Users August 2014

users@lists.einsteintoolkit.org

10 participants
13 discussions

Einstein Toolkit Meeting Reminder
by Frank Loeffler 14 May '15

14 May '15

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ I short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. My agenda contains: - Fall workshop - PLEASE let us know if you come [1]! - Hotel booking - Release planning - release date: Mon Oct 24 2011 - freeze date: Mon Sep 26 - the day of the call! - branch name: ET_2011_10 - List of release-concerning bugs [2] - ET paper: proposed "freeze" by Oct 3rd (Mon after this call) As always: feel free to add to this list. Frank Loeffler [1] https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Fall_2011#Fall_Einstei… [2] https://trac.einsteintoolkit.org/query?status=!closed&milestone=ET_2011_11&…

10 31

PARAMCHECK and non fatal but inefficient parameter choices
by Roland Haas 03 Oct '14

03 Oct '14

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello all, the PARAMCHECK routines normally abort if inconsistent parameters are given. I have a situation where the parameter choice is valid and the result of the simulation should be identical with or without the parameter set (assuming not bugs...), however setting the parameter is likely going to make the simulation slower. Im this particular case the parameter is CarpetLib::use_higher_order_restriction when used for a run with Carpet::refinement_centering = "vertex". In that case restriction is just a copy operation and independent of use_higher_order_restriction, for cell-centered runs this is not true anymore and this is the situation that use_higher_order_restriction was implemented for. However there is code in Carpet/Evolve.cc that calls POSTREGRID multiple times if use_higher_order_restriction is set (it has to in order to get symmetry, outer boundaries and also ghost zones right). For vertex centering nothing should happen (since there is a second call to POSTRESTRICT after all restriction is done). Options are: * do nothing since these parameters are perfectly valid if slow * warn with level CCTK_WARN_COMPLAIN ("the user should know about this but the problem is not terribly surprising") * warn with level CCTK_WARN_ALERT ("the results of this run will be wrong, and this will surprise the user, but we can still continue the run") * abort since the user most likely did not want to set the parameter Note that current practise in most code seems to be to use CCTK_WARN_COMPLAIN (Level 1) for warnings about situations that do not invalidate the result and CCTK_WARN_ABORT (Level 0) for anything that invalidates results, ie. we do not adhere to the meaning of the levels documented in src/include/cctk_WarnLevel.h . 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://keys.gnupg.net. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iEYEARECAAYFAlNqrvQACgkQTiFSTN7SboVuBQCg0IhvBi92zRKRVKoe216Q6wND NEYAn25pqT33i90JbhXmBJ90jKNAP4wd =+2Fk -----END PGP SIGNATURE-----

3 4

Re: [Users] Einstein Toolkit Meeting Reminder
by Frank Loeffler 23 Sep '14

23 Sep '14

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ In short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. Some tickets within the last two weeks that are still open: - 778: Compiling PittNullCode is slow - 1648: simfactory default for <1 node jobs - 1648: MPI thorn should auto configure - 1650: piraha parses "-0." incorrectly (reviewed ok - but not closed) - 1618: Compile with adaptive MPI (new patches) Other projects include - Make Illinois code work with standard ET - git transition As always, please add to this list if you like. Frank Loeffler

6 7

No Einstein Toolkit Meeting
by Frank Loeffler 29 Aug '14

29 Aug '14

Hi, There will be no Einstein Toolkit Meeting next Monday, as most of the people in the US will celebrate Labor day (doing the opposite). If you feel that something has to be discussed before the next meeting on Sep 8th, please use this email list. Frank Loeffler

1 0

Einstein Toolkit Meeting Minutes
by Frank Loeffler 29 Aug '14

29 Aug '14

Hi, I apologize for the late minutes. Present were (and I quite probably forgot someone): Peter, Erik, Zach, Philipp, and Frank > - 1648: MPI thorn should auto configure (new patch) This has in the meantime been committed. > - 1618: Compile with adaptive MPI (no new patch yet) This is still in the works. > - Make Illinois code work with standard ET There are still discrepancies between GRHydro+HLLE and other codes (Whisky, IllinoisGRMHD) and HLLE that are not understood. > - git transition Please test the new repositories. They are still checked out in /repos, but should work. Make sure you have (write) access if you think you should have. You will need a bitbucket account. > - MHD status & interest in vector potential There is currently only little attention and interest in this, with the slight hope of revival in about two months or so, according to Philipp. Frank

1 0

Any 64-bit issues I should be aware of?
by Ian Smith 25 Aug '14

25 Aug '14

Hi again list, I've just done another install onto my 64-bit Ubuntu 14.04 machine (the 32-bit Debian one is running now), and when I submit a job I get this output: $ ./simfactory/bin/sim show-output --follow static_tov Simulation name: static_tov ================================================================================ The job's Formaline output is: ================================================================================ (file does not exist) ================================================================================ The job's stdout is: ================================================================================ Simulation name: static_tov Running simulation static_tov Preparing: Checking: /home/ian/simulations/static_tov/output-0001-active bonsai Wed Aug 20 17:10:06 BST 2014 Environment: Starting: INFO (Cactus): Increasing logging level from 0 to 3 Wed Aug 20 17:10:07 BST 2014 Simfactory Done at date: 0 ================================================================================ The job's stderr is: ================================================================================ + set -e + cd /home/ian/simulations/static_tov/output-0001-active + echo Checking: + pwd + hostname + date + echo Environment: + export GMON_OUT_PREFIX=gmon.out + GMON_OUT_PREFIX=gmon.out + export OMP_NUM_THREADS=4 + OMP_NUM_THREADS=4 + env + echo Starting: ++ date +%s + export CACTUS_STARTTIME=1408551006 + CACTUS_STARTTIME=1408551006 + mpirun -np 1 /home/ian/simulations/static_tov/SIMFACTORY/exe/cactus_sim -L 3 /home/ian/simulations/static_tov/output-0001/static_tov_small.par [bonsai:02183] *** Process received signal *** [bonsai:02183] Signal: Segmentation fault (11) [bonsai:02183] Signal code: Address not mapped (1) [bonsai:02183] Failing at address: 0x44000098 [bonsai:02183] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7fefca300340] [bonsai:02183] [ 1] /usr/lib/libmpich.so.10(PMPI_Comm_rank+0x4b) [0x7fefc800d63b] [bonsai:02183] [ 2] /home/ian/simulations/static_tov/SIMFACTORY/exe/cactus_sim(CactusDefaultMyProc+0x6f) [0xc2951f] [bonsai:02183] [ 3] /home/ian/simulations/static_tov/SIMFACTORY/exe/cactus_sim(CCTKi_CommandLineFinished+0x40) [0xc16380] [bonsai:02183] [ 4] /home/ian/simulations/static_tov/SIMFACTORY/exe/cactus_sim(CCTKi_ProcessCommandLine+0x204) [0xc00744] [bonsai:02183] [ 5] /home/ian/simulations/static_tov/SIMFACTORY/exe/cactus_sim(CCTKi_InitialiseCactus+0x3c) [0xbfd8ec] [bonsai:02183] [ 6] /home/ian/simulations/static_tov/SIMFACTORY/exe/cactus_sim(main+0x1e) [0xbf542e] [bonsai:02183] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7fefc6f83ec5] [bonsai:02183] [ 8] /home/ian/simulations/static_tov/SIMFACTORY/exe/cactus_sim() [0xbfd62c] [bonsai:02183] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 0 with PID 2183 on node bonsai exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- ================================================================================ anyone else encountered or dealt with this? Cheers, Ian.

3 11

Einstein Toolkit Meeting Reminder
by Frank Loeffler 24 Aug '14

24 Aug '14

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ In short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. Some tickets within the last two weeks that are still open: - 1648: MPI thorn should auto configure (new patch) - 1618: Compile with adaptive MPI (no new patch yet) Other projects include - Make Illinois code work with standard ET - git transition - MHD status & interest in vector potential As always, please add to this list if you like. Frank Loeffler

1 0

Migration from SVN to Git
by Barry Wardell 20 Aug '14

20 Aug '14

Hi, Following on from the discussion in the last Einstein Toolkit meeting, this is an update of the status of the transition from svn to git. * (Almost) all Cactus and Einstein Toolkit arrangements have now been converted to git and merged into a one-repository-per-arrangement layout. * The repositories are available on Bitbucket under the Cactus < https://bitbucket.org/cactuscode> and EinsteinToolkit < https://bitbucket.org/einsteintoolkit> team pages. * The git testing thornlist < http://svn.einsteintoolkit.org/manifest/trunk/git_testing.th> has been updated to point to the new repositories. I have verified that it is possible to checkout and build the Einstein Toolkit using this thornlist. * The conversion process is automated using scripts provided in the ET git transition repository <https://bitbucket.org/ianhinder/etgittransition>. * All master, ET release and Cactus release branches have been checked to perfectly match (i.e. no missing commits, no file differences) their svn counterparts. Similarly for the ET and Cactus release tags. * There is a list of known outstanding issues available < https://bitbucket.org/ianhinder/etgittransition/src/master/issues.md>. It's likely that most, if not all of these issues are sufficiently minor that they can be ignored. To proceed further it would be helpful if people (particularly those responsible for maintaining thorns and those who have opinions on how the final layout should appear) could take a look at the repositories and report any issues or suggested changes. In particular, it would be helpful to have feedback on how to handle AEIThorns, LSUThorns, ExternalLibraries, GRHydro, and the TAT thorns. Regards, Barry

4 10

Cactus build problems
by Ian Smith 20 Aug '14

20 Aug '14

Hi List! I've tried building this a few times over the last couple of years, on different machines, and always get stuck at the build stage, currently I have this set of errors: ------------------------------------------------------ There were 3 errors during execution of the CST These must be corrected before compilation can proceed ------------------------------------------------------ ------------------------------------------------------ Warnings were generated during execution of the CST ------------------------------------------------------ CST error 1: -> Configuration script for thorn FORTRAN returned exit code 1 Error message: 'Fortran thorn requires that a Fortran compiler is defined, but F77 = 'none' and F90 = 'none'. Aborting.' CST error 2: -> Configuration script for thorn LORENE returned exit code 1 (no error message) CST error 3: -> Configuration script for thorn MPI returned exit code 1 (no error message) ------------------------------------------------------ I have all the compilers that I think are needed, and have also added the dependencies listed at https://docs.einsteintoolkit.org/et-docs/Simplified_Tutorial_for_New_Users I have also tried things like: export F77=/usr/bin/f77 export F90=/usr/bin/f95 to no avail. As for installed packages, these seem relevant to the errors . . . ian@bonsai Tue Jul 29 02:58 PM /opt/EinsteinToolkit/Cactus $ aptitude search fort | grep '^i' i fort77 - Invoke f2c like a real compiler i gfortran - GNU Fortran 95 compiler i A gfortran-4.8 - GNU Fortran compiler i A libgfortran-4.8-dev - Runtime library for GNU Fortran applicatio i libgfortran3 - Runtime library for GNU Fortran applicatio ian@bonsai Tue Jul 29 02:58 PM /opt/EinsteinToolkit/Cactus $ aptitude search mpi | grep '^i' i libmpich-dev - Development files for MPICH i A libmpich10 - Shared libraries for MPICH i libmpich2-dev - Transitional dummy package for MPICH devel i A libopenmpi1.6 - high performance message passing library - i A mpi-default-bin - Standard MPI runtime programs (metapackage i A mpich - Implementation of the MPI Message Passing i mpich2 - Transitional dummy package i A openmpi-bin - high performance message passing library - i A openmpi-common - high performance message passing library - Can anyone assist with this? I am using Xubuntu 14.04 64-bit. Cheers, Ian.

4 12

Re: [Users] Users Digest, Vol 52, Issue 17 Fortran -problem
by David Bradley 18 Aug '14

18 Aug '14

On 07/29/2014 12:00 PM, users-request(a)einsteintoolkit.org wrote: > Send Users mailing list submissions to > users(a)einsteintoolkit.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.einsteintoolkit.org/mailman/listinfo/users > or, via email, send a message with subject or body 'help' to > users-request(a)einsteintoolkit.org > > You can reach the person managing the list at > users-owner(a)einsteintoolkit.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Users digest..." > > > > Today's Topics: > > 1. Problem with Jenkins test system (Ian Hinder) > 2. Cactus build problems (Ian Smith) > > > > _______________________________________________ > Users mailing list > Users(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users > I have had luck with builds for some time now with openmpi. In fact builds for the last month have been with the cnf file in the attachment named david.cfg. My only recent problem ( not related) is the number of nodes not working please take a look at the file and see if it helps any. Also, any additions appreciated. What is your thoughts on .cactus file in home account. Dave

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

Users August 2014