From users at einsteintoolkit.org Mon Jun 2 15:18:02 2025 From: users at einsteintoolkit.org (users at einsteintoolkit.org) Date: Mon, 02 Jun 2025 15:18:02 -0500 Subject: [Users] Agenda for Thursday's Meeting Message-ID: <683e06fa.paDRUBAfI/NNRgT+%users@einsteintoolkit.org> Please update the Wiki with agenda items for Thursday's meeting. Thanks! https://docs.einsteintoolkit.org/et-docs/meeting_agenda --The Maintainers From s-kokauf at uni-greifswald.de Wed Jun 4 07:02:11 2025 From: s-kokauf at uni-greifswald.de (Kaufhold, Konstantin) Date: Wed, 4 Jun 2025 14:02:11 +0200 Subject: [Users] Problem installing the ETK Message-ID: <9989204a704984a6821b2cee56979101@groupware.uni-greifswald.de> Hi, I am currently trying to install the ETK to my personal laptop for a project.? I am using an ArchLinux system with linux?6.14.9. The processor in my laptop is an AMD Ryzen 7 PRO 8840U. While trying to compile the toolkit I get the error /usr/include/c++/15.1.1/cstdlib:83:15: schwerwiegender Fehler: stdlib.h: Datei oder Verzeichnis nicht gefunden ? ?83 | #include_next which then causes the compilation to fail. The only version of the bug I found, which I could reproduce locally, was using "gcc -isystem /usr/include" as described in an bug report (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=70129) from 2016 for gcc. I tried compiling a small Hello World script written in C++ with "gcc", "gcc -I" and gcc -isystem" and the last option gave me the same error, the rest worked just fine. But I'm not sure if that is the real reason as other OptionFiles indicate, that gcc can and has been successfully used to compile?the ETK and I have not seen the "-isystem" glag invoked anywhere, so I'm guessing the the error is on my side, although I have no clue where exactly. I have attached the make.log file and my OptionsList, as I had to explicitly give the ETK the HDF folders and then decided to do it for most external libraries I saw in the list and have locally on my system. I appreciate any ideas or advice on fixing this problem and thank you in advance for taking the time to look over my problem. With best regards Konstantin Kaufhold -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: make.log URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: OptionList Type: text/x-makefile Size: 3427 bytes Desc: not available URL: From jpmferreira at ua.pt Wed Jun 4 10:18:38 2025 From: jpmferreira at ua.pt (=?UTF-8?Q?Jos=C3=A9_Ferreira?=) Date: Wed, 4 Jun 2025 16:18:38 +0100 Subject: [Users] Problem installing the ETK In-Reply-To: <9989204a704984a6821b2cee56979101@groupware.uni-greifswald.de> References: <9989204a704984a6821b2cee56979101@groupware.uni-greifswald.de> Message-ID: <6ac1a168-6017-4e49-a249-61464872a5cf@ua.pt> Hello Konstantin, I've sucessfully compiled the toolkit on an Arch Linux machine with the option files that I'm sending as an attachment. The dependencies are all listed in the option file inside, and are all available and up-to-date in the official repositories. There is one small caveat: one of the updates of HDF5 in the Arch repositories somehow broke the Toolkit compilation, now it fails to find HDF5. I wanted to look into it and figure out whats going on, but I decided to be lazy instead and just downgrade HDF5. Version 1.14.5-1 in repositories works. Since I don't have any other package depending on HDF5, this works fine for me. If you figure out what happened, please do let me know. Also, when I started using the toolkit, I was getting random core dumps on Arch and Arch based distros. This hasn't happened to me in many months now, so it was probably something to do with a specific version of one of the libraries. Either way, if that does happen to you, here's the bug report that I made: https://bitbucket.org/einsteintoolkit/tickets/issues/2774/openmp-heisenbug-with-default-thornfile Best, Jos? Ferreira On 04/06/25 13:02, Kaufhold, Konstantin wrote: > Hi, > > I am currently trying to install the ETK to my personal laptop for a > project. > I am using an ArchLinux system with linux?6.14.9. The processor in my > laptop is an AMD Ryzen 7 PRO 8840U. > While trying to compile the toolkit I get the error > > /usr/include/c++/15.1.1/cstdlib:83:15: schwerwiegender Fehler: > stdlib.h: Datei oder Verzeichnis nicht gefunden > ? ?83 | #include_next > > which then causes the compilation to fail. > The only version of the bug I found, which I could reproduce locally, > was using "gcc -isystem /usr/include" as described in an bug report > (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=70129 > ) from 2016 for > gcc. I tried compiling a small Hello World script written in C++ with > "gcc", "gcc -I" and gcc -isystem" and the last option gave me the same > error, the rest worked just fine. > But I'm not sure if that is the real reason as other OptionFiles > indicate, that gcc can and has been successfully used to compile?the > ETK and I have not seen the "-isystem" glag invoked anywhere, so I'm > guessing the the error is on my side, although I have no clue where > exactly. > I have attached the make.log file and my OptionsList, as I had to > explicitly give the ETK the HDF folders and then decided to do it for > most external libraries I saw in the list and have locally on my system. > I appreciate any ideas or advice on fixing this problem and thank you > in advance for taking the time to look over my problem. > > With best regards > > Konstantin Kaufhold > > _______________________________________________ > Users mailing list > Users at einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- # Cactus configuration for Arch and Arch-based distros # NOTES: # - `-Wno-error=incompatible-pointer-types` removes error temporarily, see https://bitbucket.org/einsteintoolkit/tickets/issues/2802/compilation-faiulres-in-twopunctures_bbhsf # - AEILocalInterp defines `bool` which in `c23` is a keywork, specify C17 standard as a workaround # - The toolkit raises an error with lastest HDF5 version. Is this a toolkit or Arch errror? Version 1.14.5-1 in repos works # Packages to install (all available on official repos) # - gcc # - gcc-fortran # - hdf5 # - blas-openblas # - openmpi # - gsl # - hwloc # - libjpeg-turbo # - openssl # - fftw # - boost ## Decide which flags will be used at compile-time OPTIMISE = yes WARN = yes DEBUG = no PROFILE = no OPENMP = yes ## Preprocessors and Compilers CPP = cpp FPP = cpp CC = gcc CXX = g++ F77 = gfortran F90 = gfortran ## Default flags CPPFLAGS = -DMPICH_IGNORE_CXX_SEEK FPPFLAGS = -traditional CFLAGS = -g3 -march=native -Wno-error=incompatible-pointer-types -std=gnu17 CXXFLAGS = -g3 -march=native -Wno-error=incompatible-pointer-types -std=gnu++17 F77FLAGS = -g3 -march=native -fcray-pointer -m128bit-long-double -ffixed-line-length-none -fno-range-check F90FLAGS = -g3 -march=native -fcray-pointer -m128bit-long-double -ffixed-line-length-none -fno-range-check LDFLAGS = -rdynamic ## Optimization flags CPP_OPTIMISE_FLAGS = -DKRANC_VECTORS # -DCARPET_OPTIMISE -DNDEBUG FPP_OPTIMISE_FLAGS = # -DCARPET_OPTIMISE -DNDEBUG C_OPTIMISE_FLAGS = -O3 CXX_OPTIMISE_FLAGS = -O3 F77_OPTIMISE_FLAGS = -O3 F90_OPTIMISE_FLAGS = -O3 ## Warning flags CPP_WARN_FLAGS = -Wall FPP_WARN_FLAGS = -Wall C_WARN_FLAGS = -Wall CXX_WARN_FLAGS = -Wall F77_WARN_FLAGS = -Wall F90_WARN_FLAGS = -Wall ## Debug flags CPP_DEBUG_FLAGS = -DCARPET_DEBUG -fsanitize=undefined -fsanitize=thread FPP_DEBUG_FLAGS = -DCARPET_DEBUG -fsanitize=undefined -fsanitize=thread C_DEBUG_FLAGS = -O0 -fsanitize=undefined -fsanitize=thread CXX_DEBUG_FLAGS = -O0 -fsanitize=undefined -fsanitize=thread F77_DEBUG_FLAGS = -O0 -fsanitize=undefined -fsanitize=thread F90_DEBUG_FLAGS = -O0 -fsanitize=undefined -fsanitize=thread ## Code profiling flags CPP_PROFILE_FLAGS = FPP_PROFILE_FLAGS = C_PROFILE_FLAGS = -pg CXX_PROFILE_FLAGS = -pg F77_PROFILE_FLAGS = -pg F90_PROFILE_FLAGS = -pg ## OpenMP CPP_OPENMP_FLAGS = -fopenmp FPP_OPENMP_FLAGS = -fopenmp C_OPENMP_FLAGS = -fopenmp CXX_OPENMP_FLAGS = -fopenmp F77_OPENMP_FLAGS = -fopenmp F90_OPENMP_FLAGS = -fopenmp ## Libraries location LIBDIRS = MPI_DIR = /usr HDF5_DIR = /usr GSL_DIR = /usr BOOST_DIR = /usr PTHREADS_DIR = NO_BUILD LIBS = gfortran open-pal z # ? C_LINE_DIRECTIVES = yes # ? F_LINE_DIRECTIVES = yes # ? From users at einsteintoolkit.org Wed Jun 4 17:15:01 2025 From: users at einsteintoolkit.org (users at einsteintoolkit.org) Date: Wed, 04 Jun 2025 17:15:01 -0500 Subject: [Users] Einstein Toolkit Meeting Reminder Message-ID: <6840c565.lem0ncTmF17noOza%users@einsteintoolkit.org> 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 From sbrandt at cct.lsu.edu Thu Jun 5 10:02:27 2025 From: sbrandt at cct.lsu.edu (Steven Brandt) Date: Thu, 5 Jun 2025 10:02:27 -0500 Subject: [Users] Meeting minutes for 2025-06-05` Message-ID: <1aa3beaf-2335-45a0-9775-e22533412d33@cct.lsu.edu> June 5, 2025 Present: Roland, Steve, Lucas, Calil, Johnny, Zach, Bill Gabella, Deborah Calil called in with memory problems when running in Unigrid. Hopefully, they will create a ticket. Lessons Learned from the Release: * Issues with creating release branches. Only Roland and Steve can really do it. * Need to start testing earlier. We didn't discover some problems until after the release. * Somehow reduce the work for the release. Gallery Examples: * Zach and BBH, had trouble running it. * Steve Poisson Gallery Example * Axidilaton - Deborah Ferguson (ran it) External libraries are often a problem: * HDF5 build failures. Fedora now works, but possibly for the wrong reasons. Should be a ticket. * SILO tries to identify the machine, and has a default for "localhost." Need to disable this test for known clusters. * Add a Spack recipe? ET Summer School * Most speakers are confirmed * Amount of people registered will fit in the room * 30 participants * Online attendees should register * Remote participants will happen via zoom Update on Bahahah - Quickly drafted a documentation.tex based on AI (Gemini 2.5 Pro), then edited. Status of NRPy Elliptic ID solver. Currently, a two punctures solver. Does not allow for refinement. High mass ratios are hard. Tickets: 2873 - Disable hard-coded compiler options in Silo Proposal: CCTK_ASSERT() macro which calles CCTK_Error on failure 2872 - gcc 15 is causing issues because it is stricter. From s-kokauf at uni-greifswald.de Fri Jun 6 01:46:29 2025 From: s-kokauf at uni-greifswald.de (Kaufhold, Konstantin) Date: Fri, 6 Jun 2025 08:46:29 +0200 Subject: [Users] Problem installing the ETK In-Reply-To: <6ac1a168-6017-4e49-a249-61464872a5cf@ua.pt> References: <6ac1a168-6017-4e49-a249-61464872a5cf@ua.pt> Message-ID: Hello Jos?, I did manage to compile it on wednesday with my own OptionsList, just had to call make after the compilation stopped due to the error I've described, then it compiled without problems. I the tried it again with your OptionsList and it did not fail with that error, but at the very end of the process I got a new error involving hdf5m reading /usr/bin/ld: /home/KK/Programieren/ETK/Cactus/configs/sim/scratch/external/Silo/lib/libsiloh5.a(H5FDsilo.o): undefined reference to symbol 'H5FDregister' /usr/bin/ld: /lib/libhdf5.so.310: error adding symbols: DSO missing from command line collect2: Fehler: ld gab 1 als Ende-Status zur?ck which did not pop up with my config. The only difference in how we handle hdf5 is that I explicitly tell it where the /Lib and Include directories are. Maybe there is some effect due to the different compiler flags, but I am not that experienced with using them, so I have no clue where it would stem from. I also did not get any core dumps yet, but I have also only run the WaveToy thorn twice, so I'll have to see what happens in the future. Anyways, thank you very much for your help. With best regards Konstantin Kaufhold Am Mittwoch, den 04-06-2025 um 17:18 schrieb Jos? Ferreira: Hello Konstantin, I've sucessfully compiled the toolkit on an Arch Linux machine with the option files that I'm sending as an attachment. The dependencies are all listed in the option file inside, and are all available and up-to-date in the official repositories. There is one small caveat: one of the updates of HDF5 in the Arch repositories somehow broke the Toolkit compilation, now it fails to find HDF5. I wanted to look into it and figure out whats going on, but I decided to be lazy instead and just downgrade HDF5. Version 1.14.5-1 in repositories works. Since I don't have any other package depending on HDF5, this works fine for me. If you figure out what happened, please do let me know. Also, when I started using the toolkit, I was getting random core dumps on Arch and Arch based distros. This hasn't happened to me in many months now, so it was probably something to do with a specific version of one of the libraries. Either way, if that does happen to you, here's the bug report that I made: https://bitbucket.org/einsteintoolkit/tickets/issues/2774/openmp-heisenbug-with-default-thornfile Best, Jos? Ferreira On 04/06/25 13:02, Kaufhold, Konstantin wrote: Hi, I am currently trying to install the ETK to my personal laptop for a project.? I am using an ArchLinux system with linux?6.14.9. The processor in my laptop is an AMD Ryzen 7 PRO 8840U. While trying to compile the toolkit I get the error /usr/include/c++/15.1.1/cstdlib:83:15: schwerwiegender Fehler: stdlib.h: Datei oder Verzeichnis nicht gefunden ? ?83 | #include_next which then causes the compilation to fail. The only version of the bug I found, which I could reproduce locally, was using "gcc -isystem /usr/include" as described in an bug report (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=70129) from 2016 for gcc. I tried compiling a small Hello World script written in C++ with "gcc", "gcc -I" and gcc -isystem" and the last option gave me the same error, the rest worked just fine. But I'm not sure if that is the real reason as other OptionFiles indicate, that gcc can and has been successfully used to compile?the ETK and I have not seen the "-isystem" glag invoked anywhere, so I'm guessing the the error is on my side, although I have no clue where exactly. I have attached the make.log file and my OptionsList, as I had to explicitly give the ETK the HDF folders and then decided to do it for most external libraries I saw in the list and have locally on my system. I appreciate any ideas or advice on fixing this problem and thank you in advance for taking the time to look over my problem. With best regards Konstantin Kaufhold _______________________________________________ Users mailing list Users at einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users -------------- next part -------------- An HTML attachment was scrubbed... URL: From users at einsteintoolkit.org Mon Jun 16 15:18:02 2025 From: users at einsteintoolkit.org (users at einsteintoolkit.org) Date: Mon, 16 Jun 2025 15:18:02 -0500 Subject: [Users] Agenda for Thursday's Meeting Message-ID: <68507bfa.9nIpkaHMJb6jhxnM%users@einsteintoolkit.org> Please update the Wiki with agenda items for Thursday's meeting. Thanks! https://docs.einsteintoolkit.org/et-docs/meeting_agenda --The Maintainers From users at einsteintoolkit.org Wed Jun 18 17:15:02 2025 From: users at einsteintoolkit.org (users at einsteintoolkit.org) Date: Wed, 18 Jun 2025 17:15:02 -0500 Subject: [Users] Einstein Toolkit Meeting Reminder Message-ID: <68533a66.MO+TfDVc9bjIjEb3%users@einsteintoolkit.org> 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 From rhaas at phas.ubc.ca Thu Jun 19 18:02:42 2025 From: rhaas at phas.ubc.ca (Roland Haas) Date: Thu, 19 Jun 2025 16:02:42 -0700 Subject: [Users] Problem installing the ETK In-Reply-To: References: <6ac1a168-6017-4e49-a249-61464872a5cf@ua.pt> Message-ID: <20250619160242.50f89212@fdea4908> Hello Konstantin, "DSO missing from command line" usually happens if you are not listing all libraries. Note that with static libraries order matters and eg for libsiloh5.a which requires HDF5 functions you need to have them like this: -lsiloh5 -lhdf5 ie the library that provides the functions last. Yours, Roland > [CAUTION: Non-UBC Email] > > Hello Jos?, > > > I did manage to compile it on wednesday with my own OptionsList, just > had to call make after the compilation stopped due to the error I've > described, then it compiled without problems. > I the tried it again with your OptionsList and it did not fail with > that error, but at the very end of the process I got a new error > involving hdf5m reading > > > /usr/bin/ld: > /home/KK/Programieren/ETK/Cactus/configs/sim/scratch/external/Silo/lib/libsiloh5.a(H5FDsilo.o): > undefined reference to symbol 'H5FDregister' > /usr/bin/ld: /lib/libhdf5.so.310: error adding symbols: DSO missing > from command line > collect2: Fehler: ld gab 1 als Ende-Status zur?ck > > > which did not pop up with my config. The only difference in how we > handle hdf5 is that I explicitly tell it where the /Lib and Include > directories are. Maybe there is some effect due to the different > compiler flags, but I am not that experienced with using them, so I > have no clue where it would stem from. > I also did not get any core dumps yet, but I have also only run the > WaveToy thorn twice, so I'll have to see what happens in the future. > Anyways, thank you very much for your help. > > > With best regards > > > Konstantin Kaufhold > > Am Mittwoch, den 04-06-2025 um 17:18 schrieb Jos? Ferreira: > > > > > Hello Konstantin, > > > > > > > > > I've sucessfully compiled the toolkit on an Arch Linux machine with > the option files that I'm sending as an attachment. > > > > The dependencies are all listed in the option file inside, and are all > available and up-to-date in the official repositories. > > > > > > > > > There is one small caveat: one of the updates of HDF5 in the Arch > repositories somehow broke the Toolkit compilation, now it fails to > find HDF5. > > > > > I wanted to look into it and figure out whats going on, but I decided > to be lazy instead and just downgrade HDF5. > > > > Version 1.14.5-1 in repositories works. > > > > Since I don't have any other package depending on HDF5, this works > fine for me. > > > > If you figure out what happened, please do let me know. > > > > > > > > > Also, when I started using the toolkit, I was getting random core > dumps on Arch and Arch based distros. > > > > This hasn't happened to me in many months now, so it was probably > something to do with a specific version of one of the libraries. > > > > Either way, if that does happen to you, here's the bug report that I > made: > https://bitbucket.org/einsteintoolkit/tickets/issues/2774/openmp-heisenbug-with-default-thornfile > > > > > > > > > Best, > > > > Jos? Ferreira > > > > > > > > > On 04/06/25 13:02, Kaufhold, Konstantin wrote: > > > > Hi, > > > I am currently trying to install the ETK to my personal laptop for a > project.? > I am using an ArchLinux system with linux?6.14.9. The processor in my > laptop is an AMD Ryzen 7 PRO 8840U. > While trying to compile the toolkit I get the error > > > > /usr/include/c++/15.1.1/cstdlib:83:15: schwerwiegender Fehler: > stdlib.h: Datei oder Verzeichnis nicht gefunden > ? ?83 | #include_next > > > > which then causes the compilation to fail. > The only version of the bug I found, which I could reproduce locally, > was using "gcc -isystem /usr/include" as described in an bug report > (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=70129) from 2016 for > gcc. I tried compiling a small Hello World script written in C++ with > "gcc", "gcc -I" and gcc -isystem" and the last option gave me the same > error, the rest worked just fine. > But I'm not sure if that is the real reason as other OptionFiles > indicate, that gcc can and has been successfully used to compile?the > ETK and I have not seen the "-isystem" glag invoked anywhere, so I'm > guessing the the error is on my side, although I have no clue where > exactly. > I have attached the make.log file and my OptionsList, as I had to > explicitly give the ETK the HDF folders and then decided to do it for > most external libraries I saw in the list and have locally on my > system. > I appreciate any ideas or advice on fixing this problem and thank you > in advance for taking the time to look over my problem. > > > With best regards > > > Konstantin Kaufhold > _______________________________________________ Users mailing list > Users at einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users -- 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 . -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 833 bytes Desc: OpenPGP digital signature URL: From rhaas at phas.ubc.ca Thu Jun 19 18:27:17 2025 From: rhaas at phas.ubc.ca (Roland Haas) Date: Thu, 19 Jun 2025 16:27:17 -0700 Subject: [Users] meeting minutes for 2025-06-19 Message-ID: <20250619162717.39ba4d4f@fdea4908> Present: Peter, Roland, Johnny, Keith, Lucas, Steve, Zach Next ET release =============== * Steve will be release chair * Zach proposed BHaHAHAH * missing gallery examples: BBH (Peter & Zach both), Poisson (Steve) ET summer school ================ * workshop recordings are live on YouTube (also in https://youtube.com/@einsteintoolkit) * Johnny will share playlist with ET channel * suggestion to provide program for half-day off, viz tour would have been possible * might want some more time for questions * Lucas suggested adding back more basic lectures, maybe poll participants when registering what they would be interested in Unanswered questions ==================== * Roland will try and follow up with: https://lists.einsteintoolkit.org/pipermail/users/2025-June/009659.html Tickets ======= * https://bitbucket.org/einsteintoolkit/tickets/issues/2855 noisex-improve-noise-generation-in-carpetx Lucas mentioned that even when specifying the algorithm in STL different implementations may still produce different random number sequences. Peter will look into modern Fortran implementations if the have better specified behaviour. * Steve brought up code developed by Stellar group (HPX) at LSU that does compensated addition to improve results of sum reductions. * https://bitbucket.org/einsteintoolkit/tickets/issues/2862 update-spacetimex-z4c-robust-stability needs review, for robust stability test for Z4c. Current candidates for inclusion are LeanBSSNMoLX and Cottonmouth. 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 . -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 833 bytes Desc: OpenPGP digital signature URL: From users at einsteintoolkit.org Mon Jun 23 15:18:02 2025 From: users at einsteintoolkit.org (users at einsteintoolkit.org) Date: Mon, 23 Jun 2025 15:18:02 -0500 Subject: [Users] Agenda for Thursday's Meeting Message-ID: <6859b67a.EFDhcFFOw7Sb5E3B%users@einsteintoolkit.org> Please update the Wiki with agenda items for Thursday's meeting. Thanks! https://docs.einsteintoolkit.org/et-docs/meeting_agenda --The Maintainers From users at einsteintoolkit.org Wed Jun 25 17:15:01 2025 From: users at einsteintoolkit.org (users at einsteintoolkit.org) Date: Wed, 25 Jun 2025 17:15:01 -0500 Subject: [Users] Einstein Toolkit Meeting Reminder Message-ID: <685c74e5.PVNZAIhNEMaYcV2B%users@einsteintoolkit.org> 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 From lucas.t.s.carneiro at gmail.com Thu Jun 26 09:52:37 2025 From: lucas.t.s.carneiro at gmail.com (Lucas Timotheo Sanches) Date: Thu, 26 Jun 2025 09:52:37 -0500 Subject: [Users] Meeting Minutes for 2025-06-26 Message-ID: Present: Steve R. Brandt, Lucas (minutes), Zachariah Etienne, Bill Gabella, Maxwell Rizzo, Roland Hass, Peter Diener, Beyham, Keith Dow, Maddie Smith, Leo Rosa Werneck, Yosef Zlochower. # Pre-agenda topics - Maxwell is trying to use Baikal with CCE exporter. The CCE exporter requires the time derivative of the lapse, which Baikal does not provide. Zach and Maxwell have discussed the best way for Baikal to provide that value. Zach proposes to add a parameter that enables CCE and adds an extra loop that saves the time derivative of the lapse. - Leo asks if he can change the default value of a parameter after a thorn has been accepted? Roland says to be careful to avoid a situation where a change breaks someone's working parameter file. He suggests adding checks for consistency. # Remaining gallery examples - Zach and Peter are still to produce their examples. # Questions on the mailing list - No questions # Open tickets - 2874: NRPyElliptic had no instructions for regeneration and was probably not regenerated for the next release. Leo was tasked with adding the instructions to the documentation. - 2855: Peter says Fortran does not guarantee reproducibility of random numbers between compilers. # Tickets ready for review 2860: Peter thought the ticket was resolved. He will check to see the status of it and potentially close it. From javihernandezm at posteo.net Fri Jun 27 11:54:53 2025 From: javihernandezm at posteo.net (=?utf-8?Q?Javiera_Hern=C3=A1ndez_Morales?=) Date: Fri, 27 Jun 2025 16:54:53 +0000 Subject: [Users] Problems with output in CarpetX Message-ID: Hi all, I am starting to learn the use of CarpetX and for this I started using the WaveToyX thorn. I wanted to ask for guidance for three problems that I have encountered so far, all of them related to the output data: 1) I wanted to get 3D data, for example in .tsv format. Here I realised that there is an ambiguous definition in the documentation for the parameter ?out_tsv?, which in section 12.1 it says to control TSV output and have default value ?yes?, but in section 14 it says to control the 3D output in TSV and have default value ?no?. This last behaviour is the one that I encounter when running the parfiles. 2) When I set up ?out_tsv" to ?yes? and ?out_tsv_every? to a number, for example = 16, I get 1D output every 16 iterations, but 3D output in every iteration, therefore I suspect that ?out_tsv_every? is only controlling the frequency of the 1D output, and I cannot find a way to control the frequency of 3D output. 3) I attempted to output data in HDF5 format but I did not succeed. I first set the parameter ?openpmd_format? to ?HDF5? and also set ?out_openpmd_vars? to the variables that I wanted, but I got an error in the first iteration: INFO (CarpetX): OutputGH: iteration 0, time 0.000000, run time 1 s INFO (CarpetX): OutputOpenPMD... INFO (CarpetX): Creating openPMD object... INFO (CarpetX): options: { "adios2": { "dataset": { "operators": [ ] } } } [et-juphub:699479] *** An error occurred in MPI_Comm_create_keyval [et-juphub:699479] *** reported by process [211877889,2] [et-juphub:699479] *** on communicator MPI_COMM_WORLD [et-juphub:699479] *** MPI_ERR_ARG: invalid argument of some other kind [et-juphub:699479] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, [et-juphub:699479] *** and potentially your MPI job) [et-juphub:699473] PMIX ERROR: UNREACHABLE in file ../../../src/server/pmix_server.c at line 2193 [et-juphub:699473] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal [et-juphub:699473] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages Simfactory Done at date: Thu 26 Jun 2025 09:19:08 AM UTC And I did not know how to move on from there. I am working on the ETK Tutorial server, in case that is important. Thanks in advance to anyone who took the time to read until here, I will be looking forward to any piece of advice :) Best, Javiera H.M. -------------- next part -------------- An HTML attachment was scrubbed... URL: From schnetter at gmail.com Mon Jun 30 09:45:03 2025 From: schnetter at gmail.com (Erik Schnetter) Date: Mon, 30 Jun 2025 10:45:03 -0400 Subject: [Users] Problems with output in CarpetX In-Reply-To: References: Message-ID: Javiera I recommend using 3D output in the way others are. CarpetX supports many parameters, but not all parameter combinations are well tested, or are intended for production runs. (1, 2) Yes, there are two ways of 3D ASCII (tsv) output. This is very slow and is thus only intended for debugging. Therefore it doesn't have all the features needed for comfortable output in production runs. (3) Either OpenPMD or Silo output are the preferred ways for production runs. These formats are also supported by post-processing and visualization tools. These are not file formats, but they only describe how the metadata are arranged (i.e. what names the attributes have) in the output files. The actual file formats are ADIOS2 (preferred, faster) or HDF5. OpenPMD uses ADIOS2 by default, Silo uses HDF5 by default. I do not know why the OpenPMD/HDF5 output is not working. The error message doesn't show enough detail. If you want HDF5 output then I recommend using Silo. This will produce an HDF5 file. I'm not sure that's what you want because, whatever you are going to do with the file, you will need to understand the metadata in the file, and thus that tool or script will need to understand either the OpenMPD or Silo layout. Otherwise your HDF5 will look like a bag of 3D arrays, each array describing a Fortran array, and it will be very difficult to find out which component of which variable and which time step on which refinement level is stored in what array: That's what the metadata describes. On the other hand, if you want to have an easy way to read the file, then you could use e.g. the Julia or Python of C++ bindings of the OpenMPD library, and you then wouldn't need to care whether the low-level file format is ADIOS2 or HDF5. What do you want to do with the 3D output? -erik > On Jun 27, 2025, at 12:54, Javiera Hern?ndez Morales wrote: > > Hi all, > > I am starting to learn the use of CarpetX and for this I started using the WaveToyX thorn. I wanted to ask for guidance for three problems that I have encountered so far, all of them related to the output data: > > 1) I wanted to get 3D data, for example in .tsv format. Here I realised that there is an ambiguous definition in the documentation for the parameter ?out_tsv?, which in section 12.1 it says to control TSV output and have default value ?yes?, but in section 14 it says to control the 3D output in TSV and have default value ?no?. This last behaviour is the one that I encounter when running the parfiles. > > 2) When I set up ?out_tsv" to ?yes? and ?out_tsv_every? to a number, for example = 16, I get 1D output every 16 iterations, but 3D output in every iteration, therefore I suspect that ?out_tsv_every? is only controlling the frequency of the 1D output, and I cannot find a way to control the frequency of 3D output. > > 3) I attempted to output data in HDF5 format but I did not succeed. I first set the parameter ?openpmd_format? to ?HDF5? and also set ?out_openpmd_vars? to the variables that I wanted, but I got an error in the first iteration: > > INFO (CarpetX): OutputGH: iteration 0, time 0.000000, run time 1 s > INFO (CarpetX): OutputOpenPMD... > INFO (CarpetX): Creating openPMD object... > INFO (CarpetX): options: > { > "adios2": { > "dataset": { > "operators": [ > ] > } > } > } > > [et-juphub:699479] *** An error occurred in MPI_Comm_create_keyval > [et-juphub:699479] *** reported by process [211877889,2] > [et-juphub:699479] *** on communicator MPI_COMM_WORLD > [et-juphub:699479] *** MPI_ERR_ARG: invalid argument of some other kind > [et-juphub:699479] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, > [et-juphub:699479] *** and potentially your MPI job) > [et-juphub:699473] PMIX ERROR: UNREACHABLE in file ../../../src/server/pmix_server.c at line 2193 > [et-juphub:699473] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal > [et-juphub:699473] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages > Simfactory Done at date: Thu 26 Jun 2025 09:19:08 AM UTC > And I did not know how to move on from there. > I am working on the ETK Tutorial server, in case that is important. > Thanks in advance to anyone who took the time to read until here, I will be looking forward to any piece of advice :) > Best, > Javiera H.M. > _______________________________________________ > Users mailing list > Users at einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users -------------- next part -------------- An HTML attachment was scrubbed... URL: From schnetter at gmail.com Mon Jun 30 11:53:10 2025 From: schnetter at gmail.com (Erik Schnetter) Date: Mon, 30 Jun 2025 12:53:10 -0400 Subject: [Users] Problems with output in CarpetX In-Reply-To: References: Message-ID: <40E50047-069B-4E89-B913-37D46EB9711D@gmail.com> Javiera Unfortunately I don't recall what software is installed on the ETK tutorial server... I'm sure someone else can help us out here? -erik > On Jun 30, 2025, at 12:17, Javiera Hern?ndez Morales wrote: > > Hi Erik, > > Thanks for your answer. Maybe for more context I should mention that I am starting to learn how to use the ETK, and for that I am using the notebooks provided in the tutorial server (etk.cct.lsu.edu ), together with some of the ones used for the last ETK workshop. > > To answer your last question, I am not doing anything specific with the output, I wanted to get 3D data to see if that could help me visualise the output of the examples I did with the WaveToyX thorn. > > Unfortunately I am not familiar with SILO, so I tried to use the 1D .tsv files, but they only provide the values in a slice (for example the wave as a function of x, for y=z=0), but I wanted to create a 3D plot similar to the one found in the CreatingANewThorn-WaveEqn notebook from the tutorial server (I leave a screenshot attached), that is why I thought of outputting 3D. > > To use SILO files I understand that one has to have VisIt installed, however when I wanted to install it in the tutorial server via terminal, I got the error that I am not allowed to install software, which I suppose makes sense. > > In principle all I want to do is experiment with the WaveToyX thorn (and the other examples, like SpacetimeWaveToyX or FluxWaveToyX), changing parameters and see how things behave, but I am struggling a lot with the visualisation part. Do you have any recommendations that I could implement in the environment of the ETK Tutorial server? > > Thanks in advance. > > Best regards, > > Javiera H.M. > > > >> El 30.06.2025, a las 16:45, Erik Schnetter escribi?: >> >> Javiera >> >> I recommend using 3D output in the way others are. CarpetX supports many parameters, but not all parameter combinations are well tested, or are intended for production runs. >> >> (1, 2) Yes, there are two ways of 3D ASCII (tsv) output. This is very slow and is thus only intended for debugging. Therefore it doesn't have all the features needed for comfortable output in production runs. >> >> (3) Either OpenPMD or Silo output are the preferred ways for production runs. These formats are also supported by post-processing and visualization tools. These are not file formats, but they only describe how the metadata are arranged (i.e. what names the attributes have) in the output files. The actual file formats are ADIOS2 (preferred, faster) or HDF5. OpenPMD uses ADIOS2 by default, Silo uses HDF5 by default. >> >> I do not know why the OpenPMD/HDF5 output is not working. The error message doesn't show enough detail. >> >> If you want HDF5 output then I recommend using Silo. This will produce an HDF5 file. I'm not sure that's what you want because, whatever you are going to do with the file, you will need to understand the metadata in the file, and thus that tool or script will need to understand either the OpenMPD or Silo layout. Otherwise your HDF5 will look like a bag of 3D arrays, each array describing a Fortran array, and it will be very difficult to find out which component of which variable and which time step on which refinement level is stored in what array: That's what the metadata describes. >> >> On the other hand, if you want to have an easy way to read the file, then you could use e.g. the Julia or Python of C++ bindings of the OpenMPD library, and you then wouldn't need to care whether the low-level file format is ADIOS2 or HDF5. >> >> What do you want to do with the 3D output? >> >> -erik >> >>> On Jun 27, 2025, at 12:54, Javiera Hern?ndez Morales wrote: >>> >>> Hi all, >>> >>> I am starting to learn the use of CarpetX and for this I started using the WaveToyX thorn. I wanted to ask for guidance for three problems that I have encountered so far, all of them related to the output data: >>> >>> 1) I wanted to get 3D data, for example in .tsv format. Here I realised that there is an ambiguous definition in the documentation for the parameter ?out_tsv?, which in section 12.1 it says to control TSV output and have default value ?yes?, but in section 14 it says to control the 3D output in TSV and have default value ?no?. This last behaviour is the one that I encounter when running the parfiles. >>> >>> 2) When I set up ?out_tsv" to ?yes? and ?out_tsv_every? to a number, for example = 16, I get 1D output every 16 iterations, but 3D output in every iteration, therefore I suspect that ?out_tsv_every? is only controlling the frequency of the 1D output, and I cannot find a way to control the frequency of 3D output. >>> >>> 3) I attempted to output data in HDF5 format but I did not succeed. I first set the parameter ?openpmd_format? to ?HDF5? and also set ?out_openpmd_vars? to the variables that I wanted, but I got an error in the first iteration: >>> >>> INFO (CarpetX): OutputGH: iteration 0, time 0.000000, run time 1 s >>> INFO (CarpetX): OutputOpenPMD... >>> INFO (CarpetX): Creating openPMD object... >>> INFO (CarpetX): options: >>> { >>> "adios2": { >>> "dataset": { >>> "operators": [ >>> ] >>> } >>> } >>> } >>> >>> [et-juphub:699479] *** An error occurred in MPI_Comm_create_keyval >>> [et-juphub:699479] *** reported by process [211877889,2] >>> [et-juphub:699479] *** on communicator MPI_COMM_WORLD >>> [et-juphub:699479] *** MPI_ERR_ARG: invalid argument of some other kind >>> [et-juphub:699479] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, >>> [et-juphub:699479] *** and potentially your MPI job) >>> [et-juphub:699473] PMIX ERROR: UNREACHABLE in file ../../../src/server/pmix_server.c at line 2193 >>> [et-juphub:699473] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal >>> [et-juphub:699473] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages >>> Simfactory Done at date: Thu 26 Jun 2025 09:19:08 AM UTC >>> And I did not know how to move on from there. >>> I am working on the ETK Tutorial server, in case that is important. >>> Thanks in advance to anyone who took the time to read until here, I will be looking forward to any piece of advice :) >>> Best, >>> Javiera H.M. >>> _______________________________________________ >>> Users mailing list >>> Users at einsteintoolkit.org >>> http://lists.einsteintoolkit.org/mailman/listinfo/users >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From schnetter at gmail.com Mon Jun 30 11:53:10 2025 From: schnetter at gmail.com (Erik Schnetter) Date: Mon, 30 Jun 2025 12:53:10 -0400 Subject: [Users] Problems with output in CarpetX In-Reply-To: References: Message-ID: <40E50047-069B-4E89-B913-37D46EB9711D@gmail.com> Javiera Unfortunately I don't recall what software is installed on the ETK tutorial server... I'm sure someone else can help us out here? -erik > On Jun 30, 2025, at 12:17, Javiera Hern?ndez Morales wrote: > > Hi Erik, > > Thanks for your answer. Maybe for more context I should mention that I am starting to learn how to use the ETK, and for that I am using the notebooks provided in the tutorial server (etk.cct.lsu.edu ), together with some of the ones used for the last ETK workshop. > > To answer your last question, I am not doing anything specific with the output, I wanted to get 3D data to see if that could help me visualise the output of the examples I did with the WaveToyX thorn. > > Unfortunately I am not familiar with SILO, so I tried to use the 1D .tsv files, but they only provide the values in a slice (for example the wave as a function of x, for y=z=0), but I wanted to create a 3D plot similar to the one found in the CreatingANewThorn-WaveEqn notebook from the tutorial server (I leave a screenshot attached), that is why I thought of outputting 3D. > > To use SILO files I understand that one has to have VisIt installed, however when I wanted to install it in the tutorial server via terminal, I got the error that I am not allowed to install software, which I suppose makes sense. > > In principle all I want to do is experiment with the WaveToyX thorn (and the other examples, like SpacetimeWaveToyX or FluxWaveToyX), changing parameters and see how things behave, but I am struggling a lot with the visualisation part. Do you have any recommendations that I could implement in the environment of the ETK Tutorial server? > > Thanks in advance. > > Best regards, > > Javiera H.M. > > > >> El 30.06.2025, a las 16:45, Erik Schnetter escribi?: >> >> Javiera >> >> I recommend using 3D output in the way others are. CarpetX supports many parameters, but not all parameter combinations are well tested, or are intended for production runs. >> >> (1, 2) Yes, there are two ways of 3D ASCII (tsv) output. This is very slow and is thus only intended for debugging. Therefore it doesn't have all the features needed for comfortable output in production runs. >> >> (3) Either OpenPMD or Silo output are the preferred ways for production runs. These formats are also supported by post-processing and visualization tools. These are not file formats, but they only describe how the metadata are arranged (i.e. what names the attributes have) in the output files. The actual file formats are ADIOS2 (preferred, faster) or HDF5. OpenPMD uses ADIOS2 by default, Silo uses HDF5 by default. >> >> I do not know why the OpenPMD/HDF5 output is not working. The error message doesn't show enough detail. >> >> If you want HDF5 output then I recommend using Silo. This will produce an HDF5 file. I'm not sure that's what you want because, whatever you are going to do with the file, you will need to understand the metadata in the file, and thus that tool or script will need to understand either the OpenMPD or Silo layout. Otherwise your HDF5 will look like a bag of 3D arrays, each array describing a Fortran array, and it will be very difficult to find out which component of which variable and which time step on which refinement level is stored in what array: That's what the metadata describes. >> >> On the other hand, if you want to have an easy way to read the file, then you could use e.g. the Julia or Python of C++ bindings of the OpenMPD library, and you then wouldn't need to care whether the low-level file format is ADIOS2 or HDF5. >> >> What do you want to do with the 3D output? >> >> -erik >> >>> On Jun 27, 2025, at 12:54, Javiera Hern?ndez Morales wrote: >>> >>> Hi all, >>> >>> I am starting to learn the use of CarpetX and for this I started using the WaveToyX thorn. I wanted to ask for guidance for three problems that I have encountered so far, all of them related to the output data: >>> >>> 1) I wanted to get 3D data, for example in .tsv format. Here I realised that there is an ambiguous definition in the documentation for the parameter ?out_tsv?, which in section 12.1 it says to control TSV output and have default value ?yes?, but in section 14 it says to control the 3D output in TSV and have default value ?no?. This last behaviour is the one that I encounter when running the parfiles. >>> >>> 2) When I set up ?out_tsv" to ?yes? and ?out_tsv_every? to a number, for example = 16, I get 1D output every 16 iterations, but 3D output in every iteration, therefore I suspect that ?out_tsv_every? is only controlling the frequency of the 1D output, and I cannot find a way to control the frequency of 3D output. >>> >>> 3) I attempted to output data in HDF5 format but I did not succeed. I first set the parameter ?openpmd_format? to ?HDF5? and also set ?out_openpmd_vars? to the variables that I wanted, but I got an error in the first iteration: >>> >>> INFO (CarpetX): OutputGH: iteration 0, time 0.000000, run time 1 s >>> INFO (CarpetX): OutputOpenPMD... >>> INFO (CarpetX): Creating openPMD object... >>> INFO (CarpetX): options: >>> { >>> "adios2": { >>> "dataset": { >>> "operators": [ >>> ] >>> } >>> } >>> } >>> >>> [et-juphub:699479] *** An error occurred in MPI_Comm_create_keyval >>> [et-juphub:699479] *** reported by process [211877889,2] >>> [et-juphub:699479] *** on communicator MPI_COMM_WORLD >>> [et-juphub:699479] *** MPI_ERR_ARG: invalid argument of some other kind >>> [et-juphub:699479] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, >>> [et-juphub:699479] *** and potentially your MPI job) >>> [et-juphub:699473] PMIX ERROR: UNREACHABLE in file ../../../src/server/pmix_server.c at line 2193 >>> [et-juphub:699473] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal >>> [et-juphub:699473] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages >>> Simfactory Done at date: Thu 26 Jun 2025 09:19:08 AM UTC >>> And I did not know how to move on from there. >>> I am working on the ETK Tutorial server, in case that is important. >>> Thanks in advance to anyone who took the time to read until here, I will be looking forward to any piece of advice :) >>> Best, >>> Javiera H.M. >>> _______________________________________________ >>> Users mailing list >>> Users at einsteintoolkit.org >>> http://lists.einsteintoolkit.org/mailman/listinfo/users >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rhaas at phas.ubc.ca Mon Jun 30 12:20:48 2025 From: rhaas at phas.ubc.ca (Roland Haas) Date: Mon, 30 Jun 2025 10:20:48 -0700 Subject: [Users] Problems with output in CarpetX In-Reply-To: <40E50047-069B-4E89-B913-37D46EB9711D@gmail.com> References: <40E50047-069B-4E89-B913-37D46EB9711D@gmail.com> Message-ID: <20250630102048.4b986a9b@fdea4908> Hello all, There's no VisIt instance installed on the tutorial server (it only provides an interface using jupyter notebooks, no X11 server access). I believe Steve has written some Python code to visualize CarpetX data. Yours, Roland > [CAUTION: Non-UBC Email] > > Javiera > > Unfortunately I don't recall what software is installed on the ETK tutorial server... I'm sure someone else can help us out here? > > -erik > > > On Jun 30, 2025, at 12:17, Javiera Hern?ndez Morales wrote: > > > > Hi Erik, > > > > Thanks for your answer. Maybe for more context I should mention that I am starting to learn how to use the ETK, and for that I am using the notebooks provided in the tutorial server (etk.cct.lsu.edu ), together with some of the ones used for the last ETK workshop. > > > > To answer your last question, I am not doing anything specific with the output, I wanted to get 3D data to see if that could help me visualise the output of the examples I did with the WaveToyX thorn. > > > > Unfortunately I am not familiar with SILO, so I tried to use the 1D .tsv files, but they only provide the values in a slice (for example the wave as a function of x, for y=z=0), but I wanted to create a 3D plot similar to the one found in the CreatingANewThorn-WaveEqn notebook from the tutorial server (I leave a screenshot attached), that is why I thought of outputting 3D. > > > > To use SILO files I understand that one has to have VisIt installed, however when I wanted to install it in the tutorial server via terminal, I got the error that I am not allowed to install software, which I suppose makes sense. > > > > In principle all I want to do is experiment with the WaveToyX thorn (and the other examples, like SpacetimeWaveToyX or FluxWaveToyX), changing parameters and see how things behave, but I am struggling a lot with the visualisation part. Do you have any recommendations that I could implement in the environment of the ETK Tutorial server? > > > > Thanks in advance. > > > > Best regards, > > > > Javiera H.M. > > > > > > > >> El 30.06.2025, a las 16:45, Erik Schnetter escribi?: > >> > >> Javiera > >> > >> I recommend using 3D output in the way others are. CarpetX supports many parameters, but not all parameter combinations are well tested, or are intended for production runs. > >> > >> (1, 2) Yes, there are two ways of 3D ASCII (tsv) output. This is very slow and is thus only intended for debugging. Therefore it doesn't have all the features needed for comfortable output in production runs. > >> > >> (3) Either OpenPMD or Silo output are the preferred ways for production runs. These formats are also supported by post-processing and visualization tools. These are not file formats, but they only describe how the metadata are arranged (i.e. what names the attributes have) in the output files. The actual file formats are ADIOS2 (preferred, faster) or HDF5. OpenPMD uses ADIOS2 by default, Silo uses HDF5 by default. > >> > >> I do not know why the OpenPMD/HDF5 output is not working. The error message doesn't show enough detail. > >> > >> If you want HDF5 output then I recommend using Silo. This will produce an HDF5 file. I'm not sure that's what you want because, whatever you are going to do with the file, you will need to understand the metadata in the file, and thus that tool or script will need to understand either the OpenMPD or Silo layout. Otherwise your HDF5 will look like a bag of 3D arrays, each array describing a Fortran array, and it will be very difficult to find out which component of which variable and which time step on which refinement level is stored in what array: That's what the metadata describes. > >> > >> On the other hand, if you want to have an easy way to read the file, then you could use e.g. the Julia or Python of C++ bindings of the OpenMPD library, and you then wouldn't need to care whether the low-level file format is ADIOS2 or HDF5. > >> > >> What do you want to do with the 3D output? > >> > >> -erik > >> > >>> On Jun 27, 2025, at 12:54, Javiera Hern?ndez Morales wrote: > >>> > >>> Hi all, > >>> > >>> I am starting to learn the use of CarpetX and for this I started using the WaveToyX thorn. I wanted to ask for guidance for three problems that I have encountered so far, all of them related to the output data: > >>> > >>> 1) I wanted to get 3D data, for example in .tsv format. Here I realised that there is an ambiguous definition in the documentation for the parameter ?out_tsv?, which in section 12.1 it says to control TSV output and have default value ?yes?, but in section 14 it says to control the 3D output in TSV and have default value ?no?. This last behaviour is the one that I encounter when running the parfiles. > >>> > >>> 2) When I set up ?out_tsv" to ?yes? and ?out_tsv_every? to a number, for example = 16, I get 1D output every 16 iterations, but 3D output in every iteration, therefore I suspect that ?out_tsv_every? is only controlling the frequency of the 1D output, and I cannot find a way to control the frequency of 3D output. > >>> > >>> 3) I attempted to output data in HDF5 format but I did not succeed. I first set the parameter ?openpmd_format? to ?HDF5? and also set ?out_openpmd_vars? to the variables that I wanted, but I got an error in the first iteration: > >>> > >>> INFO (CarpetX): OutputGH: iteration 0, time 0.000000, run time 1 s > >>> INFO (CarpetX): OutputOpenPMD... > >>> INFO (CarpetX): Creating openPMD object... > >>> INFO (CarpetX): options: > >>> { > >>> "adios2": { > >>> "dataset": { > >>> "operators": [ > >>> ] > >>> } > >>> } > >>> } > >>> > >>> [et-juphub:699479] *** An error occurred in MPI_Comm_create_keyval > >>> [et-juphub:699479] *** reported by process [211877889,2] > >>> [et-juphub:699479] *** on communicator MPI_COMM_WORLD > >>> [et-juphub:699479] *** MPI_ERR_ARG: invalid argument of some other kind > >>> [et-juphub:699479] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, > >>> [et-juphub:699479] *** and potentially your MPI job) > >>> [et-juphub:699473] PMIX ERROR: UNREACHABLE in file ../../../src/server/pmix_server.c at line 2193 > >>> [et-juphub:699473] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal > >>> [et-juphub:699473] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages > >>> Simfactory Done at date: Thu 26 Jun 2025 09:19:08 AM UTC > >>> And I did not know how to move on from there. > >>> I am working on the ETK Tutorial server, in case that is important. > >>> Thanks in advance to anyone who took the time to read until here, I will be looking forward to any piece of advice :) > >>> Best, > >>> Javiera H.M. > >>> _______________________________________________ > >>> Users mailing list > >>> Users at einsteintoolkit.org > >>> http://lists.einsteintoolkit.org/mailman/listinfo/users > >> > > > 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 . -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 833 bytes Desc: OpenPGP digital signature URL: From users at einsteintoolkit.org Mon Jun 30 15:18:02 2025 From: users at einsteintoolkit.org (users at einsteintoolkit.org) Date: Mon, 30 Jun 2025 15:18:02 -0500 Subject: [Users] Agenda for Thursday's Meeting Message-ID: <6862f0fa.rxj2BNPRjo0Sncr3%users@einsteintoolkit.org> Please update the Wiki with agenda items for Thursday's meeting. Thanks! https://docs.einsteintoolkit.org/et-docs/meeting_agenda --The Maintainers From javihernandezm at posteo.net Mon Jun 30 11:17:17 2025 From: javihernandezm at posteo.net (=?utf-8?Q?Javiera_Hern=C3=A1ndez_Morales?=) Date: Mon, 30 Jun 2025 16:17:17 +0000 Subject: [Users] Problems with output in CarpetX In-Reply-To: References: Message-ID: Hi Erik, Thanks for your answer. Maybe for more context I should mention that I am starting to learn how to use the ETK, and for that I am using the notebooks provided in the tutorial server (etk.cct.lsu.edu ), together with some of the ones used for the last ETK workshop. To answer your last question, I am not doing anything specific with the output, I wanted to get 3D data to see if that could help me visualise the output of the examples I did with the WaveToyX thorn. Unfortunately I am not familiar with SILO, so I tried to use the 1D .tsv files, but they only provide the values in a slice (for example the wave as a function of x, for y=z=0), but I wanted to create a 3D plot similar to the one found in the CreatingANewThorn-WaveEqn notebook from the tutorial server (I leave a screenshot attached), that is why I thought of outputting 3D. To use SILO files I understand that one has to have VisIt installed, however when I wanted to install it in the tutorial server via terminal, I got the error that I am not allowed to install software, which I suppose makes sense. In principle all I want to do is experiment with the WaveToyX thorn (and the other examples, like SpacetimeWaveToyX or FluxWaveToyX), changing parameters and see how things behave, but I am struggling a lot with the visualisation part. Do you have any recommendations that I could implement in the environment of the ETK Tutorial server? Thanks in advance. Best regards, Javiera H.M. ? > El 30.06.2025, a las 16:45, Erik Schnetter escribi?: > > Javiera > > I recommend using 3D output in the way others are. CarpetX supports many parameters, but not all parameter combinations are well tested, or are intended for production runs. > > (1, 2) Yes, there are two ways of 3D ASCII (tsv) output. This is very slow and is thus only intended for debugging. Therefore it doesn't have all the features needed for comfortable output in production runs. > > (3) Either OpenPMD or Silo output are the preferred ways for production runs. These formats are also supported by post-processing and visualization tools. These are not file formats, but they only describe how the metadata are arranged (i.e. what names the attributes have) in the output files. The actual file formats are ADIOS2 (preferred, faster) or HDF5. OpenPMD uses ADIOS2 by default, Silo uses HDF5 by default. > > I do not know why the OpenPMD/HDF5 output is not working. The error message doesn't show enough detail. > > If you want HDF5 output then I recommend using Silo. This will produce an HDF5 file. I'm not sure that's what you want because, whatever you are going to do with the file, you will need to understand the metadata in the file, and thus that tool or script will need to understand either the OpenMPD or Silo layout. Otherwise your HDF5 will look like a bag of 3D arrays, each array describing a Fortran array, and it will be very difficult to find out which component of which variable and which time step on which refinement level is stored in what array: That's what the metadata describes. > > On the other hand, if you want to have an easy way to read the file, then you could use e.g. the Julia or Python of C++ bindings of the OpenMPD library, and you then wouldn't need to care whether the low-level file format is ADIOS2 or HDF5. > > What do you want to do with the 3D output? > > -erik > >> On Jun 27, 2025, at 12:54, Javiera Hern?ndez Morales wrote: >> >> Hi all, >> >> I am starting to learn the use of CarpetX and for this I started using the WaveToyX thorn. I wanted to ask for guidance for three problems that I have encountered so far, all of them related to the output data: >> >> 1) I wanted to get 3D data, for example in .tsv format. Here I realised that there is an ambiguous definition in the documentation for the parameter ?out_tsv?, which in section 12.1 it says to control TSV output and have default value ?yes?, but in section 14 it says to control the 3D output in TSV and have default value ?no?. This last behaviour is the one that I encounter when running the parfiles. >> >> 2) When I set up ?out_tsv" to ?yes? and ?out_tsv_every? to a number, for example = 16, I get 1D output every 16 iterations, but 3D output in every iteration, therefore I suspect that ?out_tsv_every? is only controlling the frequency of the 1D output, and I cannot find a way to control the frequency of 3D output. >> >> 3) I attempted to output data in HDF5 format but I did not succeed. I first set the parameter ?openpmd_format? to ?HDF5? and also set ?out_openpmd_vars? to the variables that I wanted, but I got an error in the first iteration: >> >> INFO (CarpetX): OutputGH: iteration 0, time 0.000000, run time 1 s >> INFO (CarpetX): OutputOpenPMD... >> INFO (CarpetX): Creating openPMD object... >> INFO (CarpetX): options: >> { >> "adios2": { >> "dataset": { >> "operators": [ >> ] >> } >> } >> } >> >> [et-juphub:699479] *** An error occurred in MPI_Comm_create_keyval >> [et-juphub:699479] *** reported by process [211877889,2] >> [et-juphub:699479] *** on communicator MPI_COMM_WORLD >> [et-juphub:699479] *** MPI_ERR_ARG: invalid argument of some other kind >> [et-juphub:699479] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, >> [et-juphub:699479] *** and potentially your MPI job) >> [et-juphub:699473] PMIX ERROR: UNREACHABLE in file ../../../src/server/pmix_server.c at line 2193 >> [et-juphub:699473] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal >> [et-juphub:699473] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages >> Simfactory Done at date: Thu 26 Jun 2025 09:19:08 AM UTC >> And I did not know how to move on from there. >> I am working on the ETK Tutorial server, in case that is important. >> Thanks in advance to anyone who took the time to read until here, I will be looking forward to any piece of advice :) >> Best, >> Javiera H.M. >> _______________________________________________ >> Users mailing list >> Users at einsteintoolkit.org >> http://lists.einsteintoolkit.org/mailman/listinfo/users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2025-06-30 at 17.12.42 p.m..png Type: image/png Size: 72975 bytes Desc: not available URL: