Users July 2024

users@lists.einsteintoolkit.org

9 participants
17 discussions

Problem installation Einstein Toolkit
by Elena Luisa Goria 28 Aug '24

28 Aug '24

Good morning, I am Elena Goria and I want to use the Einstein Toolkit. I am writing to you because of a problem encountered in installing the Einstein Toolkit. In particular when I write the command: ./simfactory/bin/sim build -j2 --thornlist thornlists/einsteintoolkit.th I get the error: COMPILING EinsteinInitialData/Meudon_Mag_NS/src/check_parameters.cc /Users/elenaluisagoria/Cactus/configs/sim/build/Meudon_Mag_NS/Mag_NS.cc: In function 'void ID_Mag_NS_initialise(cGH*)': /Users/elenaluisagoria/Cactus/configs/sim/build/Meudon_Mag_NS/Mag_NS.cc:202:25: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 202 | } catch (ios::failure e) { | ^ Checking status of thorn NPScalars Checking status of thorn NPScalars_Proca Creating /Users/elenaluisagoria/Cactus/configs/sim/lib/libthorn_Meudon_Mag_NS.a Checking status of thorn NRPyEllipticET Checking status of thorn NaNCatcher COMPILING EinsteinInitialData/NRPyEllipticET/src/conformally_flat_BBH/NRPyEllipticET_conformally_flat_BBH_Initialize_ADMBase.c COMPILING CactusUtils/NaNCatcher/src/catch_nans.c /Users/elenaluisagoria/Cactus/configs/sim/build/NRPyEllipticET/conformally_flat_BBH/NRPyEllipticET_conformally_flat_BBH_Initialize_ADMBase.c: In function 'NRPyEllipticET_conformally_flat_BBH_Initialize_ADMBase': /Users/elenaluisagoria/Cactus/configs/sim/build/NRPyEllipticET/conformally_flat_BBH/NRPyEllipticET_conformally_flat_BBH_Initialize_ADMBase.c:147:71: error: passing argument 6 of 'NRPyEllipticET_conformally_flat_BBH_interpolate_solution_to_ADMBase' from incompatible pointer type [-Wincompatible-pointer-types] 147 | input_array, | ^~~~~~~~~~~ | | | CCTK_REAL8 (*)[Nxx_plus_2NGHOSTS1][Nxx_plus_2NGHOSTS0] {aka double (*)[Nxx_plus_2NGHOSTS1][Nxx_plus_2NGHOSTS0]} In file included from /Users/elenaluisagoria/Cactus/configs/sim/build/NRPyEllipticET/conformally_flat_BBH/NRPyEllipticET_conformally_flat_BBH_Initialize_ADMBase.c:3: /Users/elenaluisagoria/Cactus/arrangements/EinsteinInitialData/NRPyEllipticET/src/conformally_flat_BBH/./conformally_flat_BBH_NRPy_function_prototypes.h:74:92: note: expected 'const CCTK_REAL8 *' {aka 'const double *'} but argument is of type 'CCTK_REAL8 (*)[Nxx_plus_2NGHOSTS1][Nxx_plus_2NGHOSTS0]' {aka 'double (*)[Nxx_plus_2NGHOSTS1][Nxx_plus_2NGHOSTS0]'} 74 | const CCTK_REAL *input_gf, | ~~~~~~~~~~~~~~~~~^~~~~~~~ make[3]: *** [NRPyEllipticET_conformally_flat_BBH_Initialize_ADMBase.c.o] Error 1 make[2]: *** [conformally_flat_BBH/make.checked] Error 2 make[1]: *** [/Users/elenaluisagoria/Cactus/configs/sim/lib/libthorn_NRPyEllipticET.a] Error 2 make[1]: *** Waiting for unfinished jobs.... COMPILING configs/sim/bindings/build/NaNCatcher/cctk_ThornBindings.c Creating /Users/elenaluisagoria/Cactus/configs/sim/lib/libthorn_NaNCatcher.a make: *** [sim] Error 2 I don't understand the reason for this error, could you help me solve it? Thank you, Best regards, Elena Goria

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Segmentation fault in TOV test
by Rhiannon Silva 02 Aug '24

02 Aug '24

Hi, I've managed to compile ET after switching to gnu compilers and openmpi, but I'm getting this warning: /usr/bin/ld: warning: libgfortran.so.3, needed by /usr/lib64/../lib64/liblapack.so, may conflict with libgfortran.so.5 The code passed the Hello World test but when I run the TOV test I get a segmentation fault, which seems to happen when it's testing vectorisation: Rank 0 with PID 139005 received signal 11 Writing backtrace to tov_ET/backtrace.0.txt -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun noticed that process rank 0 with PID 139005 on node ccs0135 exited on signal 11 (Segmentation fault). --- I also get this at the start of the .out file: [1721961556.411313] [ccs0135:139005:0] ucp_context.c:1529 UCX WARN UCP version is incompatible, required: 1.11, actual: 1.9 (release 0 /lib64/libucp.so.0) I'm also wondering about another message I get: "This OpenMPI build is integrated with Slurm. Use 'srun' to launch in a Slurm job rather than 'mpirun'." When I tried to use srun in the run script, I had problems, so I changed it back to mpirun. Not sure if that is causing a problem? Here is what happened when I used srun: [ccs0001:248227] mca_base_component_repository_open: unable to open mca_pmix_s2: libpmi2.so.0: cannot open shared object file: No such file or directory (ignored) [ccs0001:248227] mca_base_component_repository_open: unable to open mca_pmix_s1: libpmi.so.0: cannot open shared object file: No such file or directory (ignored) [ccs0001:248227] OPAL ERROR: Not initialized in file pmix2x_client.c at line 112 -------------------------------------------------------------------------- The application appears to have been direct launched using "srun", but OMPI was not built with SLURM's PMI support and therefore cannot execute. There are several options for building PMI support under SLURM, depending upon the SLURM version you are using: version 16.05 or later: you can use SLURM's PMIx support. This requires that you configure and build SLURM --with-pmix. Versions earlier than 16.05: you must use either SLURM's PMI-1 or PMI-2 support. SLURM builds PMI-1 by default, or you can manually install PMI-2. You must then build Open MPI using --with-pmi pointing to the SLURM PMI library location. Please configure as appropriate and try again. -------------------------------------------------------------------------- *** 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) [ccs0001:248227] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed! srun: error: ccs0001: task 0: Exited with exit code 1 --- I'm not sure where to start. Is any of the above likely to be causing the segmentation fault? Thanks, Rhiannon.

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Einstein Toolkit Meeting Reminder
by rhaas＠illinois.edu 31 Jul '24

31 Jul '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

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Agenda for Thursday's Meeting
by rhaas＠illinois.edu 29 Jul '24

29 Jul '24

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

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25 Jul '24

Hello, I am trying to create an account but never get the link to request an account after the 403 error. I deactivate protections and accept cookies without success. Could help me or send me the link ? ORCiD : 0009-0007-0965-8246 Thanks for your help Sandrine Lescaudron

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meeting minutes for 2024-07-25
by Roland Haas 25 Jul '24

25 Jul '24

Present: Steve, Peter, Roland, Bing-Ran HE, Lucas, Johnny, Nan Dong, Jake, Johnny, Cheng-Hsin, Liwei, Maxwell, Yosef ET release ========== * Maxwell will be release co-chair Unanswered questions ==================== * https://lists.einsteintoolkit.org/pipermail/users/2024-July/009393.html is caused by gcc being stricter about pointer types in C. Roland will respond. * Steve will address http://lists.einsteintoolkit.org/pipermail/users/2024-July/009391.html Open tickets ============ * https://bitbucket.org/einsteintoolkit/tickets/issues/2811 is ready to be applied * Steve will look into #2786: support CarpetX in Multipole https://bitbucket.org/einsteintoolkit/tickets/issues/2786 * Steve is looking into #2179: NaNChecker: fix output of NaNMask https://bitbucket.org/einsteintoolkit/tickets/issues/2179 * #2520: update gauge settings in TOV example to be more typical seems ok to apply (Steve), https://bitbucket.org/einsteintoolkit/tickets/issues/2520 * #2808: prevent wvuthorns/IllinoisGRMHD from compiling in release past 2024_05, https://bitbucket.org/einsteintoolkit/tickets/issues/2808 Leo will discuss this locally. Had a discussion on how the old and new IGM thorns agree / disagree * Peter and Zach will work on #963: Improve McLachlan accuracy, https://bitbucket.org/einsteintoolkit/tickets/issues/963/improve-mclachlan-… Einstein Toolkit translation ============================ Bing-Ran reported on efforts on creating Chinese language documentation for the ET. Currently have MPI set up and working on local cluster. Had a discussion on how to best incorporate this into the existing ET site. Steve suggests to have each language on a site and have link from one to the other. Steve and Bing-Ran will discuss this via email. 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 .

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

24 Jul '24

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Fortran compile errors
by Rhiannon Silva 22 Jul '24

22 Jul '24

Hi, I'm getting fortran errors while trying to build ET on my local cluster (Hawk, in Cardiff), as well as lots of warnings. Any suggestions? I'm using intel compilers and have tried these options F90FLAGS = -g -xCORE-AVX512 -safe-cray-ptr -traceback -align -pad These are the error messages: /nfshome/store04/users/c.c941286329/Cactus/configs/sim/build/GRHydro/GRHydro_HLLE.f90(2694): error #7844: Invalid directive. /nfshome/store04/users/c.c941286329/Cactus/configs/sim/build/GRHydro/GRHydro_HLLE.f90(2700): error #6410: This name has not been declared as an array or a function. [EOS_C] /nfshome/store04/users/c.c941286329/Cactus/configs/sim/build/GRHydro/GRHydro_HLLE.f90(2718): error #6410: This name has not been declared as an array or a function. [XPRESS] /nfshome/store04/users/c.c941286329/Cactus/configs/sim/build/GRHydro/GRHydro_HLLE.f90(2721): error #6410: This name has not been declared as an array or a function. [EOS_C] /nfshome/store04/users/c.c941286329/Cactus/configs/sim/build/GRHydro/GRHydro_HLLE.f90(2728): error #6410: This name has not been declared as an array or a function. [EOS_C] /nfshome/store04/users/c.c941286329/Cactus/configs/sim/build/GRHydro/GRHydro_HLLE.f90(2736): error #6790: This is an invalid statement; an END [PROGRAM] statement is required. /nfshome/store04/users/c.c941286329/Cactus/configs/sim/build/GRHydro/GRHydro_HLLE.f90(2736): error #6785: This name does not match the unit name. [H_VISCOSITY] The many warnings are mostly like this: /nfshome/store04/users/c.c941286329/Cactus/configs/sim/build/GRHydro/GRHydro_HLLE.f90(2710): warning #6717: This name has not been given an explicit type. [ANYERR] /nfshome/store04/users/c.c941286329/Cactus/configs/sim/build/GRHydro/GRHydro_HLLE.f90(2713): warning #8889: Explicit declaration of the EXTERNAL attribute is required. [RHO] What am I missing? Thanks, Rhiannon.

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Agenda for Thursday's Meeting
by rhaas＠illinois.edu 22 Jul '24

22 Jul '24

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

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Difference of running BNS template between reference result and my run
by Long, Sinan 22 Jul '24

22 Jul '24

Dear ET, I have run the template of the BNS merger with different versions of ET, specifically 202305 and 202211. The difference between the two versions is negligible. However, there is a noticeable difference between my run and the reference data provided on the ET website. Since I used the same files provided by the template, I am wondering what could the difference be and whether it indicates my running has certain faults. Thank you for your assistance. Best, Sinan

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hwloc build in ET: libtool error on NAS/Pleiades
by Bernard Kelly 18 Jul '24

18 Jul '24

Hi all. I may have asked this before, but does anyone encounter issues when building hwloc during an ET compilation? I recently downloaded the ET_2024_05 release on the machine Pleiades (NAS), and since hwloc isn't part of a loadable module on that machine, I have to build it myself. If I just let Cactus build hwloc as part of the ET build process for my configuration, this hwloc build fails somewhere in the linking stage -- error message below. It doesn't appear to be an issue with the hwloc source code itself --I've taken the source tar.gz file from hwloc/dist/ and gone through a standard "configure/make/make install" by hand, installing in my own $HOME/lib. Obviously I can keep doing this. But it would be more convenient to have Cactus build it automatically as it's supposed to. Any suggestions about what might be going wrong? Are there HWLOC-specific options I should have in my config-info (right now, I have nothing). Final note: the libtool installed on this machine isn't a particularly new version: pfe26.bjkelly1 57> libtool --version libtool (GNU libtool) 2.4.6 Written by Gordon Matzigkeit, 1996 Copyright (C) 2014 Free Software Foundation, Inc. Any input appreciated, Bernard --------------- error message -------------- hwloc: Building... Making all in include Making all in hwloc CC topology.lo CC traversal.lo CC distances.lo CC memattrs.lo CC cpukinds.lo CC components.lo CC bind.lo CC bitmap.lo CC pci-common.lo CC diff.lo CC shmem.lo CC misc.lo CC base64.lo CC topology-noos.lo CC topology-synthetic.lo CC topology-xml.lo CC topology-xml-nolibxml.lo CC topology-linux.lo CC topology-hardwired.lo CC topology-x86.lo CCLD libhwloc.la ../libtool: line 7759: cd: -W: invalid option cd: usage: cd [-L|[-P [-e]] [-@]] [dir] libtool: error: cannot determine absolute directory name of '-Wl,-R/nasa/pkgsrc/toss4/2022Q1-rome/lib' make[5]: *** [Makefile:928: libhwloc.la] Error 1 make[4]: *** [Makefile:664: all-recursive] Error 1 make[3]: *** No rule to make target '/nobackupp19/bjkelly1/codes/Cactus_ET_2024_05/configs/sim/scratch/done/hwloc', needed by 'version.c.o'. Stop. make[2]: *** [/nobackupp19/bjkelly1/codes/Cactus_ET_2024_05/lib/make/make.thornlib:113: make.checked] Error 2 make[1]: *** [/nobackupp19/bjkelly1/codes/Cactus_ET_2024_05/lib/make/make.configuration:179: /nobackupp19/bjkelly1/codes/Cactus_ET_2024_05/configs/sim/lib/libthorn_hwloc.a] Error 2 make: *** [Makefile:265: sim] Error 2 ------------------- -- ------------------------------------------------------------------ Bernard Kelly -- CRESST Assistant Research Scientist, NASA/GSFC Gravitational Astrophysics Laboratory --- Code 663 Phone: +1 (301) 286-7243 *** Fax: +1 (301) 286-2226 Web: http://science.gsfc.nasa.gov/sed/bio/bernard.j.kelly ORCID: orcid.org/0000-0002-3326-4454 ------------------------------------------------------------------

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Meeting minutes for 2024-07-18
by Leo Rosa Werneck 18 Jul '24

18 Jul '24

Hi all, Here are the minutes of today’s meeting. Chair: Sam Minutes: Leo Present: A (student from China), Sam Cupp, Steve Brandt, David Boyer, Keith Dow, Lucas Sanches, Zach Etienne, Leo Werneck, Johnny Tsao, Yosef Zlochower, Roland Haas, Bing-Ran HE * ET Release Timeline - Proposed new thorns and updates: - David's new TOV initial data thorn. - Probably SpacetimeX. - Zach wants to upgrade NRPyPN to the latest version. - Still no vice-manager, no volunteers yet. - Nothing else to discuss since Roland is not present. - testsuites: needs to be updated to include Mac OS. * Unanswered Questions - None. * Open Tickets - #2809: Cactus Makefile needs to be updated in the ET_2024_05 release. Steve will check. - #2179: mask bug in NaNChecker has been fixed and is ready for review. - #2520: David updated the parameters in the TOV example to use more usual values to the ML_BSSN settings. * Tickets Ready for Review: - #2179: See above. * Zach reports on some faculty members in China who are interested in using the Einstein Toolkit, some of which are experts in numerical relativity and some which are enthusiastic about the field. * Lucas reports on some good progress on trying to use Bear to setup clangd for the Einstein Toolkit. As clangd is a C/C++ LSP, this could provide a more friendly experience when using an IDE that supports it, such as VS Code and neovim. Next chair: Steve Next minutes: Roland Best, 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/>

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Einstein Toolkit Meeting Reminder
by rhaas＠illinois.edu 17 Jul '24

17 Jul '24

1 0

Agenda for Thursday's Meeting
by rhaas＠illinois.edu 15 Jul '24

15 Jul '24

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

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Meeting minutes for 2024-07-11
by Lucas Timotheo Sanches 11 Jul '24

11 Jul '24

Present: Lucas (Minutes), Roland (chair), David Boyer, Leo, Sam, Yosef # Current Etk release timeline * Things are looking OK for the release. * Test results OK (some failures on thorns known to be sensitive). * BNS gallery example is probably finished, the page is still to be updated. * BBH gallery example still missing. Deborah needs to be poked but may not have time. Roland will do the poking. # Next ETK release * We need to form a release coordination. Roland will be the release chair. * We need a release co-chair. There have been no volunteers so far. * Decide on features we will include (needs to be done now). Start querying people for possible features they would like to include. * Roland reports that Hayley J. Macpherson may have something to the cosmology toolkit. She needs to be further questioned on this. * David Boyer, a member of Zach's group has an inclusion: David Made a TOV solver that handles multiple ODEs, tabulated and piecewise EOS. He reports that adaptive RK4 is enabled for the ETK version but more can be enabled if the community desires. It is separated from the Nrpy EOS solver but was tested against that. # Mailing list * No unanswered questions on the mailing list. # Tickets * 2748: Yosef will review SpacetimeX (Z4C). He says his schedule may not be compatible, so this may have to change. * 2520: Assigned to David Boyer. * 2780: Sam suggested that this ticket should be closed and the inclusion of Baikal X dropped. Sam reports that Zach's group (the developers of Baikal/BaikalX) are not actively working on CarpetX thorns and the RIT group originally interested in it may no longer be using it.

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Einstein Toolkit Meeting Reminder
by rhaas＠illinois.edu 10 Jul '24

10 Jul '24

1 0

Agenda for Thursday's Meeting
by rhaas＠illinois.edu 08 Jul '24

08 Jul '24

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

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