Re: Google Summer of Code, Debian Science
Dear Debian Science team,
as discussed, I have submitted a proposal to GSoC 2022 [1].
I have a feedback that a second ("backup") person is needed as
a mentor.
If somebody wants to join this initiative, please drop me an email.
[1]
https://wiki.debian.org/SummerOfCode2022/PendingProjects/QualityAssuranceDebianScience
Thanks
Anton
Am Mo., 21. Feb. 2022 um 17:42 Uhr schrieb Anton Gladky :
> Dear all,
>
> Google Summer of Code call for Debian is announced [1].
> I am going to apply Debian Science Team as one of the projects.
>
> Main topic is QA-Work: Autopkgtests for high-popcon packages,
> gitlab-CI for most of packages, bringing not-in-testing packages
> into the proper shape to let them migrate to testing.
>
> If somebody wants to be a co-mentor or if you have better ideas
> for the project, please let me know.
>
> [1] https://lists.debian.org/debian-devel-announce/2022/02/msg2.html
>
> Best regards
>
> Anton
>
Re: Google Summer of Code, Debian Science
Hi Anton, I suggest this wording for an MPI Performance Testing project cc: Lucas: I'm aiming to set up MPI testing protocols that could be run on g5k to validate the parallel performance of Debian packages Project: Debian Cloud Computing (MPI) Performance Testing --- Aim: to characterize and monitor the performance of debian cloud computing (MPI) packages --- Objective: to establish Standard Operating Procedures for monitoring performance of debian MPI packages - 1) protocol for managing test launching on cloud computing installations 2) protocol for managing test results (e.g. database) 3) protocol for reporting results Background -- Complex (large-scale) scientific computation is facilitated by parallelization of numerical libraries and end-use packages, typically via MPI (Message Passing Interface). The numerical library stack for applications is usually complex. For instance FEniCS is a library providing automated solutions to differential equations using Finite Element Methods. The numerical stack for FEniCS (python3-dolfinx) could be summarized as python3-dolfinx | numpy - libdolfinx-dev - petc4py - PETSc | hypre - scotch - superlu-dist - mumps | scalapack - libhdf5-openmpi - mpi4py - openmpi | BLAS - xsimd - lapack - basix An upgrade of any package, or in the configuration of any package, at any point along the chain has the potential to greatly impact the parallel performance of the end-user application, both positively or negatively depending on the change. We want to be certain that the integrity of the parallel performance of Debian packages is maintained. This complements the existing CI testing reported at https://ci.debian.net/. CI testing helps ensure packages continue to run correctly. With Performance Testing, we want also to be confident that they continue to scale satisfactorily in the HPC or cloud computing sense. Complementary to monitoring MPI package performance over time, we also want to be able to report comparative performance in the case where alternative packages are available. This point is particularly relevant to the Debian BLAS packages. BLAS clients are expected to build against generic BLAS (libblas3) but run against optimized BLAS implementations (e.g. openblas, blis, atlas). In the case of openblas, serial, pthread and openmpi threading variants are available. How does the performance of the end-user application compare using these different BLAS implementations? Task The FEniCS project provides a package for performance testing (fenicsx-performance-tests). This will be used as the starting point for the project. 1) What runtime parameters should fenicsx-performance-tests be launched with in order to provide sufficiently meaningful scaling tests? 2) How should the launch of tests be managed? (should we use https://reframe-hpc.readthedocs.io/ ?) 2b)How should test machines be managed (e.g. how to configure g5k machines to run tests)? How to manage BLAS comparisons? 3) How should the record of test results be managed? (what kind of database or flatfile?) 4) How should test results be presented? (FEniCS uses plotly to generate https://fenics.github.io/performance-test-results/. Should we follow this or use different presentation?) 5) How should we integrate test result pages with Debian websites? (e.g. link from https://ci.debian.net/ or manage elsewhere?) 6) Can we apply these procedures to benchmark other packages, e.g. nwchem, lammps ? GSOC Candidate -- The candidate is expected to be competent in shell scripting, general coding (e.g. python, C), managing installation of debian packages and building software. MPI and HPC experience is not mandatory but would be an advantage. Drew On 2022-02-22 13:06, Anton Gladky wrote: Hello Drew, It is a very good idea! Though I would separate this task from QA-work on Debian Science packages. If you want, we could apply one-more project (something like HPC-testing of MPI-based science packages) and point special requirements for possible applicants. Feel free to propose a text for that. Thanks again! Regards Anton Am Di., 22. Feb. 2022 um 12:52 Uhr schrieb Drew Parsons : On 2022-02-21 17:42, Anton Gladky wrote: > Dear all, > > Google Summer of Code call for Debian is announced [1]. > I am going to apply Debian Science Team as one of the projects. > > Main topic is QA-Work: Autopkgtests for high-popcon packages, > gitlab-CI for most of packages, bringing not-in-testing packages > into the proper shape to let them migrate to testing. > > If somebody wants to be a co-mentor or if you have better ideas > for the project, please let me know. > > [1] > https://lists.debian.org/debian-devel-announce/2022/02/msg2.html It would be helpful to run parallel/HPC
Re: Google Summer of Code, Debian Science
Gimme a few minutes, I'll line up my text On 2022-03-01 15:04, Anton Gladky wrote: Hi Nilesh, yes, thanks for the reminder. I will do it today. News from the last few days beated me personally. So, it is difficult to concentrate on the work. Regards Anton Am Di., 1. März 2022 um 14:51 Uhr schrieb Nilesh Patra : On 2/22/22 5:36 PM, Anton Gladky wrote: > Hello Drew, > > It is a very good idea! > > Though I would separate this task from QA-work on Debian Science > packages. [...] Anton, Google is reviewing our projects (as I saw one of the admins saying that on IRC) So you might want to add atleast one project to the wiki rather quickly, so we don't run out of time to do so. Regards, Nilesh
Re: Google Summer of Code, Debian Science
Hi Nilesh, yes, thanks for the reminder. I will do it today. News from the last few days beated me personally. So, it is difficult to concentrate on the work. Regards Anton Am Di., 1. März 2022 um 14:51 Uhr schrieb Nilesh Patra : > > On 2/22/22 5:36 PM, Anton Gladky wrote: > > Hello Drew, > > > > It is a very good idea! > > > > Though I would separate this task from QA-work on Debian Science > > packages. [...] > > Anton, Google is reviewing our projects (as I saw one of the admins saying > that on IRC) > So you might want to add atleast one project to the wiki rather quickly, > so we don't run out of time to do so. > > Regards, > Nilesh
Re: Google Summer of Code, Debian Science
On 2/22/22 5:36 PM, Anton Gladky wrote: > Hello Drew, > > It is a very good idea! > > Though I would separate this task from QA-work on Debian Science > packages. [...] Anton, Google is reviewing our projects (as I saw one of the admins saying that on IRC) So you might want to add atleast one project to the wiki rather quickly, so we don't run out of time to do so. Regards, Nilesh signature.asc Description: PGP signature
Re: Google Summer of Code, Debian Science
Am Wed, Feb 23, 2022 at 09:39:24AM +0100 schrieb Drew Parsons: > > I'd look forward to such a project but my capacity to become involved is > > limited and I also need to admit that I have no real competence if it > > comes to HPC and MPI questions. > > We can share the load, you can provide back-up supervision if I'm offline > camping during summer :) > > What I'm envisioning shouldn't require MPI programming as such. It's more > about setting up a test management system to get the MPI programs to test > themselves. Shell scripting as much as anything, maybe python for > extracting numbers from output files. Feel free to consider me a backup for this kind of things and enjoy camping Andreas. -- http://fam-tille.de
Re: Google Summer of Code, Debian Science
On 2022-02-23 07:21, Andreas Tille wrote: Hi, > It would be helpful to run parallel/HPC performance testing for our MPI > numerical packages. Am Tue, Feb 22, 2022 at 01:06:30PM +0100 schrieb Anton Gladky: It is a very good idea! +1 Though I would separate this task from QA-work on Debian Science packages. I support that this is a separate idea. If you ask me it should be ranked even higher. If you want, we could apply one-more project (something like HPC-testing of MPI-based science packages) and point special requirements for possible applicants. Feel free to propose a text for that. Thanks again! I'd look forward to such a project but my capacity to become involved is limited and I also need to admit that I have no real competence if it comes to HPC and MPI questions. We can share the load, you can provide back-up supervision if I'm offline camping during summer :) What I'm envisioning shouldn't require MPI programming as such. It's more about setting up a test management system to get the MPI programs to test themselves. Shell scripting as much as anything, maybe python for extracting numbers from output files. Drew
Re: Google Summer of Code, Debian Science
Hi, Am Tue, Feb 22, 2022 at 01:06:30PM +0100 schrieb Anton Gladky: > It is a very good idea! +1 > Though I would separate this task from QA-work on Debian Science > packages. I support that this is a separate idea. If you ask me it should be ranked even higher. > If you want, we could apply one-more project (something > like HPC-testing of MPI-based science packages) and point special > requirements for possible applicants. Feel free to propose a text > for that. Thanks again! I'd look forward to such a project but my capacity to become involved is limited and I also need to admit that I have no real competence if it comes to HPC and MPI questions. Kind regards Andreas. > Am Di., 22. Feb. 2022 um 12:52 Uhr schrieb Drew Parsons : > > > > On 2022-02-21 17:42, Anton Gladky wrote: > > > Dear all, > > > > > > Google Summer of Code call for Debian is announced [1]. > > > I am going to apply Debian Science Team as one of the projects. > > > > > > Main topic is QA-Work: Autopkgtests for high-popcon packages, > > > gitlab-CI for most of packages, bringing not-in-testing packages > > > into the proper shape to let them migrate to testing. > > > > > > If somebody wants to be a co-mentor or if you have better ideas > > > for the project, please let me know. > > > > > > [1] > > > https://lists.debian.org/debian-devel-announce/2022/02/msg2.html > > > > > > It would be helpful to run parallel/HPC performance testing for our MPI > > numerical packages. > > > > This would be a type of CI testing that we would set up to run regularly > > and report. > > Lucas Nussbaum is in charge of an academic supercomputing cluster that > > we can access to run such tests. > > > > Some packages have benchmarks already at hand. The FEniCS project for > > instance offers fenicsx-performance-tests (both prebuilt and source). > > > > The project would determined how to set up MPI CI testing (how to > > activate it on Lucas' system), and what parameters (test size etc) to > > use to get meaningful numbers. > > A suggested tools for managing test parameters and results might be > > https://reframe-hpc.readthedocs.io/en/stable/ > > > > The report format could be similar to > > https://fenics.github.io/performance-test-results/ > > or perhaps the GSoC worker could come up with a better way of presenting > > results. > > > > It would be useful to be able to quantify how well our HPC packages > > actually scale (in cloud computing environments) and monitor if there's > > any drop in performance (e.g. with version updates) > > > > Also useful to report their performance with the various BLAS > > alternatives. > > > > This would be valuable GSoC project I think. > > > > Drew > > -- http://fam-tille.de
Re: Google Summer of Code, Debian Science
You are aware of https://wiki.debian.org/DebianScience/ROOT ? On 22.02.22 17:19, Stephan Lachnit wrote: On Mon, Feb 21, 2022 at 5:43 PM Anton Gladky wrote: If somebody wants to be a co-mentor or if you have better ideas for the project, please let me know. I would love to have a student to bring up packaging of common HEP packages (High Energy Physics), most notably ROOT [1] and Geant4 [2]. I've already done a bit ([3] resp. [4]), but I'm currently not working actively on it anymore. If anyone would be interested to co-mentor this, I would consider mentoring this. However it's unlikely that I will do it alone as I'm hopefully a Summer Student myself (not at GSoC). Regards, Stephan [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=981113 [2] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=965964 [3] https://salsa.debian.org/science-team/root [4] https://salsa.debian.org/science-team/geant4
Re: Google Summer of Code, Debian Science
Hi Anton, https://salsa.debian.org/med-team/community/helper-scripts/-/blob/master/debian-science-tests.txt :-) It should be updated twice a day. Kind regards Andreas. Am Tue, Feb 22, 2022 at 01:04:01PM +0100 schrieb Anton Gladky: > Hello Andreas, > > thank you very much for offering a help! Yes, it would be fine > if you run the script. > > Best regards > > Anton > > Am Di., 22. Feb. 2022 um 11:28 Uhr schrieb Andreas Tille : > > > > Hi, > > > > Am Mon, Feb 21, 2022 at 05:42:56PM +0100 schrieb Anton Gladky: > > > Google Summer of Code call for Debian is announced [1]. > > > I am going to apply Debian Science Team as one of the projects. > > > > > > Main topic is QA-Work: Autopkgtests for high-popcon packages, > > > gitlab-CI for most of packages, bringing not-in-testing packages > > > into the proper shape to let them migrate to testing. > > > > > > If somebody wants to be a co-mentor or if you have better ideas > > > for the project, please let me know. > > > > I'm basically running the same GSoC project in Debian Med (as in > > previous years) and to my experience this is an extremely valuable > > project. Students have a low entry barrier and its quite granted that > > you get sensible output since it is split into tiny tasks which are all > > helpful once solved. > > > > If you want me to run this script[1] also for Debian Science as I do it > > in a cron job for Debian Med I can very easily do it. The text file[2] > > (result of the cron job) has turned out to be very helpful for the > > intern (and others!) to pick sensible packages. > > > > Kind regards > > > > Andreas. > > > > [1] > > https://salsa.debian.org/med-team/community/helper-scripts/-/blob/master/missing-autopkgtest > > [2] > > https://salsa.debian.org/med-team/community/helper-scripts/-/blob/master/debian-med-tests.txt > > > > -- > > http://fam-tille.de > > > -- http://fam-tille.de
Re: Google Summer of Code, Debian Science
On Mon, Feb 21, 2022 at 5:43 PM Anton Gladky wrote: > > If somebody wants to be a co-mentor or if you have better ideas > for the project, please let me know. I would love to have a student to bring up packaging of common HEP packages (High Energy Physics), most notably ROOT [1] and Geant4 [2]. I've already done a bit ([3] resp. [4]), but I'm currently not working actively on it anymore. If anyone would be interested to co-mentor this, I would consider mentoring this. However it's unlikely that I will do it alone as I'm hopefully a Summer Student myself (not at GSoC). Regards, Stephan [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=981113 [2] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=965964 [3] https://salsa.debian.org/science-team/root [4] https://salsa.debian.org/science-team/geant4
Re: Google Summer of Code, Debian Science
On Tue, 2022-02-22 at 12:52 +0100, Drew Parsons wrote: > > Also useful to report their performance with the various BLAS > alternatives. Looking forward to it. I'm glad to provide pointers in terms of our BLAS and LAPACK packaging.
Re: Google Summer of Code, Debian Science
Hello Andreas, thank you very much for offering a help! Yes, it would be fine if you run the script. Best regards Anton Am Di., 22. Feb. 2022 um 11:28 Uhr schrieb Andreas Tille : > > Hi, > > Am Mon, Feb 21, 2022 at 05:42:56PM +0100 schrieb Anton Gladky: > > Google Summer of Code call for Debian is announced [1]. > > I am going to apply Debian Science Team as one of the projects. > > > > Main topic is QA-Work: Autopkgtests for high-popcon packages, > > gitlab-CI for most of packages, bringing not-in-testing packages > > into the proper shape to let them migrate to testing. > > > > If somebody wants to be a co-mentor or if you have better ideas > > for the project, please let me know. > > I'm basically running the same GSoC project in Debian Med (as in > previous years) and to my experience this is an extremely valuable > project. Students have a low entry barrier and its quite granted that > you get sensible output since it is split into tiny tasks which are all > helpful once solved. > > If you want me to run this script[1] also for Debian Science as I do it > in a cron job for Debian Med I can very easily do it. The text file[2] > (result of the cron job) has turned out to be very helpful for the > intern (and others!) to pick sensible packages. > > Kind regards > > Andreas. > > [1] > https://salsa.debian.org/med-team/community/helper-scripts/-/blob/master/missing-autopkgtest > [2] > https://salsa.debian.org/med-team/community/helper-scripts/-/blob/master/debian-med-tests.txt > > -- > http://fam-tille.de >
Re: Google Summer of Code, Debian Science
Hello Drew, It is a very good idea! Though I would separate this task from QA-work on Debian Science packages. If you want, we could apply one-more project (something like HPC-testing of MPI-based science packages) and point special requirements for possible applicants. Feel free to propose a text for that. Thanks again! Regards Anton Am Di., 22. Feb. 2022 um 12:52 Uhr schrieb Drew Parsons : > > On 2022-02-21 17:42, Anton Gladky wrote: > > Dear all, > > > > Google Summer of Code call for Debian is announced [1]. > > I am going to apply Debian Science Team as one of the projects. > > > > Main topic is QA-Work: Autopkgtests for high-popcon packages, > > gitlab-CI for most of packages, bringing not-in-testing packages > > into the proper shape to let them migrate to testing. > > > > If somebody wants to be a co-mentor or if you have better ideas > > for the project, please let me know. > > > > [1] > > https://lists.debian.org/debian-devel-announce/2022/02/msg2.html > > > It would be helpful to run parallel/HPC performance testing for our MPI > numerical packages. > > This would be a type of CI testing that we would set up to run regularly > and report. > Lucas Nussbaum is in charge of an academic supercomputing cluster that > we can access to run such tests. > > Some packages have benchmarks already at hand. The FEniCS project for > instance offers fenicsx-performance-tests (both prebuilt and source). > > The project would determined how to set up MPI CI testing (how to > activate it on Lucas' system), and what parameters (test size etc) to > use to get meaningful numbers. > A suggested tools for managing test parameters and results might be > https://reframe-hpc.readthedocs.io/en/stable/ > > The report format could be similar to > https://fenics.github.io/performance-test-results/ > or perhaps the GSoC worker could come up with a better way of presenting > results. > > It would be useful to be able to quantify how well our HPC packages > actually scale (in cloud computing environments) and monitor if there's > any drop in performance (e.g. with version updates) > > Also useful to report their performance with the various BLAS > alternatives. > > This would be valuable GSoC project I think. > > Drew
Re: Google Summer of Code, Debian Science
On 2022-02-21 17:42, Anton Gladky wrote: Dear all, Google Summer of Code call for Debian is announced [1]. I am going to apply Debian Science Team as one of the projects. Main topic is QA-Work: Autopkgtests for high-popcon packages, gitlab-CI for most of packages, bringing not-in-testing packages into the proper shape to let them migrate to testing. If somebody wants to be a co-mentor or if you have better ideas for the project, please let me know. [1] https://lists.debian.org/debian-devel-announce/2022/02/msg2.html It would be helpful to run parallel/HPC performance testing for our MPI numerical packages. This would be a type of CI testing that we would set up to run regularly and report. Lucas Nussbaum is in charge of an academic supercomputing cluster that we can access to run such tests. Some packages have benchmarks already at hand. The FEniCS project for instance offers fenicsx-performance-tests (both prebuilt and source). The project would determined how to set up MPI CI testing (how to activate it on Lucas' system), and what parameters (test size etc) to use to get meaningful numbers. A suggested tools for managing test parameters and results might be https://reframe-hpc.readthedocs.io/en/stable/ The report format could be similar to https://fenics.github.io/performance-test-results/ or perhaps the GSoC worker could come up with a better way of presenting results. It would be useful to be able to quantify how well our HPC packages actually scale (in cloud computing environments) and monitor if there's any drop in performance (e.g. with version updates) Also useful to report their performance with the various BLAS alternatives. This would be valuable GSoC project I think. Drew
Re: Google Summer of Code, Debian Science
Hi, Am Mon, Feb 21, 2022 at 05:42:56PM +0100 schrieb Anton Gladky: > Google Summer of Code call for Debian is announced [1]. > I am going to apply Debian Science Team as one of the projects. > > Main topic is QA-Work: Autopkgtests for high-popcon packages, > gitlab-CI for most of packages, bringing not-in-testing packages > into the proper shape to let them migrate to testing. > > If somebody wants to be a co-mentor or if you have better ideas > for the project, please let me know. I'm basically running the same GSoC project in Debian Med (as in previous years) and to my experience this is an extremely valuable project. Students have a low entry barrier and its quite granted that you get sensible output since it is split into tiny tasks which are all helpful once solved. If you want me to run this script[1] also for Debian Science as I do it in a cron job for Debian Med I can very easily do it. The text file[2] (result of the cron job) has turned out to be very helpful for the intern (and others!) to pick sensible packages. Kind regards Andreas. [1] https://salsa.debian.org/med-team/community/helper-scripts/-/blob/master/missing-autopkgtest [2] https://salsa.debian.org/med-team/community/helper-scripts/-/blob/master/debian-med-tests.txt -- http://fam-tille.de
Google Summer of Code, Debian Science
Dear all, Google Summer of Code call for Debian is announced [1]. I am going to apply Debian Science Team as one of the projects. Main topic is QA-Work: Autopkgtests for high-popcon packages, gitlab-CI for most of packages, bringing not-in-testing packages into the proper shape to let them migrate to testing. If somebody wants to be a co-mentor or if you have better ideas for the project, please let me know. [1] https://lists.debian.org/debian-devel-announce/2022/02/msg2.html Best regards Anton
