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

1 0

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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