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Issue with ExternalLibraries/HDF5 in dev version
by Christian D. Ott 16 Oct '15

16 Oct '15

Hi All, so I just got a fresh checkout of the development version and noticed that there is a problem with ExternalLibraries/HDF5: I have my own pre-compiled version of HDF5 and I am setting HDF5_DIR=... in my options list. When I do that, the script detect.sh in ExternalLibraries/HDF5 fails to set HDF5_LIB_DIRS and HDF5_LIBS and the compile fails at the link stage. Could this possibly be fixed? I fixed the problem locally by introducing HDF5_LIB_DIRS="${HDF5_DIR}/lib" HDF5_LIBS="${HDF5_CXX_LIBS} ${HDF5_FORTRAN_LIBS} ${HDF5_C_LIBS}" Near line 156 of detect.sh. Thanks, - Christian

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Test failures in CT_MultiLevel
by Ian Hinder 16 Oct '15

16 Oct '15

Hi Eloisa and Erik, I am running the CT_MultiLevel elliptic solver tests on Datura. I ran into two problems. 1. BLAS/LAPACK vs OpenBLAS 2. Differences above tolerance in the Hamiltonian constraint The first is that the test parameter files ask for thorns BLAS and LAPACK, which are disabled on Datura. The ET thornlist contains ExternalLibraries/BLAS ExternalLibraries/LAPACK #DISABLED ExternalLibraries/OpenBLAS whereas datura.ini contains disabled-thorns = <<EOT ExternalLibraries/BLAS ExternalLibraries/LAPACK enabled-thorns = <<EOT ExternalLibraries/OpenBLAS So by default, machines will use BLAS and LAPACK, but datura is configured to use OpenBLAS instead. I don't quite understand this, because parameter files will activate one or the other thorns, so a parameter file which requires either of these cannot work both on datura and on a machine which does not do this enabling/disabling. There is a ticket (https://trac.einsteintoolkit.org/ticket/1674) in which the suggestion is made to switch to OpenBLAS across the ET, but as far as is written in the ticket, this was not implemented. If we follow the suggestion in the ticket, then this would be solved by using OpenBLAS all the time, and editing all parameter files to use that instead. If not, then it would probably be better for the choice of library to be a machine-specific option, and not something that needs to be selected in a parameter file by activating the right thorn. Also, I'm not sure how the other options in datura.cfg affect this, since on Datura, the intention is to use MKL anyway. LDFLAGS = -rdynamic -Wl,-rpath,/cluster/Compiler/Intel/ics_2013.1.039/mkl/lib/intel64 -Wl,-rpath,/cluster/Compiler/Intel/ics_2013.1.039/lib/intel64 # -Wl,-rpath,/usr/lib64 BLAS_DIR = /cluster/Compiler/Intel/ics_2013.1.039/mkl/lib/intel64 BLAS_LIBS = -Wl,--start-group mkl_intel_lp64 mkl_intel_thread mkl_core -Wl,--end-group iomp5 pthread LAPACK_DIR = /cluster/Compiler/Intel/ics_2013.1.039/mkl/lib/intel64 LAPACK_LIBS = -Wl,--start-group mkl_intel_lp64 mkl_intel_thread mkl_core -Wl,--end-group OPENBLAS_DIR = NO_BUILD OPENBLAS_LIBS = -mkl What is the best way forward? The second problem is that when I switch to OpenBLAS in the test parameter files, all tests pass except for CTThorns/CT_MultiLevel/test/boostedpuncture.par, which fails with ml_bssn-ml_ham.d.asc: substantial differences significant differences on 56 (out of 109) lines maximum absolute difference in column 13 is 16.796401082424 maximum relative difference in column 13 is 10.214243488001 (insignificant differences on 45 lines) ml_bssn-ml_ham.x.asc: substantial differences significant differences on 88 (out of 182) lines maximum absolute difference in column 13 is 5.30707663071086 maximum relative difference in column 13 is 0.897391183181081 (insignificant differences on 94 lines) ml_bssn-ml_ham.y.asc: substantial differences significant differences on 88 (out of 182) lines maximum absolute difference in column 13 is 5.30900732375572 maximum relative difference in column 13 is 0.897408813491657 (insignificant differences on 94 lines) ml_bssn-ml_ham.z.asc: substantial differences significant differences on 56 (out of 109) lines maximum absolute difference in column 13 is 5.30900949367607 maximum relative difference in column 13 is 0.8974032303582 (insignificant differences on 53 lines) All other solution variables are within tolerance, suggesting that the solver is getting the right answer, though ml_ham would be more sensitive to small solution differences anyway. None of the other CT_MultiLevel tests seem to be checking ml_ham, so it might be that if ml_ham was checked, it would also differ. Could this be related to the McLachlan rewrite, or is the Hamiltonian constraint expected to be the same across the rewrite? It could be the usual roundoff-error problem, but the differences listed are quite large. Or maybe this comes from the method used by the elliptic solver, which may not be 100% deterministic due to thread ordering in the Gauss Seidel method? -- Ian Hinder http://members.aei.mpg.de/ianhin

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Re: [Users] Numerical arrangement
by Ian Hinder 13 Oct '15

13 Oct '15

On 13 Oct 2015, at 19:20, Barry Wardell <barry.wardell(a)ucd.ie> wrote: > On Tue, Oct 13, 2015 at 5:47 PM, Ian Hinder <ian.hinder(a)aei.mpg.de> wrote: > I just realised that AEILocalInterp was moved to > > https://bitbucket.org/einsteintoolkit/numerical > > Would it be better for this to be under the cactuscode team instead, i.e. > > https://bitbucket.org/cactuscode/numerical > > AEILocalInterp is nothing to do with the Einstein equations. > > I believe the reasoning for including it in the Numerical arrangement as opposed to, for example, CactusNumerical is that AEILocalInterp is licensed under the GPL and the author does not wish to relicense it under the LGPL. Since Cactus thorns are required to be licensed under the LGPL it cannot be include with Cactus, and so the idea was to have it as part of a new arrangement under the Einstein Toolkit instead. Hi Barry, Yes, we didn't want to (couldn't) make it part of Cactus, i.e. in an arrangement starting with "Cactus". But I thought we were going to still host it under the Cactus BitBucket account, since being under Einstein Toolkit doesn't make much sense. It is of interest to a wider community than just those using Cactus for GR. The idea was to have a generic location for free software Cactus thorns which are not part of Cactus. -- Ian Hinder http://members.aei.mpg.de/ianhin

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Numerical arrangement
by Ian Hinder 13 Oct '15

13 Oct '15

Hi Barry, I just realised that AEILocalInterp was moved to https://bitbucket.org/einsteintoolkit/numerical Would it be better for this to be under the cactuscode team instead, i.e. https://bitbucket.org/cactuscode/numerical AEILocalInterp is nothing to do with the Einstein equations. -- Ian Hinder http://members.aei.mpg.de/ianhin

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 12 Oct '15

12 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/ I short: the number is (+1) 225-578-4942 and the conference id is 118682#. Steve will host the meeting. Frank Loeffler

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trac server down
by Roland Haas 11 Oct '15

11 Oct '15

Hello all, it seems as if the trac server is down. I get: rhaas@horizon:.../rhaas/tmp$ curl --verbose https://trac.einsteintoolkit.org/ * Trying 130.39.21.34... * connect to 130.39.21.34 port 443 failed: Connection refused * Failed to connect to trac.einsteintoolkit.org port 443: Connection refused * Closing connection 0 curl: (7) Failed to connect to trac.einsteintoolkit.org port 443: Connection refused Yours, Roland

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 09 Oct '15

09 Oct '15

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Ideas for a new I/O file format
by Erik Schnetter 06 Oct '15

06 Oct '15

This Monday we briefly discussed various concepts related to a new I/O file format for Cactus, and I presented a graphical overview of these concepts. I have now written things up in a C++-like style and added it to the wiki < https://docs.einsteintoolkit.org/et-docs/A_new_I/O_file_format>. -erik -- Erik Schnetter <eschnetter(a)perimeterinstitute.ca> http://www.perimeterinstitute.ca/personal/eschnetter/ AIM: eschnett247, Skype: eschnett, Google Talk: schnetter(a)gmail.com

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Simulation olog
by Erik Schnetter 05 Oct '15

05 Oct '15

[image: Inline image 1] -- Erik Schnetter <schnetter(a)gmail.com> http://www.perimeterinstitute.ca/personal/eschnetter/

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Re: [Users] HDF5 Error, Hilbert
by Geraint Pratten 05 Oct '15

05 Oct '15

Hi, I am trying to run a simulation with the same output directory - though I've been removing the simulations after each run while trying to fix the above issue. I should have write access to the file and there should be sufficient storage. Geraint On 5 October 2015 at 11:34, Ian Hinder <ian.hinder(a)aei.mpg.de> wrote: > > On 1 Oct 2015, at 15:49, Erik Schnetter <schnetter(a)cct.lsu.edu> wrote: > > Geraint > > Some very fundamental HDF5 operations fail. This could be due to a file > system problem; maybe you don't have write access to the file, or your disk > is full. It could also be that there exists a corrupted HDF5 file, and you > are trying to write to it (extend it). > > HDF5 files can get corrupted if you have opened it for writing, and then > the application is interrupted or crashes, or you run out of disk space. > Even if you make free space later, a corrupted file remains corrupted. > > > Hi Geraint, > > Are you trying to run a simulation with output in the same directory as > one that was run before? > > > -erik > > > On Thu, Oct 1, 2015 at 9:30 AM, Geraint Pratten <g.pratten(a)sussex.ac.uk> > wrote: > >> Hi all, >> >> I recently built the latest release (Hilbert) on the local cluster and >> I've been getting a HDF5 error. I've tried building Cactus with both the >> local HDF5 package on the cluster as well as letting Cactus build HDF5 from >> scratch. Does anyone have any insight into the error I've attached below >> (extract of a long chain of errors of the same form)? >> >> I can dump the output to file or give configuration files if needed. >> >> Thanks in advance! >> Geraint >> >> ---------- >> >> HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0: >> #000: H5Ddeprec.c line 193 in H5Dcreate1(): unable to create dataset >> major: Dataset >> minor: Unable to initialize object >> #001: H5Dint.c line 453 in H5D__create_named(): unable to create and >> link to dataset >> major: Dataset >> minor: Unable to initialize object >> #002: H5L.c line 1638 in H5L_link_object(): unable to create new link >> to object >> major: Links >> minor: Unable to initialize object >> #003: H5L.c line 1882 in H5L_create_real(): can't insert link >> major: Symbol table >> minor: Unable to insert object >> #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal >> failed >> major: Symbol table >> minor: Object not found >> #005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator >> failed >> major: Symbol table >> minor: Callback failed >> #006: H5L.c line 1674 in H5L_link_cb(): name already exists >> major: Symbol table >> minor: Object already exists >> WARNING level 1 from host node207.cm.cluster process 0 >> while executing schedule bin (none), routine (no thorn)::(no routine) >> in thorn CarpetIOHDF5, file >> /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc >> :677: >> -> HDF5 call 'dataset = H5Dcreate (outfile, datasetname.str().c_str(), >> filedatatype, dataspace, plist)' returned error code -1 >> WARNING level 1 from host node207.cm.cluster process 0 >> while executing schedule bin (none), routine (no thorn)::(no routine) >> in thorn CarpetIOHDF5, file >> /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc >> :689: >> -> HDF5 call 'H5Dwrite (dataset, memdatatype, H5S_ALL, H5S_ALL, >> H5P_DEFAULT, data)' returned error code -1 >> WARNING level 1 from host node207.cm.cluster process 0 >> while executing schedule bin (none), routine (no thorn)::(no routine) >> in thorn CarpetIOHDF5, file >> /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc >> :725: >> -> HDF5 call 'attr = H5Acreate (dataset, "level", H5T_NATIVE_INT, >> dataspace, H5P_DEFAULT)' returned error code -1 >> WARNING level 1 from host node207.cm.cluster process 0 >> while executing schedule bin (none), routine (no thorn)::(no routine) >> in thorn CarpetIOHDF5, file >> /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc >> :726: >> -> HDF5 call 'H5Awrite (attr, H5T_NATIVE_INT, &refinementlevel)' >> returned error code -1 >> WARNING level 1 from host node207.cm.cluster process 0 >> >> -- >> 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 >> >> _______________________________________________ >> Users mailing list >> Users(a)einsteintoolkit.org >> http://lists.einsteintoolkit.org/mailman/listinfo/users >> >> > > > -- > Erik Schnetter <schnetter(a)cct.lsu.edu> > http://www.perimeterinstitute.ca/personal/eschnetter/ > _______________________________________________ > Users mailing list > Users(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users > > > -- > 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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