Trac October 2011

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[Einstein Toolkit] #647: Thornlist http://www.simfactory.org/einsteintoolkit-pysim.th contains old python simfactory repository
by Einstein Toolkit 25 Oct '11

25 Oct '11

#647: Thornlist http://www.simfactory.org/einsteintoolkit-pysim.th contains old python simfactory repository ----------------------------------------------+----------------------------- Reporter: alexander.beck-ratzka@… | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: SimFactory | Version: Keywords: | ----------------------------------------------+----------------------------- The "new users guides" for Simfactory 2: https://docs.einsteintoolkit.org/et-docs/Pysim_Tutorial_for_New_Users instructs to get the example thornlist with simfactory with the command: ./GetComponents -a http://www.simfactory.org/einsteintoolkit-pysim.th The Thornlist of the command above contains the path to the old simfactory 2 repository: [snip] # Pysim Simulation Factory !TARGET = $ROOT !TYPE = svn !URL = https://svn.cct.lsu.edu/repos/numrel/$1/branches/PYSIM_2010 !CHECKOUT = simfactory [snip] -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/647> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #633: Need a transition guide for SimFactory
by Einstein Toolkit 25 Oct '11

25 Oct '11

#633: Need a transition guide for SimFactory -------------------------+-------------------------------------------------- Reporter: hinder | Owner: eschnett Type: enhancement | Status: new Priority: critical | Milestone: ET_2011_10 Component: SimFactory | Version: Keywords: | -------------------------+-------------------------------------------------- People who are using the Perl version of SimFactory will need to know how to change their usage for the Python version for the ET release. Do we have such a document? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/633> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #648: ET wiki should not show a captcha for new links when the user is logged in
by Einstein Toolkit 25 Oct '11

25 Oct '11

#648: ET wiki should not show a captcha for new links when the user is logged in -------------------------------------+-------------------------------------- Reporter: hinder | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit website | Version: Keywords: | -------------------------------------+-------------------------------------- The ET wiki shows a captcha to verify the humanity of any user submitting links to external sites. This does not need to happen if the user is logged in. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/648> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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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] #640: Simulation domain volume and reduction weight sum differ
by Einstein Toolkit 23 Oct '11

23 Oct '11

#640: Simulation domain volume and reduction weight sum differ --------------------+------------------------------------------------------- Reporter: hinder | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: ET_2011_10 Component: Carpet | Version: Keywords: | --------------------+------------------------------------------------------- When I run qc0-mclachlan.par with the current trunk, I get this warning {{{ WARNING level 1 in thorn CarpetReduce processor 0 host kop70.datura.admin (line 120 of /home/ianhin/Cactus/EinsteinToolkit/arrangements/Carpet/CarpetReduce/src/mask_test.c): -> Simulation domain volume and reduction weight sum differ INFO (CarpetReduce): Simulation domain volume: 432000 INFO (CarpetReduce): Reduction weight sum: 431999.996160507 }}} This happens very frequently - more frequently than the CarpetIOBasic output. I think people who try the released ET with the example BBH parameter file will be concerned by this warning. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/640> 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] #639: Change default of VECTORISE_INLINE to "no" in Vectors
by Einstein Toolkit 22 Oct '11

22 Oct '11

#639: Change default of VECTORISE_INLINE to "no" in Vectors -----------------------------------+---------------------------------------- Reporter: hinder | Owner: Type: enhancement | Status: new Priority: major | Milestone: ET_2011_10 Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- Most of the machines supported by SimFactory that use the Intel compiler have to set this to "no" to avoid the compiler running out of memory when compiling ML_BSSN. We choose "no" as the default now to avoid problems for users of machines not supported in SimFactory. OK to commit for the release? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/639> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #636: PITTNullCode does not compile on IBM P7 using the ibm compilers.
by Einstein Toolkit 21 Oct '11

21 Oct '11

#636: PITTNullCode does not compile on IBM P7 using the ibm compilers. -----------------------------------+---------------------------------------- Reporter: diener | Owner: Type: defect | Status: new Priority: major | Milestone: ET_2011_10 Component: EinsteinToolkit thorn | Version: development version Keywords: | -----------------------------------+---------------------------------------- When attempting to run the test suites on an IBM P7 machine using the IBM fortran and C compilers several source files didn't compile for different reasons. In NullDecomp/src/NullDecomp_IO.F90 extra commas was present in some write statements. In the attached patch I have removed these commas. In NullEvolve/src/NullEvol_DissipMask.F90 the min and max functions was used with arguments of different type. The constants 1.0 and 0.0 are by default single precision while CCTK_REAL are double precision. In the patch I have added CCTK_REAL parameters one and zero that are used throughout. In SphericalHarmonicDecomp/src/h5read.cc and SphericalHarmonicRecon/src/Recon.cc the function sqrt was applied to variables of integer type and the compiler didn't know what to convert them to. In the attached patch I explicitly convert the integers to double before taking the sqrt. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/636> 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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