Users September 2014

users@lists.einsteintoolkit.org

10 participants
16 discussions

Einstein Toolkit Meeting Reminder
by Frank Loeffler 14 May '15

14 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#. My agenda contains: - Fall workshop - PLEASE let us know if you come [1]! - Hotel booking - Release planning - release date: Mon Oct 24 2011 - freeze date: Mon Sep 26 - the day of the call! - branch name: ET_2011_10 - List of release-concerning bugs [2] - ET paper: proposed "freeze" by Oct 3rd (Mon after this call) As always: feel free to add to this list. Frank Loeffler [1] https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Fall_2011#Fall_Einstei… [2] https://trac.einsteintoolkit.org/query?status=!closed&milestone=ET_2011_11&…

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PARAMCHECK and non fatal but inefficient parameter choices
by Roland Haas 03 Oct '14

03 Oct '14

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello all, the PARAMCHECK routines normally abort if inconsistent parameters are given. I have a situation where the parameter choice is valid and the result of the simulation should be identical with or without the parameter set (assuming not bugs...), however setting the parameter is likely going to make the simulation slower. Im this particular case the parameter is CarpetLib::use_higher_order_restriction when used for a run with Carpet::refinement_centering = "vertex". In that case restriction is just a copy operation and independent of use_higher_order_restriction, for cell-centered runs this is not true anymore and this is the situation that use_higher_order_restriction was implemented for. However there is code in Carpet/Evolve.cc that calls POSTREGRID multiple times if use_higher_order_restriction is set (it has to in order to get symmetry, outer boundaries and also ghost zones right). For vertex centering nothing should happen (since there is a second call to POSTRESTRICT after all restriction is done). Options are: * do nothing since these parameters are perfectly valid if slow * warn with level CCTK_WARN_COMPLAIN ("the user should know about this but the problem is not terribly surprising") * warn with level CCTK_WARN_ALERT ("the results of this run will be wrong, and this will surprise the user, but we can still continue the run") * abort since the user most likely did not want to set the parameter Note that current practise in most code seems to be to use CCTK_WARN_COMPLAIN (Level 1) for warnings about situations that do not invalidate the result and CCTK_WARN_ABORT (Level 0) for anything that invalidates results, ie. we do not adhere to the meaning of the levels documented in src/include/cctk_WarnLevel.h . Yours, Roland - -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://keys.gnupg.net. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iEYEARECAAYFAlNqrvQACgkQTiFSTN7SboVuBQCg0IhvBi92zRKRVKoe216Q6wND NEYAn25pqT33i90JbhXmBJ90jKNAP4wd =+2Fk -----END PGP SIGNATURE-----

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Jenkins temporarily offline
by Barry Wardell 01 Oct '14

01 Oct '14

Hi all, The Jenkins automated build and test system which runs the tests for the Einstein Toolkit will be offline for a period starting today, while the machine it is running on is physically relocated to a new building. I hope to complete the relocation and bring the system back online today, although it may end up taking a bit longer. I will send an update once the system is back online. Regards, Barry

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Meeting Minutes
by Roland Haas 30 Sep '14

30 Sep '14

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Present: Steve, Zach, Roland, Frank, Peter, Matt, Barry, Erik tickets: * change GetComponents such that it asks for one user name per host rather than per repository * check why/if GetComponents asks for a user name for anonymous checkouts at all * disable pciutils by default right now since we don't know how strongly they rely on being compiled with gcc. Currently we have compiled them with gcc (on Linux workstations) and intel 13 (on Datura). Compilers we would not know what would happen would be eg pgi compiler. PAPI does not require it anyway but only optionally uses it. * interpolation in MoL substeps: need more input from Ian * Steve to implement backwards compatible API for expression evaluator * we notice that there are many undocumented routines in Cactus Please test git checkout of full toolkit. Yours, Roland -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iEYEARECAAYFAlQpmQIACgkQTiFSTN7SboUHbwCgujIzGWnWr53CYKsGd/Z8myyn DEsAniA4BydG3wY6ANbX00pFuunceUFK =itb8 -----END PGP SIGNATURE-----

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 28 Sep '14

28 Sep '14

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Re: [Users] Einstein Toolkit Meeting Reminder
by Frank Loeffler 23 Sep '14

23 Sep '14

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/ In short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. Some tickets within the last two weeks that are still open: - 778: Compiling PittNullCode is slow - 1648: simfactory default for <1 node jobs - 1648: MPI thorn should auto configure - 1650: piraha parses "-0." incorrectly (reviewed ok - but not closed) - 1618: Compile with adaptive MPI (new patches) Other projects include - Make Illinois code work with standard ET - git transition As always, please add to this list if you like. Frank Loeffler

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issues when compiling
by Francisco S. Guzman 23 Sep '14

23 Sep '14

Hi all, I'm kind of new at ET and am trying to compile the einsteintoolkit.th set of thorns. I get the following problem: /home/guzman/ET/Cactus/configs/ejemplo/scratch/external/MPI/lib/libmpi.a(ompi_mpi_init.o): In function `ompi_warn_fork': ompi_mpi_init.c:(.text+0x8a): undefined reference to `pthread_atfork' collect2: ld returned status exit 1 make[1]: *** [/home/guzman/ET/Cactus/exe/cactus_ejemplo] Error 1 make: *** [ejemplo] Error 2 I'm using F77=gfortran F90=gfortran CC=gcc CXX=g++ PERL=/usr/bin/perl CPP=/usr/bin/cpp FPP=/usr/bin/cpp -traditional F77_OPTIMISE_FLAGS=-O2 -fcray-pointer F90_OPTIMISE_FLAGS=-O2 -fcray-pointer WITH gfortran -- gcc --g++ 4.6.3 openmpi 1.8.2 GNU make 3.81 Any clue, hint suggestion to fix this? Versions mixed up or so? contradicting options? environment variables wrongly set? a thorn missing? It also happens that when compiling ET doesn't like any options on MPI (=MPICH or =OpenMPI) and states it is deprecated and refers to MPI instead. How can I handle this sophisticated statement? Thanks in advance, Francisco -- Francisco S. Guzman Murillo. ----------------------------------------------------------------------------- Instituto de Fisica y Matematicas. Universidad Michoacana de San Nicolas de Hidalgo. -----------------------------------------------------------------------------

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 22 Sep '14

22 Sep '14

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/ In short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. We will shortly mention some of the current tickets, but nothing much happened here since last week. The one major issue at the moment is the git transition which will be happening this week by the looks of it. Jenkins is up again (although not pointing to git yet), and no problems with the new repos have been found so far. This means that next week we will close the svn repositories for write access, and after a final svn to git conversion will open the git repositories for general use. Note that releases will be still be available in svn, and if important changes need to be made there, we will do so too (as well as in git). If you are using a release right now there is nothing you have to change right now. Frank Loeffler

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Git transition
by Barry Wardell 21 Sep '14

21 Sep '14

Hi all, We now have almost everything in place for the transition from svn to git. Jenkins is back online and the tests are passing (although it is still running from svn, not the new git repositories yet), so I think we can consider the current svn trunk versions reasonably 'stable'. I propose that we now freeze the svn repositories and not allow any further commits to them. The primary reason for this is that it will help make the transition easier; every time there is a new commit to one of the svn repositories I have to go through a time consuming process of updating the git arrangement repositories and manually checking everything is still working. Does anyone object to this proposal? Barry

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CarpetHDF5 Package Build error
by Garrison, David 17 Sep '14

17 Sep '14

Hello, I am attempting to build the CarpetHDF5 VisIt Plugin on a Mac 10.9.4 using version 2.8.0 of VisIt. I get the following error. Any ideas? -DG bash-3.2$ ./install Running: xmledit2.8.0 CarpetHDF5.xml Running: xml2cmake2.8.0 CarpetHDF5.xml ----------------------------------------------------------------- Parsed document of type Plugin ----------------------------------------------------------------- Plugin: CarpetHDF5 ("Carpet AMR/curvilinear HDF5 output generated by the Cactus Computational Toolkit", type=database) -- version 2.1 Attribute: () -- The C compiler identification is AppleClang 5.1.0.5030040 -- The CXX compiler identification is AppleClang 5.1.0.5030040 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Configuring done CMake Warning (dev): Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake --help-policy CMP0042" for policy details. Use the cmake_policy command to set the policy and suppress this warning. MACOSX_RPATH is not specified for the following targets: ECarpetHDF5Database_par ECarpetHDF5Database_ser ICarpetHDF5Database MCarpetHDF5Database This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done -- Build files have been written to: /Users/garrison/Downloads/CarpetHDF5 Scanning dependencies of target ECarpetHDF5Database_par [ 6%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5EnginePluginInfo.C.o [ 12%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5PluginInfo.C.o [ 18%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/CarpetHDF5CommonPluginInfo.C.o [ 25%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/avtCarpetHDF5FileFormat.C.o [ 31%] Building CXX object CMakeFiles/ECarpetHDF5Database_par.dir/H5Index.C.o Linking CXX shared library /Users/garrison/.visit/2.8.0/darwin-x86_64/plugins/databases/libECarpetHDF5Database_par.dylib Undefined symbols for architecture x86_64: "avtFileFormat::AddMeshToMetaData(avtDatabaseMetaData*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, avtMeshType, double const*, int, int, int, int, int const*)", referenced from: avtCarpetHDF5FileFormat::PopulateDatabaseMetaData(avtDatabaseMetaData*, int) in avtCarpetHDF5FileFormat.C.o "avtScalarMetaData::avtScalarMetaData(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, avtCentering)", referenced from: avtCarpetHDF5FileFormat::PopulateDatabaseMetaData(avtDatabaseMetaData*, int) in avtCarpetHDF5FileFormat.C.o "avtVectorMetaData::avtVectorMetaData(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, avtCentering, int)", referenced from: avtCarpetHDF5FileFormat::PopulateDatabaseMetaData(avtDatabaseMetaData*, int) in avtCarpetHDF5FileFormat.C.o "avtDatabaseMetaData::AddGroupInformation(int, int, std::__1::vector<int, std::__1::allocator<int> >&)", referenced from: avtCarpetHDF5FileFormat::PopulateDatabaseMetaData(avtDatabaseMetaData*, int) in avtCarpetHDF5FileFormat.C.o "avtDatabaseMetaData::SetTimes(std::__1::vector<double, std::__1::allocator<double> > const&)", referenced from: avtCarpetHDF5FileFormat::PopulateDatabaseMetaData(avtDatabaseMetaData*, int) in avtCarpetHDF5FileFormat.C.o "avtDatabaseMetaData::SetCycles(std::__1::vector<int, std::__1::allocator<int> > const&)", referenced from: avtCarpetHDF5FileFormat::PopulateDatabaseMetaData(avtDatabaseMetaData*, int) in avtCarpetHDF5FileFormat.C.o "avtDatabaseMetaData::GetMesh(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const", referenced from: avtCarpetHDF5FileFormat::PopulateDatabaseMetaData(avtDatabaseMetaData*, int) in avtCarpetHDF5FileFormat.C.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[2]: *** [/Users/garrison/.visit/2.8.0/darwin-x86_64/plugins/databases/libECarpetHDF5Database_par.dylib] Error 1 make[1]: *** [CMakeFiles/ECarpetHDF5Database_par.dir/all] Error 2 make: *** [all] Error 2 bash-3.2$ -- David Garrison, Ph.D. Associate Professor and Chair of Physics University of Houston-Clear Lake Bayou 3531 Houston, TX 77058 Tel: 281-283-3796 Fax: 281-283-3709 http://sce.uhcl.edu/garrison For more information about the UHCL Physics Program go to http://www.uhcl.edu/physics or sign up for UHCL newsletters at https://ecommunications.houston.edu/uhcl/join.html "If we knew what it was we were doing, it would not be called research, would it?" — Albert Einstein.

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Users September 2014