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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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Re: [Users] [ET Trac] [Einstein Toolkit] #1653: ExternalLibraries/MPI missing C++ library names
by Erik Schnetter 15 Sep '14

15 Sep '14

The flesh file flesh.cc which contains main() is written in C++. -erik On Mon, Sep 15, 2014 at 3:52 PM, Einstein Toolkit <trac-noreply(a)einsteintoolkit.org> wrote: > #1653: ExternalLibraries/MPI missing C++ library names > ------------------------------------+--------------------------------------- > Reporter: barry.wardell | Owner: > Type: defect | Status: new > Priority: major | Milestone: > Component: EinsteinToolkit thorn | Version: development version > Resolution: | Keywords: > ------------------------------------+--------------------------------------- > > Comment (by knarf): > > I can confirm the problem, and that the proposed change fixes it. I think > it should also be save to assume that C++ can be allowed to be required. > > -- > Ticket URL: <https://trac.einsteintoolkit.org/ticket/1653#comment:1> > Einstein Toolkit <http://einsteintoolkit.org> > The Einstein Toolkit > _______________________________________________ > Trac mailing list > Trac(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/trac -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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Einstein Toolkit Meeting Minutes
by Frank Loeffler 15 Sep '14

15 Sep '14

Hi, We had 12 people present: Phillip, Josh, Peter, Steven, Frank, Jonah, Erik, Barry, Zach, Matt, Ian, and Roland. Besides mentioning a few "minor" tickets, the top discussions were: - how to expand variables in parameter files (a question which now seems to be settled, more here: https://trac.einsteintoolkit.org/ticket/1651) - git move: should wait until Jenkins comes up again, at least if this isn't too far into the future (hopefully this week) - GRHydro/Illinois/Whisky inconsistency: reason still unknown. Zach has more puzzle pieces, but they also pose more questions. It seems that we don't have an edge or even corner yet, and attention and interest is waining. What we know so far (please correct me if I am wrong): - The 2-norm of the Ham. constraint is about 2x high with GRHydro than both with Whisky and the Illinois code, plus there are differences in the drift of the central density (probably related). - This does happen with HLLE, but not Marquina - It does not happen in Cowling - Nobody could find a major difference in the HLLE code - The Illinois code uses another definition for the velocity - a possible source for this difference, but Whisky uses the same as GRHydro Frank

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 15 Sep '14

15 Sep '14

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Einstein Toolkit Meeting Minutes
by Frank Loeffler 08 Sep '14

08 Sep '14

Hi Present at todays meeting were: Roland, Jonah, Erik, Matt, Steve, Peter, Frank. We've talked about a couple of active tickets, in particular: - 1396: GetComponents: Display prompts of executed commands (discussion) Steve will look into bash-magic (or something else) to solve this. - 1517: Make Simfactory tell you what it's doing (discussion) Steve accepted the ticket. - 1388: New thorn MemSpeed (reviewed ok) Erik will add the thorn to the ET thornlist. - 1651: Problems with expansions in parameter files (new patch) Roland will look at the new patch. Nobody really tested the new git transition repositories, but at least Steve and Peter volunteered to do so soon. The URL for the thornlist to test is: https://svn.einsteintoolkit.org/manifest/trunk/git_testing.th Frank Loeffler

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Fwd: Blue Waters Advanced User Workshop and yt development workshop
by Matthew Turk 05 Sep '14

05 Sep '14

Hi everyone, I just wanted to bring to your attention that there's going to be a yt (yt-project.org) development workshop at NCSA in mid-October, if anyone is interested in attending. For the last couple months, Roland, Sherwood and I have been working on and off on yt+Cactus work. The last remaining sticking point seems to be refinement boundaries that coincide with processor tiles; I'm prepping a detailed question-laden email that hopefully covers this last case, which I'll send to this list. But, this workshop would also give a good opportunity to meet in person and see what other items are remaining, and how best to shift yt to accommodate ET data. -Matt ---------- Forwarded message ---------- From: <help+bw(a)ncsa.illinois.edu> Date: Mon, Sep 1, 2014 at 3:16 PM Subject: Blue Waters Advanced User Workshop and yt development workshop To: Blue Waters Announcements <noreply(a)ncsa.illinois.edu> We are pleased to announce a three-day, hands-on oriented advanced user workshop about using Blue Waters to its fullest potential. Representatives from Cray, Allinea, PGI and NVIDIA will be on-site to present material and interact with attendees so bring your own code. This work shop is targeting existing or recently allocated, advanced users of Blue Waters. In conjunction with the Blue Waters Advanced User workshop, we are pleased to invite people who are interested in participating in development of the yt project (yt-project.org) to a two-day hands-on development workshop, focusing on parallel and in situ analysis, stabilizing existing data format front-ends, and expanding the capabilities of yt to take advantage of supercomputing resources. Blue Waters Advanced User workshop https://bluewaters.ncsa.illinois.edu/blue-waters-advanced-user-workshop-oct… yt development workshop https://bluewaters.ncsa.illinois.edu/yt-development-workshop-oct-16-17-2014 We hope to see you here.

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