Trac April 2015

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[Einstein Toolkit] #1193: CarpetReduce uses lsh for index calculations
by Einstein Toolkit 24 Oct '17

24 Oct '17

#1193: CarpetReduce uses lsh for index calculations --------------------+------------------------------------------------------- Reporter: knarf | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: ET_2013_05 Component: Carpet | Version: development version Keywords: | --------------------+------------------------------------------------------- CarpetReduce (e.g. reduce.cc:644) uses lsh to calculate GF indices. This is wrong in case lsh!=ash. Either use ash or the Cactus macros (which would probably be even better). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1193> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1181: Parameter file parsing error message is hidden
by Einstein Toolkit 24 Oct '17

24 Oct '17

#1181: Parameter file parsing error message is hidden ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | ----------------------+----------------------------------------------------- Parse errors in parameter files are hidden among other output, and are thus difficult to spot. This example shows this: {{{ cactus::cctk_itlast = 3 ; ActiveThorns = "HDF5" }}} The problem is that the error message is output among the activation messages. If the parameter file is long and the syntax error is in the beginning, then several hundred lines may be output after the error message, which makes it very difficult to spot it. The parsing errors should be output in the same way as other parameter errors, which are prefixed by WARNING etc. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1181> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1100: Correct backtrace generation in Carpet
by Einstein Toolkit 24 Oct '17

24 Oct '17

#1100: Correct backtrace generation in Carpet ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: Carpet | Version: Keywords: | ----------------------+----------------------------------------------------- The file backtrace.cc in CarpetLib does not #include <cctk.h>; hence all HAVE_BACKTRACE* macros are undefined, and only basic backtraces are generated. Correcting this is non-trivial, since the backtrace code is arcane, is written in C, probably expects glibc, contains (I'm fairly certain) memory allocation errors, and doesn't build e.g. on Mac OSX. The code also spends an inordinate amount of time allocating and freeing string buffers, which should be replaced by simply using C++ streams. The backtrace code also probably requires a few more autoconf tests, so that it can be disabled where it does not work. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1100> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1494: Allow skipping of MoL_PostStep and MoL_PseudoEvolutionBoundaries in POSTRESTRICT
by Einstein Toolkit 24 Oct '17

24 Oct '17

#1494: Allow skipping of MoL_PostStep and MoL_PseudoEvolutionBoundaries in POSTRESTRICT -------------------------+-------------------------------------------------- Reporter: hinder | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: development version Keywords: | -------------------------+-------------------------------------------------- It is not always necessary to call MoL_PostStep and MoL_PseudoEvolutionBoundaries in POSTRESTRICT, and it can introduce a performance penalty. The main reason for these calls is that restriction does not fill (outer or symmetry) boundary points, and this is usually done in MoL_PostStep. MoL_PseudoEvolutionBoundaries also sets boundary conditions. However, if restriction does not modify boundary points, for example in the case that boundary points are always far from refined regions, there is no reason to apply boundary conditions (e.g. by calling MoL_PostStep) after restriction. Eventually, Carpet and MoL should be modified to determine automatically whether the BCs need to be applied, but until that is implemented, the attached patch provides parameters for careful users to optimise their simulations in the case where this is safe to do. Additionally, recalculations performed in MoL_PostStep may replace more accurate restricted values computed on finer grids, leading to a loss of accuracy. OK to commit? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1494> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #914: Don't use fork()
by Einstein Toolkit 24 Oct '17

24 Oct '17

#914: Don't use fork() -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- It seems that it is in many cases not safe to call fork() in MPI applications. This page <http://www.open-mpi.de/faq/?category=openfabrics #ofa-fork> has some information. The upshot seems to be: - In many (most) cases, one can call system() or popen() to execute external processes while waiting for them. - It is generally not safe to call fork() to execute a certain task in the background. However, it should be possible to use threads in this case. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/914> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #260: produce map of ET users
by Einstein Toolkit 24 Oct '17

24 Oct '17

#260: produce map of ET users -------------------------------------+-------------------------------------- Reporter: knarf | Owner: Type: enhancement | Status: new Priority: optional | Milestone: Component: EinsteinToolkit website | Version: Keywords: | -------------------------------------+-------------------------------------- It would be nice to produce an (autmatically generated) map of the locations of ET users -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/260> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1542: Define variants of CCTK_FullName and CCTK_GroupName that don't require calling free
by Einstein Toolkit 24 Oct '17

24 Oct '17

#1542: Define variants of CCTK_FullName and CCTK_GroupName that don't require calling free -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: development version Keywords: | -------------------------+-------------------------------------------------- 'nuff said. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1542> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1581: Clean up ET web site menu
by Einstein Toolkit 24 Oct '17

24 Oct '17

#1581: Clean up ET web site menu -------------------------------------+-------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit website | Version: development version Keywords: | -------------------------------------+-------------------------------------- The menu entries "support" and "issue tracker" should be separated from "wiki", "blog", and "seminars". The first two are about the code, the latter two about the community. I suggest to move the first two to the "download" section that currently has no sub-menus. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1581> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1547: issues with stampede
by Einstein Toolkit 24 Oct '17

24 Oct '17

#1547: issues with stampede ----------------------------+----------------------------------------------- Reporter: jchsma@… | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Other | Version: ET_2013_11 Keywords: | ----------------------------+----------------------------------------------- Over the past few months, I have been using RIT's LazEv code with only minor hiccups on stampede (particularly, the unreproducible 'dapl_conn_rc' crashes that I'm sure other stampede users are familiar with). This checkout was of the previous release, ET_2013_05, and compiled with Intel MPI. Most of the jobs I ran took advantage of some symmetry, and I was able to run on 12-16 nodes at about 50-60% memory usage. After the sync issue was backported, I checked out the new release, ET_2013_11 and immediately ran into problems. The first issue was with the run performance and LoopControl, which, with the mailing lists help, we sorted out. The second was with crashes and checkpointing. With both Intel MPI and MVAPICH2 configurations, the code would hang (~50% of the time) when dumping checkpoints, and 100% when dumping a termination checkpoint. Further, the crashes seem more frequent, and I couldn't get a simulation to run for a full 24 hours without crashing (either by stalling on checkpointing or otherwise). So, I checked out a clean version of the toolkit, with only toolkit thorns, and removed any thorns specific to RIT. I compiled with both the Intel MPI and MVAPICH2 configurations in simfactory. In both cases, I can run the 'qc0-mclachlan.par' file to completion with no issues. So I edited the qc0 parfile to update the grid, remove the symmetries, and update the initial data to match my test parameter file. I ran the job on 20 nodes, and with either configuration, I was not successful in running the job to completion on any of my numerous attempts. Intel MPI runs die with the standard unhelpful "dapl_conn_rc" error at random times in the evolution, and the MVAPICH2 dies with: [c431-903.stampede.tacc.utexas.edu:mpispawn_7][readline] Unexpected End- Of-File on file descriptor 6. MPI process died? [c431-903.stampede.tacc.utexas.edu:mpispawn_7][mtpmi_processops] Error while reading PMI socket. MPI process died? [c431-903.stampede.tacc.utexas.edu:mpispawn_7][child_handler] MPI process (rank: 15, pid: 106620) terminated with signal 9 -> abort job [c429-501.stampede.tacc.utexas.edu:mpirun_rsh][process_mpispawn_connection] mpispawn_7 from node c431-903 aborted: Error while reading a PMI socket (4) The IMPI jobs died with the same dapl_conn_rc error at run times of 2 hours, 8 hours, and 21 hours. I also had one job that hung and did not exit until it was killed by the queue manager. The MVAPICH2 jobs died at around 3 hours and 8 hours with the error above. We've been in contact with TACC and they said it was a Cactus issue, so I am sending this report. Attached is the parameter file I used for the tests. They should work with a stock ET_2013_11 checkout. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1547> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #980: Remove support for the flesh-based MPI mechanism
by Einstein Toolkit 24 Oct '17

24 Oct '17

#980: Remove support for the flesh-based MPI mechanism -------------------------+-------------------------------------------------- Reporter: hinder | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- The flesh-based MPI mechanism has just been deprecated in favour of ExternalLibraries/MPI. Even though the latter is new, it is probably a good idea to completely disable the old mechanism since having any mixture of thorns/optionlists using the old and new mechanisms is completely untested and will likely lead to problems and confusion. It's better to give a useful fatal error message if someone still specifies "MPI = " in their optionlist than to have things break in other weird and wonderful ways. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/980> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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