Users December 2024

users@lists.einsteintoolkit.org

7 participants
15 discussions

meeting minutes for 2024-12-05
by Roland Haas 05 Dec '24

05 Dec '24

Present: Roland, Bill, Peter, Zach, Johnny, Leo, Maxwell, Lucas, Steve ET Cannon release ================= * waiting for TOVola commit rights, Zach will try and follow up * some failing tests, likely due to tight tolerances * Peter finished BBH gallery example, everything looks fine, will skip VisIt visualization unless QB cooporates, Bill mentions a singularity image for VisIt that he has used successfully in the past. Lucas reports having successfully used sshfs to access the files on the cluster from one's workstation. * Running VisiIt via singularity, singularity run docker://symerio/visit and see halfway down the ticket for Multipatch https://bitbucket.org/einsteintoolkit/tickets/issues/2174/test-multi-patch-… Next ET release =============== * possibly inclusions for next release, Maxwell Rizzo is chair ** Z4c ** BHaHAHA horizon finder ** CCE code to hook up to Spectre ** possibly more modules for cosmology Updated tickets =============== * 2520 update gauge settings in TOV example to be more typical, will postpone until 2025 * will close 2171 since issue can no longer be reproduced * 2773 "make CarpetX-ThornDoc is confused in InterLatex.pl", Steve will take a look * 2282 "gallery examples use low-order integration n Multipole", Peter tested some of this but has not quite gotten all results. Will continue and report next week. * 2606 "Inconsistent LAPACK versions in ExternalLibraries/BLAS & LAPACK", Zach will look into it again * 2576 "`after` statements in scheduler in `IllinoisGRMHD`", Zach&Leo&Sam will check and close ticket if posible * 1566 "Update Cactus autoconf", Roland has change ready, will apply shortly after release to have lots of time for testing * 2831 "ExternalLibraries/MPI creates MPI_INC_DIRS that have double quotes in their value", Steve has a fix in mind * 2761 "some ExternalLibraries require cmake to build", to be included in master now, since it limits things on expanse * 2719 "GetCompnents does not handle symbolic links correctly when checking repository inter-dependencies", still persists, mostly affects FUKA * 2820 "NewRadX boundary condition conflicts with symmetry condition", just did not make for this release, should make it for the next Yours, Roland -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu .

1 0

Einstein Toolkit Meeting Reminder
by rhaas＠illinois.edu 04 Dec '24

04 Dec '24

Hello, Please consider joining the weekly Einstein Toolkit phone call at 9:00 am US central time on Thursdays. For details on how to connect and what agenda items are to be discussed, use the link below. https://docs.einsteintoolkit.org/et-docs/Main_Page#Weekly_Users_Call --The Maintainers

1 0

Re: [Users] need help running simulation on slurm
by Roland Haas 04 Dec '24

04 Dec '24

Hello Maya, Sorry for the long delay in responding. > My name is Maya Baireddy. I am working on my school research project trying > to run the simulation of BNS merger on amarel supercomputer from my local > university. Thanks for contacting me. I will try and see if I can provide some help. > Could you please help me to start my simulation on SLURM. I have followed > the ETK gallery example for BNS simulation steps 1-5. But I am not able to > proceed to successfully create a machine to run the simulation. > > I run the following steps > /home/sb1554/BNS/simfactory/bin/sim create bns --parfile > /home/sb1554/BNS/bns.par --machine slurmbns > > srun bns.sh -o slurm.bns.%N.%j.out Looks ok to me. > and got the error: > > **** An error occurred in MPI_Init_thread*** on a NULL communicator*** > MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,*** > and potentially your MPI job)* With errors like this my first guess is usually that he MPI stack used to compile and the one used at runtime is not the same. SLURM in particular can be dicey in that respect since it can try and directly interface with MPI. > I am attaching my machine, submit script, run script, log files. Thank you. > I would appreciate any pointers from you. Or if you could point me to the > right person. > > I was trying to post this on EKT forum, but need one credit to post. To the gitter chat? I though that was open to all with no requirements? This one: https://gitter.im/EinsteinToolkit/EinsteinToolkit The mailing list users(a)einsteintoolkit.org was unavailable for a while due to required maintenance. You would have to sign up to post, otherwise the post will be held for "moderator approval" (which it will receive, just may take a little bit of time). Now for the actual question. The machine.ini file (slurmbns.ini-machine.txt) looks strange (eg it contains two [slurmbns] sections). The line submit = sbatch /home/sb1554/BNS/simfactory/mdb/runscripts/slurmbns.run will always make is use the file "/home/sb1554/BNS/simfactory/mdb/runscripts/slurmbns.run" as the file passed to SLURM as the job script. The "submit" entry should be just "sbatch" without the extra file name. There is no "envsetup" section so you will have to yourself make sure that he same modules (in particular mpi modules) are loaded when you compile and when you submit the job, otherwise SLURM (and srun) may use the wrong MPI stack. The run script "slurmbns.ini-runscript.txt" is also strange since it contains a "/home/sb1554/BNS/simfactory/bin/sim run" which would again call the runscript. Instead it should contain the "srun" call. The submitscript is also strange since it should end with a line calling "sim run". It may be best to first directly add the srun command to the SLURM batch file (the "submitscript" mostly since it has the SBATCH headers) and set the headers by hand, load the modules, and call srun from there. This should make it look very similar to a MPI+OpenMP "Hybrid" parallelization example submit script that your cluster admins may provide. For SLURM based machines, the machine ini files usually look very similar. In your case I would suggest taking a look at say the ones for the Delta cluster at NCSA: https://bitbucket.org/simfactory/simfactory2/src/master/mdb/machines/delta.… https://bitbucket.org/simfactory/simfactory2/src/master/mdb/optionlists/del… https://bitbucket.org/simfactory/simfactory2/src/master/mdb/runscripts/delt… https://bitbucket.org/simfactory/simfactory2/src/master/mdb/submitscripts/d… You may also want to call in to the Einstein Toolkit weekly call on Thursday (the Gitter chat may also work for real time communication). Yours, Roland -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu .

1 0

Agenda for Thursday's Meeting
by rhaas＠illinois.edu 02 Dec '24

02 Dec '24

Please update the Wiki with agenda items for Thursday's meeting. Thanks! https://docs.einsteintoolkit.org/et-docs/meeting_agenda --The Maintainers

1 0

Meeting minutes for 2024-11-21
by Leo Rosa Werneck 01 Dec '24

01 Dec '24

Hi all, I apologize for the long delay, but I just realized I forgot to send the minutes from the Nov. 21 meeting. Here they are: Chair: Lucas Minutes: Leo Present: Lucas, Leo, Roland, Peter, Maxwell, Bill, Johnny ET Release * Timeline - Testing should be completed by tomorrow. - Leo "fixed the issue" in GRHayLHDX with a temporary fix that circumvents the fact that CarpetX currently doesn't respect the "STORAGE" statement in the schedule.ccl file. - Folks are running tests on different HPC clusters; progressing well. - TOVola: no news. Leo will ping David regarding contributors. * Gallery example: - Poisson (Lucas): ran example and seems correct; still needs to generate plots, update documentation, and add instructions on how to use VisIt. - BNS (Maxwell): performance issues on Anvil, will try somewhere else. - BBH (Peter): running, looks fine, but will know more next week. - TOV (David): completed and is working, not sure if ticket was updated. - Scalar Wave (UIUC Student): progressing well, confused about visualization, but Lucas clarified it is correct. Unanswered questions on the mailing list * None Open Tickets * #2503: FishboneMoncriefID still needs to be updated. * #2773: Piraha issuing a "Confused" message that needs to be understood. * #2282: if example runners are up for it, they should update Multipole. Tickets ready for review * #1566: Roland is handling it. * #2761: added CMake to the list of compiled external libraries. * #2807: no assignee, no updates. * #2820: some proposed fix, but hasn't been merged in yet. VolumeIntegrals-GRMHD * Maxwell asked about the output of the center-of-mass, and Leo clarified that typically one must divide the coordinates by the mass of the star. Maxwell will see if doing this yields result that match what he would expect, then will let Leo so so he can update either the documentation or the thorn. ** No meeting next week due to American Thanksgiving ** Next Chair: Peter Next Minutes: Roland Cheers, Leo ------ Leonardo R. Werneck, Ph.D. Postdoctoral researcher Office EP 314 | Department of Physics | University of Idaho 875 Perimeter Dr. MS 0903 Moscow, ID 83844-0903, USA leonardo(a)uidaho.edu <mailto:leonardo@uidaho.edu> https://leowerneck.github.io <https://leowerneck.github.io/>

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

Users December 2024