Hi! Just a minimal update: I now tested with open-mpi 4.0.2 from Homebrew and that also worked well. Best, Hans Ekkehard On 28 Oct 2019, at 13:19, Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> wrote: Hi Benjamin, This is curious. My setup seems very similar (macOS 10.14.6 with the newest XCode and Clang 10, OpenMPI 4.0.1_2 from Homebrew) and it works out of the box. It is a long time since I had trouble compiling NEST with MPI on my system. Could you run CMake again in an empty directory with additional flags --trace --debug-output and see if that generates some indication on what might go wrong with MPI detection? In my case, I end up with the following configuration Use MPI : Yes (MPI: /usr/local/bin/mpicxx) FLAGS : Includes : /usr/local/Cellar/open-mpi/4.0.1_2/include Link Flags : -L/usr/local/Cellar/libevent/2.1.11_1/lib Libraries : /usr/local/Cellar/open-mpi/4.0.1_2/lib/libmpi.dylib You could also try with -Dwith-mpi=/usr/local/Cellar/open-mpi/4.0.2/ but I haven't tested that. Best, Hans Ekkehard On 28 Oct 2019, at 08:58, Benjamin Staude <benjamin.staude@gmail.com<mailto:benjamin.staude@gmail.com>> wrote: Hi Hans-Ekkehard, Here is some info on my mpicxx installations (after a brew uninstall and brew install): staude:bld staude$ which mpicxx /usr/local/bin/mpicxx staude:bld staude$ ls -la /usr/local/bin/mpicxx lrwxr-xr-x 1 staude admin 35 Oct 28 08:42 /usr/local/bin/mpicxx -> ../Cellar/open-mpi/4.0.2/bin/mpicxx staude:bld staude$ mpicxx --version Apple LLVM version 9.0.0 (clang-900.0.38) Target: x86_64-apple-darwin18.7.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin Does that help? Best, Benjamin On 27. Oct 2019, at 22:01, Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> wrote: Hi Benjamin, It is curious that MPI is not found on your system. Could you double check that you have installed open-mpi via Homebrew? What does which mpicxx return on your system? Best, Hans Ekkehard On 26 Oct 2019, at 17:04, Benjamin Staude <benjamin.staude@gmail.com<mailto:benjamin.staude@gmail.com>> wrote: Hi Hans-Ekkehard, Thanks for the support, that solved one issue. But now, I get the same for OPEN_MPI: -- Could NOT find MPI_C (missing: MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) (I need open_mpi because I need the MUSIC interface). This is my cmake-call: cmake \ -DCMAKE_C_COMPILER=gcc-9 \ -DCMAKE_CXX_COMPILER=g++-9 \ -Dwith-music=ON \ -Dwith-mpi=ON \ -Dwith-openmp=ON \ -DCMAKE_INSTALL_PREFIX=/Users/staude/.pyenv/versions/3.7.2/ \ /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0 And the output: -- The CXX compiler identification is GNU 9.2.0 -- The C compiler identification is GNU 9.2.0 -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/local/bin/g++-9 -- Check for working CXX compiler: /usr/local/bin/g++-9 -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/local/bin/gcc-9 -- Check for working C compiler: /usr/local/bin/gcc-9 -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file mach-o/dyld.h -- Looking for include file mach-o/dyld.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for C++ include istream -- Looking for C++ include istream - not found -- Looking for C++ include ostream -- Looking for C++ include ostream - not found -- Looking for C++ include sstream -- Looking for C++ include sstream - not found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of long long -- Check size of long long - done -- Check size of u_int16_t -- Check size of u_int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of u_int64_t -- Check size of u_int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Looking for NAN -- Looking for NAN - found -- Looking for isnan -- Looking for isnan - found -- Looking for M_E -- Looking for M_E - found -- Looking for M_PI -- Looking for M_PI - found -- Looking for expm1 -- Looking for expm1 - found -- Host triple: x86_64-apple-darwin -- Target triple: x86_64-apple-darwin -- Found LTDL: /usr/local/lib/libltdl.dylib (found version "2.4.6") -- Found Readline: /usr/lib/libreadline.dylib (found version "4.2") -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/local/Cellar/gsl/2.6/include (found version "2.6") -- Found PythonInterp: /Users/staude/.pyenv/shims/python (found version "3.7.2") -- Found PythonLibs: /Users/staude/.pyenv/versions/3.7.2/lib/libpython3.7m.a (found suitable exact version "3.7.2") -- Found Cython: /Users/staude/.pyenv/shims/cython (found version "0.29.13") -- Found OpenMP_C: -fopenmp -- Found OpenMP_CXX: -fopenmp -- Found OpenMP: TRUE -- Could NOT find MPI_C (missing: MPI_C_WORKS) -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND) CMake Error at cmake/ProcessOptions.cmake:528 (message): MUSIC requires -Dwith-mpi=ON. Call Stack (most recent call first): CMakeLists.txt:167 (nest_process_with_music) And the cmake-version: cmake --version cmake version 3.15.3 On 26. Oct 2019, at 14:11, Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> wrote: Hi Benjamin, The CMake output shows that you are using the AppleClang compiler, which does not support OpenMP. If you want to use that compiler, you need to turn off OpenMP with -Dwith-openmp=OFF. If you want NEST with OpenMP on the Mac, I would recommend using the GCC compiler installed via Homebrew, see https://nest-simulator.readthedocs.io/en/latest/installation/mac_install.ht… for instructions. Best, Hans Ekkehard On 25 Oct 2019, at 18:12, Benjamin Staude <benjamin.staude@gmail.com<mailto:benjamin.staude@gmail.com>> wrote: Hi there, I am trying to install nest under OSX Mojave and run into the following cmake-error (see below for a full trace): -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) I already tried various tricks (http://stechschulte.net/2016/03/20/openmp-osx-cmake.html, https://stackoverflow.com/questions/48825416/missing-openmp-c-flags-openmp-…), but had no success. Does anybody have experience? Thanks in advance, Benjamin ######################################################### -- The CXX compiler identification is AppleClang 9.0.0.9000038 -- The C compiler identification is AppleClang 9.0.0.9000038 -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file mach-o/dyld.h -- Looking for include file mach-o/dyld.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file stdint.h -- Looking for include file stdint.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for C++ include istream -- Looking for C++ include istream - found -- Looking for C++ include ostream -- Looking for C++ include ostream - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of long long -- Check size of long long - done -- Check size of u_int16_t -- Check size of u_int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of u_int64_t -- Check size of u_int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Looking for NAN -- Looking for NAN - found -- Looking for isnan -- Looking for isnan - found -- Looking for M_E -- Looking for M_E - found -- Looking for M_PI -- Looking for M_PI - found -- Looking for expm1 -- Looking for expm1 - found -- Host triple: x86_64-apple-darwin -- Target triple: x86_64-apple-darwin -- Found LTDL: /usr/local/lib/libltdl.dylib (found version "2.4.6") -- Found Readline: /usr/lib/libreadline.dylib (found version "4.2") -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/local/Cellar/gsl/2.6/include (found version "2.6") -- Found PythonInterp: /Users/staude/.pyenv/shims/python (found version "3.7.2") -- Found PythonLibs: /Users/staude/.pyenv/versions/3.7.2/lib/libpython3.7m.a (found suitable exact version "3.7.2") -- Found Cython: /Users/staude/.pyenv/shims/cython (found version "0.29.13") -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) CMake Error at cmake/ProcessOptions.cmake:452 (message): CMake can not find OpenMP. Call Stack (most recent call first): CMakeLists.txt:164 (nest_process_with_openmp) _______________________________________________ NEST Users mailing list -- users@nest-simulator.org<mailto:users@nest-simulator.org> To unsubscribe send an email to users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org> -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude@gmail.com<mailto:benjamin.staude@gmail.com> -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser _______________________________________________ NEST Users mailing list -- users@nest-simulator.org<mailto:users@nest-simulator.org> To unsubscribe send an email to users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org> -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude@gmail.com<mailto:benjamin.staude@gmail.com> -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no Home http://arken.nmbu.no/~plesser _______________________________________________ NEST Users mailing list -- users@nest-simulator.org<mailto:users@nest-simulator.org> To unsubscribe send an email to users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org> -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no Home http://arken.nmbu.no/~plesser

Hi Benjamin, This seems to be a deeper problem on OSX, see https://stackoverflow.com/questions/58144137/gcc-missing-headers-on-macos10… Interestingly, it works for me on Mojave. The quick-fix would be to build NEST with MPI but without OpenMP using the Clang compiler. With llvm and libomp from brew installed, the following also works for me cmake -E env LDFLAGS="-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib" \ cmake -DCMAKE_INSTALL_PREFIX:PATH=$PWD/install \ -DCMAKE_C_COMPILER=/usr/local/opt/llvm/bin/clang \ -DCMAKE_CXX_COMPILER=/usr/local/opt/llvm/bin/clang++ \ -Dwith-mpi=ON ../src This builds NEST using the Clang compiler from llvm with OpenMP and MPI support. The only problem is that some Python tests crash, complaining about two different OpenMP libraries imported (libomp and libiomp5, where the latter comes from Anaconda's MKL library). One can (with a certain risk of problems) set KMP_DUPLICATE_LIB_OK=TRUE which will make macOS ignore the duplicate libraries. Tests then pass, but behavior may be unpredictable. Alternatively, one can create a Conda environment without MKL as describe on StackOverflow (https://stackoverflow.com/questions/38345519/how-to-install-scipy-without-m…). I haven't tested this yet. I also tried compiling with the Apple Clang, configuring as cmake -DCMAKE_INSTALL_PREFIX:PATH=$PWD/install \ -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp" -DOpenMP_CXX_LIB_NAMES="omp" \ -DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp" -DOpenMP_C_LIB_NAMES="omp" \ -DOpenMP_omp_LIBRARY=/usr/local/lib/libomp.dylib \ -Dwith-mpi=ON ../src based on https://iscinumpy.gitlab.io/post/omp-on-high-sierra/, but this failed when linking, since the library information probably is not used properly by our CMake script. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no Home http://arken.nmbu.no/~plesser

Hi Hans Ekkehard, hi Lakshmi, Thank you for your suggestions, unfortunately none have worked for me so far. Here’s what happened: ----------------------------------------------------------- HANS EKKEHARDS FIRST OPTION cmake -E env LDFLAGS="-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib" \ cmake -DCMAKE_INSTALL_PREFIX:PATH=$PWD/install \ -DCMAKE_C_COMPILER=/usr/local/opt/llvm/bin/clang \ -DCMAKE_CXX_COMPILER=/usr/local/opt/llvm/bin/clang++ \ -Dwith-mpi=ON ../src Here, the cmake command went through, but make failed during Scanning dependencies of target nestkernel with lots of errors like: In file included from /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0/nestkernel/clopath_archiving_node.cpp:26: In file included from /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0/nestkernel/kernel_manager.h:27: In file included from /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0/nestkernel/connection_manager.h:42: In file included from /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0/nestkernel/source_table.h:35: /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0/nestkernel/mpi_manager.h:313:3: error: use of undeclared identifier 'MPI' MPI::Intracomm comm; Also, I am not sure if that really built without OpenMP. At least cmake outputs -- Found Cython: /Users/staude/.pyenv/shims/cython (found version "0.29.13") -- Found OpenMP_C: -fopenmp=libomp (found version "3.1") -- Found OpenMP_CXX: -fopenmp=libomp (found version "3.1") -- Found OpenMP: TRUE (found version "3.1") and the Nest Configuration Summary says: C compiler : /usr/local/opt/llvm/bin/clang C compiler flags : -O2 -Wall -fopenmp=libomp C++ compiler : /usr/local/opt/llvm/bin/clang++ C++ compiler flags : -std=c++11 -O2 -Wall -fopenmp=libomp ----------------------------------------------------------- HANS EKKEHARDS SECOND OPTION Haven’t tried yet, but also don’t know really what I would have to do in practice... ----------------------------------------------------------- HANS EKKEHARDS THIRD OPTION cmake -DCMAKE_INSTALL_PREFIX:PATH=$PWD/install \ -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp" -DOpenMP_CXX_LIB_NAMES="omp" \ -DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp" -DOpenMP_C_LIB_NAMES="omp" \ -DOpenMP_omp_LIBRARY=/usr/local/lib/libomp.dylib \ -Dwith-mpi=ON ../src That indeed failed during linking: [ 24%] Linking CXX shared library libsli.dylib Undefined symbols for architecture x86_64: "___kmpc_critical", referenced from: SLIInterpreter::message(int, char const*, char const*, char const*) const in interpret.cc.o "___kmpc_end_critical", referenced from: SLIInterpreter::message(int, char const*, char const*, char const*) const in interpret.cc.o "___kmpc_global_thread_num", referenced from: SLIInterpreter::message(int, char const*, char const*, char const*) const in interpret.cc.o "_omp_in_parallel", referenced from: Name::insert(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in name.cc.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]: *** [sli/libsli.dylib] Error 1 make[1]: *** [sli/CMakeFiles/sli_lib.dir/all] Error 2 make: *** [all] Error 2 ----------------------------------------------------------- LEKSHMIS OPTION When running your command, cmake worked fine, but make results in clang: error: unsupported option '-fopenmp’ Also, I need the -Dwith-mpi=ON -Dwith-music=ON flags. If I set them, I get the familiar -- Could NOT find MPI_C (missing: MPI_C_WORKS) during cmake. This I can fix by using the g++-9 compiler. But then I get lots of errors during make. They start during Scanning dependencies of target nestkernel and look like this: In file included from /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0/nestkernel/source_table.h:35, from /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0/nestkernel/connection_manager.h:42, from /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0/nestkernel/kernel_manager.h:27, from /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0/nestkernel/common_synapse_properties.cpp:27: /Users/staude/Projekte/RainerDunkel/SensoryNetwork/Skripte/snn/NEST/nest-simulator-2.18.0/nestkernel/mpi_manager.h:313:3: error: 'MPI' does not name a type; did you mean 'M_PI'? 313 | MPI::Intracomm comm; | ^~~ | M_PI -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com

Hi Hans-Ekkehard, Thanks for asking, I have not continued to install nest on osx. I guess I will simply use a vm with Ubuntu for the simulation. But since you’re asking: are you aware of an example of music in python that uses a chain-like architecture? I only found one in c++. Best, Benjamin