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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] #1826: config file in current directory overwrites default
by Einstein Toolkit 19 Oct '15

19 Oct '15

#1826: config file in current directory overwrites default ------------------------+--------------------------------------------------- Reporter: knarf | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: SimFactory | Version: development version Keywords: | ------------------------+--------------------------------------------------- I configured like usual: {{{ sim build --thornlist ./thornlists/einsteintoolkit.th }}} This is supposed to use the default optionlist for that machine: debian.cfg, in the simfactory mdb. However, I had another (different) debian.cfg in my current directory (the Cactus root dir), which simfactory used instead. Simfactory should only use files other than "it's own" if specified by the user, even if there happen to have to be files in `pwd` with the same name. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1826> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1818: HDF5 configuration fails on Datura
by Einstein Toolkit 19 Oct '15

19 Oct '15

#1818: HDF5 configuration fails on Datura -----------------------------------+---------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: blocker | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: HDF5 | -----------------------------------+---------------------------------------- With the current ET trunk, I get the following error on a clean build on Datura: ******************************************************************************** Running configuration script for thorn HDF5: Additional requested language support: Fortran ERROR: ERROR in HDF5 configuration: ERROR: H5pubconf.h not found in The build then hangs at that point with no further output. This may be related to the recent changes to the HDF5 thorn to factor out common code in external libraries. The error message is one issue, the hanging build is another I think. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1818> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1815: simfactory: sim show-output selects inactive, queued restart
by Einstein Toolkit 19 Oct '15

19 Oct '15

#1815: simfactory: sim show-output selects inactive, queued restart ------------------------+--------------------------------------------------- Reporter: knarf | Owner: Type: defect | Status: new Priority: minor | Milestone: ET_2015_11 Component: SimFactory | Version: development version Keywords: | ------------------------+--------------------------------------------------- {{{ sim show-output NAME }}} currently selects the 'maximum' restart for output, which in case of queued up restarts is one that isn't (yet) running. It should select the currently active restart (if there is one), given that this version of simfactory is going to be retired anyway .... The patch could probably be done 'nicer', but this is the minimally invasive version. Patch: {{{ diff --git a/lib/sim-manage.py b/lib/sim-manage.py index 87a26fd..c0e8343 100755 --- a/lib/sim-manage.py +++ b/lib/sim-manage.py @@ -300,7 +300,12 @@ def command_show_output(): if simenv.OptionsManager.HasOption('restart-id'): restart_id = simenv.OptionsManager.GetOption('restart-id') else: - restart_id = restartlib.GetMaxRestartID(simulationName) + restart = simrestart.SimRestart() + restart.load(simulationName) + restart_id = restartlib.GetActiveRestartId(restart) + restart.done() + if (restart_id == None): + restart_id = restartlib.GetMaxRestartID(simulationName) restart = simrestart.SimRestart() ret = restart.load(simulationName, restart_id) }}} -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1815> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1814: Make git repository names conform to Cactus CamelCase name convention.
by Einstein Toolkit 19 Oct '15

19 Oct '15

#1814: Make git repository names conform to Cactus CamelCase name convention. -------------------------+-------------------------------------------------- Reporter: bmundim | Owner: Type: enhancement | Status: new Priority: minor | Milestone: ET_2015_11 Component: Other | Version: development version Keywords: | -------------------------+-------------------------------------------------- https://bitbucket.org/einsteintoolkit/manifest/pull-requests/4/make-git- repository-names-conform-to/diff -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1814> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1822: requested and suggested references no longer automatically updated on website
by Einstein Toolkit 19 Oct '15

19 Oct '15

#1822: requested and suggested references no longer automatically updated on website ----------------------------+----------------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: critical | Milestone: Component: Cactus website | Version: development version Keywords: ET_2015_11 | ----------------------------+----------------------------------------------- With the switch of the manifest repo to git, the web-server stopped updating the requested/suggested references for each thorn automatically (since it uses the old svn repo). This should be fixed, if it still persists. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1822> 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] #1802: move AEIThorns into git repositories
by Einstein Toolkit 08 Oct '15

08 Oct '15

#1802: move AEIThorns into git repositories -----------------------------------------------------------------------------+ Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: ADMMass AEILocalInterp PunctureTracker SystemStatistics Trigger | -----------------------------------------------------------------------------+ Currently the ET contains the following AEI thorns: * AEIThorns/ADMMass * AEIThorns/AEILocalInterp * AEIThorns/PunctureTracker * AEIThorns/SystemStatistics * AEIThorns/Trigger since the AEI would like to shut down the svn server (or at least change it to read only mode) it would be good to move these thorns into: EinsteinAnalysis:: ADMMass PunctureTracker CactusUtils:: SystemStatistics Trigger (need change of license to LGPL) Numerical:: AEILocalInterp (license must stay GPL) For the ET thorns Barry kindly did the conversion using a set of scripts of his. If you were to make the scripts accessible (or give the whole thing a try yourself), then this could be started as soon as the authors (Ian and Frank are main authors if SystemStatistics and Trigger, Erik, Barry and I contributed, I am fine with a license change) agree to the license change where required. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1802> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1803: Move LSUThorns into git repositories at Bitbucket
by Einstein Toolkit 08 Oct '15

08 Oct '15

#1803: Move LSUThorns into git repositories at Bitbucket -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: unset | Milestone: Component: Other | Version: development version Keywords: | -------------------------+-------------------------------------------------- -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1803> 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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