Trac April 2014

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[Einstein Toolkit] #697: Repository and thorn names cannot be different
by Einstein Toolkit 10 Nov '15

10 Nov '15

#697: Repository and thorn names cannot be different ---------------------------+------------------------------------------------ Reporter: eschnett | Owner: eric9 Type: defect | Status: new Priority: critical | Milestone: Component: GetComponents | Version: Keywords: | ---------------------------+------------------------------------------------ I am accessing some thorns stored in git repositories at bitbucket.org, which insists that all repository names are all lower case. I don't know how to specify this in GetComponents. When I say !TARGET = $ARR !TYPE = git !URL = git@bitbucket.org:user/thorn.git !AUTH_URL = git@bitbucket.org:user/thorn.git !CHECKOUT = Arrangement/Thorn then GetComponents does not create a symbolic link from Thorn to ../../repos/thorn, but to ../../repos/thorn/Arrangement/Thorn instead. How do I avoid this? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/697> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #241: Thorns should be able to specify implementation versions, and other thorns should be able to depend on those
by Einstein Toolkit 26 Oct '15

26 Oct '15

#241: Thorns should be able to specify implementation versions, and other thorns should be able to depend on those -------------------------+-------------------------------------------------- Reporter: knarf | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- Cactus thorns implement 'implementations', and other thorns can then depend on particular implementations being present. However, quite often those are updated, and incompatibilities occur. Usually this is resolved by the developer in both thorns - the implementing and the using thorn. However, a user might just update one of them, and Cactus would not catch this error. Thus, I suggest to think about, and implement how to: - specify implementation versions e.g. IMPLEMENTS: Cactus (4.0) The version string within () would have be sorted in an intelligent way to allow comparisons [1]. - specify dependencies on particular versions of other implementations In particular I suggest the following dependencies: depends, and conflicts, both with comparisons < <= == >= > != e.g. DEPENDS: Cactus (>= 4.0) DEPENDS: BadImplementation (!=3.14) <-- this introduces a dependency CONFLICTS: BadImplementation (==3.14) <-- this doesn't introduce a depencency [1] First the initial part of each string consisting entirely of non-digit characters is determined. These two parts (one of which may be empty) are compared lexically. If a difference is found it is returned. The lexical comparison is a comparison of ASCII values modified so that all the letters sort earlier than all the non-letters. Then the initial part of the remainder of each string which consists entirely of digit characters is determined. The numerical values of these two parts are compared, and any difference found is returned as the result of the comparison. For these purposes an empty string (which can only occur at the end of one or both version strings being compared) counts as zero. These two steps (comparing and removing initial non-digit strings and initial digit strings) are repeated until a difference is found or both strings are exhausted. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/241> 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] #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] #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] #649: simfactory should create the "simulations" directory
by Einstein Toolkit 14 Aug '15

14 Aug '15

#649: simfactory should create the "simulations" directory ------------------------+--------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: SimFactory | Version: Keywords: | ------------------------+--------------------------------------------------- when following the new users tutorial one gets: {{{ [rhaas@qb1 Cactus]$ ./simfactory/bin/sim submit static_tov --parfile=par/static_tov.par --procs=32 --walltime=8:0:0 Parameter file: /home/rhaas/Cactus/par/static_tov.par Error: could not access simulation base directory /scratch/rhaas/simulations for reading and writing Aborting Simfactory. [137450 refs] }}} This happens each time I set up a fresh simfactory on a machine. It might be useful if simfactory would create the simulation base directory if it does not exist. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/649> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1059: simfactory silent error
by Einstein Toolkit 13 Aug '15

13 Aug '15

#1059: simfactory silent error --------------------------------------+------------------------------------- Reporter: anonymous | Owner: eschnett Type: enhancement | Status: new Priority: optional | Milestone: Component: SimFactory | Version: Keywords: simfactory error message | --------------------------------------+------------------------------------- When sim submit -remote ... fails to queue a job because the allocation has been overdrawn, simfactory does not print any error message to screen (it is only hidden in the log file). Could it be made to print an error message to screen? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1059> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #959: Move pthreads to ExternalLibraries
by Einstein Toolkit 13 Aug '15

13 Aug '15

#959: Move pthreads to ExternalLibraries -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- We should move pthreads support to ExternalLibraries (or to the flesh). I have asked CCT to create the respective repository. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/959> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1579: GRHydro does not build on Blue Gene/Q
by Einstein Toolkit 09 Aug '15

09 Aug '15

#1579: GRHydro does not build on Blue Gene/Q ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Other | Version: development version Keywords: | ----------------------+----------------------------------------------------- Some of the C++ source files in GRHydro do not build on a Blue Gene/Q with IBM's compiler. The problem is that the compiler takes a very long time (>8h) even without (sic!) optimization. "The usual" playing with compiler options or changes to the source files had no effect. I consider this to be a bug in the compiler. A work-around may be to switch to Clang as C++ compiler. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1579> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #816: include SphericalHarmonicReconASCII from incoming in PITTNULLCode
by Einstein Toolkit 04 Aug '15

04 Aug '15

#816: include SphericalHarmonicReconASCII from incoming in PITTNULLCode -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: optional | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- Christian Reisswig provided a copy of SphericalHarmonicReconASCII and alternative thorn that reads in CCE boundary data (similar SphericalHarmonicRecon) but supporting a wider variety of input file formats (HDF5 among them, irrespective of the name). Used by SpEC and Llama. There are no docs or test cases as of now. Test data would be welcome (SpEC, Llama or Cactus provided, I don't think it makes a difference). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/816> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac April 2014