularity images or import docker images. In my ad-hoc testing I was having
much more problems with building singularity images (e.g FS corruption ) than
importing docker images with singularity. The latter worked really well and
fast.
So perhaps it makes sense to focus on integrating Docker builds into EB as one
could deliver a more comprehensive solution to bigdata, devops and HPC people.
Interested to hear some thoughts
DP
On Thu, May 4, 2017 at 9:53 AM, Siddiqui, Shahzeb
<shahzeb.siddi...@pfizer.com<mailto:shahzeb.siddi...@pfizer.com>> wrote:
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<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.<https://urldefense.proofpoint.com/v2/url?u=http-3A__1.2.8.&d=DwMFaQ&c=UE1eNsedaKncO0Yl_u8bfw&r=RMJdCm7m5fiPWhajwKUnEW5yn4eK2YdUWW-MLVShghg&m=U1Ye_dBtCfKKvzdeYTPD9IUfYLhVCCQYcTW04W3jMFI&s=2DbV7b8CLu85Uado7mlKmdBIcJvdmaZr0IIo3nO0XtU&e=>..
== 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
