Trac August 2013

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[Einstein Toolkit] #605: Simfactory does not find the right 'path' for symlinked cactus directories
by Einstein Toolkit 13 Aug '13

13 Aug '13

#605: Simfactory does not find the right 'path' for symlinked cactus directories ------------------------+--------------------------------------------------- Reporter: knarf | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: ET_2011_10 Component: SimFactory | Version: development version Keywords: | ------------------------+--------------------------------------------------- Simfactory currently does not detect the 'right' path to a Cactus sourcetree if this is from within a symlink, e.g. Cactus -> /mnt/data/Cactus. This is because while `pwd` returns '/home/user/Cactus', simfactory uses a wrapper to the C-library getcwd(), which dereferences symlinks. Simfactory then gets '/mnt/data/Cactus' and tries to use this path on remote machines when syncing - which of course does not work. The attached patch fixes this by using os.environ.get("PWD") and, if this is not defined, using os.getcwd() as workaround. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/605> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1415: GRHydro updates
by Einstein Toolkit 13 Aug '13

13 Aug '13

#1415: GRHydro updates -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: GRHydro | -----------------------------------+---------------------------------------- accumulated GRHydro changes since before the CGWAS school (July 22nd). Includes the PPM changes from the workshop. Does not yet include the staggered vector potential work since this seems to be still in early stages. Will commit after Thursday unless objections are raised. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1415> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1422: Subscribing to commit notifications for the ET should be made easier
by Einstein Toolkit 13 Aug '13

13 Aug '13

#1422: Subscribing to commit notifications for the ET should be made easier -------------------------+-------------------------------------------------- Reporter: hinder | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Other | Version: development version Keywords: | -------------------------+-------------------------------------------------- At the moment, if you want to receive commit notification emails about changes to components of the ET, you have to subscribe to a number of separate mailing lists. There is a "commits" mailing list for the ET, but this currently only includes notifications for components which are not announced on other lists. I propose that subscribing to the ET "commits" mailing list should be enough to receive commit notifications for all components in the toolkit, so that only one subscription is needed. This will also simplify mail filtering on the receiving end. Note that the individual components could continue to manage their own mailing lists if needed, but a copy of the commit notification would be sent to the ET commits list. The components with separate lists that I currently know about are: * SimFactory * Cactus * AEIThorns * Kranc * LSUThorns Probably the easiest way to implement this would be to modify the VC commit hooks to send the notification to the ET commits list in addition to wherever it is currently being sent. The commits list may have to be configured to accept email from these additional addresses. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1422> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #117: Error while building multiple configurations
by Einstein Toolkit 12 Aug '13

12 Aug '13

#117: Error while building multiple configurations ------------------------+--------------------------------------------------- Reporter: eschnett | Owner: mthomas Type: defect | Status: new Priority: major | Milestone: Component: SimFactory | Version: Keywords: | ------------------------+--------------------------------------------------- I wanted to build multiple configurations at once with the command ./simfactory/sim build sim-debug sim sim-debug is a debug configuration, sim is optimised. SimFactory built sim-debug, then aborted with the error: optionlist is: /Users/eschnett/EinsteinToolkit-hg/configs/sim/OptionList Error: pattern '^\s*DEBUG\s*=.*$' exists already It assumes that SimFactory doesn't properly distinguish between the different build options of the different configurations. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/117> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1303: document syntax of new parameter file parser
by Einstein Toolkit 12 Aug '13

12 Aug '13

#1303: document syntax of new parameter file parser --------------------+------------------------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | --------------------+------------------------------------------------------- currently we have no documentation as to what format the new parser accepts. As a matter of fact the documentation in the UsersGuide (see http://einsteintoolkit.org/documentation/UsersGuide/UsersGuidech7.html#x10-…) is in contradiction with what the parser will allow: {{{ * The parameter file is read sequentially from top to bottom, this means that if you set the value of a parameter twice in the parameter file, the second value will be used. * String parameter values can be specified either as unquoted tokens (not containing any whitespace), or as quoted values. If a quoted string parameter value spans multiple lines, all whitespaces, including newline characters, are preserved. }}} which will fail. Actually the first one is already incorrect with the current implementation which does not allow a parameter to be set twice (since this is often a sign of a user error). While this is "just" documentation, I'll still flag it as major since the parser is so fundamental. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1303> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1306: problem with creating a new project with an existing cactus directory
by Einstein Toolkit 12 Aug '13

12 Aug '13

#1306: problem with creating a new project with an existing cactus directory ----------------------------------------+----------------------------------- Reporter: srichers@… | Owner: sbrandt Type: defect | Status: new Priority: minor | Milestone: Component: Mojave | Version: Keywords: | ----------------------------------------+----------------------------------- When a new project is created and fed the location of a local Cactus directory, the Mojave 'build' command does not work right away because it tries to execute simfactory from the workspace directory. It would be nice if the commands were executed in the existing directory rather than the workspace one so the .mojave.xml file doesn't have to be changed. (or a basedir variable in the mojave.xml file could be added and prepended to each filename) Also, the indexer does not work properly for new projects with an existing cactus directory. It does not recognize anything (cactus types, functions from other files, etc). It works somewhat better, though not completely, if the Cactus directory is put into the appropriate folder in workspace/ before creating the project. (recognizes Cactus internals, but not e.g. functions defined in other thorns) -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1306> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1270: Formaline doesn't understand CACTUS_CONFIGS_DIR
by Einstein Toolkit 12 Aug '13

12 Aug '13

#1270: Formaline doesn't understand CACTUS_CONFIGS_DIR -----------------------+---------------------------------------------------- Reporter: sbrandt | Owner: Type: defect | Status: new Priority: major | Milestone: ET_2013_05 Component: Other | Version: development version Keywords: Formaline | -----------------------+---------------------------------------------------- When building with Formaline and CACTUS_CONFIGS_DIR one sees error messages of the form seen below. It is easily fixed though. See patch. COMPILING /home/sbrandt/workspace/funwave2/Cactus/src/main/Parameters.c Updating /home/sbrandt/.mojaveconfig/funwave2/Cfg1/lib/libthorn_Cactus.a Checking status of thorn CactusBindings find: `configs/Cfg1/ThornList': No such file or directory find: `configs/Cfg1/config-data': No such file or directory find: `configs/Cfg1/config-info': No such file or directory -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1270> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1423: CarpetIOHDF5 corrupts memory when readingi compressed grid structure strings
by Einstein Toolkit 12 Aug '13

12 Aug '13

#1423: CarpetIOHDF5 corrupts memory when readingi compressed grid structure strings --------------------+------------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: Carpet | Version: development version Keywords: | --------------------+------------------------------------------------------- Input.cc uses H5Dget_storage_size to determine how much memory to allocate for the large string attributes (Paramters and grid structure). However this function literally returns the space used on disk which differs from the space in memory when compression is used (or when the dataset is sparse, or when the datatype on disk is different from that in memory eg float vs double). The attached patch instead queries the dataspace for the number of points. Ok to apply? Is there a preferred way of getting this size othewise? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1423> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #874: Reduce warnings during an ET build
by Einstein Toolkit 12 Aug '13

12 Aug '13

#874: Reduce warnings during an ET build --------------------+------------------------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Other | Version: Keywords: | --------------------+------------------------------------------------------- A new user of the ET might be disconcerted to see warnings during compilation such as: {{{ /home/ianhin/Cactus/EinsteinToolkit/arrangements/Carpet/CarpetLib/src/bboxset.hh(206): warning #1224: #warning directive: "TODO: this is incorrect" #warning "TODO: this is incorrect" ^ }}} I propose that such directives are replaced with a comment and a link to a TRAC ticket concerning the problem. Further, we should aim to eliminate as many warnings as possible from the build, similarly to avoid eroding confidence. Warnings can also make it hard to find the real error messages, when a build fails with errors. Other warnings I see are similar to: {{{ In file included from /home/ianhin/Cactus/GBSC12/arrangements/CactusUtils/Formaline/src/thornlist.cc:13: /home/ianhin/Cactus/GBSC12/configs/bbh/bindings/include/thornlist.h:61: warning: deprecated conversion from string constant to ‘char*’ }}} {{{ /home/ianhin/Cactus/GBSC12/arrangements/EinsteinInitialData/TwoPunctures/src/Newton.c: In function ‘TestRelax’: /home/ianhin/Cactus/GBSC12/arrangements/EinsteinInitialData/TwoPunctures/src/Newton.c:287: warning: passing argument 6 of ‘resid’ from incompatible pointer type /home/ianhin/Cactus/GBSC12/arrangements/EinsteinInitialData/TwoPunctures/src/Newton.c:75: note: expected ‘const int * const restrict* const restrict’ but argument is of type ‘int **’ }}} {{{ /home/ianhin/Cactus/GBSC12/configs/bbh/bindings/Variables/ADMBase.c: In function ‘CCTKi_BindingsFortranWrapperADMBase’: /home/ianhin/Cactus/GBSC12/configs/bbh/bindings/Variables/ADMBase.c:34: warning: passing argument 22 of ‘function’ from incompatible pointer type /home/ianhin/Cactus/GBSC12/configs/bbh/bindings/Variables/ADMBase.c:34: note: expected ‘const struct cGH * const*’ but argument is of type ‘struct cGH **’ }}} This last warning appears very many times during a build (though I believe it may be triggered only by GCC and not by the Intel compiler). {{{ /home/ianhin/Cactus/GBSC12/src/main/Parameters.c: In function ‘ParameterSetBoolean’: /home/ianhin/Cactus/GBSC12/src/main/Parameters.c:2394: warning: passing argument 4 of ‘Util_ExpressionEvaluate’ discards qualifiers from pointer target type /home/ianhin/Cactus/GBSC12/src/include/util_Expression.h:38: note: expected ‘void *’ but argument is of type ‘const int *’ }}} There are probably more as well. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/874> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1424: CarpetLib 2dedcb0e7340b0682d530dc26e764408b301e3b8 "CarpetLib: Do not reallocate communication buffers; instead, keep them around" breaks QLM qlm-bl.par test
by Einstein Toolkit 12 Aug '13

12 Aug '13

#1424: CarpetLib 2dedcb0e7340b0682d530dc26e764408b301e3b8 "CarpetLib: Do not reallocate communication buffers; instead, keep them around" breaks QLM qlm-bl.par test --------------------+------------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: Carpet | Version: development version Keywords: | --------------------+------------------------------------------------------- With the commit in a up-to-date (trunk) Cactus tree the test (and others) fails with: {{{ }}} Without (reverting it on top of it 7671fa71925aebfd787497bae61cf6da6ddeac54 "CarpetIOHDF5: support IO->alias option in reader") succeeds. I attach the test log. parfile, thorn list and option list. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1424> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac August 2013