Trac February 2017

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95 discussions

[Einstein Toolkit] #1753: hwloc: move pkg-config based detection into Search phase
by Einstein Toolkit 13 Dec '17

13 Dec '17

#1753: hwloc: move pkg-config based detection into Search phase -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: hwloc | -----------------------------------+---------------------------------------- the attacheched patch changes detect.sh such that pkg-config is treated on the same footing as the search at commonly known places. It also adds the option for the user to specify HWLOC_LIBS rather than hard-coding it to hwloc. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1753> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1917: sim setup should automatically set up the machine for common OSes
by Einstein Toolkit 21 Nov '17

21 Nov '17

#1917: sim setup should automatically set up the machine for common OSes -------------------------+-------------------------------------------------- Reporter: hinder | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: SimFactory | Version: development version Keywords: | -------------------------+-------------------------------------------------- There are instructions at https://docs.einsteintoolkit.org/et- docs/Simplified_Tutorial_for_New_Users for users to configure simfactory for common operating systems when their machine is not recognised by SimFactory. This logic should be implemented in sim setup instead, so that users can use the ET out of the box on supported OSes. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1917> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #2004: example in New User Tutorial maybe wrong
by Einstein Toolkit 21 Nov '17

21 Nov '17

#2004: example in New User Tutorial maybe wrong --------------------------------------+------------------------------------- Reporter: b.gabella@… | Owner: Bill Gabella Type: defect | Status: new Priority: minor | Milestone: Component: Other | Version: development version Keywords: | --------------------------------------+------------------------------------- Running the static_tov.par that comes in the ETK_2016_11, I see different results for the two plots hydrobase-rho.maximum and admbase-lapse.minimum. See the mail list post Users Digest, Vol 83, Issue 3 on 1 Feb 2017 at 3:10pm. New User Tutorial https://docs.einsteintoolkit.org/et-docs/Tutorial_for_New_Users bill e.g. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/2004> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #2013: piraha breaks ThornDoc building
by Einstein Toolkit 19 Nov '17

19 Nov '17

#2013: piraha breaks ThornDoc building --------------------+------------------------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: development version Keywords: | --------------------+------------------------------------------------------- Doing {{{make ThornDocHTML}}} I get an error message in eg in echo RELOADAGENT | gpg-connect-agent of {{{ Undefined subroutine &piraha::parse_peg_file called at /home/rhaas/postdoc/gr/cactus/ET_trunk/lib/sbin/ScheduleParser.pl line 83. }}} -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/2013> 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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Trac February 2017