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 

Am 06.11.2019 um 16:54 schrieb Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.no>:



Hi Benjamin,

Have you made any progress in the meantime? Unfortunately, I have only very limited time to explore this at the moment.

Best,
Hans Ekkehard



On 29 Oct 2019, at 20:28, Benjamin Staude <benjamin.staude@gmail.com> wrote:

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
On 29. Oct 2019, at 16:36, Rajalekshmi Deepu <r.deepu@fz-juelich.de> wrote:

H Hans, Hi Benjamin,

    Some months back, one of our colleague had some issues and we fixed it with the following command:

cmake -DCMAKE_INSTALL_PREFIX:PATH=/../NEST/bld -DCMAKE_C_COMPILER=gcc -DOpenMP_C_FLAGS="-fopenmp -I/usr/local/opt/libomp/include" -DOpenMP_C_LIB_NAMES="omp" -DOpenMP_omp_LIBRARY=/usr/local/opt/libomp -DCMAKE_CXX_COMPILER=g++ -DOpenMP_CXX_FLAGS="-fopenmp -I/usr/local/opt/libomp/include" -DOpenMP_CXX_LIB_NAMES="omp" /../NEST/nest-simulator

Best regards,

Lekshmi

On 29.10.19 16:04, Hans Ekkehard Plesser wrote:

Hi Benjamin,

This seems to be a deeper problem on OSX, see


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-mkl). 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@nmbu.no
Home  http://arken.nmbu.no/~plesser


_______________________________________________
NEST Users mailing list -- users@nest-simulator.org
To unsubscribe send an email to users-leave@nest-simulator.org

-- 
Rajalekshmi Deepu
Simulation Lab Neuroscience
Division HPC in Neuroscience         Phone:  +49 2461 61 8945
Jülich Supercomputing Centre (JSC)   E-mail: r.deepu@fz-juelich.de
Institute for Advanced Simulation    http://www.fz-juelich.de/ias/jsc
Forschungszentrum Jülich GmbH

 -- -- -- 
Dr. Benjamin Staude  |  Paul-Lincke-Ufer 7  |  10999 Berlin  |  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
Home  http://arken.nmbu.no/~plesser