Users October 2015

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14 participants
25 discussions

Re: [Users] [ET Trac] [Einstein Toolkit] #1326: running loopcontrol on strange number of threads fails
by Erik Schnetter 11 Apr '19

11 Apr '19

Do you have a backtrace? -erik On Sunday, March 22, 2015, Einstein Toolkit < trac-noreply(a)einsteintoolkit.org> wrote: > #1326: running loopcontrol on strange number of threads fails > ------------------------------------+--------------------------------------- > Reporter: rhaas | Owner: > Type: defect | Status: new > Priority: minor | Milestone: > Component: EinsteinToolkit thorn | Version: > Resolution: | Keywords: LoopControl > ------------------------------------+--------------------------------------- > > Comment (by rhaas): > > This still happens even with current (Sun Mar 22 18:46:21 CET 2015) trunk, > though failure looks a bit different now: > {{{ > actus_sim: > /data/rhaas/postdoc/gr/ET_trunk/configs/sim/build/LoopControl/loopcontrol.cc:312: > T {anonymous}::divexact(T, T) [with T = int]: Assertion `i % j == 0' > failed > }}} > > -- > Ticket URL: <https://trac.einsteintoolkit.org/ticket/1326#comment:1> > Einstein Toolkit <http://einsteintoolkit.org> > The Einstein Toolkit > _______________________________________________ > Trac mailing list > Trac(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/trac > -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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meeting minutes for 2015-08-31
by Roland Haas 11 Apr '16

11 Apr '16

Present: Frank, Roland, Steve, Peter, Matt, Josh, Erik, Zach, Jonah, Elo There will be no ET call next week due to labour day/Thanksgiving weekend in North America. IllnoisGRMHD: * report is with Zach, was send via private email * separate repo is fine, Zach will create a repository * volunteer needed for the compatibility thorn * Zach will move compatibility thorns into same repo as IllinoisGRMHD GetComponents on OSX: * no OSX user has written * Roland will propose a patch simfactory on BeeGFS: * Erik will look into Bruno's proposed patch writing timeseries data into hdf5: * Frank would like to use this for things like the Hamiltonian norm * HDF5 supports extensible datasets, an example on how to use this is the HDF5 output of Multipole SPH in Cactus: * Matt has a more or less working version of SPH on grid background * came out of work at a national lab on generic grid methods * currently linked in a shared objects for mesh handling and nearest neighbour finding * currently writing his thesis, so code is not changing much right now * load balancing through bisection initially then times the RHS and neighbour looked up push particles around * no octree, instead a hierarchical hash * particle to grid data currently uses SPH approximation for Tmunu at gridpoints of Cactus grid * will arrange for time for presentation through mailing 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://keys.gnupg.net.

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Exact meaning of prolongation tags
by Federico Guercilena 31 Oct '15

31 Oct '15

Hello, could anyone tell me a few details regarding the Carpet prolongation operators? It appears there's no real documentation about them. Looking at Carpet source code I can see these operators are available: none sync restrict copy Lagrange ENO ENOVOL WENO TVD Lagrange_monotone STAGGER011 STAGGER101 STAGGER110 STAGGER111 The "polynomial" ones (Lagrange, ENO, etc) appear to be self explanatory, more or less. I'm particularly interested in the exact behaviour of "none", "sync" and "copy". "none" and "sync" are the same thing apparently. I find the "restrict" operator very confusing, since these are supposed to take care of prolongation. I'm asking because in a thorn I'm working on, a certain GF has prolongation set to "None". This resulted in buffer zones on finer grids not to be initialized (full of NaNs) when switching on mesh refinement. Although I think I found a workaround, I'd like to take care of this by using some already provided mechanism, if available. Thank you very much, Federico Guercilena -- Federico Guercilena Institut für Theoretische Physik Johann Wolfgang Goethe-Universität Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany Telephone: +49 69 798 47887 Email: guercilena[at]th.physik.uni-frankfurt.de

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Odd CCTK_VarDataPtrI behaviour?
by Federico Guercilena 28 Oct '15

28 Oct '15

(I write this second question in different message so it can be answered separately) Hello, when asking for a vector variable index with CCTK_VarIndex, it correctly returns an increasing index for every variable component, for example: CCTK_VarIndex (example_gf[0]) --> 180 CCTK_VarIndex (example_gf[1]) --> 181 However when the index is fed to CCTK_VarDataPtrI to get a pointer to the grid function, it always points to the 0th component. To get the pointer to the component I wanted, I had to increment the pointer by the correct amount. This not a major inconvenience, but it is quite counterintuitive. Is there a reason for such behaviour? Thanks again, Federico Guercilena -- Federico Guercilena Institut für Theoretische Physik Johann Wolfgang Goethe-Universität Max-von-Laue-Str. 1 60438 Frankfurt am Main, Germany Telephone: +49 69 798 47887 Email: guercilena[at]th.physik.uni-frankfurt.de

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Time change: Einstein Toolkit Meeting Reminder
by Frank Loeffler 27 Oct '15

27 Oct '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/ NOTE: Most of Europe, and maybe other parts of the world too, changed to winter time last week end. This means for those the meeting will be ONE HOUR EARLIER than usual. This change will only affect this week, as Louisiana will change its time on Nov 1st too, one week later than Europe. The number to call is (+1) 225-578-4942 and the conference id is 118682#. Frank Loeffler

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BitBucket down
by Ian Hinder 23 Oct '15

23 Oct '15

Hi, BitBucket appears to be down at the moment. This will make it impossible to check out the ET or Cactus until it is fixed. See http://status.bitbucket.org for current status. -- Ian Hinder http://members.aei.mpg.de/ianhin

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Re: [Users] HDF5 Error, Hilbert
by Geraint Pratten 21 Oct '15

21 Oct '15

Thanks Ian, I think that did the trick! I rebuilt Cactus with a different MPI infrastructure and made sure that the appropriate MPI environment was loaded. Seems to be working now, e.g. INFO (Carpet): MPI is enabled INFO (Carpet): Carpet is running on 12 processes INFO (Carpet): This is process 0 INFO (Carpet): OpenMP is enabled INFO (Carpet): This process contains 1 threads, this is thread 0 INFO (Carpet): There are 12 threads in total INFO (Carpet): There are 1 threads per process INFO (Carpet): This process runs on host node203, pid=28712 INFO (Carpet): This process runs on 24 cores: 0-23 INFO (Carpet): Thread 0 runs on 24 cores: 0-23 Thanks! Geraint On 20 October 2015 at 14:55, Ian Hinder <ian.hinder(a)aei.mpg.de> wrote: > > On 20 Oct 2015, at 15:44, Geraint Pratten <g.pratten(a)sussex.ac.uk> wrote: > > Thanks! I'll take a look into that - changing to $MPIDIR/bin/mpirun didn't > help but I suspect that the MPI version used in the options list may not be > correct. Will see if this is the issue and confirm. > > > You could also check to see which MPI module is loaded. Do you load any > modules in envsetup in the machine definition file? > > -- > Ian Hinder > http://members.aei.mpg.de/ianhin > > -- Geraint Pratten Postdoctoral Research Associate Mobile: +44(0) 7581709282 E-mail: G.Pratten(a)sussex.ac.uk Skype: geraint.pratten School of Mathematical and Physical Sciences Pevensey 3 Building University of Sussex Falmer Campus Brighton BN1 9QH United Kingdom

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Simpler certificates for einsteintoolkit.org
by Erik Schnetter 20 Oct '15

20 Oct '15

It seems that <https://letsencrypt.org> is a new CA that we could use to provide certificates for domains. Two of the advertised features seem interesting: - automatic renewal - free of charge It is sponsored by Mozilla and the EFF (and others) so it seems legit. It seems too good to be true, so I wonder whether there is a catch. -erik -- Erik Schnetter <schnetter(a)gmail.com> http://www.perimeterinstitute.ca/personal/eschnetter/

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Re: [Users] HDF5 Error, Hilbert
by Geraint Pratten 20 Oct '15

20 Oct '15

Thanks! I'll take a look into that - changing to $MPIDIR/bin/mpirun didn't help but I suspect that the MPI version used in the options list may not be correct. Will see if this is the issue and confirm. On 20 October 2015 at 14:16, Ian Hinder <ian.hinder(a)aei.mpg.de> wrote: > > On 20 Oct 2015, at 14:49, Geraint Pratten <g.pratten(a)sussex.ac.uk> wrote: > > Sorry, fixed the typo (though error is still there - having tried > different parallel environments). I've attached a chunk of the output but > killed it before it carried on until error. Do you need further output? > > > Hi Geraint, > > In apollo.run, you call "mpirun". This might not be the right mpirun. It > might be better to call it using $MPIDIR/bin/mpirun, if that is where it is > located. > > From the output file, you can see that there are multiple Cactus banners > appearing. This indicates that each mpi process is starting thinking it is > the only one there. This is a smoking gun for a mismatch between the MPI > versions used to compile and run, so I would focus on that possibility. > > -- > Ian Hinder > http://members.aei.mpg.de/ianhin > > -- Geraint Pratten Postdoctoral Research Associate Mobile: +44(0) 7581709282 E-mail: G.Pratten(a)sussex.ac.uk Skype: geraint.pratten School of Mathematical and Physical Sciences Pevensey 3 Building University of Sussex Falmer Campus Brighton BN1 9QH United Kingdom

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Re: [Users] HDF5 Error, Hilbert
by Geraint Pratten 20 Oct '15

20 Oct '15

Sorry, fixed the typo (though error is still there - having tried different parallel environments). I've attached a chunk of the output but killed it before it carried on until error. Do you need further output? The double comment is ignored - will confirm though... On 20 October 2015 at 13:24, Ian Hinder <ian.hinder(a)aei.mpg.de> wrote: > > On 20 Oct 2015, at 13:44, Geraint Pratten <g.pratten(a)sussex.ac.uk> wrote: > > Hi, > > So I'm getting a problem passing the correct number of MPI processes > through to Carpet. I'm not sure what I've messed up in the configurations, > the error I am getting is: > > The environment variable CACTUS_NUM_PROCS is set to 4, but there are 1 MPI > processes. This may indicate a severe problem with the MPI startup > mechanism. > > I've attached the .run and .sub scripts that I use. Can anyone see > anything obviously wrong? The local cluster uses the UNIVA Grid Engine for > submission scripts. > > > Hi Geraint, > > In your submission script, you have > > #! /bin/bash > #$ -cwd > #$ -j y > #$ -o output/@SIMULATION_NAME@.out > #$ -e output/@SIMULATION_NAME@.err > > ## Error and ouput > #$ -m abe > #$ -M geraint.pratten(a)gmail.com > > ## Set up parallel environment > ##$ -pe openmpi_mixed_32 @PROCS_REQUESTED@ > #$ -pe mpich @PROC_REQUESTEDS@ > > ## Request queue and job class > #$ -q mps.q > #$ -jc mps.medium > > ## Walltime, simulation name and memory > #$ -l h_rt=@WALLTIME@ > #$ -N @SHORT_SIMULATION_NAME@ > > > Specifically, you say @PROC_REQUESTED@ instead of @PROCS_REQUESTED@. > i.e. a missing S on PROCS. Can you also post your output and error > files? It would be good if simfactory could detect errors like this. It > would also be good if the queuing system on that machine would complain if > it got a number of procs that it doesn't understand. Maybe it does > complain, but it's only a warning? > > I'm also not sure what happens if you do a double comment ##. It may > treat it as a single comment, and use the first pe that you specify. > > -- > Ian Hinder > http://members.aei.mpg.de/ianhin > > -- Geraint Pratten Postdoctoral Research Associate Mobile: +44(0) 7581709282 E-mail: G.Pratten(a)sussex.ac.uk Skype: geraint.pratten School of Mathematical and Physical Sciences Pevensey 3 Building University of Sussex Falmer Campus Brighton BN1 9QH United Kingdom

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Users October 2015