Trac July 2011

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130 discussions

[Einstein Toolkit] #145: EOS_Omni requires HDF5 library. What about if it only uses HDF5 instead?
by Einstein Toolkit 13 Nov '11

13 Nov '11

#145: EOS_Omni requires HDF5 library. What about if it only uses HDF5 instead? ---------------------------+------------------------------------------------ Reporter: bmundim | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: Other | Version: Keywords: EOS_Omni HDF5 | ---------------------------+------------------------------------------------ At the moment EOS_Omni requires the HDF5 library to read the nuclear EOS values from a table. Since not all distros have fortran support for the HDF5 library as a default, I propose to change this requirement and provide a fall back in case this support is not present. Perhaps not using the nuclear EOS, or reading from an ASCII file instead. This could be just a temporary solution until the HDF5 library build script becomes more robust. Opinions? Thanks, Bruno. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/145> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #470: Check is wrong inside prolongate_3d_o1_rf2.cc
by Einstein Toolkit 10 Nov '11

10 Nov '11

#470: Check is wrong inside prolongate_3d_o1_rf2.cc ---------------------+------------------------------------------------------ Reporter: sbrandt | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Other | Version: Keywords: | ---------------------+------------------------------------------------------ The problem materialized when creating wave equation tutorials for the Teragrid conference. I was unable to run an FMR application in parallel. The check comprises lines 76-80 of the file: if (not regbbox.expand(offsetlo, offsethi).is_contained_in(srcbbox) or not regbbox .is_contained_in(dstbbox)) { CCTK_WARN (0, "Internal error: region extent is not contained in array extent"); } -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/470> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #365: ADMBase: evolving with evolution_method="static" does not apply boundary conditions
by Einstein Toolkit 10 Nov '11

10 Nov '11

#365: ADMBase: evolving with evolution_method="static" does not apply boundary conditions ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | ----------------------+----------------------------------------------------- When one uses the evolution method ADMBASE::evolution_method = "static" (which is very tempting e.g. for Cowling), then no boundary conditions are applied. This means that the ADMBase variables remain unset on the boundaries after regridding, leading to all sorts of (rather unexpected) problems. The easy solution is to use thorn Exact instead, which applies an exact solution at each time step, including on the boundary. I suggest to remove the ADMBase functionality to provide a "static" evolution method, since this evolution method does not know which boundary condition to apply, and hence is bound to fail in non-trivial situations. Alternatively, ADMBase needs to synchronise in postregrid (and probably a few other bins as well). ADMBase should then also offer to apply an outer boundary condition, in this case probably a Minkowski Dirichlet boundary condition or a von Neumann condition. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/365> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #410: CarpetIOHDF5 may segfault when one_file_per_group is selected
by Einstein Toolkit 09 Nov '11

09 Nov '11

#410: CarpetIOHDF5 may segfault when one_file_per_group is selected --------------------------------+------------------------------------------- Reporter: bmundim | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: Carpet | Version: Keywords: Carpet git version | --------------------------------+------------------------------------------- I was facing one of those cryptic MPI error messages on Ranger, where your job quits without any useful error message. It turns out that this parameter file had CarpetIOHDF5::one_file_per_group = "yes" CarpetIOHDF5::out2D_vars = " ADMBase::gxx" and CarpetIOHDF5 would try to loop over the group variables when just one of them was selected. As a result it has accessed memory address that it was not supposed to, consequently killing the job. I have attached the stack back trace. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/410> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #431: Update some external libraries
by Einstein Toolkit 09 Nov '11

09 Nov '11

#431: Update some external libraries -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- Several external libraries have new versions available: LAPACK PETSc curl git These are only minor updates. I suggest to apply them. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/431> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #467: Make table printing functions publicly accessible
by Einstein Toolkit 09 Nov '11

09 Nov '11

#467: Make table printing functions publicly accessible -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- The table data types (util_Table.h) have internal routines that print the table contents to screen. This can be helpful for debugging. The attached patch makes these functions publicly available. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/467> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #136: Don't rebuild external libraries so often
by Einstein Toolkit 08 Nov '11

08 Nov '11

#136: Don't rebuild external libraries so often -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- One way to keep the external libraries that have been built would be the following. Create a dummy configuration "ext" where all external libraries are built. When another configuration is built, it should be easy to specify to look there for the external libraries, or maybe this should even be the default. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/136> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #222: Dubious code in Hydro_InitExcision.c
by Einstein Toolkit 08 Nov '11

08 Nov '11

#222: Dubious code in Hydro_InitExcision.c ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | ----------------------+----------------------------------------------------- Hydro_InitExcision.c contains the following code: if ( (hydro_initexcision_coordinate_length <= 0.0) && ( ( x_frac > 0.5 - hydro_initexcision_fraction) && ( x_frac < 0.5 + hydro_initexcision_fraction) && ( y_frac > 0.5 - hydro_initexcision_fraction) && ( y_frac < 0.5 + hydro_initexcision_fraction) && ( z_frac > 0.5 - hydro_initexcision_fraction) && ( z_frac < 0.5 + hydro_initexcision_fraction) ) || ( (hydro_initexcision_coordinate_length > 0.0) && ( fabs(x[point]-hydro_initexcision_position_x) <= hydro_initexcision_coordinate_length*0.5) && ( fabs(y[point]-hydro_initexcision_position_y) <= hydro_initexcision_coordinate_length*0.5) && ( fabs(z[point]-hydro_initexcision_position_z) <= hydro_initexcision_coordinate_length*0.5) ) ) This code has an "and" (&&) and an "or" (||) operation at top level. Is this intended? The code would be clearer with an additional set of parenthesis, or by introducing a suitable set of temporaries for sub- expressions. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/222> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #235: Improve performance of Fortran index calculations
by Einstein Toolkit 27 Oct '11

27 Oct '11

#235: Improve performance of Fortran index calculations -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- In Fortran, Cactus currently declares grid functions e.g. as (this is the expansion of DECLARE_CCTK_ARGUMENTS) REAL*8 gxx (X0metric,X1metric,X2metric) where X0metric etc. are integers passed into the routine. Each grid function group has its own, independent size. This has two disadvantages: 1. The compiler does not know that all grid functions have the same size (namely cctk_lsh), and thus has to perform array index calculations separately for each group 2. The argument list is longer than neded The enclosed patch declares grid functions via cctk_lsh. Grid arrays are still declared independently. This reduces the code size of e.g. GRHydro/GRHydro_Tmunu.F90 from 6836 to 6241 bytes on my system. I have not attempted to measure a performance difference. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/235> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #458: Improve bboxset efficiency (e.g. for regridding)
by Einstein Toolkit 27 Oct '11

27 Oct '11

#458: Improve bboxset efficiency (e.g. for regridding) -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: eschnett Type: enhancement | Status: new Priority: major | Milestone: Component: Carpet | Version: Keywords: | -------------------------+-------------------------------------------------- The attached patch modifies the algorithm used to insert a new bbox into an existing bboxset. It reduces the computational complexity of this operation from O(n^2) to O(n), where n is the number of elements in the bboxset. This has the potential to speed up regridding significantly. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/458> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac July 2011