Users July 2014

users@lists.einsteintoolkit.org

16 participants
16 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&…

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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-----

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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.

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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

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Stampede
by Ian Hinder 07 Aug '14

07 Aug '14

Hi all, Has anyone run into problems recently with Cactus jobs on Stampede? I've had jobs die when checkpointing, and also mysteriously hanging for no apparent reason. These might be separate problems. The checkpointing issue occurred when I submitted several jobs and they all started checkpointing at the same time after 3 hours. The hang happened after a few hours of evolution, with GDB reporting > MPIDI_CH3I_MRAILI_Get_next_vbuf (vc_ptr=0x7fff00d9a8d8, vbuf_ptr=0x13) > at src/mpid/ch3/channels/mrail/src/gen2/ibv_channel_manager.c:296 > 296 for (; i < mv2_MPIDI_CH3I_RDMA_Process.polling_group_size; > ++i) Unfortunately I didn't ask for a backtrace. I'm using mvapich2. I've been in touch with support and they said the dying while checkpointing coincided with the filesystems being hit hard by my jobs, which makes sense, but they didn't see any problems in their logs, and they have no idea about the mysterious hang. I repeated the hanging job and it ran fine. -- Ian Hinder http://numrel.aei.mpg.de/people/hinder

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Problem with Jenkins test system
by Ian Hinder 29 Jul '14

29 Jul '14

Hi all, I noticed today that the Jenkins automated build and test system which runs the tests for the Einstein Toolkit was not actually checking out the latest version of the code. This means that the reports of success do not correspond to the latest versions. I have added a workaround to the problem, and I think it is now fixed. It is possible that we will now see failures due to changes introduced since the last tested version. I do not know which is the last version which was actually tested. It is definitely before 11-Jun-2014, so no commits since then will have been tested. I suspect that the problem started some time in May. -- Ian Hinder http://numrel.aei.mpg.de/people/hinder

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 28 Jul '14

28 Jul '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 week that are still open: - 1640: RK2-MR2-1 test fails - 1641: Switching Slab from alltoall to irecv/isend Other projects include - Make Illinois code work with standard ET - git transition As always, please add to this list if you like. Frank Loeffler

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 28 Jul '14

28 Jul '14

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simfactory job restart
by Vassilios Mewes 28 Jul '14

28 Jul '14

Hello all, a simulation has crashed without checkpointing (there was a filesystem error on the cluster) how can i restart it? do I need to delete the uncompleted output-xxxx and output-xxx-active folder? or is that not necessary and simfactory will automatically find the latest valid checkpoint in simulation time and restart from there? best wishes, Vassili

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[trac-noreply@einsteintoolkit.org: Re: [Einstein Toolkit] #1338: Rename Carpet output files]
by Frank Loeffler 25 Jul '14

25 Jul '14

----- Forwarded message from Einstein Toolkit <trac-noreply(a)einsteintoolkit.org> ----- Date: Sat, 26 Jul 2014 04:01:29 -0000 From: Einstein Toolkit <trac-noreply(a)einsteintoolkit.org> Cc: trac(a)einsteintoolkit.org Subject: Re: [Einstein Toolkit] #1338: Rename Carpet output files Content-Type: text/plain; charset="utf-8" Reply-To: users(a)einsteintoolkit.org #1338: Rename Carpet output files -----------------------+---------------------------------------------------- Reporter: eschnett | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: Carpet | Version: Resolution: | Keywords: -----------------------+---------------------------------------------------- Comment (by knarf): We should do something about this, so I now (again) suggest "." as separator, replacing the "::". The default should change too, but the old behaviour should be allowed using a parameter. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1338#comment:21> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit ----- End forwarded message -----

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Users July 2014