On Tue, Apr 11, 2017 at 1:04 PM, Siddiqui, Shahzeb
<shahzeb.siddi...@pfizer.com <mailto:shahzeb.siddi...@pfizer.com>> wrote:
Hello Gregory,
It was easy for me to create a single singularity container that has
all my collection of software packages, but it was difficult for me to
figure out how to create individual containers that can interact together.
Ahh, and there-in lies orchestration of containers.
Initially I would try to setup Lmod in container, I was able to figure
this out and then I was able to build EB packages. My concern is a
single collection scheme seems to be limited in the sense that
software packages are not truly independent.
I would expect that I can install Singularity containers like rpm
which have all the dependencies that pick up other singularity
containers. Initially I can start out by installing dependency for GCC
as separate containers but the one thing that caused issues was
setting up Lmod on each container to allow EB to build properly. In a
1-1 app to container scenario how will I implement the module behavior
to pick up paths installed in different containers.
Again, as soon as you start talking about multiple containers
interacting with each other, and dependencies, we end up with a layer
of orchestration.
This is both a good and bad thing. Thinking in terms of
reproducibility in it's simplest form, we have a single Singularity
image that has within it all of the "bits" necessary for a given
software workflow. The moment we start requiring other containers, we
do not have a single point of reproducibility anymore. Not that this
is a bad thing, but it compounds the problem of complexity exponentially.
Assuming EB installs in some path /usr/local/easybuild and there is a
module file for GCC. Users can execute commands against the container:
singularity exec GCC-5.4.0-2.27.img gcc –V provided that GCC module
is loaded. I don’t think this would still work since dependent
modules need to exist in same container. Single container solution
would be simple but I only see this useful for managing a group of
software in a container. There would be no way to interact between two
containers.
Perhaps a standardized method to interacting with an orchestration
system like Kubernetes (not HPC ready, but Slurm doesn't have the
necessary bits to deal with this easily).
Ken, is there anyone from EB working on this, I would like to get
started on this approach. Looking forward to hearing back from both of
you.
Thoughts?
Regards,
*From:*Gregory M. Kurtzer [mailto:gmkurt...@gmail.com
<mailto:gmkurt...@gmail.com>]
*Sent:* Tuesday, April 11, 2017 1:25 PM
*To:* Siddiqui, Shahzeb
*Cc:* Kenneth Hoste
*Subject:* Re: Singularity + EasyBuild
Hello Shahzeb,
I think this is a very interesting idea, but I will have to defer to
Kenneth to comment as it pertains to EB.
My initial feeling is that this should be possible, and I would love
to see EB generate the build commands for the package and the
dependencies such that it can be transposed into a Singularity build
definition file. That way we can bring the deffile and build it
anywhere (e.g. Singularity-hub) and create packages from that.
Thoughts?
Greg
Thoughts?
On Mon, Apr 10, 2017 at 8:00 AM, Siddiqui, Shahzeb
<shahzeb.siddi...@pfizer.com <mailto:shahzeb.siddi...@pfizer.com>> wrote:
Hello Greg/Ken,
My name is Shahzeb Siddiqui, I am a HPC Engineer at Pfizer and I
manage our software applications. I am currently using EasyBuild to
build out our software collection, and I have briefly played out with
Singularity to build out Easybuild packages. I have already build my
EB pkgs with RPM and in the next few months I would like to get EB
pkgs in Singularity. Before I start on this journey, I would like to
know if you guys have started work on this. If so, I would like to
know what is the current progress and potentially find command grounds
for collaboration. Do you have a timeframe when EB + Singularity will
work together. I see Singularity as an alternate to RPM packages which
can ease deployment of packages without relying on FPM.
At Pfizer, we retain software packages for 10 years that were built on
older architecture and OS. I think Singularity would be able to
address some of these issues, by allowing EB to build Singularity
containers for any OS. Before we introduce Singularity at our HPC
site, we would like to have a support model, potentially a consultant
that can help architect this for us. Do you provide commercial support
for this tool, we would need to address some of the security concerns
to comply with Pfizer policies.
I look forward to hearing back from you.
Regards,
Shahzeb Siddiqui
HPC Linux Engineer
B2220-447.2
Groton, CT
*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
