Trac July 2015

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[Einstein Toolkit] #1796: Include IllinoisGRMHD into the Toolkit, as an Arrangement
by Einstein Toolkit 20 Oct '15

20 Oct '15

#1796: Include IllinoisGRMHD into the Toolkit, as an Arrangement -----------------------------------+---------------------------------------- Reporter: zachetie@… | Owner: Zachariah Etienne Type: enhancement | Status: new Priority: major | Milestone: ET_2015_11 Component: EinsteinToolkit thorn | Version: development version Keywords: GRMHD IllinoisGRMHD | -----------------------------------+---------------------------------------- IllinoisGRMHD, an open-source, compact rewrite of the Illinois NR group's GRMHD code, has been graciously hosted by the ET community in its BitBucket repo for more than a year, under the EinsteinEvolve arrangement. This ticket requests official inclusion of an updated IllinoisGRMHD and closely-related thorns into the ET, as an arrangement. IllinoisGRMHD brings a number of key new features to the Toolkit, including: 1) a staggered, vector-potential-based, AMR-compatible GRMHD scheme that automatically preserves divergenceless B-fields without the need for specialized interpolation schemes or divergence cleaning. 2) excision-less, robust modeling of GRMHD flows into black hole interiors 3) a highly-robust conservative-to-primitive solver, which checks the physicality of the conservative variables *prior* to inversion, and modifies them minimally to restore physicality. The proposed arrangement will include: 1) IllinoisGRMHD: Core GRMHD evolution routines, some significant bugfixes since the original version currently in the ET's bitbucket repo; about 3,400 lines of code (cloc) 2) ID_converter_ILGRMHD: Converts HydroBase variables into variables IllinoisGRMHD can read (e.g., IllinoisGRMHD uses a velocity definition consistent with the magnetic induction equation, not the Valencia formulation); about 209 lines of code (cloc) 3) convert_to_HydroBase: Does the reverse of ID_converter_ILGRMHD, needed for compatibility with HydroBase-based analysis thorns; 126 lines of code. All codes are written in C99 and are fully OpenMP-ified. You can read more about IllinoisGRMHD in its code announcement paper (CQG in press): http://arxiv.org/abs/1501.07276 Additionally, a Guide to Getting Started with IllinoisGRMHD has also been written and is available at the IllinoisGRMHD webpage: http://math.wvu.edu/~zetienne/ILGRMHD/ You may now download all three of these thorns (licensed GNU GPL v2 or higher) from: math.wvu.edu/~zetienne/IllinoisGRMHD_arrangement_July_20_2015.tar.gz -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1796> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1794: Backport MPI detect.pl changes from development to release version
by Einstein Toolkit 19 Oct '15

19 Oct '15

#1794: Backport MPI detect.pl changes from development to release version ----------------------+----------------------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Other | Version: development version Keywords: backport | ----------------------+----------------------------------------------------- According to the ET mailing list discussion at http://lists.einsteintoolkit.org/pipermail/users/2015-July/004312.html, the ET does not build on Mac OS with MacPorts in the released version, probably due to changes in MacPorts since the release. The fix was committed to the MPI thorn detect.pl script and needs to be backported to the release. Comer Duncan confirms that this fixes the problem. The required commit seems to be http://git.barrywardell.net/?p=arrangements/ExternalLibraries/MPI.git;a=blo…. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1794> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1033: support a combined "map" file in CarpetIOHDF5
by Einstein Toolkit 07 Oct '15

07 Oct '15

#1033: support a combined "map" file in CarpetIOHDF5 --------------------------+------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: enhancement | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: CarpetIOHDF5 | --------------------------+------------------------------------------------- recovering on different number of processes than was used to write a checkpoint is painfully slow. Part of the reason seems to be that each process essentially has to read all files to find out where each piece of data it requires is located. The attached patch (not to be included in the main code due to bad file formats and coding) enables CarpetIOHDF5 to read all the information stored in the union of index files to from a single file. This means (together with the other patches proposed today) that CarpetIOHDF5 only ever opens those HDF5 files that are required to restore the simulation on a given process. It significantly (factor > 4 where I don't quite know how fast since the unpatched version ran out of walltime) speeds up recovery with many more processors than wrote the files. It also adds an optimization for CCTK_VarIndex calls inside CarpetIOHDF5 (which happens for every dataset in the file). This is intended only as a proof of what might speed up recovery. A proper implementation would need a more sensible file format. Two option seem possible: 1) extend the index file format by a "filename" or "filenum" attribute to each dataset and use a concatenation of all index files as the map file 2) define a custom hdf5 data type corresponding to the information in a single patch_t, which would have mostly integer field plus two variable length / enumerated ASCII fields (for the patch name, variable name) -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1033> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1737: upate CarpetHDF5 reader in VisIt
by Einstein Toolkit 15 Sep '15

15 Sep '15

#1737: upate CarpetHDF5 reader in VisIt ------------------------------+--------------------------------------------- Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Other | Version: development version Keywords: VisIt CarpetHDF5 | ------------------------------+--------------------------------------------- Since the CarpetHDF5 reader (https://svn.cactuscode.org/VizTools/CarpetHDF5) was included in VisIt's main source code repo, we have not attempted to update that copy to the most current version. The coding style in that branch matches the official code but the patches do not apply on top of the official code due to ordering issues as well as some minor new changes to code formatting in the current (2.8.0) VisIt codebase. Since then, I have collected a number of bugfixes/improvements that are collected in various branches at https://bitbucket.org/rhaas80/carpethdf5 . It would be good to eventually try and get the for_VisIt branch (https://bitbucket.org/rhaas80/carpethdf5/branch/for_VisIt) included in the main source code repo again. It contains some bug-fixes wrt how file metadata is cached, as well as number of fixes to reduce memory footprint, number of open files (required to work on large datasets on machines that limit the total number of open files), some improvements to error reporting and robustness when dealing with partially corrupted filesets as well as changes that allow a user to combine multiple HDF5 files into a single "virtual" VisIt database using .visit files. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1737> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1045: URL field should be optional
by Einstein Toolkit 01 Sep '15

01 Sep '15

#1045: URL field should be optional ---------------------------+------------------------------------------------ Reporter: hinder | Owner: eric9 Type: defect | Status: new Priority: minor | Milestone: Component: GetComponents | Version: Keywords: | ---------------------------+------------------------------------------------ In a CRL file, it should be possible to have only an AUTH_URL field and omit the URL field, since it might be that there is no unauthenticated way to access the repository (e.g. for private repositories). At the moment, when I omit the URL field for a Git repository, the error message is: {{{ Use of uninitialized value $git_repo in substitution (s///) at ./GetComponents line 589. Use of uninitialized value $git_repo in substitution (s///) at ./GetComponents line 590. Use of uninitialized value $rec{"GIT_REPO"} in substitution (s///) at ./GetComponents line 593. Use of uninitialized value $rec{"GIT_REPO"} in substitution (s///) at ./GetComponents line 594. ... }}} -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1045> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1772: Simfactory: potentially serious problem with CACHE directory in the simulations directory
by Einstein Toolkit 31 Aug '15

31 Aug '15

#1772: Simfactory: potentially serious problem with CACHE directory in the simulations directory ------------------------+--------------------------------------------------- Reporter: bmundim | Owner: Type: defect | Status: new Priority: critical | Milestone: ET_2015_05 Component: SimFactory | Version: development version Keywords: CACHE | ------------------------+--------------------------------------------------- Is the directory CACHE in the simulation directory really necessary? We are talking about executables with at most 400MB of size, which is nothing compared to current HPC storage systems. I think I might have found a design flaw on simfactory use of CACHE directory which can go unnoticed until it is too late with potential loss of thousands of SUs. Suppose we have the following situation: 1) We build a configuration A and send a simulation A1 with with parameter file 1. So simfactory copies the executable from configuration A to simulation A1 simfactory directory and creates a symlink from /scratch/simulations/CACHE/exe/cactus_A to /scratch/simulations/A1/SIMFACTORY/exe/cactus_A. 2) We then create a new simulation A2 with a different parameter file 2. This time simfactory symlink the simulation executable /scratch/simulations/A2/SIMFACTORY/exe/cactus_A to the cached one /scratch/simulations/CACHE/exe/cactus_A. 3) After a few days (or restarts) of simulations A1 and A2, you come up with a better idea/fix/new parameter which requires to recompile your configuration A. Note that we don't want to build a new configuration from scratch since cactus configurations consume both a lot of time and space to build. So you rebuild your configuration A and its executable cactus_A is updated. 4) Let's say now we submit the updated configuration with the same parameter file 2 in order to test your new idea/fix/parameter and compare it with the simulation A2, which is still running and have a few extra restarts to completion. Call this simulation A2_updated. Simfactory then copy the new updated executable cactus_A from the Cactus/exe/cactus_A to the simulation directory /scratch/simulations/A2_updated/SIMFACTORY/exe/cactus_A *and* update the CACHE symlink to that new simulation directory, ie: $ cd /scratch/simulations/CACHE/exe $ ls -l cactus_A cactus_A -> ../../../../scratch/simulations/A2_updated/SIMFACTORY/exe/cactus_A 5) The problem: now my simulation A2 restarts are compromised with a new executable. Remember that that simulation executable is actually a symlink to the one in the CACHE directory, which has just been updated. I think this whole cache directory intermediate step introduces unnecessary complexity for the user to track; it is really unnecessary and in my opinion not a good design choice. I would vote to eliminate it from simfactory completely as soon as possible, ideally even for this release. Just use one copy of the executable from cactus/exe to simulation/SIMFACTORY/exe and that's it. This is all we need to have that simulation and future ones running consistently with the same executable. Thanks! PS: I have actually noticed this issue on Hershel release (there is no option pointing to Hershel release on trac). I am working on tests for development version to confirm this issue, but give simfactory commits I believe it is still there. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1772> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1749: avoid creating temporary links to files in Formaline
by Einstein Toolkit 18 Aug '15

18 Aug '15

#1749: avoid creating temporary links to files in Formaline -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: Formaline | -----------------------------------+---------------------------------------- the patch in https://bitbucket.org/cactuscode/cactusutils/branch/rhaas %2Fupdate-index changes the way Formaline populates the configjar git repository with changed files. Instead of making a hard linked copy of every file in the thorn, it used plumbing commands git-update-index to add them to the index. This deals gracefully with files in symbolically linked directories (but will dereference a symbolic link if the file *itself* is a symgolic link) and also works when CACTUS_CONFIGS_DIR is not on the same file system as the source tree (eg Cactus is in $HOME which has a small quota but is backed up and $CACTUS_CONFIGS_DIR is in $SCRATCH which is not backed up). Not being able to have $CACTUS_CONFIGS_DIR on a different file system than Cactus is a minor bug, in particular since this method is described in the UserGuide. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1749> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #334: unsuccessful qsub not recognized / submit succeeds for finished simulation
by Einstein Toolkit 18 Aug '15

18 Aug '15

#334: unsuccessful qsub not recognized / submit succeeds for finished simulation ------------------------+--------------------------------------------------- Reporter: knarf | Owner: mthomas Type: defect | Status: new Priority: minor | Milestone: Component: SimFactory | Version: Keywords: | ------------------------+--------------------------------------------------- python version: I submitted a simulation 'sim submit' but the corresponding qsub failed due to wrong numbers of procs/node (philip cluster). I changed the number given on the command line and did a 'sim submit' again, this time successful. Several things happend which I think could be done better: - the unsuccessful qsub was not detected during the new submit - it attempted a restart and didn't simply clean the unsuccessful submit - when trying the restart, it went ahead and queued the job, but this later failed when run with "cannot rerun a restart that has been finished". This could have been caught earlier - without the wait time in the queue. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/334> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1790: ADMMass: Properly distinguish between int and CCTK_INT
by Einstein Toolkit 17 Aug '15

17 Aug '15

#1790: ADMMass: Properly distinguish between int and CCTK_INT -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: | -----------------------------------+---------------------------------------- Patch attached. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1790> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1795: PITTNullCode results depend on number of processors
by Einstein Toolkit 17 Aug '15

17 Aug '15

#1795: PITTNullCode results depend on number of processors -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: PITTNullCode | -----------------------------------+---------------------------------------- As part of trying to add SphericalHarmonicReconGen to the ET I noticed that PITTNullCode produces different results depending on the number of cores used. This already happens with the %%regression_test%% test if SphericalHarmonicRecon that is already in the ET. The issue is hidden right now since the test uses very lose tolerances of {{{ ABSTOL 1.5e-5 RELTOL 1.5e-4 }}} Changing them to the standard Cactus accuracies and regenerating the tests shows that the test that was generated using 2 processors fails when run with a single MPI process. Test data is in the branch rhaas/procdependency . This needs to be fixed or the arrangement must be marked as broken unless this is the intended behaviour in which case this needs to be documented prominently in the documenation. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1795> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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