Trac September 2011

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[Einstein Toolkit] #147: Write transition guide for EOS_Omni
by Einstein Toolkit 24 Oct '11

24 Oct '11

#147: Write transition guide for EOS_Omni -------------------------------------+-------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit website | Version: Keywords: | -------------------------------------+-------------------------------------- The Einstein Toolkit pages need a wiki tutorial for switching to EOS_Omni. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/147> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #162: Document CCTK_GFINDEX3D and friends in reference manual
by Einstein Toolkit 23 Oct '11

23 Oct '11

#162: Document CCTK_GFINDEX3D and friends in reference manual ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | ----------------------+----------------------------------------------------- I believe the reference manual does not describe any of the CCTK_GFINDEX* and CCTK_VECTGFINDEX* functions. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/162> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #534: Checkpointing fails on LoneStar
by Einstein Toolkit 23 Oct '11

23 Oct '11

#534: Checkpointing fails on LoneStar --------------------------+------------------------------------------------- Reporter: hinder | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: Carpet | Version: Keywords: CarpetIOHDF5 | --------------------------+------------------------------------------------- Hi, I am starting to run on LoneStar, but find that I cannot checkpoint. This is for a production simulation. I see: INFO (CarpetIOHDF5): --------------------------------------------------------- INFO (CarpetIOHDF5): Dumping periodic checkpoint at iteration 9876, simulation time 18.5175 INFO (CarpetIOHDF5): --------------------------------------------------------- on stdout, and there is nothing on stderr. The checkpoint files are partially written: -rw------- 1 hinder G-25181 61M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_0.h5 -rw------- 1 hinder G-25181 47M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_10.h5 -rw------- 1 hinder G-25181 47M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_11.h5 -rw------- 1 hinder G-25181 47M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_12.h5 -rw------- 1 hinder G-25181 46M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_13.h5 -rw------- 1 hinder G-25181 46M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_14.h5 -rw------- 1 hinder G-25181 47M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_15.h5 -rw------- 1 hinder G-25181 47M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_16.h5 -rw------- 1 hinder G-25181 47M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_17.h5 -rw------- 1 hinder G-25181 46M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_18.h5 -rw------- 1 hinder G-25181 46M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_19.h5 -rw------- 1 hinder G-25181 60M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_1.h5 -rw------- 1 hinder G-25181 47M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_20.h5 -rw------- 1 hinder G-25181 47M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_21.h5 -rw------- 1 hinder G-25181 47M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_22.h5 -rw------- 1 hinder G-25181 46M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_23.h5 -rw------- 1 hinder G-25181 58M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_24.h5 -rw------- 1 hinder G-25181 58M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_25.h5 -rw------- 1 hinder G-25181 58M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_26.h5 -rw------- 1 hinder G-25181 57M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_27.h5 -rw------- 1 hinder G-25181 58M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_28.h5 -rw------- 1 hinder G-25181 58M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_29.h5 -rw------- 1 hinder G-25181 60M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_2.h5 -rw------- 1 hinder G-25181 58M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_30.h5 -rw------- 1 hinder G-25181 57M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_31.h5 -rw------- 1 hinder G-25181 59M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_3.h5 -rw------- 1 hinder G-25181 46M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_4.h5 -rw------- 1 hinder G-25181 47M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_5.h5 -rw------- 1 hinder G-25181 47M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_6.h5 -rw------- 1 hinder G-25181 47M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_7.h5 -rw------- 1 hinder G-25181 46M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_8.h5 -rw------- 1 hinder G-25181 46M Aug 25 15:58 checkpoint.chkpt.tmp.it_9876.file_9.h5 and invalid: c334-106$ h5ls checkpoint.chkpt.tmp.it_9876.file_0.h5 checkpoint.chkpt.tmp.it_9876.file_0.h5: unable to open file The job and the processes are all still running. Logging into one of the nodes and attaching gdb to the Cactus process yields: 0x00002b8eb3f6a287 in MPIDI_CH3I_MRAILI_Get_next_vbuf (vc_ptr=0x7fff50b96cb0, vbuf_ptr=0x7fff50b96cb8) at ibv_channel_manager.c:367 367 if (*head && vc->mrail.rfp.p_RDMA_recv != vc->mrail.rfp.p_RDMA_recv_tail) (gdb) bt #0 0x00002b8eb3f6a287 in MPIDI_CH3I_MRAILI_Get_next_vbuf (vc_ptr=0x7fff50b96cb0, vbuf_ptr=0x7fff50b96cb8) at ibv_channel_manager.c:367 #1 0x00002b8eb3f0426c in MPIDI_CH3I_read_progress (vc_pptr=0x7fff50b96cb0, v_ptr=0x7fff50b96cb8, is_blocking=259164064) at ch3_read_progress.c:130 #2 0x00002b8eb3f023dd in MPIDI_CH3I_Progress (is_blocking=1354329264, state=0x7fff50b96cb8) at ch3_progress.c:206 #3 0x00002b8eb3f6852c in MPIC_Wait (request_ptr=0x7fff50b96cb0) at helper_fns.c:518 #4 0x00002b8eb3f67e9c in MPIC_Recv (buf=0x7fff50b96cb0, count=1354329272, datatype=259164064, source=30, tag=0, comm=-788556288, status=0x1) at helper_fns.c:76 #5 0x00002b8eb3eee47e in MPIR_Bcast_OSU (buffer=0x7fff50b96cb0, count=1354329272, datatype=259164064, root=30, comm_ptr=0x0) at bcast_osu.c:283 #6 0x00002b8eb3eed0c6 in PMPI_Bcast (buffer=0x7fff50b96cb0, count=1354329272, datatype=259164064, root=30, comm=0) at bcast.c:1274 #7 0x0000000000c12fc4 in CarpetIOHDF5::WriteVarChunkedParallel (cctkGH=0x7fff50b96cb0, outfile=1354329272, io_bytes=@0xf7287a0, request=0x1e, called_from_checkpoint=false, indexfile=-788556288, $q8=<value optimized out>, $q9=<value optimized out>, $r0=<value optimized out>, $r1=<value optimized out>, $r2=<value optimized out>, $r3=<value optimized out>) at /work/00915/hinder/Cactus/llama/arrangements/Carpet/CarpetIOHDF5/src/Output.cc:519 #8 0x0000000000bf3f7f in CarpetIOHDF5::Checkpoint (cctkGH=0x7fff50b96cb0, called_from=1354329272, $W3=<value optimized out>, $W4=<value optimized out>) at /work/00915/hinder/Cactus/llama/arrangements/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc:973 #9 0x0000000000bf360b in CarpetIOHDF5::CarpetIOHDF5_EvolutionCheckpoint (cctkGH=0x7fff50b96cb0) at /work/00915/hinder/Cactus/llama/arrangements/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc:186 #10 0x0000000000413a5f in CCTK_CallFunction (function=0x7fff50b96cb0, fdata=0x7fff50b96cb8, data=0xf7287a0) at /work/00915/hinder/Cactus/llama/src/main/ScheduleInterface.c:291 #11 0x00000000011c2eb1 in Carpet::CallFunction (function=0x7fff50b96cb0, attribute=0x7fff50b96cb8, data=0xf7287a0, $01=<value optimized out>, $04=<value optimized out>, $05=<value optimized out>) at /work/00915/hinder/Cactus/llama/arrangements/Carpet/Carpet/src/CallFunction.cc:135 #12 0x0000000000418dea in CCTKi_ScheduleCallFunction (function=0x7fff50b96cb0, attribute=0x7fff50b96cb8, data=0xf7287a0) at /work/00915/hinder/Cactus/llama/src/main/ScheduleInterface.c:2826 #13 0x000000000041bc26 in CCTKi_DoScheduleTraverse (group_name=0x7fff50b96cb0 "", item_entry=0x7fff50b96cb8, item_exit=0xf7287a0, while_check=0x1e, if_check=0, function_process=0x2aabd0ff9600, data=0x7fff50b97848) at /work/00915/hinder/Cactus/llama/src/schedule/ScheduleTraverse.c:158 #14 0x0000000000414f19 in CCTK_ScheduleTraverse (where=0x7fff50b96cb0 "", GH=0x7fff50b96cb8, CallFunction=0xf7287a0) at /work/00915/hinder/Cactus/llama/src/main/ScheduleInterface.c:812 #15 0x000000000116f6c0 in Carpet::CallAnalysis (cctkGH=0x7fff50b96cb0, $=2=<value optimized out>) at /work/00915/hinder/Cactus/llama/arrangements/Carpet/Carpet/src/Evolve.cc:556 #16 0x000000000116e755 in Carpet::Evolve (fc=0x7fff50b96cb0, $<1=<value optimized out>) at /work/00915/hinder/Cactus/llama/arrangements/Carpet/Carpet/src/Evolve.cc:81 #17 0x000000000040ccc5 in main (argc=4, argv=0x7fff50b98888) at /work/00915/hinder/Cactus/llama/src/main/flesh.cc:84 I'm not sure why CarpetIOHDF5 is performing MPI calls. This is with the stable version of Carpet. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/534> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #367: When a repo URL changes, GetComponents should offer more help
by Einstein Toolkit 19 Oct '11

19 Oct '11

#367: When a repo URL changes, GetComponents should offer more help ---------------------------+------------------------------------------------ Reporter: eschnett | Owner: eric9 Type: enhancement | Status: new Priority: major | Milestone: Component: GetComponents | Version: Keywords: | ---------------------------+------------------------------------------------ When a repo URL changes, GetComponents currently suggests to check out the repo from scratch (and presumably delete/ignore the old repo). This is very inflexible, in particular when the user has changes in the old repository, which often happens during development. SVN (and presumably all other VC software) offer commands to update the URL, so that one can keep the current checkout. Of course, this makes only sense if this is the same repository that only moved to a new URL, but this seems to happen often enough. GetComponents should at least output instructions for updating the URL. It would be even better if GetComponents detected that new and old repo are the same, and then update the repo URL by itself. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/367> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #494: CarpetReduce tests nonstaggered and staggered fail with development version of Carpet
by Einstein Toolkit 19 Oct '11

19 Oct '11

#494: CarpetReduce tests nonstaggered and staggered fail with development version of Carpet --------------------+------------------------------------------------------- Reporter: hinder | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: Carpet | Version: Keywords: | --------------------+------------------------------------------------------- The CarpetReduce tests nonstaggered and staggered fail with the development version of Carpet and pass with the stable version. The failure is reported as: weight.d.asc: substantial differences did not reproduce 3 NaNs from old weight.d.asc significant differences on 3 (out of 9) lines Were the NaNs wrong before, and somehow got into the test output incorrectly? Or are the NaNs supposed to be there? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/494> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #414: --parallel option not documented in GetComponents
by Einstein Toolkit 19 Oct '11

19 Oct '11

#414: --parallel option not documented in GetComponents ---------------------------+------------------------------------------------ Reporter: bmundim | Owner: eric9 Type: defect | Status: new Priority: minor | Milestone: Component: GetComponents | Version: Keywords: | ---------------------------+------------------------------------------------ The --parallel option is not documented in both versions of GetComponents, the released and development ones. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/414> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #219: ExternalLibraries method should be documented
by Einstein Toolkit 19 Oct '11

19 Oct '11

#219: ExternalLibraries method should be documented ---------------------------+------------------------------------------------ Reporter: hinder | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: documentation | ---------------------------+------------------------------------------------ The Cactus documentation http://einsteintoolkit.org/info/documentation/UsersGuide/UsersGuidech6.html… (scroll down to Compiling with Extra Packages) currently tells people to use the "extras" method for enabling access to external libraries such as HDF5, MPI etc. As I understand it, this method is deprecated in favour of the ExternalLibraries method, and both should not be used at the same time for the same library. The documentation should be updated to describe the ExternalLibraries method, and the old method description should be moved to an appendix with a clear warning that this is deprecated. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/219> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #206: Add --xml option to GetComponents
by Einstein Toolkit 19 Oct '11

19 Oct '11

#206: Add --xml option to GetComponents ---------------------------+------------------------------------------------ Reporter: eric9 | Owner: eric9 Type: enhancement | Status: new Priority: minor | Milestone: Component: GetComponents | Version: Keywords: | ---------------------------+------------------------------------------------ GetComponents should support machine readable output using XML. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/206> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #481: Tests should be converted to use new symmetry thorns
by Einstein Toolkit 19 Oct '11

19 Oct '11

#481: Tests should be converted to use new symmetry thorns -----------------------------------+---------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- It was decided (http://cactuscode.org/pipermail/developers/2010-September/006087.html) that the built-in CartGrid3D symmetries are deprecated and will not work with the Mercurial version of Carpet. Any test cases that use Grid::domain != "full" should be modified to use ReflectionSymmetry instead. In general, this should be possible without regenerating the test output. However, for the case of AHFinderDirect, the horizon finder actually uses a different internal multipatch grid structure if it detects that a CartGrid3D symmetry is being used. This means that the horizon shapes and quantities are different at the level of numerical error with ReflectionSymmetry. I propose to convert the tests to use ReflectionSymmetry and regenerate the test data (the grid function phi is the same with the new symmetry thorn, it's only the horizons which are different). The failing tests are related to checkpoint and recovery, and are not designed to test the symmetry mechanism. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/481> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #395: Thorns providing interpolator routines should provide testcases for them
by Einstein Toolkit 18 Oct '11

18 Oct '11

#395: Thorns providing interpolator routines should provide testcases for them -------------------------+-------------------------------------------------- Reporter: knarf | Owner: Type: enhancement | Status: new Priority: minor | Milestone: ET_2011_11 Component: Other | Version: Keywords: | -------------------------+-------------------------------------------------- Errors in the interpolator often show up in the output of other thorns, depending on those interpolating routines. Figuring out that this is caused by problem while interpolating can take quite a bit of time, which could be saved if the interpolating thorns would include testsuites themselves. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/395> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac September 2011