Trac May 2015

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[Einstein Toolkit] #1283: Missing data in HDF5 files
by Einstein Toolkit 24 Oct '17

24 Oct '17

#1283: Missing data in HDF5 files --------------------+------------------------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | --------------------+------------------------------------------------------- If a simulation runs out of disk space while writing an HDF5 file, the simulation will terminate. The hdf5 file being written might then be corrupt, and all data from it may be irretrievable. In that case, restarting from the last-written checkpoint file may leave a "gap" in the data corresponding to the period between the start of the failed restart and the last checkpoint file written. Steps to reproduce: • Start a simulation which checkpoints periodically and consists of several restarts • Keep all checkpoint files • Restart 0000 completes successfully and checkpoints at iteration i1 • Restart 0001 checkpoints once after some evolution at iteration i2 • Restart 0001 terminates abnormally while writing an HDF5 output file at iteration i3 • The output file is corrupted and nonrecoverable, so there is no data from iteration i1 to iteration i3 • Restart 0002 starts at iteration i2 as this is the last checkpoint available • The simulation continues until the end, but the data from the corrupted HDF5 file between iteration i1 and i2 is lost Possible solutions: 1. Write HDF5 files safely, e.g. by first copying the file to a new temporary file, performing the write, then atomically moving the temporary file over the original file. The original file would then remain in the event of a crash while writing the new file. This could be very expensive for 3D output files. 2. Start a new set of HDF5 files after each checkpoint. This seems to be the most efficient and simplest solution, but requires readers of HDF5 files to be modified to take it into account. 3. Check the consistency of all HDF5 files in the previous restart(s) on recovery, and recover from the latest checkpoint file for which all previous HDF5 files are valid. We could use code to check the HDF5 file, or some other flagging mechanism to indicate that HDF5 writes were completed successfully; e.g. we could rename the HDF5 file to .tmp during writes, and rename it back after a successful write. This is complex and requires Cactus or simfactory to look into previous restarts. It also only applies to HDF5 files, and requires breaking several abstraction barriers. 4. Wait for HDF5 journalling support. As far as I know only metadata journalling is planned, which is probably not enough, and in any case, they are not actively working on the next version of HDF5 at the moment due to lack of funding. 5. Checkpoint only on termination of the simulation In reality, we do not keep all checkpoint files. I usually keep just the last checkpoint file. I believe that a Cactus simulation will only delete checkpoint files which it has itself written, which means that there will generally be one checkpoint file kept per restart; the last one written. This means that you can always recover from the above situation by rerunning the restart during which the problem occurred. However, keeping one checkpoint file per restart is a problem in itself, and we should fix this as well, which would then mean the potential for losing data in the case of an interrupted write operation. Thoughts? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1283> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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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] #1781: Outflow: wrong column labels in 2D output
by Einstein Toolkit 24 Oct '17

24 Oct '17

#1781: Outflow: wrong column labels in 2D output -----------------------------------+---------------------------------------- Reporter: dradice@… | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: | -----------------------------------+---------------------------------------- This is a trivial fix (I am attaching a patch) -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1781> 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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