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[Einstein Toolkit] #745: the flesh allows two implemantion of the same interface to have different default values for restricted parameters
by Einstein Toolkit 05 Sep '12

05 Sep '12

#745: the flesh allows two implemantion of the same interface to have different default values for restricted parameters --------------------+------------------------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | --------------------+------------------------------------------------------- since the flesh creates paramters for all compiled in (rather than activated) thorns initially, this affects the default value that a thorn sees. Thorns seem to be initialized (and thus their parameter structures being created) in alphabetical order, which means that the thorn alphabetically '''last''' (How, I have no idea, the parameter handling logic seems a bit of a mess) will determine the default parameter value. Attached is a parameter file to demonstrate this with Carpet and PUGH who both declare parameters periodic and periodic_[xyz] but differ in their defaults. To demonstrate, create an executable with only Carpet compiled in and run the parameter file. Then look at the paramters in the checkpoint it creates eg. {{{ h5dump -r -d /Parameters\ and\ Global\ Attributes/All\ Parameters output/checkpoint.chkpt.it_0.h5 | grep periodic }}} Do the same with an executable that contains both PUGH and Carpet. Notice that parameter values are now PUGH's defaults. This can actually cause a runs to abort when recovering from a checkpoint when one switches from an executable with PUGH compiled in to one that does not. (Beyond the fact that some thorn might actually use it's parameters rather than the Carpet/PUGH pair where happily Carpet ignores these parameters and PUGH who actually used them gets to set the default). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/745> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1058: Add "lapsefactor" parameter to EinsteinExact
by Einstein Toolkit 05 Sep '12

05 Sep '12

#1058: Add "lapsefactor" parameter to EinsteinExact -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- I suggest introducing a "lapsefactor" parameter to EinsteinExact. This defines a transformation for the time coordinate between the underlying metric and the metric as will be used by Cactus. For example, setting lapsefactor=1/2 will lead to alpha=0.5 for the Minkowski metric, with the other metric components unchanged. This complements the "shiftadd" parameters, and is very useful for testing. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1058> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1053: CarpetIOHDF5: it doesn't honor out3D_every parameter
by Einstein Toolkit 05 Sep '12

05 Sep '12

#1053: CarpetIOHDF5: it doesn't honor out3D_every parameter --------------------------------------+------------------------------------- Reporter: bmundim | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: Carpet | Version: Keywords: CarpetIOHDF5 out3D_every | --------------------------------------+------------------------------------- Hi, I have noticed a strange behaviour of CarpetIOHDF5 when running a bbh simulation with Lovelace release: it doesn't seem to follow the parameter out3D_every. I have attached a modified version of CarpetWaveToyCheckpointTest.par that reproduces this error. I tried to mimic a bbh simulation setup I am using in terms of number of refinement levels (it also helps to slow down the simulation a bit) and what I was interested to output. The experiment goes as follows: 1) create two directories, 000 and 001, where you can copy the attached par file to. Symlink a cactus executable for ET on each directory. Both development and lovelace releases will show this problem. You should have something like this: {{{ [bruno@frozenstar wavetoytest]$ ls 0* 000: cactus_einstein@ CarpetWaveToyCheckpointTest.par 001: cactus_einstein@ CarpetWaveToyCheckpointTest.par }}} 2) Run the executable on both directories. First on 000 and then on 001. {{{ ./cactus_einstein CarpetWaveToyCheckpointTest.par }}} 3) Analyze the results. Everything goes all right on the first directory, 000: {{{ [bruno@frozenstar CarpetWaveToyCheckpointTest]$ h5ls wavetoy::scalarevolve.xyz.h5 Parameters\ and\ Global\ Attributes Group WAVETOY::phi\ it=0\ tl=0\ rl=0 Dataset {43, 43, 43} WAVETOY::phi\ it=0\ tl=0\ rl=1 Dataset {41, 41, 41} WAVETOY::phi\ it=0\ tl=0\ rl=2 Dataset {33, 33, 33} WAVETOY::phi\ it=0\ tl=0\ rl=3 Dataset {33, 33, 33} WAVETOY::phi\ it=0\ tl=0\ rl=4 Dataset {33, 33, 33} WAVETOY::phi\ it=0\ tl=0\ rl=5 Dataset {33, 33, 33} WAVETOY::phi\ it=0\ tl=0\ rl=6 Dataset {33, 33, 33} WAVETOY::phi\ it=0\ tl=0\ rl=7 Dataset {33, 33, 33} WAVETOY::phi\ it=0\ tl=0\ rl=8 Dataset {33, 33, 33} WAVETOY::phi\ it=128\ tl=0\ rl=1 Dataset {41, 41, 41} WAVETOY::phi\ it=128\ tl=0\ rl=2 Dataset {33, 33, 33} WAVETOY::phi\ it=128\ tl=0\ rl=3 Dataset {33, 33, 33} WAVETOY::phi\ it=128\ tl=0\ rl=4 Dataset {33, 33, 33} WAVETOY::phi\ it=128\ tl=0\ rl=5 Dataset {33, 33, 33} WAVETOY::phi\ it=128\ tl=0\ rl=6 Dataset {33, 33, 33} WAVETOY::phi\ it=128\ tl=0\ rl=7 Dataset {33, 33, 33} WAVETOY::phi\ it=128\ tl=0\ rl=8 Dataset {33, 33, 33} WAVETOY::phi\ it=256\ tl=0\ rl=0 Dataset {43, 43, 43} WAVETOY::phi\ it=256\ tl=0\ rl=1 Dataset {41, 41, 41} WAVETOY::phi\ it=256\ tl=0\ rl=2 Dataset {33, 33, 33} WAVETOY::phi\ it=256\ tl=0\ rl=3 Dataset {33, 33, 33} WAVETOY::phi\ it=256\ tl=0\ rl=4 Dataset {33, 33, 33} WAVETOY::phi\ it=256\ tl=0\ rl=5 Dataset {33, 33, 33} WAVETOY::phi\ it=256\ tl=0\ rl=6 Dataset {33, 33, 33} WAVETOY::phi\ it=256\ tl=0\ rl=7 Dataset {33, 33, 33} WAVETOY::phi\ it=256\ tl=0\ rl=8 Dataset {33, 33, 33} }}} You can see above that all refinement levels were correctly output every 128 iterations as it was set on the par file. That doesn't happen anymore after recovery, ie on the second directory, 001: {{{ [bruno@frozenstar CarpetWaveToyCheckpointTest]$ h5ls wavetoy::scalarevolve.xyz.h5 Parameters\ and\ Global\ Attributes Group WAVETOY::phi\ it=262\ tl=0\ rl=7 Dataset {33, 33, 33} WAVETOY::phi\ it=262\ tl=0\ rl=8 Dataset {33, 33, 33} WAVETOY::phi\ it=390\ tl=0\ rl=7 Dataset {33, 33, 33} WAVETOY::phi\ it=390\ tl=0\ rl=8 Dataset {33, 33, 33} }}} neither 262 or 390 are multiples of 128! So something is going really wrong here. Note however that the respective 2D slice is correct: {{{ [bruno@frozenstar CarpetWaveToyCheckpointTest]$ h5ls wavetoy::scalarevolve.xy.h5 Parameters\ and\ Global\ Attributes Group WAVETOY::phi\ it=384\ tl=0\ rl=1 Dataset {41, 41} WAVETOY::phi\ it=384\ tl=0\ rl=2 Dataset {33, 33} WAVETOY::phi\ it=384\ tl=0\ rl=3 Dataset {33, 33} WAVETOY::phi\ it=384\ tl=0\ rl=4 Dataset {33, 33} WAVETOY::phi\ it=384\ tl=0\ rl=5 Dataset {33, 33} WAVETOY::phi\ it=384\ tl=0\ rl=6 Dataset {33, 33} WAVETOY::phi\ it=384\ tl=0\ rl=7 Dataset {33, 33} WAVETOY::phi\ it=384\ tl=0\ rl=8 Dataset {33, 33} }}} 384 is a multiple of 128 and as you can see all active refinement levels for that iteration were written down. Any idea on how to fix this? Thanks! -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1053> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1031: write index files for checkpoints
by Einstein Toolkit 05 Sep '12

05 Sep '12

#1031: write index files for checkpoints --------------------------+------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: enhancement | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: CarpetIOHDF5 | --------------------------+------------------------------------------------- this patch writes index files for checkpoints if output_index is set. This is (only) useful if the checkpoints will be read in by a different number of processes than written. In that case, parsing the index files is faster than parsing the heavy data files. The two patches provide read and write functionality. The attached C code creates index files from existing HDF5 files (not necessary checkpoints). It is a modified copy of hdf5_extract from the HDF5 thorn. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1031> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1063: GRHydro_InitData update
by Einstein Toolkit 05 Sep '12

05 Sep '12

#1063: GRHydro_InitData update -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: GRHydro_InitData | -----------------------------------+---------------------------------------- attach please find patches to bring Zelmani and trunk GRhydro_InitData in sync again. Mostly they add hot EOS support, but also there is a fix for a double definition of initial_Bvec both as a restricted parameter in HydroBase and a private parameter in GRHydro. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1063> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1072: User guide does not explain how to use boolean parameters from Fortran.
by Einstein Toolkit 05 Sep '12

05 Sep '12

#1072: User guide does not explain how to use boolean parameters from Fortran. ---------------------------+------------------------------------------------ Reporter: hinder | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: documentation | ---------------------------+------------------------------------------------ The Cactus user guide does not explain how to use boolean parameters from Fortran. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1072> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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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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