Users January 2015

users@lists.einsteintoolkit.org

10 participants
14 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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ETK test suite build fails for me in linking
by So Ra Chung 26 Jan '15

26 Jan '15

Hi, I'm following the instructions on the page https://docs.einsteintoolkit.org/et-docs/Simplified_Tutorial_for_New_Users and during the final link I get an 'undefined reference' error (see below). It seems that the routine Util_CacheMalloc is defined in the Fortran thorn in the file cctk_Cache.F90, however the object code never seems to be supplied, i.e. % nm cctk_Cache.F90.o appears to contain no symbols. So, perhaps this is a compiler error, however no errors were thrown during the build process. I'm not sure what to do at this point. Can anyone advise me? Thanks, Sara Chung ./simfactory/bin/sim build --thornlist=manifest/einsteintoolkit.th ... ..._______________________________________________________________ Formaline: Done. Formaline: (Formaline has finished updating the git repositories. Formaline: If the build process seems to hang, some other command Formaline: is still running, e.g. the final link stage.) Creating cactus_sim in /home/sorachung/Cactus/exe from EinsteinAnalysis/ADMAnalysis EinsteinBase/ADMBase EinsteinBase/ADMCoupling EinsteinBase/ADMMacros AEIThorns/ADMMass AEIThorns/AEILocalInterp EinsteinAnalysis/AHFinder EinsteinAnalysis/AHFinderDirect ExternalLibraries/BLAS CactusBase/Boundary EinsteinAnalysis/CalcK Carpet/Carpet Carpet/CarpetEvolutionMask Carpet/CarpetIOASCII Carpet/CarpetIOBasic Carpet/CarpetIOHDF5 Carpet/CarpetIOScalar Carpet/CarpetIntegrateTest Carpet/CarpetInterp Carpet/CarpetInterp2 Carpet/CarpetLib Carpet/CarpetMask Carpet/CarpetProlongateTest Carpet/CarpetReduce Carpet/CarpetRegrid Carpet/CarpetRegrid2 Carpet/CarpetRegridTest Carpet/CarpetSlab Carpet/CarpetTracker CactusBase/CartGrid3D CactusNumerical/Cartoon2D EinsteinBase/Constants CactusBase/CoordBase EinsteinBase/CoordGauge Carpet/CycleClock CactusExamples/DemoInterp CactusNumerical/Dissipation EinsteinInitialData/DistortedBHIVP EinsteinAnalysis/EHFinder EinsteinBase/EOS_Base EinsteinEOS/EOS_Hybrid EinsteinEOS/EOS_IdealFluid EinsteinEOS/EOS_Omni EinsteinEOS/EOS_Polytrope EinsteinExact/EinsteinExact_Test CactusElliptic/EllBase CactusElliptic/EllSOR EinsteinInitialData/Exact EinsteinAnalysis/Extract ExternalLibraries/FFTW3 CactusExamples/FleshInfo CactusUtils/Formaline CactusBase/Fortran EinsteinEvolve/GRHydro EinsteinEvolve/GRHydro_InitData ExternalLibraries/GSL EinsteinExact/GaugeWave KrancNumericalTools/GenericFD ExternalLibraries/HDF5 CactusConnect/HTTPD CactusConnect/HTTPDExtra CactusExamples/HelloWorld Carpet/HighOrderWaveTest EinsteinBase/HydroBase EinsteinAnalysis/Hydro_Analysis EinsteinInitialData/Hydro_InitExcision EinsteinInitialData/IDAnalyticBH EinsteinInitialData/IDAxiBrillBH EinsteinInitialData/IDAxiOddBrillBH EinsteinInitialData/IDBrillData EinsteinInitialData/IDConstraintViolate EinsteinInitialData/IDFileADM EinsteinInitialData/IDLinearWaves CactusWave/IDScalarWave CactusWave/IDScalarWaveC CactusWave/IDScalarWaveCXX CactusWave/IDScalarWaveElliptic CactusExamples/IDWaveMoL CactusBase/IOASCII CactusBase/IOBasic CactusPUGHIO/IOHDF5 CactusPUGHIO/IOHDF5Util CactusIO/IOJpeg CactusBase/IOUtil CactusBase/InitBase CactusNumerical/InterpToArray EinsteinExact/KerrSchild ExternalLibraries/LAPACK ExternalLibraries/LORENE CactusNumerical/LocalInterp CactusNumerical/LocalReduce Carpet/LoopControl McLachlan/ML_ADMConstraints McLachlan/ML_ADMQuantities McLachlan/ML_BSSN McLachlan/ML_BSSN_Helper McLachlan/ML_BSSN_Test McLachlan/ML_CCZ4 McLachlan/ML_CCZ4_Helper McLachlan/ML_CCZ4_Test McLachlan/ML_WaveToy McLachlan/ML_WaveToy_Test ExternalLibraries/MPI CactusUtils/MemSpeed EinsteinInitialData/Meudon_Bin_BH EinsteinInitialData/Meudon_Bin_NS EinsteinInitialData/Meudon_Mag_NS EinsteinExact/Minkowski CactusNumerical/MoL EinsteinExact/ModifiedSchwarzschildBL EinsteinAnalysis/Multipole CactusUtils/NaNCatcher CactusUtils/NaNChecker EinsteinEvolve/NewRad CactusUtils/Nice EinsteinInitialData/NoExcision CactusUtils/NoMPI CactusNumerical/Noise CactusNumerical/Norms PITTNullCode/NullConstr PITTNullCode/NullDecomp PITTNullCode/NullEvolve PITTNullCode/NullExact PITTNullCode/NullGrid PITTNullCode/NullInterp PITTNullCode/NullNews PITTNullCode/NullPsiInt PITTNullCode/NullSHRExtract PITTNullCode/NullVars ExternalLibraries/OpenSSL EinsteinAnalysis/Outflow ExternalLibraries/PAPI CactusPUGH/PUGH CactusPUGH/PUGHInterp CactusPUGH/PUGHReduce CactusPUGH/PUGHSlab CactusNumerical/Periodic LSUThorns/PeriodicCarpet AEIThorns/PunctureTracker LSUThorns/QuasiLocalMeasures Carpet/ReductionTest Carpet/ReductionTest2 Carpet/ReductionTest3 CactusNumerical/ReflectionSymmetry Carpet/RegridSyncTest EinsteinInitialData/RotatingDBHIVP CactusNumerical/RotatingSymmetry180 CactusNumerical/RotatingSymmetry90 CactusExamples/SampleBoundary CactusExamples/SampleIO EinsteinUtils/SetMask_SphericalSurface EinsteinExact/ShiftedGaugeWave CactusNumerical/Slab CactusNumerical/SlabTest CactusConnect/Socket CactusNumerical/SpaceMask PITTNullCode/SphericalHarmonicDecomp PITTNullCode/SphericalHarmonicRecon CactusNumerical/SphericalSurface EinsteinBase/StaticConformal LSUThorns/SummationByParts CactusBase/SymBase AEIThorns/SystemStatistics CactusElliptic/TATelliptic EinsteinUtils/TGRtensor EinsteinInitialData/TOVSolver CactusUtils/TerminationTrigger CactusTest/TestArrays Carpet/TestCarpetGridInfo CactusTest/TestComplex CactusTest/TestCoordinates CactusTest/TestFortranCrayPointers CactusTest/TestFortranDependencies1 CactusTest/TestFortranDependencies2 CactusTest/TestFpointerNULL CactusTest/TestFreeF90 CactusTest/TestGlobalReduce CactusTest/TestInclude1 CactusTest/TestInclude2 CactusNumerical/TestLocalReduce CactusTest/TestLoop Carpet/TestLoopControl CactusTest/TestMath CactusTest/TestMoL CactusTest/TestPar CactusTest/TestReduce CactusTest/TestSchedule CactusTest/TestStrings CactusTest/TestTable CactusTest/TestTimers CactusTest/TestTypes CactusBase/Time CactusExamples/TimerInfo CactusUtils/TimerReport Carpet/Timers EinsteinBase/TmunuBase AEIThorns/Trigger EinsteinInitialData/TwoPunctures EinsteinExact/Vaidya2 LSUThorns/Vectors CactusWave/WaveBinarySource CactusExamples/WaveMoL CactusExamples/WaveToy1DF77 CactusExamples/WaveToy2DF77 CactusWave/WaveToyC CactusWave/WaveToyCXX CactusWave/WaveToyExtra CactusWave/WaveToyF77 CactusWave/WaveToyF90 CactusWave/WaveToyFreeF90 EinsteinAnalysis/WeylScal4 ExternalLibraries/hwloc ExternalLibraries/libjpeg ExternalLibraries/zlib /home/sorachung/Cactus/configs/sim/lib/libthorn_PUGH.a(Storage.c.o): In function `PUGH_EnableGArrayDataStorage': /home/sorachung/Cactus/arrangements/CactusPUGH/PUGH/src/Storage.c:646: undefined reference to `Util_CacheMalloc' collect2: error: ld returned 1 exit status make[1]: *** [/home/sorachung/Cactus/exe/cactus_sim] Error 1 make: *** [sim] Error 2 sorachung@sorachung-N550JK:~/Cactus$ sorachung@sorachung-N550JK:~/Cactus$ grep -rnw . -e "Util_CacheMalloc" ./repos/cactusbase/Fortran/src/cctk_Cache.F90:8: subroutine Util_CacheMalloc (pointer, index, size, realstart) ./repos/cactusbase/Fortran/src/cctk_Cache.F90:14: end subroutine Util_CacheMalloc ./repos/cactuspugh/PUGH/src/Storage.c~:538: @calls Util_CacheMalloc ./repos/cactuspugh/PUGH/src/Storage.c~:646: GA->data = Util_CacheMalloc (GA->arrayid, ./repos/cactuspugh/PUGH/src/Storage.c:538: @calls Util_CacheMalloc ./repos/cactuspugh/PUGH/src/Storage.c:646: GA->data = Util_CacheMalloc (GA->arrayid, ./.svn/pristine/de/def745e3379fad4f949c40f811f7efd7acc3d4bf.svn-base:40: @routine Util_CacheMalloc ./.svn/pristine/de/def745e3379fad4f949c40f811f7efd7acc3d4bf.svn-base:75:void *Util_CacheMalloc(unsigned int idx, ./.svn/pristine/8c/8c6f37c22be6bcd98ee2b3825f12269b225b6a77.svn-base:19:void *Util_CacheMalloc(unsigned _index, Binary file ./configs/sim/lib/libthorn_PUGH.a matches Binary file ./configs/sim/build/PUGH/Storage.c.o matches ./configs/sim/build/PUGH/Storage.c:539: @calls Util_CacheMalloc ./configs/sim/build/PUGH/Storage.c:647: GA->data = Util_CacheMalloc (GA->arrayid, ./configs/sim/build/Fortran/cctk_Cache.f90:7: subroutine Util_CacheMalloc (pointer, index, size, realstart) ./configs/sim/build/Fortran/cctk_Cache.f90:13: end subroutine Util_CacheMalloc

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meeting minutes for 2015-01-26
by Roland Haas 26 Jan '15

26 Jan '15

Present: Frank, Roland, Jonah, Peter, Steve, Erik, Matt, Ian, Yosef Tickets up for application with no discussion happening: Decision to make it a policy to apply tickets that are up for review for a long time, for which no comments are made. This decision is then up to the person proposing the change in the commit. ML rewrite branch: * Ian commented on the proposed changes * further discussion will continue to happen on Trac Yours, Roland

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 25 Jan '15

25 Jan '15

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segfault on ubuntu 14.10
by Jonah Miller 24 Jan '15

24 Jan '15

Hello everyone, I recently switched from using Debian stable to Ubuntu 14.10 on my development laptop, and I'm now having trouble getting the Einstein Toolkit to run. It compiles fine, but even the simplest simulations segfault consistently. Does anyone have any advice on how to approach debugging this? I've attached the error output from my attempt to run the example static tov star in the simplified tutorial for new users (https://docs.einsteintoolkit.org/et-docs/Simplified_Tutorial_for_New_Users) as well as the two sets of build options that I've tried using (the first, ubuntu.cfg, is the default, the second, yugoth.cfg, is a set of options that I've used successfully in the past). I know your time is precious and I appreciate any that you can spare. Thanks in advance! Best, Jonah Miller

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Cactus build on local HPC
by Geraint Pratten 22 Jan '15

22 Jan '15

Hi, I am running into some problems building Cactus/Einstein Toolkit on our local HPC. The .ini file I am using looks okay to me. As far as I can tell, there seems to be an issue with PAPI? I've attached a copy of the error message. Does anyone have any insight into this? If you need to see any particular files (e.g. .ini or .cfg files) then just let me know which ones (including directory would be helpful!) and I'll post back asap. Thanks in advance! Your time taken is very much appreciated! Regards Geraint ---------- *Checking status of thorn CoordBase...Checking status of thorn PUGHInterpChecking status of thorn PUGHReduce/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c: In function ‘PAPI_Cactus_outinfo’:/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c:51:0: warning: ignoring #pragma omp master [-Wunknown-pragmas] #pragma omp master ^/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c: In function ‘PAPI_Cactus_chkerr’:/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c:62:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical ^/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c: In function ‘PAPI_init’:/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c:231:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel private(ierr) ^/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c:262:0: warning: ignoring #pragma omp master [-Wunknown-pragmas] #pragma omp master ^/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c:267:7: warning: implicit declaration of function ‘strdup’ [-Wimplicit-function-declaration] char *const eventnames = strdup(eventset_eventnames[n]); ^/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c:267:32: warning: initialization makes pointer from integer without a cast [enabled by default] char *const eventnames = strdup(eventset_eventnames[n]); ^/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c:270:7: warning: implicit declaration of function ‘strtok_r’ [-Wimplicit-function-declaration] for (char *event_name = strtok_r(eventnames, sep, &lasts); ^/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c:270:31: warning: initialization makes pointer from integer without a cast [enabled by default] for (char *event_name = strtok_r(eventnames, sep, &lasts); ^/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c:270:7: error: declaration of non-variable ‘strtok_r’ in ‘for’ loop initial declaration for (char *event_name = strtok_r(eventnames, sep, &lasts); ^/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c:272:23: warning: assignment makes pointer from integer without a cast [enabled by default] event_name = strtok_r(NULL, sep, &lasts)) ^/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c:274:0: warning: ignoring #pragma omp master [-Wunknown-pragmas] #pragma omp master ^/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c:301:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel private(ierr) ^/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c: In function ‘output_stats’:/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c:333:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel private(ierr) ^/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/build/PAPI/stats.c:351:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical(PAPI_output_stats_add) ^make[3]: *** [stats.c.o] Error 1make[2]: *** [make.checked] Error 2make[1]: *** [/mnt/pact/gp234/NR/Cactus/configs/apollo-login.cm.cluster.ini/lib/libthorn_PAPI.a] Error 2make[1]: *** Waiting for unfinished jobs....make: *** [apollo-login.cm.cluster.ini] Error 2* -- Geraint Pratten Mobile: +44(0) 7581709282 E-mail: G.Pratten(a)sussex.ac.uk Skype: geraint.pratten Astronomy Centre Pevensey 3 Building University of Sussex Falmer Campus Brighton BN1 9QH United Kingdom

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Spurious test failures due to now bboxset code in Carpet
by Erik Schnetter 20 Jan '15

20 Jan '15

We enabled a new, much scalable implementation of the bboxset class in Carpet. This class describes sets of "bounding boxes", i.e. the locations and shapes of the components of Carpet's grids. (This new implementation requires C++11 features, and is thus only available by default if the C++ compiler supports the C++11 standard.) As it turns out, the new class numbers these components differently than the old code. This numbering scheme is ultimately arbitrary; if there are two refined regions, then it does not matter for physics which one is labelled #0 and which one is labelled #1. However, since the old and the new code differ, some ASCII output will now differ. In the Einstein Toolkit test cases, this is triggered by the test ml-gw1d-small-amr of PeriodicCarpet. Inspection shows that, apart from this re-labelling, the test output is identical. The new bboxset code has a defined ordering of the bboxes; they are ordered lexicographically by their upper left corner. (This is implemented in the "less" functions in bbox.hh and vect.hh, following STL conventions.) The old code used no particular ordering, although the ordering was guaranteed to remain the same between runs. I suggest to ignore the test case failures caused by this transition, and to update this (and potentially other) test cases. I plan to update the old bboxset code to explicitly sort bboxes in the same order. -erik -- Erik Schnetter <schnetter(a)gmail.com> http://www.perimeterinstitute.ca/personal/eschnetter/ My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from https://sks-keyservers.net.

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Re: [Users] [Test] EinsteinToolkit - Build #409 - Failure
by Ian Hinder 20 Jan '15

20 Jan '15

On 19 Jan 2015, at 18:23, ian.hinder(a)aei.mpg.de wrote: > BUILD FAILURE > > Build URL: https://build.barrywardell.net/job/EinsteinToolkit/409/ > Project: EinsteinToolkit > Date of build: Mon, 19 Jan 2015 17:13:41 +0000 > Build duration: 9 min 29 sec > > Changes > > Revision: 68cdcc5ecc34e0fac714e13a5a53016651a64903 > Author: Einstein Toolkit Git Server > Log: > Updated submodules: > > * arrangements/CactusBase 11f4180...9b1bab2 (1): > > CactusBase: Support CCTK_INT16 > > * arrangements/CactusNumerical 93a286d...49912fb (1): > > CactusNumerical: Support CCTK_INT16 > > * arrangements/CactusPUGH 0ac5c78...cb3c70f (1): > > PUGH: Support CCTK_INT16 > > * arrangements/CactusTest 8c3b35b...48004a2 (1): > > TestAllTypes: Test CCTK_INT16 > > * repos/carpet 7ddf438...2efdefc (2): > > CarpetLib: Disable new bboxset class if the compiler does not support C++11 > > Merge branch 'eschnett/int16' Hi, This test failure was caused by the git super-repository update system not successfully updating the flesh in its working copy. I believe this was caused by somebody pushing a commit which rewrote the flesh history. From the repository history I can see, I think this was the push by Erik at 15-Jan-2015 19:12 which added commit 104612e - Cactus: Output schedule routine when outputting warnings (2014-12-31) <Erik Schnetter> with parent c7fd13a - Merged in redirect_root (pull request #2) (2014-12-30) <Frank Löffler> The master branch then evolved from this commit. However, there were already more commits on master, including 065b00c - Merged in simple_make_for_single_config (pull request #6) (2015-01-12) <Frank Löffler> f47e1d0 - (origin/simple_make_for_single_config) Don't require configuration name when only one is present anyway. (2014-12-25) <Frank Loeffler> 9c7a72a - Merged in Makefile_invalid_configuration_names (pull request #5) (2015-01-12) <Frank Löffler> which were then lost. These commits were then added onto the end of master (I think again by Erik?), so that the code was correct, but the history was different. I'm basing this on the history I can see in the update server's copy of the repository, and the commit email notifications which give the timeline of pushes. This could have been caused by Erik rebasing his master branch off a feature branch, instead of the other way around, and then overriding the warning when pushing to bitbucket by adding the --force option to "git push". Erik, is it possible that this is what happened? The super-repo update system should have detected the failure to update and sent me an email, but there is a bug there which means it ignored the error. I have corrected the repository problem on the update server. I believe the current master branch contains all the code that it should, and that it will now update correctly, unless another forced push is performed. Possible actions: – We could disable forced pushes in bitbucket for the master branch to stop this happening again (this should presumably be done for all the repositories, so it should be done by a script). – The super-repo update system should be fixed so that errors like this are detected and reported -- Ian Hinder http://members.aei.mpg.de/ianhin

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meeting minutes for 2015-01-19
by Roland Haas 19 Jan '15

19 Jan '15

Present: Frank, Zach, Jonah, Roland, Yosef, Josh, Erik * EU ET meeting in August around MICRA meeting * accept support for INT16 * McLachlan rewrite branch: ** waiting for feedback and testing. Needs "Please apply". ** a good test would be a qc0 run with both old and new code and comparing results if they are within error * hwloc configuration: ** problem is that when hwloc builds itself, Cactus would need to know in advance which libraries hwloc will pull in ** original proposed solution to split up build and configure stages and run configure stage at CST time ** alternative solution is to defer determination of the required link libraries until jsut before Cactus links. Attempt this first. Yours, Roland

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 18 Jan '15

18 Jan '15

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