Trac August 2012

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[Einstein Toolkit] #669: Rewrite users of deprecated HDF5 C++ API
by Einstein Toolkit 04 Sep '12

04 Sep '12

#669: Rewrite users of deprecated HDF5 C++ API ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: task | Status: new Priority: minor | Milestone: Component: Other | Version: Keywords: | ----------------------+----------------------------------------------------- The C++ API for HDF5 is decprecated. We should examine which code uses it, and rewrite it to use the C API instead. This would allow us to use more system-provided HDF5 installations. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/669> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1042: Cactus should know more about allowed configuration options
by Einstein Toolkit 03 Sep '12

03 Sep '12

#1042: Cactus should know more about allowed configuration options -------------------------+-------------------------------------------------- Reporter: hinder | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- Currently, thorns can specify which configuration options their configuration scripts use in their configuration.ccl file. Cactus itself also reads a certain set of options. There should be a list of such options, and Cactus could warn or abort if unrecognised options are included in an optionlist. This would help to avoid user error where options are misspelled or omitted. Maintaining such a list would also help with documentation: we could ensure that each such option was documented. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1042> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1050: [PATCH]CarpetIOHDF5: make WriteLargeAttribute write a string, not an array of ints
by Einstein Toolkit 28 Aug '12

28 Aug '12

#1050: [PATCH]CarpetIOHDF5: make WriteLargeAttribute write a string, not an array of ints -------------------------------+-------------------------------------------- Reporter: anton@… | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: | -------------------------------+-------------------------------------------- The data that's supplied to it is to be interpreted as a string. Before the attached patch the data is written as an array of int8, e.g.: h5dump -d '/Parameters and Global Attributes/Datasets' alpha.h5 HDF5 "alpha.h5" { DATASET "/Parameters and Global Attributes/Datasets" { DATATYPE H5T_STD_I8LE DATASPACE SIMPLE { ( 16 ) / ( 16 ) } DATA { (0): 77, 76, 95, 66, 83, 83, 78, 58, 58, 97, 108, 112, 104, 97, 10, 0 } } } After the patch: h5dump -d '/Parameters and Global Attributes/Datasets' alpha.h5 HDF5 "alpha.h5" { DATASET "/Parameters and Global Attributes/Datasets" { DATATYPE H5T_STRING { STRSIZE 16; STRPAD H5T_STR_NULLTERM; CSET H5T_CSET_ASCII; CTYPE H5T_C_S1; } DATASPACE SIMPLE { ( 1 ) / ( 1 ) } DATA { (0): "ML_BSSN::alpha " } } } -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1050> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1064: Dissipation tests failing
by Einstein Toolkit 28 Aug '12

28 Aug '12

#1064: Dissipation tests failing -----------------------------------+---------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- The tests Dissipation/test_ah Dissipation/test_ob are currently failing. The commits since the last time the test passed are: {{{ GRHydro_InitData remove unused GRHydro_reflevel declaration that causes compilation to fail carpet CarpetInterp2: White space change carpet Carpet: Initialise outer_boundaries during recursive load balancing carpet Carpet: Improve layout of grid structure files GRHydro GRHydro: clear atmosphere_mask_real in MHD AtmosphereReset GRHydro GRHydro: add OpenMP parallelization to IntialAtmosphereReset GRHydro GRHydro: remove unused file GRHydro GRHydro: Option to reconstruct W*vel (W = Lorentz factor) instead of just the primitive velocity 'vel'. This ensures that the Lorentz factor can never become unphysical during reconstruction. This patch is necessary for NS collapse when ePPM+Refluxing is used. GRHydro GRHydro: Changes fixing issues with hot EOS treatment: 1) Set correct keytemp in C2P 2) Fix OpenMP private variable declaration in HLLEM 3) Fix velocity arguments for Y_e 1D PPM reconstruction 4) If in atmosphere and if evolve a Y_e also reset Y_e with cell averaged value in Reconstruction 5) Fix index permutation bug in ReconstructPoly routines for divergence cleaning field 6) Remove extra comment character in UpdateMaskM 7) Fix a missing velocity permutation when calling 1D reconstruction for Y_e. 8) Insert missing sqrt(det) factor for pressure term in resetting tau when temperature got too cold with a hot EOS. GRHydro GRHydro: Adding back OpenMP support to HLLEM.F90 GRHydro GRHydro: improve error handling in C2P hot routine GRHydro GRHydro: use inverse Jacobian to transform Bvec back to global basis GRHydro GRHydro: MP pointer stuff for MHD GRHydro GRHydro: Changes to make GRHydro MHD work with nuclear/hot equation of state: }}} http://damiana2.aei.mpg.de/~ianhin/testreports/EinsteinToolkitTests/results… -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1064> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1057: GRHydro updates
by Einstein Toolkit 27 Aug '12

27 Aug '12

#1057: GRHydro updates -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: GRHydro | -----------------------------------+---------------------------------------- attached please find cahnges to Zelmani/GRHydro that I would like to commit to trunk. Philipp: this contains your hot EOS and MHD work as it is currently present in Zelmani. If this is not to be pushed yet, please let me know. There is one new feature: reconstruct_Wv which used v^i*w_lorentz in the PPM reconstruction scheme (non-MHD only) and which can be useful to avoid PPM reconstructing speeds > c. The other patches are mostly bugfixes to MHD and the hot EOS, plus more boilerplate (and as of yet not fully covering all routines) pointer stuff for multipatch and MHD. The bugfix "clear atmosphere mask" is required for the real valued atmosphere mask to be correct. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1057> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1062: the flesh allows a private parameter and a shared parameter of the same name
by Einstein Toolkit 27 Aug '12

27 Aug '12

#1062: the flesh allows a private parameter and a shared parameter of the same name -------------------+-------------------------------------------------------- Reporter: rhaas | Type: defect Status: new | Priority: major Milestone: | Component: Cactus Version: | Keywords: -------------------+-------------------------------------------------------- eg. currently GRHydro_InitData::initial_Bvec it should instead fail during the consistency checks in the configuration phase. For GRHydro_InitData I'll fix this by making the private pieces part of the EXTEND (which they should have anyway I think). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1062> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1060: CarpetRegrid2 error message improvement
by Einstein Toolkit 25 Aug '12

25 Aug '12

#1060: CarpetRegrid2 error message improvement -----------------------------------------------------+---------------------- Reporter: anonymous | Owner: eschnett Type: enhancement | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: CarpetRegrid2 error message improvement | -----------------------------------------------------+---------------------- I ran cactus with the parameter CarpetRegrid2::num_levels_1=2 but without setting CarpetRegrid2::radius_1[1] That is wrong, of course. The error message was: WARNING level 0 in thorn CarpetRegrid2 processor 0 host mb2.local (line 93 of /Users/mb/Cactus/arrangements/Carpet/CarpetRegrid2/src/regrid.cc): -> The radius of refinement level 1 of region 1 is [4.94066e-323,4.88063e+252,5.03503e+175], which is non-negative This error message does not seem to make sense. Could it be improved? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1060> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1056: do not attempt reductions in local mode in SphericalSurface unless auto_res[n] is set
by Einstein Toolkit 24 Aug '12

24 Aug '12

#1056: do not attempt reductions in local mode in SphericalSurface unless auto_res[n] is set -------------------+-------------------------------------------------------- Reporter: rhaas | Type: defect Status: new | Priority: minor Milestone: | Component: EinsteinToolkit thorn Version: | Keywords: SphericalSurface -------------------+-------------------------------------------------------- currently SphericalSurface_SetupRes will attempt a reduction in local mode even if all auto_res values are false, ie if there are no spheres whose resolution is to be set automatically. This causes MPI hangs if different processors own different numbers of components, as produced by the recursive load balancer and carpet::same_number_of_components_on_each_process = false (true by default but might change). The attached patch ameliorates the situation by only attempting a reduction if auto_res[n] is set, thus at least allowing SphericalSurface to be used when all ntheta, nphi are giving explicitly. It also adds a comment warning about auto_res. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1056> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1038: remove compiled documentation from Cactus repository
by Einstein Toolkit 22 Aug '12

22 Aug '12

#1038: remove compiled documentation from Cactus repository ---------------------------+------------------------------------------------ Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: optional | Milestone: Component: Cactus | Version: Keywords: documentation | ---------------------------+------------------------------------------------ the current Cactus repository contains pdf versions of the Reference and User guides. Are these present to allow users without a working LaTeX installation to view the documentation (of the flesh, thorns tend to not include PDF files anyway)? We could instead point to the online HTML version on the ET website. This would reduce the number of times the tex file and pdf file are out of sync. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1038> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1055: Don't write multiple variables to the same file
by Einstein Toolkit 21 Aug '12

21 Aug '12

#1055: Don't write multiple variables to the same file -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- IOASCII writes variables into files that are named after the variable. If multiple variables have the same name (but are in different groups), then multiple output is written to the same file, confusing people. All output thorns should check for this condition, and then modify the file name e.g. to VARNAME.GROUPNAME. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1055> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac August 2012