Users December 2020

users@lists.einsteintoolkit.org

9 participants
14 discussions

Einstein Toolkit Telecon Minutes: Dec 10, 2020
by Zach Etienne 14 Jan '21

14 Jan '21

Present: Zach, Steve, Roland, Peter, David Bradley, Maria, Ken Sible, Leo Werneck, Liu Haoyang, Miguel Gracia, Sam Cupp, Bill Gabella, Yosef - *SPEC benchmark*: Steve reports no progress, but says we should do it. Roland wrote a to-do list for this task: https://bitbucket.org/einsteintoolkit/tickets/issues/2470 . Some details regarding this to-do list were discussed. - *Webserver issues*: einsteintoolkit.org was down for ~70 hours (including Dec 5-6 weekend). - Roland: was it a glitch or something systemic? - Steve: glitch. Machine hosting virtual webserver went down -- just needed LSU CCT support to reboot machine. Will work with Roland & Peter to ensure there's more redundancy in the future. After ticket, machine was back within an hour. - Bill: cactuscode.org has problems redirecting to new github.io page. Roland: Only sometimes, and not with Chrome. Firefox indeed doesn't redirect unless www.cactuscode.org is used. Roland: *Always* use *www.cactuscode.org <http://www.cactuscode.org>* - *Updates for next release*: - POWER: Used for waveform extraction on Scri+ -- Maria & Zach are interested in this code. Roland is improving interface, etc. - GRHydro con2prim updates -- Roland: A number of improvements have been reported from various groups. - selfforce1D updates -- Peter: new features are in progress, depending on progress might be a candidate for inclusion - Canuda updates -- Roland has been in touch with authors, privately. - *Unanswered mailing list queries*: One MPI query (failure) discussed, will need more details to help. Peter said he'd send an email. - *Tickets*: - #2335 ( https://bitbucket.org/einsteintoolkit/tickets/issues/2335/switch-simfactory… ) Steve: Patch makes SimFactory compatible with Python3. Pull request ready for review. Bill said he'd test it out. Roland has started to review. - Roland: other tickets ready for review, nothing super urgent at the moment. - *NRPy+ LaTeX parser update*: Ken Sible reports ability to now parse another of the BSSN equations. \gamma and \phi (using W variable) can now be parsed. Continued robustness improvements. Hope to have remaining equations parsed within the week. Bill asked for a progress report on parsing non-tensorial expressions, like those in PN expressions. Ken: we're very close to being ready to parse those expressions. - *Tabulated EOS with single TOV star*: Some discussion on whether this has been done with GRHydro. Roland pointed out a TOVHot code that may be on stellarcollapse.org ( https://svn.einsteintoolkit.org/incoming/TOVSolverHot/); Miguel: RNS thorn may have a parfile with tabEOS as well, could try out (HydroRNSID: test/RNS_a2.par). - *Jan 7 meeting*: Minute taker: Bill. Chair: Maria -Zach * * * Prof. Zachariah Etienne Physics & Astronomy Dept. West Virginia University http://astro.phys.wvu.edu/zetienne/ http://blackholesathome.net <https://blackholesathome.net>

2 1

MPI killing issue
by Karima Shahzad 04 Jan '21

04 Jan '21

Hello there, I am running a simple binary black hole simulation from the parameter file kept in the Cactus/par/arXiv-1111.3344 where I simulated high resolution. Furthermore, I assume simulation for lower resolution is less costly than higher, but I wonder it keeps giving me errors in the low-resolution run. (kernel dies for the MedResolution). I tried almost all the ways of adjusting the par file according to my local machine strength, but I failed. The error is below along with the par file, *.err, and *.out filesgenerators attached. Note: There is no storage issue at all. Any help would be highly appreciated. Warning: Too many threads per process specified: specified num-threads=2 (ppn-used is 2) Warning: Total number of threads and number of threads per process are inconsistent: procs=1, num-threads=2 (procs*num-smt must be an integer multiple of num-threads) Warning: Total number of threads and number of cores per node are inconsistent: procs=1, ppn-used=2 (procs must be an integer multiple of ppn-used) + set -e + cd /home/karima/simulations/bbhL/output-0000-active + echo Checking: + pwd + hostname + date + echo Environment: + export CACTUS_NUM_PROCS=1 + export CACTUS_NUM_THREADS=2 + export GMON_OUT_PREFIX=gmon.out + export OMP_NUM_THREADS=2 + env + sort + echo Starting: + date +%s + export CACTUS_STARTTIME=1608653732 + [ 1 = 1 ] + [ 0 -eq 0 ] + /home/karima/simulations/bbhL/SIMFACTORY/exe/cactus_sim -L 3 /home/karima/simulations/bbhL/output-0000/BBHLowRes.par WARNING level 0 from host karima-Latitude-E5470 process 0 in thorn cactus, file BBHLowRes.par:1: -> ERROR IN PARAMETER FILE:Parse Error Expected one of the following characters: ':' CarpetMask::excluded_surface_factor[1] = 1.0 CarpetMask::excluded_surface [2] = 2 CarpetMask::excluded_surface_factor[2] = 1.0 Contents successfully written to /home/karima/Cactus/repos/simfactory2/etc/defs.local.ini ^ -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. Thanks in advance best, Karima S

3 5

MPI killing issue in running the simulation
by Karima Shahzad 22 Dec '20

22 Dec '20

Hi there, I am running a simple test (parameter file) using simfactory. Input: > ./simfactory/bin/sim create-run tstadm \ > --parfile repos/einsteinanalysis/testADM-0018.par Error: > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > with errorcode 1. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them along with the warning, > Warning: Too many threads per process specified: specified num-threads=2 (ppn-used is 2) > Warning: Total number of threads and number of threads per process are inconsistent: procs=1, num-threads=2 (procs*num-smt must be an integer multiple of num-threads). How to resolve the issue? Thanks in advance, Best karima

2 1

Einstein Toolkit Telecon Minutes: Dec 17, 2020
by Ken Sible 17 Dec '20

17 Dec '20

Present: Ken S., Karim S., Yosef Z., Peter D., Atul K., David B., Roland H., William G., Miguel G., Zach E., Steve B., Maria H. Chair: Steve B. Minutes: Ken S. - *SPEC benchmark*: Steve filled out the web form and performed a 5 min test; waiting for approval; submitted proposal; more than 1 million LOC in the Einstein Toolkit - *NRPy+ LaTeX parser*: Ken parsed a PN equation that Bill provided using the new capture group feature (string replacement macro) to resolve non-tensorial ambiguities. Ken also moved the parser config into a json file for config retention and sharing. - *Unanswered questions / open tickets / tickets ready to review: MPI killing issue in running the simulation (Karima Shahzad): Peter will respond No new open tickets / tickets ready to review since last week - *Other*: Steve submitted a pull request addressing SymFactory 2 concerns because the documentation was confusing. He added a --test flag that shows the number of nodes and node processors and an option to specify nodes using a --nodes flag and processors using a --nodeprocs flag; SymFactory missing test suite, making transition to Python 3 difficult. Zach mentioned LGMT Python linter for SymFactory 2 (lgtm.com/projects/b/simfactory/simfactory2/?mode=list) - *Dec 24/31* No ET meeting, due to winter break. - *Next meeting Jan 7* Minutes: Bill. Chair: Maria

1 0

Einstein Toolkit Telecon Minutes: Dec 17, 2020
by Ken Sible 17 Dec '20

17 Dec '20

1 0

Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 14 Dec '20

14 Dec '20

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

1 0

Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 09 Dec '20

09 Dec '20

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

Fwd: GRAPPA Postdoctoral Prize Fellowship at the University of Amsterdam: deadline 20/12/2020
by Helvi Witek 08 Dec '20

08 Dec '20

FYI --------------------------------------------- Dr. Helvi Witek Assistant Professor Department of Physics University of Illinois at Urbana-Champaign 247 Loomis Lab 1110 W Green St Urbana, IL 61801 --------------------------------------------- -------- Forwarded Message -------- Subject: GRAPPA Postdoctoral Prize Fellowship at the University of Amsterdam: deadline 20/12/2020 Date: Tue, 8 Dec 2020 12:19:49 +0100 From: Samaya Nissanke <samaya.nissanke(a)uva.nl> Reply-To: Samaya Nissanke <samaya.nissanke(a)uva.nl> To: virgo-l(a)ego-gw.it, consortium(a)lisamission.org Dear colleagues, We are pleased to announce an opening of the GRAPPA Postdoctoral Prize Fellowship starting from fall 2021 for three years. We invite applications in the areas of astroparticle physics, cosmology, and gravitation. Established in 2012, GRAPPA Institute (grappa.amsterdam) strives for revealing fundamental aspects of the Universe and laws of physics. The GRAPPA Fellowship has been our flagship postdoctoral program, which fully ensures academic freedom to pursue any theoretical and experimental research subjects that are relevant to the GRAPPA’s scientific focus. In this round, we are paying particular attention to increasing the diversity and inclusivity of our group. To this end, we strongly encourage applications from people of diverse backgrounds and from underrepresented groups. We also welcome active contribution by the fellow to our discussions on diversity, equity and inclusion. The deadline is rather tight, and is 20 December 2020. We aim to spread this ad as broadly as possible, and appreciate for your help. Please forward this message to those who you think might be interested in such an opportunity. More details of the position is found from www.uva.nl/en/content/vacancies/2020/12/20-756-grappa-postdoctoral-fellowsh… <https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.uva.nl…> Best regards, Shin’ichiro Ando, on behalf of selection committee

1 0

Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 07 Dec '20

07 Dec '20

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

1 0

FW: Meeting Minutes 2020-12-03
by Hamilton, Maria 03 Dec '20

03 Dec '20

Hello, Just a short update regarding the current version of ETK on Big Sur. I tested it on my laptop, following the instructions from https://einsteintoolkit.org/download.html Download - Einstein Toolkit<https://einsteintoolkit.org/download.html> Tools The Einstein Toolkit provides more than the main toolkit. It comes with a variety of tools that might be used with the main toolkit, or also might be used stand-alone. einsteintoolkit.org I am running macOS Big Sur version 11.01.1 and Homebrew with gcc-10 and OpenMP. It compiled smoothly, in 45 min. I also ran the test suites, which passed, and took about 15 min to run. I'll test next Maria _______________________ Maria C. Babiuc Hamilton, Ph.D. Professor, Department of Physics College of Science, Marshall University, 1 John Marshall Drive, Huntington, WV, 25755 Room S 257, Phone: (304)696-2754 ________________________________ From: users-bounces(a)einsteintoolkit.org <users-bounces(a)einsteintoolkit.org> on behalf of Miguel Gracia <mgracia(a)austin.utexas.edu> Sent: Thursday, December 3, 2020 11:37 AM To: users(a)einsteintoolkit.org <users(a)einsteintoolkit.org> Subject: [Users] Meeting Minutes 2020-12-03 Present: Peter D., Roland H., Miguel G., Kenneth S. , David B., Steven B., Atul K, Nicolas C., Maria H. , Zach E. Chair: Roland H. Minutes: Miguel G. * SPEC benchmark contribution [RH, SB] -Roland: mentioned that February is the due date. The SPEC CPU 2017 McLachlan submission is going to be submitted again. Let -Steve and Roland if you want to contribute or help. The link to tasks list is https://bitbucket.org/einsteintoolkit/tickets/issues/2470<https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fbitbucket.org%2feinstei…> -Steve: SPEC install worked fine in his own friendly environment. He thinks it would be relatively easy to do it in any other system. The installation instructions should be simple except (possibly) for MacOS . * cactuscode.org<https://linkprotect.cudasvc.com/url?a=http%3a%2f%2fcactuscode.org&c=E,1,AX6…> now hosted on Github pages [RH] Cactus website was moved to Github with minor changes to the original site. Loading the website with https always work but using http sometimes doesn’t. Roland doesn’t know the reason. * Proposed ET tutorial by Nick Choustikov -Nick an undergraduate student in Cambridge, put together a tutorial for the ET. He ran the ET on Amazon Web Services (AWS) following the same process as in any regular computer except that he needed to add lamboot command due to an error in simfactory. -It was proposed with no objections to include Frank’s, Miguel’s and Nick’s tutorial on wiki and website (will require pdf to html conversion) . * Post release report -Roland: some small issues. TeX to HTML conversion is failing. Might be due to Ubuntu and Debian configuration differences. -The guide for next release should be upgraded to a more linear version. -If somebody wish to include something in the next release it should be mentioned in the mailing list or weekly meeting before February 2021. * ET on macOS BigSur[RH] Macport works but OpenMPI is not working, some works arounds. MPICH problems with hwloc. In conclusion for the moment ET is not supporting BigSur. New M1 Macs. Homebrew is partially working but it is not clear if all the components to run the toolkit will work. It would be helpful if somebody in the ET community with an M1-Mac try to run it. * Take a minute taker search[RH] December 10 Chair: Peter D. Minutes: Zach E. December 17 Chair: Steve B. Minutes: Kenneth S. Last meeting of the year is December 17,2020 coming back on January 7, 2021. * LaTeX parser -Kenneth is cleaning the BSSN code and adding more features. He successfully created a validation test between the sympy expression created by the parser and the NRPy expression. -Kenneth has made some improvements to the documentation. -Zach said early 2021 an official presentation of the LaTeX parser should be given. * Unanswered questions / open tickets / tickets ready to review Roland encourages the ET community to review the list of open tickets and help. (no expertise is required to do it) * Other comments -Zach is having a problem running BBH simulations with 8th order finite difference example BBH. Peter mentioned he has no problem using 8th order stencils with 5 ghost zones. Roland mentioned that there’s a gallery example that uses 8th order stencils. -Steve mentioned that simfactory should work with python3 in the early future. Roland said that this could be an oportunity to clean the simfactory script and remove some features that are not being used. End of the meeting.

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

Users December 2020