Trac September 2013

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[Einstein Toolkit] #1368: add env option for commands in .mojave.xml
by Einstein Toolkit 07 May '18

07 May '18

#1368: add env option for commands in .mojave.xml -------------------------+-------------------------------------------------- Reporter: sbrandt | Owner: sbrandt Type: enhancement | Status: new Priority: major | Milestone: Cactus_4.3.0 Component: Mojave | Version: Keywords: | -------------------------+-------------------------------------------------- add env option for commands in .mojave.xml -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1368> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1170: ExtrenalLibraries handle XXX_DIR XXX_INC_DIRS and XXX_LIB_DIRS incosistently
by Einstein Toolkit 20 Mar '18

20 Mar '18

#1170: ExtrenalLibraries handle XXX_DIR XXX_INC_DIRS and XXX_LIB_DIRS incosistently -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: ExternalLibraries | -----------------------------------+---------------------------------------- This is a companion ticket to #1006. Different thorns (eg. MPI and HDF5 and LAPACK) handle XXX_DIR and XXX_INC_DIRS etc differently. MPI for example sets the include path to $MPI_DIR/include if MPI_INC_DIRS is not explicitly set and to MPI_INC_DIRS if it is set. HDF5 has no HDF5_INC_DIRS option and always sets the include path to HDF5_DIR/include. LAPACK has not INC_DIRS option and sets the linker path to LAPACK_DIR while the other two thorns set it to XXX_DIR/lib (unless overridden by MPI_LIB_DIRS in the case of MPI). I would be good to present a uniform set of option for all these thorns. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1170> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1396: Display prompts of executed commands
by Einstein Toolkit 19 Nov '17

19 Nov '17

#1396: Display prompts of executed commands ---------------------------+------------------------------------------------ Reporter: rhaas | Owner: eric9 Type: enhancement | Status: new Priority: optional | Milestone: Component: GetComponents | Version: development version Keywords: | ---------------------------+------------------------------------------------ the attached patch goes to some lengths to capture both stdout and stderr when executing commands and displays each line of output as it is generated by the command. This is useful for programs that output prompts to stdout and wait for user input afterwards. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1396> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #68: GetComponents hang due to certificate issues.
by Einstein Toolkit 19 Nov '17

19 Nov '17

#68: GetComponents hang due to certificate issues. --------------------------------+------------------------------------------- Reporter: diener@… | Owner: eric9 Type: defect | Status: new Priority: major | Milestone: Component: GetComponents | Version: ET_2010_06 Keywords: | --------------------------------+------------------------------------------- I did a complete new checkout of the EinsteinToolkit on numrel06 using the version of GetComponents available on the EinsteinToolkit web pages and had GetComponents hang with no errors or warnings when checking out AEIThorns/AEILocalInterp. Trying the checkout manually I got: Error validating server certificate for 'https://svn.aei.mpg.de:443': - The certificate is not issued by a trusted authority. Use the fingerprint to validate the certificate manually! Certificate information: - Hostname: svn.aei.mpg.de - Valid: from Tue, 23 Feb 2010 16:02:12 GMT until Sun, 22 Feb 2015 16:02:12 GMT - Issuer: Max-Planck-Gesellschaft, DE - Fingerprint: 03:b4:e8:6e:d9:09:e9:93:72:e9:ff:fa:df:e4:2c:6d:1d:2a:e4:66 (R)eject, accept (t)emporarily or accept (p)ermanently? p After accepting the certificate and restarting the checkout proceeded without problems. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/68> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #181: AEILocalInterp should not off-centre the interpolation stencil by default
by Einstein Toolkit 19 Nov '17

19 Nov '17

#181: AEILocalInterp should not off-centre the interpolation stencil by default ----------------------------+----------------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: AEILocalInterp | ----------------------------+----------------------------------------------- AEILocalInterp by default will off-centre the interpolation stencil if there are insufficient points to perform the interpolation. In a parallel setting, this could happen due to there being insufficient ghost points for the interpolator chosen. The off-centering leads to an interpolation error which is of the correct order but larger than for a centered stencil. More importantly, it leads to different results on different numbers of processes. This violates a basic design principle of Cactus, and the expectation of users, that changing the number of processors should not change the results of a simulation. I propose that instead of silently off-centering the stencil, AEILocalInterp should abort with an error indicating that there are insufficient ghost-zones. The interpolator options corresponding to this are: boundary_off_centering_tolerance={0.0 0.0 0.0 0.0 0.0 0.0} boundary_extrapolation_tolerance={0.0 0.0 0.0 0.0 0.0 0.0} -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/181> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #778: Compiling PittNullCode is slow
by Einstein Toolkit 24 Oct '17

24 Oct '17

#778: Compiling PittNullCode is slow -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- Compiling PittNullCode is very slow on some systems (e.g. with gcc). I believe this is because files such as NullConstr_R00.F90 contain many whole-array operations that the compiler has to analyse. I suggest to rewrite these routines, using e.g. forall or do loops. If we want to keep the elegant, index-free notation, then I suggest to add an elemental subroutine for the actual calculations and calling it with whole arrays. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/778> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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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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Trac September 2013