Trac October 2012

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[Einstein Toolkit] #1112: simfactory's option parser termination option values on "; "
by Einstein Toolkit 22 Oct '12

22 Oct '12

#1112: simfactory's option parser termination option values on ";" ------------------------+--------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: SimFactory | Version: Keywords: | ------------------------+--------------------------------------------------- I have (on my local machine horizon.tapir.caltech.edu): {{{ rhaas@horizon:/mnt/data/rhaas/postdoc/gr/ET_trunk$ tail -n2 simfactory/etc/defs.local.ini [horizon.tapir.caltech.edu] user = rhaas3 ; missing }}} and get {{{ rhaas@horizon:/mnt/data/rhaas/postdoc/gr/ET_trunk$ sim print-mdb-entry horizon.tapir.caltech.edu | grep rhaas sourcebasedir = /mnt/data/rhaas/postdoc/gr basedir = /home/rhaas/data/postdoc/runs user = rhaas3 email = rhaas }}} ie. the option parser truncates the option value for "user" at the ";" character (seem to treat it as a comment marger like "#"). This makes it impossible to have a ";" eg. in the envsetup command. I tried escaping the ";" with backslashes and double quotes. No luck. In my specific case I wanted to do: hash module && module purge ; bash ... ie clear all module information if the module command exists (I have a workaround for this particular application). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1112> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1120: CarpetInterp2: New ENO2 interpolator
by Einstein Toolkit 22 Oct '12

22 Oct '12

#1120: CarpetInterp2: New ENO2 interpolator ----------------------------------------+----------------------------------- Reporter: reisswig@… | Owner: eschnett Type: enhancement | Status: new Priority: optional | Milestone: Component: Carpet | Version: Keywords: CarpetInterp2, eno2 | ----------------------------------------+----------------------------------- The above patch introduces eno2 to CarpetInterp2. It works very similar to the the original Lagrange interpolator. The only difference is that the new interpolator uses a new class fasterp_eno2_src_loc_t instead of the original fasterp_src_loc_t. Similar to what is done in fasterp_src_loc_t, fasterp_eno2_src_loc_t computes the stencil coefficients and stores them. The interpolation algorithm with fasterp_eno2_src_loc_t is adapted for eno2. I had to introduce templates to recycle the surrounding code in which fasterp_src_loc_t/fasterp_eno2_src_loc_t is used. The above patch was tested with a 2-patch and a 7-patch system, a shock tube and an excited TOV. The necessary changes to Llama/Interpolate2 are contained in a different patch. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1120> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1126: Ubuntu.cfg does not link with libmpl
by Einstein Toolkit 22 Oct '12

22 Oct '12

#1126: Ubuntu.cfg does not link with libmpl ------------------------+--------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: SimFactory | Version: Keywords: | ------------------------+--------------------------------------------------- mpich2 on ubuntu seems to require an explicit -lmpl to link with libmpl on my test system. The fix is obviously to include this library in MPI_LIBS. {{{#!diff Index: mdb/optionlists/ubuntu.cfg =================================================================== --- mdb/optionlists/ubuntu.cfg (revision 1828) +++ mdb/optionlists/ubuntu.cfg (working copy) @@ -79,6 +79,6 @@ MPI_DIR = /usr MPI_INC_DIRS = /usr/include/mpich2 MPI_LIB_DIRS = /usr/lib -MPI_LIBS = mpich fmpich +MPI_LIBS = mpich fmpich mpl PTHREADS = yes }}} This makes ubuntu.cfg almost a superset of the options set in debian.cfg. If we either have a willing maintainer for ubuntu.cfg or Frank is willing to take over ubuntu.cfg I'd think it might be a good idea to drop the explicit debian.cfg in favor of ubuntu.cfg since ubuntu is the more populer distribution. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1126> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1043: RotatingSymmetry180::poison_boundaries should not check for NaNs
by Einstein Toolkit 20 Oct '12

20 Oct '12

#1043: RotatingSymmetry180::poison_boundaries should not check for NaNs -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: McLachlan | -----------------------------------+---------------------------------------- currently poison_boundaries causes RotatingSymmetry180 checks for both the poison value and for nonfinite values in the boundary. It should probably not check for NaN in case there are grid functions that do actually contain nan values near the boundaries (right not I have a run where this is true for ML_BSSN::H where I don't care about the NaNs). RotatingSymmetry's output completely clutters stdout since it list every single nan point it find. If one wants to check for NaN values in the constraints one can always use NaNChecker so no functionality is lost. Also RotatingSymmetry might well see NaN values when combined with say ReflectionSymmetry if the NaNs would be overwritten by say a z-reflection symmetry afterwards (I am not sure what the order in which symmetries are applied is). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1043> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #704: Carpet complains about lack of mpi after ExternalLibraries/OpenMPI is built
by Einstein Toolkit 20 Oct '12

20 Oct '12

#704: Carpet complains about lack of mpi after ExternalLibraries/OpenMPI is built ---------------------+------------------------------------------------------ Reporter: bmundim | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | ---------------------+------------------------------------------------------ I was able to compile ExternalLibraries/OpenMPI successfully, but the Cactus compilation stops afterwards with the message: /home/bruno/tmp/einstein_dev_maxwell/Cactus/arrangements/Carpet/CarpetLib/src/make.configuration.defn:5: *** Configuration error: The Carpet thorns require MPI. Please configure with MPI, or remove the Carpet thorns from the ThornList.. Stop. make: *** [einstein] Error 2 I indicated in my configuration file the following options: OPENMPI_DIR = BUILD OPENMPI_INSTALL_DIR = /home/bruno/local/gcc4.6.1/openmpi-1.5.4 I have then tried to indicate in my config file these extra options after the library was built (and the rest of Cactus compilation stopped): OPENMPI_DIR = /home/bruno/local/gcc4.6.1/openmpi-1.5.4 OPENMPI_INC_DIRS = /home/bruno/local/gcc4.6.1/openmpi-1.5.4/include OPENMPI_LIB_DIRS = /home/bruno/local/gcc4.6.1/openmpi-1.5.4/lib The config-info file does reflect these choices afterwards, and apparently the flag indicating the presence of mpi library, HAVE_MPI, was set correctly at ~/Cactus/configs/einstein/bindings/Configuration/Capabilities: grep -i have_mpi * cctki_MPI.h:#define HAVE_MPI 1 make.MPI.defn:HAVE_MPI = 1 however since I didn't use the old mechanism to tell Cactus about MPI, the ~/Cactus/configs/einstein/config-data/make.extra.defn doesn't have anything indicating the presence of mpi library there. It seems to me a compilation order issue. Somehow HAVE_MPI definition is coming after Carpet compilation, triggering this error then. Does anyone have any idea where I should look at in order to fix this problem? Thanks, Bruno. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/704> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #918: Usage of appendix in both UsersGuide and ReferenceManual
by Einstein Toolkit 20 Oct '12

20 Oct '12

#918: Usage of appendix in both UsersGuide and ReferenceManual -------------------------+-------------------------------------------------- Reporter: knarf | Owner: Type: enhancement | Status: new Priority: minor | Milestone: ET_2012_11 Component: Cactus | Version: development version Keywords: | -------------------------+-------------------------------------------------- The usage of the appendix of the UsersGuide inside the ReferenceManual led to a lot of internal references being commented out. This probably happened when UsersGuide and ReferenceManual had been divided, but it means that currently a lot of useful information is missing. In #885 there is agreement that the best solution would be to have the appendix included only by one of the two documents, and to restore references as much as possible. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/918> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #990: Cacuts documentation describes staggering
by Einstein Toolkit 20 Oct '12

20 Oct '12

#990: Cacuts documentation describes staggering ---------------------------+------------------------------------------------ Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: Documentation | ---------------------------+------------------------------------------------ didn't we recently remove this? The docs are at: http://einsteintoolkit.org/documentation/UsersGuide/UsersGuidech9.html#x13-… It also still mentions cctk_lssh which was removed. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/990> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1021: Fortran example for CCTK_Equals in the reference guide has multiple issues
by Einstein Toolkit 20 Oct '12

20 Oct '12

#1021: Fortran example for CCTK_Equals in the reference guide has multiple issues ---------------------------+------------------------------------------------ Reporter: hinder | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: documentation | ---------------------------+------------------------------------------------ The example for CCTK_Equals in the reference guide (http://cactuscode.org/documentation/referencemanual/ReferenceManualch2.html…) has an errant semicolon and does not include the macro DECLARE_CCTK_FUNCTIONS which seems to be needed for CCTK_Equals to be used. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1021> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1081: Add index file support for sliced output to CarpetIOHDF5
by Einstein Toolkit 20 Oct '12

20 Oct '12

#1081: Add index file support for sliced output to CarpetIOHDF5 -------------------------+-------------------------------------------------- Reporter: hinder | Owner: eschnett Type: enhancement | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: | -------------------------+-------------------------------------------------- CarpetIOHDF5 has support for writing an "index" file alongside the normal HDF5 output files. This is an HDF5 file in which the datasets are present but contain no data. This index file is much faster to read than the full HDF5 file (due to locality of data in the index file and block reads on slow filesystems) and can significantly speed up analysis of the data. Index files are currently written for the "standard" (typically 3D) data in Output.cc, but are not written for the "sliced" data in OutputSlice.cc. Since visualisation of 2D data is very common, OutputSlice.cc should be modified to output index files as well. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1081> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1118: Incorrect header info for 2d CarpetIOASCII when "compact_format=yes"
by Einstein Toolkit 20 Oct '12

20 Oct '12

#1118: Incorrect header info for 2d CarpetIOASCII when "compact_format=yes" ----------------------------------------+----------------------------------- Reporter: reisswig@… | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: | ----------------------------------------+----------------------------------- I am outputting a 2d array using 2d CarpetIOASCII output. I use CarpetIOASCII::compact_format = yes. The header incorrectly reports that the data starts in column 7. The data really starts in column 5. The header reports that there are x and y coordinates present, which is not the case for 2d arrays, which then presumedly leads to the incorrect column counting. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1118> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac October 2012