Interesting discussion about Singularity, there was an older thread here https://mail.google.com/mail/u/0/#search/singularity/159045c3913ad572
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/ 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 < [email protected]> 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. > > 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 > > >
