Trac October 2014

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[Einstein Toolkit] #1685: Access of freed memory in CarpetIOHDF5 during 1-Proc test of recoverML-EE.par
by Einstein Toolkit 05 Nov '14

05 Nov '14

#1685: Access of freed memory in CarpetIOHDF5 during 1-Proc test of recoverML- EE.par ---------------------+------------------------------------------------------ Reporter: sbrandt | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: Carpet | Version: development version Keywords: | ---------------------+------------------------------------------------------ I originally found the problem with clang, but have verified it with valgrind. A parameter is being freed by CCTK_SetString() in Misc.c, but is reused by CarpetIOHDF5. To reproduce, I build with clang, after commenting out the papi and hwloc thorns. Commenting out the call to free in CCTK_SetString() reveals alignment errors in LoopControl. I'm attaching the cfg file I used to build with clang. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1685> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1661: ExternalLibraries/PAPI does not build with gcc 4.8.2
by Einstein Toolkit 05 Nov '14

05 Nov '14

#1661: ExternalLibraries/PAPI does not build with gcc 4.8.2 -----------------------------------+---------------------------------------- Reporter: tbode | Owner: tbode Type: defect | Status: new Priority: major | Milestone: ET_2014_11 Component: EinsteinToolkit thorn | Version: development version Keywords: PAPI | -----------------------------------+---------------------------------------- This seems to be a repeat of #1459 whose fix was never re-applied after updating to PAPI-5.3.0. With the newer version of PAPI and newer compiler, there are quite a few newer complaints (see attached make.log). This is done on a machine running Ubuntu 14.04 Trusty. I am attaching an equivalent set of patches to #1459 which seems to work as a workaround for the moment (namely removing the -Werror flags). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1661> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1598: ExternalLibraries/MPI does not auto-detect openmpi on Debian/testing
by Einstein Toolkit 01 Nov '14

01 Nov '14

#1598: ExternalLibraries/MPI does not auto-detect openmpi on Debian/testing -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: development version Keywords: MPI | -----------------------------------+---------------------------------------- configure.sh expects to find libmpi.a in $MPI_DIR/lib however Debian no longer delivers a static libmpi.a but only libmpi.so so the tests fails. The fix is likely similar to what HDF5 already does (ie accept any of .a .so .dylib as extensions for libraries). The fix is a bit complex though, so (given that Debian/stable is still fine) this is a reminder for after the release. Explictly specifying MPI_DIR, MPI_INC_DIRS, MPI_LIB_DIRS and MPI_LIBS allows this to be worked around in the current release. For reference, the fragment from HDF5 looks like this: {{{ # We look in these directories DIRS="/usr /usr/local /usr/local/hdf5 /usr/local/packages/hdf5 /usr/local/apps/hdf5 /opt/local ${HOME} ${HOME}/hdf5 c:/packages/hdf5" # look into each directory for dir in $DIRS; do # libraries might have different file extensions for libext in a so dylib; do # libraries can be in /lib or /lib64 for libdir in lib64 lib; do # These files must exist FILES="include/hdf5.h $(for lib in ${HDF5_CXX_LIBS} ${HDF5_FORTRAN_LIBS} ${HDF5_C_LIBS}; do echo ${libdir}/lib${lib}.${libext}; done)" # assume this is the one and check all needed files HDF5_DIR="$dir" for file in $FILES; do # discard this directory if one file was not found if [ ! -r "$dir/$file" ]; then unset HDF5_DIR break fi done # don't look further if all files have been found if [ -n "$HDF5_DIR" ]; then break fi done # don't look further if all files have been found if [ -n "$HDF5_DIR" ]; then break fi done # don't look further if all files have been found if [ -n "$HDF5_DIR" ]; then break fi done }}} -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1598> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1684: Add PETSc and friends to Jenkins
by Einstein Toolkit 28 Oct '14

28 Oct '14

#1684: Add PETSc and friends to Jenkins -------------------------------------+-------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: EinsteinToolkit website | Version: development version Keywords: | -------------------------------------+-------------------------------------- Can we add PETSc (and related thorns) to Jenkins, so that they are tested automatically? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1684> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1677: Support attribute((nonnull)), attribute((returns_nonnull))
by Einstein Toolkit 27 Oct '14

27 Oct '14

#1677: Support attribute((nonnull)), attribute((returns_nonnull)) -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: Other | Version: development version Keywords: | -------------------------+-------------------------------------------------- GCC (and probably other compilers) have attributes nonnull and returns_nonnull. These describe functions that require either arguments or return values to be not null, allowing both additional optimizations and consistency checks. I would like to add support for Cactus's autoconf mechanism to detect this, and then use these attributes in a few central places such as CCTK_ARGUMENTS or CCTK_PARAMETERS. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1677> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1683: build error TATPETSc
by Einstein Toolkit 27 Oct '14

27 Oct '14

#1683: build error TATPETSc ---------------------+------------------------------------------------------ Reporter: knarf | Owner: Type: defect | Status: new Priority: blocker | Milestone: ET_2014_11 Component: Cactus | Version: development version Keywords: | ---------------------+------------------------------------------------------ While building TATPETSc I get: {{{ /home/knarf/ET_trunk/configs/openblas/build/TATPETSc/solve.c:291:23: error: ‘MPI_UINT32_T’ undeclared (first use in this function) /home/knarf/ET_trunk/configs/openblas/build/TATPETSc/solve.c:291:23: note: each undeclared identifier is reported only once for each function it appears in /home/knarf/ET_trunk/configs/openblas/build/TATPETSc/solve.c:292:23: error: ‘MPI_UINT64_T’ undeclared (first use in this function) }}} -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1683> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1681: Switch SimFactory2 to git
by Einstein Toolkit 24 Oct '14

24 Oct '14

#1681: Switch SimFactory2 to git -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: Other | Version: development version Keywords: | -------------------------+-------------------------------------------------- Pull request at <https://bitbucket.org/einsteintoolkit/manifest/pull- request/2/switch-simfactory2-to-git/diff>. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1681> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1641: Switch Slab default from "alltoall" to "irecv/isend"
by Einstein Toolkit 21 Oct '14

21 Oct '14

#1641: Switch Slab default from "alltoall" to "irecv/isend" -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: major | Milestone: ET_2014_11 Component: EinsteinToolkit thorn | Version: development version Keywords: | -----------------------------------+---------------------------------------- The "alltoall" algorithm in Slab does not scale well. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1641> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1678: Update OpenSSL to 1.0.1j
by Einstein Toolkit 20 Oct '14

20 Oct '14

#1678: Update OpenSSL to 1.0.1j -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: Other | Version: development version Keywords: | -------------------------+-------------------------------------------------- I have a patch that updates OpenSSL to version 1.0.1j. Ok to apply? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1678> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1075: Test cases with specific number of processes
by Einstein Toolkit 20 Oct '14

20 Oct '14

#1075: Test cases with specific number of processes -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- Some test cases require a specific number of processes. Instead not running, they should run on that number of processes. This would ensure that all tests execute all the time. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1075> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac October 2014