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Dear , Online Issue of "Open Journal of Social Sciences" for You
by Open Journal of Social Sciences 22 May '15

22 May '15

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failed build on local mac osx yosemite
by Comer Duncan 20 May '15

20 May '15

I have tried to build the new release on my local macbook. I am running Yosemite and am using the optionlist for macports. Here is the part of the make which chokes: . . . Undefined symbols for architecture x86_64: "MPI::Win::Free()", referenced from: vtable for MPI::Win in libthorn_PeriodicCarpet.a(periodic.cc.o) vtable for MPI::Win in libthorn_Carpet.a(helpers.cc.o) vtable for MPI::Win in libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o) vtable for MPI::Win in libthorn_CarpetIOASCII.a(ioascii.cc.o) vtable for MPI::Win in libthorn_CarpetIOBasic.a(iobasic.cc.o) vtable for MPI::Win in libthorn_CarpetIOHDF5.a(Input.cc.o) vtable for MPI::Win in libthorn_CarpetIOHDF5.a(CarpetIOHDF5.cc.o) ... "MPI::Comm::Comm()", referenced from: MPI::Intercomm::Merge(bool) const in libthorn_PeriodicCarpet.a(periodic.cc.o) MPI::Intracomm::Split(int, int) const in libthorn_PeriodicCarpet.a(periodic.cc.o) MPI::Intracomm::Create(MPI::Group const&) const in libthorn_PeriodicCarpet.a(periodic.cc.o) MPI::Graphcomm::Clone() const in libthorn_PeriodicCarpet.a(periodic.cc.o) MPI::Cartcomm::Clone() const in libthorn_PeriodicCarpet.a(periodic.cc.o) MPI::Intracomm::Clone() const in libthorn_PeriodicCarpet.a(periodic.cc.o) MPI::Intracomm::Create_graph(int, int const*, int const*, bool) const in libthorn_PeriodicCarpet.a(periodic.cc.o) ... "MPI::Datatype::Free()", referenced from: vtable for MPI::Datatype in libthorn_PeriodicCarpet.a(periodic.cc.o) vtable for MPI::Datatype in libthorn_Carpet.a(helpers.cc.o) vtable for MPI::Datatype in libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o) vtable for MPI::Datatype in libthorn_CarpetIOASCII.a(ioascii.cc.o) vtable for MPI::Datatype in libthorn_CarpetIOBasic.a(iobasic.cc.o) vtable for MPI::Datatype in libthorn_CarpetIOHDF5.a(Input.cc.o) vtable for MPI::Datatype in libthorn_CarpetIOHDF5.a(CarpetIOHDF5.cc.o) ... "_ompi_mpi_cxx_op_intercept", referenced from: MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool) in libthorn_PeriodicCarpet.a(periodic.cc.o) MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool) in libthorn_Carpet.a(helpers.cc.o) MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool) in libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o) MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool) in libthorn_CarpetIOASCII.a(ioascii.cc.o) MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool) in libthorn_CarpetIOBasic.a(iobasic.cc.o) MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool) in libthorn_CarpetIOHDF5.a(Input.cc.o) MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool) in libthorn_CarpetIOHDF5.a(CarpetIOHDF5.cc.o) ... ld: symbol(s) not found for architecture x86_64 collect2: error: ld returned 1 exit status make[1]: *** [/Users/comerduncan/Cactus/exe/cactus_sim] Error 1 make: *** [sim] Error 2 Here is the build I did: simfactory/bin/sim build --optionlist=/Users/comerduncan/Cactus/simfactory/mdb/optionlists/osx-macports.cfg Can you please help me figure out what went wrong? Thanks. Comer

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Re: [Users] TAT/Slab error
by Geraint Pratten 19 May '15

19 May '15

Thanks! I've submitted a job with more processes, will let you know how this goes. On 19 May 2015 at 11:32, Ian Hinder <ian.hinder(a)aei.mpg.de> wrote: > > On 19 May 2015, at 20:14, Geraint Pratten <g.pratten(a)sussex.ac.uk> wrote: > > Hi all, > > I am getting the following error and I'm not sure what could be causing > it: > > (line 447 of > /mnt/pact/gp234/NR/Cactus/arrangements/CactusNumerical/RotatingSymmetry180/src/rotatingsymmetry180.c): > -> TAT/Slab can only be used if there is a single local component per > MPI process > > Typically the simulation (e.g. the qc0-mclachlan or the pre-packaged > BBHLowRes) will run for a few hundred iterations before hitting this error > and terminating. Has anyone come across this error before? Or is it just a > case of re-submitting the job from a checkpoint? > > If anyone needs more information, just let me know! > > > You need to have at least as many MPI processes as "components" which > are the rectangular regions that Carpet splits the domain into. Try > increasing the number of processes you are running on. > > -- > Ian Hinder > http://members.aei.mpg.de/ianhin > > -- Geraint Pratten Mobile: +44(0) 7581709282 E-mail: G.Pratten(a)sussex.ac.uk Skype: geraint.pratten School of Mathematical and Physical Sciences Pevensey 3 Building University of Sussex Falmer Campus Brighton BN1 9QH United Kingdom

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TAT/Slab error
by Geraint Pratten 19 May '15

19 May '15

Hi all, I am getting the following error and I'm not sure what could be causing it: (line 447 of /mnt/pact/gp234/NR/Cactus/arrangements/CactusNumerical/RotatingSymmetry180/src/rotatingsymmetry180.c): -> TAT/Slab can only be used if there is a single local component per MPI process Typically the simulation (e.g. the qc0-mclachlan or the pre-packaged BBHLowRes) will run for a few hundred iterations before hitting this error and terminating. Has anyone come across this error before? Or is it just a case of re-submitting the job from a checkpoint? If anyone needs more information, just let me know! Thanks, Geraint -- Geraint Pratten Mobile: +44(0) 7581709282 E-mail: G.Pratten(a)sussex.ac.uk Skype: geraint.pratten School of Mathematical and Physical Sciences Pevensey 3 Building University of Sussex Falmer Campus Brighton BN1 9QH United Kingdom

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Re: [Users] Lots of warnings
by Ian Hinder 19 May '15

19 May '15

On 19 May 2015, at 00:50, Comer Duncan <comer.duncan(a)gmail.com> wrote: > Hi Ian, > > Thanks for the reply. I am using MacOSX 10.4 and from what you say, I have not gotten macports svn installed, so am using whatever Xcode uses. I will now go get svn from macports and procede. > > Thanks again for your help. Hi Comer, Glad to be of help! 10.4 (Tiger) is very old though; it was released 10 years ago. Are you sure that is what you are using? We don't have any machines with 10.4 available for testing (nor the manpower to test on very old versions), so you might have to do some work to get it running. Apple change things from time to time. We have tested the Hilbert release on 10.10, 10.9, and expect it to also work on 10.8. -- Ian Hinder http://members.aei.mpg.de/ianhin

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Lots of warnings
by Comer Duncan 18 May '15

18 May '15

I just checked out Hilbert and get a 'pile' of warnings. Here is the list: Could not checkout module AEIThorns/ADMMass svn: E175002: Unable to connect to a repository at URL ' https://svn.aei.mpg.de/numrel/AEIThorns/ADMMass/branches/ET_2015_05' svn: E175002: OPTIONS of ' https://svn.aei.mpg.de/numrel/AEIThorns/ADMMass/branches/ET_2015_05': Server certificate verification failed: issuer is not trusted ( https://svn.aei.mpg.de) Could not checkout module AEIThorns/Trigger svn: E175002: Unable to connect to a repository at URL ' https://svn.aei.mpg.de/numrel/AEIThorns/Trigger/branches/ET_2015_05' svn: E175002: OPTIONS of ' https://svn.aei.mpg.de/numrel/AEIThorns/Trigger/branches/ET_2015_05': Server certificate verification failed: issuer is not trusted ( https://svn.aei.mpg.de) Could not checkout module ExternalLibraries/GSL svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/GSL/branches/ET_2015_… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/GSL/branches/ET_2015_…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module ExternalLibraries/MPI svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/MPI/branches/ET_2015_… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/MPI/branches/ET_2015_…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module ExternalLibraries/BLAS svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/BLAS/branches/ET_2015… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/BLAS/branches/ET_2015…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module ExternalLibraries/HDF5 svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/HDF5/branches/ET_2015… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/HDF5/branches/ET_2015…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module ExternalLibraries/PAPI svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/PAPI/branches/ET_2015… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/PAPI/branches/ET_2015…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module ExternalLibraries/zlib svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/zlib/branches/ET_2015… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/zlib/branches/ET_2015…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module ExternalLibraries/PETSc svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/PETSc/branches/ET_201… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/PETSc/branches/ET_201…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module ExternalLibraries/FFTW3 svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/FFTW3/branches/ET_201… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/FFTW3/branches/ET_201…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module ExternalLibraries/hwloc svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/hwloc/branches/ET_201… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/hwloc/branches/ET_201…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module ExternalLibraries/OpenCL svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/OpenCL/branches/ET_20… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/OpenCL/branches/ET_20…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module ExternalLibraries/LAPACK svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/LAPACK/branches/ET_20… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/LAPACK/branches/ET_20…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module ExternalLibraries/LORENE svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/LORENE/branches/ET_20… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/LORENE/branches/ET_20…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module AEIThorns/AEILocalInterp svn: E175002: Unable to connect to a repository at URL ' https://svn.aei.mpg.de/numrel/AEIThorns/AEILocalInterp/branches/ET_2015_05' svn: E175002: OPTIONS of ' https://svn.aei.mpg.de/numrel/AEIThorns/AEILocalInterp/branches/ET_2015_05': Server certificate verification failed: issuer is not trusted ( https://svn.aei.mpg.de) Could not checkout module ExternalLibraries/libjpeg svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/libjpeg/branches/ET_2… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/libjpeg/branches/ET_2…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module ExternalLibraries/OpenSSL svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/OpenSSL/branches/ET_2… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/OpenSSL/branches/ET_2…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module ExternalLibraries/OpenBLAS svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/OpenBLAS/branches/ET_… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/OpenBLAS/branches/ET_…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module ExternalLibraries/pciutils svn: E175002: Unable to connect to a repository at URL ' https://svn.cactuscode.org/projects/ExternalLibraries/pciutils/branches/ET_… ' svn: E175002: OPTIONS of ' https://svn.cactuscode.org/projects/ExternalLibraries/pciutils/branches/ET_…': Server certificate verification failed: issuer is not trusted ( https://svn.cactuscode.org) Could not checkout module AEIThorns/PunctureTracker svn: E175002: Unable to connect to a repository at URL ' https://svn.aei.mpg.de/numrel/AEIThorns/PunctureTracker/branches/ET_2015_05' svn: E175002: OPTIONS of ' https://svn.aei.mpg.de/numrel/AEIThorns/PunctureTracker/branches/ET_2015_05': Server certificate verification failed: issuer is not trusted ( https://svn.aei.mpg.de) Could not checkout module AEIThorns/SystemStatistics svn: E175002: Unable to connect to a repository at URL ' https://svn.aei.mpg.de/numrel/AEIThorns/SystemStatistics/branches/ET_2015_05 ' svn: E175002: OPTIONS of ' https://svn.aei.mpg.de/numrel/AEIThorns/SystemStatistics/branches/ET_2015_05': Server certificate verification failed: issuer is not trusted ( https://svn.aei.mpg.de) Time Elapsed: 2 minutes, 42 seconds My question is how come so many warnings of inability to checkout occurs? One would have thought that the checkout of a new release would be completely clean. What am I missing? Comer

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New Einstein Toolkit Release (Hilbert)
by Frank Loeffler 18 May '15

18 May '15

We are pleased to announce the eleventh release (code name "Hilbert") of the Einstein Toolkit, an open, community developed software infrastructure for relativistic astrophysics. This release includes, among other things, various improvements in the handling of external libraries (and with that, installations), discontinue the direct support for Fortran 77 (use Fortran 90 instead), and enable the C++ code in GRHydro by default. In addition, bug fixes accumulated since the previous release in November 2014 have been included. For more detailed information about the "Hilbert" release please read the long release announcement on the Einstein Toolkit web pages: http://einsteintoolkit.org/about/releases/ET_2015_05_announcement.php. The Einstein Toolkit is a collection of software components and tools for simulating and analyzing general relativistic astrophysical systems that builds on numerous software efforts in the numerical relativity community including CactusEinstein, the Carpet AMR infrastructure and the relativistic magneto-hydrodynamics code GRHydro. The Cactus Framework is used as the underlying computational infrastructure providing large-scale parallelization, general computational components, and a model for collaborative, portable code development. The toolkit includes modules to build complete codes for simulating black hole spacetimes as well as systems governed by relativistic magneto-hydrodynamics. The Einstein Toolkit uses a distributed software model and its different modules are developed, distributed, and supported either by the core team of Einstein Toolkit Maintainers, or by individual groups. Where modules are provided by external groups, the Einstein Toolkit Maintainers provide quality control for modules for inclusion in the toolkit and help coordinate support. The Einstein Toolkit Maintainers currently involve postdocs and faculty from six different institutions, and host weekly meetings that are open for anyone to join in. Guiding principles for the design and implementation of the toolkit include: open, community-driven software development; well thought out and stable interfaces; separation of physics software from computational science infrastructure; provision of complete working production code; training and education for a new generation of researchers. For more information about using or contributing to the Einstein Toolkit, or to join the Einstein Toolkit Consortium, please visit our web pages at http://einsteintoolkit.org. The Einstein Toolkit is primarily supported by NSF 1212401/1212426/1212433/1212460 (Einstein Toolkit), and also by 0905046/0941653 (PetaCactus) and 0710874 (LONI Grid). The Einstein Toolkit contains about 200 regression test cases. On a large portion of the tested machines, almost all of these test suites pass, using both MPI and OpenMP parallelization. The changes between this and the previous release include: === Larger changes since last release === * Repositories - New components: - CactusExamples/Poisson - CactusNumerical/LocalInterp2: a C++ drop-in replacement for LocalInterp - CactusNumerical/TestLocalInterp2: containing tests for LocalInterp2 - CactusUtils/SystemTopology: Utility thorn - Moved components: - McLachlan moved to Bitbucket * Simfactory - Updates to many machines and some new machines - Mac OS: Optionlists have been updated and simplified. There is now osx-macports.cfg and osc-homebrew.cfg which should work on OS X 10.8, 10.9 and 10.10. MacPorts updated to use GCC 4.9 to match Homebrew. Both optionlists contain comments with the necessary "port" and "brew" commands to install the expected packages. For MacPorts, you also need the osx-macports.run runscript. * External Libraries - Delay build of external libraries so they can be 'made' in parallel. - Several updates to accommodate changes in system library paths, and update some built versions of libraries. * Cactus: - Change default output filename format from implementation::groupname to implementation-groupname (parameter IOUtil::out_group_separator). - 'make' (without configuration name) works now, as long as there is only one configuration present. - Piraha replaced parts of the old Cactus parser (but that should not be a user visible change). === How to upgrade from Wheeler (ET_2014_11) === To upgrade from the previous release, use GetComponents with the new thornlist to check out the new version. Switching to the new branch is not possible for most repositories due to the repository move. See the [http://einsteintoolkit.org/download Download] page on the Einstein Toolkit website for download instructions. === Remaining issues with this release === * Certain machines need to be configured specially in Simfactory because the remote directories cannot be determined automatically just from the user name. See the Machine notes below. * Recovering with Carpet: Carpet stores metadata (such as the simulation time) only for Carpet::max_timelevels time levels, although it is possible to allocate more time levels. These additional time levels then cannot be recovered; the symptom is an assertion failure during recovery. The solution is to either increase Carpet::max_timelevels, or to decrease the number of active time levels. === Machine notes === Supported (tested) machines include: - Default Debian, Fedora and MacOS installations - Bluewaters * - Carver - Comet - Datura - Edison - Fermi - Galileo - Hopper - Loewe - Supermike II - Nvidia - Orca * - Philip - Queenbee 2 - Shelob - Stampede (CPU) - Zwicky A * means that a small number of tests fail on that machine. Almost all tests pass on the other machines. * Stampede: defs.local.ini needs to have sourcebasedir = $WORK and basedir = $SCRATCH/simulations configured for this machine. You need to determine $WORK and $SCRATCH by logging in to the machine. All repositories participating in this release carry a branch ET_2015_05 marking this release. These release branches will be updated if severe errors are found. The "Hilbert" Release Team on behalf of the Einstein Toolkit Consortium (2015-05-18) Steven R. Brandt Peter Diener Roland Haas Ian Hinder Frank Löffler Bruno C. Mundim Erik Schnetter Barry Wardell May 18, 2015

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Meeting Minutes
by Frank Loeffler 18 May '15

18 May '15

Hi, Present today were Erik, Peter, Steven, Frank, Matt, Eloisa, Ian, and Christine. The new release is now almost good to go, and will be release today, after a few minor things are handled. Boost might be added as thorn in the future, but will be disabled by default, at least until an ET actually needs Boost. At that point we will again pick up the discussion how to handle the size of Boost. The next Einstein Toolkit Meeting will be in *two* weeks, on June 1st. Frank Loeffler

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release branches created
by Frank Loeffler 15 May '15

15 May '15

Hi, The release branches and tags have now been created. This means that every change that should make it into the release now has to be committed to this branch (in addition to possibly being committed to trunk/master). Also, the release tag should be reset in that case. These two should only differ after the release (if at all). This also means that the development branch is now open again. Frank

3 4

Einstein Toolkit Meeting Reminder
by Frank Loeffler 15 May '15

15 May '15

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ I short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. Until the call, everything concerning the release should be ready, with the call being the final place to actually do the release. This means, most of the time of the call can be devoted to things that had to be left aside because of the release. Frank Loeffler

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