Users

users@lists.einsteintoolkit.org

3 participants
3984 discussions

Meeting minutes for 2023-02-23
by Bing-Jyun Tsao 23 Feb '23

23 Feb '23

- Present: Steve, Helvi, Peter, Leo, Cheng-Hsin, Keith, Roland, Yosef, Zach, Johnny - seminar proposal: Adam J. Peterson, "Code generation for AMReX with applications to numerical relativity", 2301.08354 <https://arxiv.org/abs/2301.08354>, which uses AMReX for Z4c evolution - March 09th, recording available on seminar <https://www.einsteintoolkit.org/seminars/> page and youtube - Unanswered questions on mailing list - email <http://lists.einsteintoolkit.org/pipermail/users/2023-February/008847.html> from Roland: nobody used Anvil before - [SB] Another email regarding running on Rome powered supercomputer: [RH] Delta is powered by Rome, Steve or Roland will ask the user to provide the files for compiling (optionlists, etc.) and send this email to the mailing list - New GRMHD library: take IllinoisGRMHD and NRPyEOS and make it into a library, [LW] No need to review NRPyEOS and NRPyLeakage, will need reviewers for other parts. Terrence will review particle code, Peter can review NPSolverSX (?), [HW] have reviewers and champions in contact - [RH] People who agree to test the cluster, Steven Brandt - deep bayou, Peter - sunrise, Roland - stampede2, expanse, Summit, Frontera, [LW] add detail to the release - Open tickets - SummationByParts <https://bitbucket.org/einsteintoolkit/tickets/issues/2700/summationbyparts-…>: [RH] prefix needs to be fix to not pollute namespace, fix name conflict when Fortran code add underscore at the end, warning: might break something in Llama - Mac os Ventura <https://bitbucket.org/einsteintoolkit/tickets/issues/2699/etk-fails-on-mac-…>: [RH] duplicate from the mailing list, could be listed as solved - Compile on the M1 system <https://bitbucket.org/einsteintoolkit/tickets/issues/2682/updates-to-compil…> [RH] PAPI needs significant changes, HomeBrew changes the links - Slab fails <https://bitbucket.org/einsteintoolkit/tickets/issues/2683/slab-fails-to-com…> [RH] Slab claim to optionally use MPI and Kranc tutorial did without it, but it actually does use MPI so a pull request is made to fix this - Include NRPyLeakage <https://bitbucket.org/einsteintoolkit/tickets/issues/2689/include-nrpyleaka…> [LW]: will be included for the next release - EHFinder parfile <https://bitbucket.org/einsteintoolkit/tickets/issues/2698/misner_22_80_3dpa…>: [PD] will look into it - [YZ] Large ET jobs on Frontera, startup overwhelming the system, every MPI proc starts reading files. Proposed solution: at a checkpoint, only a group of MPI procs to open files, workaround by staggering when the job starts, issue might also occur with CarpetX. [RH] Assign token barrier to MPI. Roland can send the token to Yosef. Frontera should fix their file system. - Next week: Chair: Zach Minute: Roland

1 0

Re: [Users] ETK on mac os Ventura -- unsupported tapi file error
by Hamilton, Maria 23 Feb '23

23 Feb '23

It worked by adding the path to F90FLAGS. Thank you! _______________________ Maria C. Babiuc Hamilton, Ph.D. Professor, Department of Physics College of Science, Marshall University, 1 John Marshall Drive, Huntington, WV, 25755 Room S 257, Phone: (304)696-2754 ________________________________ From: Roland Haas Sent: Tuesday, February 21, 2023 4:03 PM To: Hamilton, Maria Cc: users(a)einsteintoolkit.org Subject: Re: [Users] ETK on mac os Ventura -- unsupported tapi file error Hello Maria, > The problem was that the ld path for anaconda3 was above the one for > /usr/bin, even after uninstalling anaconda3. Ah, yes, I could see that causing problems. > The compilation stopped at: > > Cactus/configs/sim/build/FLRWSolver/flrw_powerspecics.f90:833:0: > include 'fftw3.f03' > Fatal Error: Cannot open included file 'fftw3.f03'. > > Is there a fix? Hmm. Interesting. fftw3.f03 looks like some include file for Fortran 2003 bindings for fftw3. If macports / homebrew does not install it, then you should be able to use the FFTW3_DIR = BUILD option in your option list to force Cactus to compile its own copy from source. Looking at my own setup this does produce a file fftw3.f03 in configs/sim/scratch/external/FFTW3/include/fftw3.f03 which one hopes is included in the Fortran include search path or CPP search path. This would be the -J or -I options though FLRWsolver needs -J since it used a Fortran include statement (I think, I am no Fortran expert). If you verify that the file fftw3.f03 exists (either in the Cactus compiled FFTW3 or in macports / homebrew) but is not found then the quickest fix for you right now is likely to add: -J<PATH-TO-INCLUDE-DIR-WITH-FFTW3.F03> to you F90FLAGS in the option list. 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 .

2 1

Einstein Toolkit Meeting Reminder
by reminders＠einsteintoolkit.org 22 Feb '23

22 Feb '23

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

1 0

Re: [Users] ETK on mac os Ventura -- unsupported tapi file error
by Hamilton, Maria 21 Feb '23

21 Feb '23

Hello Roland, My laptop is x86 based. I succeeded to get gcc-12 to work! It still complained after uninstalling and reinstalling XCode and CommandLineTools. The problem was that the ld path for anaconda3 was above the one for /usr/bin, even after uninstalling anaconda3. The compilation stopped at: Cactus/configs/sim/build/FLRWSolver/flrw_powerspecics.f90:833:0: include 'fftw3.f03' Fatal Error: Cannot open included file 'fftw3.f03'. Is there a fix? Maria _______________________ Maria C. Babiuc Hamilton, Ph.D. Professor, Department of Physics College of Science, Marshall University, 1 John Marshall Drive, Huntington, WV, 25755 Room S 257, Phone: (304)696-2754 ________________________________ From: Roland Haas Sent: Monday, February 20, 2023 6:32 AM To: Hamilton, Maria Cc: users(a)einsteintoolkit.org Subject: Re: [Users] ETK on mac os Ventura -- unsupported tapi file error Hello Maria, Is you laptop M1 or x86 based? Only the most recent release (ET_2022_11) has been tested on M1 macOS. The error you are getting is strange since it reports trying to compile for x86 which of course should not happen on M1 system. Beyond that I unfortunately cannot help since I do not myself use macOS (I compiler precisely 4 times a year, once for macports, once for homebrew for each release). You could try and re-install the commandlinetools and xcode. The official way is actually to remove the folder directly (no uninstall, https://stackoverflow.com/a/29949289): sudo rm -rf /Library/Developer/CommandLineTools Yours, Roland > While trying to create a configuration, I got this error: > ____________ > cat configs/sim/config-data/config.log > This file contains any messages produced by compilers while > running configure, to aid debugging if configure makes a mistake. > > configure:922: checking host system type > configure:948: checking for mawk > configure:948: checking for gawk > configure:948: checking for nawk > configure:948: checking for awk > configure:1017: checking whether make sets ${MAKE} > configure:1082: checking whether the C compiler (gcc-12 -g -std=gnu99 -rdynamic) works > configure:1099: gcc-12 -o conftest -g -std=gnu99 -rdynamic conftest.c 1>&5 > ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/lib/libSystem.tbd' for architecture x86_64 > collect2: error: ld returned 1 exit status > configure: failed program was: > > #line 1094 "configure" > #include "confdefs.h" > > int main(){return(0);} int PilotMain(){return(0);} > (base) > ____________ > > Browsing the internet I founnd that this might appear if Anaconda is installed. I uninstalled it and the error is still there. > Any suggestion on how to fix it? > > Thanks, > Maria > > > _______________________ > Maria C. Babiuc Hamilton, Ph.D. > Professor, Department of Physics > College of Science, Marshall University, > 1 John Marshall Drive, Huntington, WV, 25755 > Room S 257, Phone: (304)696-2754 > -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://keys.gnupg.net.

2 1

simfactory files for Anvil system at Purdue
by Roland Haas 21 Feb '23

21 Feb '23

Hello all, Does anyone have (tested, in use, trustworthy) simfactory (or batchtools) files for Purdue's Anvil cluster? https://www.rcac.purdue.edu/knowledge/anvil/overview If so, would you be ok to share them with me and / or contribute them to simfactory? Yours, Roland -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu .

1 0

Agenda for Thursday's Meeting
by reminders＠einsteintoolkit.org 20 Feb '23

20 Feb '23

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

1 0

ETK on mac os Ventura -- unsupported tapi file error
by Hamilton, Maria 20 Feb '23

20 Feb '23

While trying to create a configuration, I got this error: ____________ cat configs/sim/config-data/config.log This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. configure:922: checking host system type configure:948: checking for mawk configure:948: checking for gawk configure:948: checking for nawk configure:948: checking for awk configure:1017: checking whether make sets ${MAKE} configure:1082: checking whether the C compiler (gcc-12 -g -std=gnu99 -rdynamic) works configure:1099: gcc-12 -o conftest -g -std=gnu99 -rdynamic conftest.c 1>&5 ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/usr/lib/libSystem.tbd' for architecture x86_64 collect2: error: ld returned 1 exit status configure: failed program was: #line 1094 "configure" #include "confdefs.h" int main(){return(0);} int PilotMain(){return(0);} (base) ____________ Browsing the internet I founnd that this might appear if Anaconda is installed. I uninstalled it and the error is still there. Any suggestion on how to fix it? Thanks, Maria _______________________ Maria C. Babiuc Hamilton, Ph.D. Professor, Department of Physics College of Science, Marshall University, 1 John Marshall Drive, Huntington, WV, 25755 Room S 257, Phone: (304)696-2754

2 1

SummationByParts c_file_processor issues
by Samuel Tootle 18 Feb '23

18 Feb '23

For the compiling gurus: I've been working towards finalizing the FUKA importer build system for inclusion into the ETK and I've recently added additional thorns to the build list to run the test par. For completeness, I'm compiling in the following way: yes | make test-config THORNLIST=thornlist/test.th options=test.cfg; make test: Currently, all thorns compile successfully except for SummationByParts which gives the following error: /home/user/lib/ETKREL/Cactus/arrangements/CactusNumerical/SummationByParts/src/get_offset.c:49:17: error: redefinition of ‘get_shiftout’ 49 | void CCTK_FCALL CCTK_FNAME(get_shiftout)( const CCTK_POINTER_TO_CONST cctkGH_, | ^~~~~~~~~~~~ /home/user/lib/ETKREL/Cactus/arrangements/CactusNumerical/SummationByParts/src/get_offset.c:11:6: note: previous definition of ‘get_shiftout’ with type ‘void(const void * const, CCTK_INT4 *)’ {aka ‘void(const void * const, int *)’} 11 | void get_shiftout ( const CCTK_POINTER_TO_CONST cctkGH_, What appears to be happening is that the c_file_processor.pl is not handling the generation of creating a fortran function in place of CCTK_FNAME so far as I understand it. For instance, if I check the `Cactus/configs/test/build/SummationByParts/get_offset.c` file, the CCTK_FNAME statement is still there. Conversely, if I check `Cactus/configs/test/build/Boundary/FlatBoundary.c` which also uses CCTK_FNAME, these statements have been correctly removed by the pre-processor. Oddly enough, if I run `make test --just-print` I obtain the following which suggests that it is at least executing the processor correctly. Checking status of thorn SummationByParts if [ ! -d ./ ] ; then mkdir -p ./ ; fi cd ./ ; make CCTK_TARGET=make.checked TOP=/home/user/lib/ETKREL/Cactus/configs/test CONFIG=/home/user/lib/ETKREL/Cactus/configs/test/config-data SRCDIR=/home/user/lib/ETKREL/Cactus/arrangements/CactusNumerical/SummationByParts/src THORN=SummationByParts USESTHORNS="" -f /home/user/lib/ETKREL/Cactus/lib/make/make.subdir{if test yes = 'yes'; then echo '#line 1 "'/home/user/lib/ETKREL/Cactus/arrangements/CactusNumerical/SummationByParts/src/get_offset.c'"'; fi; cat /home/user/lib/ETKREL/Cactus/arrangements/CactusNumerical/SummationByParts/src/get_offset.c; } | perl -s /home/user/lib/ETKREL/Cactus/lib/sbin/c_file_processor.pl -line_directives=yes -source_file_name=/home/user/lib/ETKREL/Cactus/arrangements/CactusNumerical/SummationByParts/src/get_offset.c /home/user/lib/ETKREL/Cactus/configs/test/config-data > get_offset.c echo COMPILING CactusNumerical/SummationByParts/src/get_offset.c I have compared the above to the compilation of Boundary/src/FlatBoundary.c which compiles successfully and also includes the generation of a number of Fortran functions using CCTK_FNAME. So far, no discrepancies have been found that would highlight why summationbyparts is failing. I will continue to try and resolve this, but I hope someone with more experience with the pre-processors will be able to shed some light on the issue. Cheers, Samuel

2 3

Minutes for 2023-02-16 meeting
by Yosef Zlochower 16 Feb '23

16 Feb '23

Present: H Witek, L Werneck, J Tsao, K Dow, R Haas, S Cupp, S Tootle Z Etienne, Y Zlochower * Proposal for seminar on "Code generation for AMReX with applications to numerical relativity" [https://arxiv.org/abs/2301.08354] Will try scheduling for March 9 (before most spring breaks) * Next release updates Reviewers: Fuka reader : Konrad Topolski Elliptica : Beyhan Karakaş NRPyLeakage: Terrence Pierre Jacques TwoPunctures: Thiago Assumpção NP Scalars: Possible Peter Diener Kuibit: Cheng-Hsin Cheng NRPyEOS: Possibly a UIdaho student * SSL certificate for lists.einsteintoolkit.org will be generated [currently the server does not use a good certificate]. Plan is also to update mailman. * Summary of Mexican NR School https://sites.google.com/ciencias.unam.mx/numericalrelativity/home?authuser… 4 days of both theoretical lectures and hands-on sessions Was very successful (60+ attendees daily) Chair for next meeting: Helvi Minute taker for next meeting: Johnny -- Dr. Yosef Zlochower Center for Computational Relativity and Gravitation Professor School of Mathematical Sciences Rochester Institute of Technology 85 Lomb Memorial Drive Rochester, NY 14623 Office:74-2067 Phone: +1 585-475-6103 yrzsma(a)rit.edu CONFIDENTIALITY NOTE: The information transmitted, including attachments, is intended only for the person(s) or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and destroy any copies of this information.

1 0

Einstein Toolkit Meeting Reminder
by reminders＠einsteintoolkit.org 15 Feb '23

15 Feb '23

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

Users