NEST compilation issues in connection with conda environment

Created by: mschmidt87

This issue deal with our compilation problems with NEST and the conda environment. This is our current status of knowledge:

We found two different solutions for the simulations on the one hand and mean-field theory calculation on the other hand:

Simulations

Deactivate conda environment, execute cmake with explicite python paths of the conda environment.

MFT

Activate conda environment and compile NEST inside this conda environment, but without MPI, OpenMP, readline and ncurses, with such a cmake line:

cmake -Dwith-gsl=$HOME/miniconda3/envs/multiarea_model -Dwith-readline=OFF -Dwith-ltdl=OFF -Dwith-openmp=OFF -DCMAKE_INSTALL_PREFIX:PATH=$HOME/nest-2.14.0-conda-mam

For your interest: @AlexVanMeegen , @albada , @heplesser, @jougs, @terhorstd

Created by: mschmidt87

I think that the solution for the MFT problem is actually the appropriate one. We somehow have to manage to link to all the packages inside the Conda Environment. It is, however, not clear to me whether this will also work with MPI.

I tried to reproduce it including MPI, OpenMP, readline and ncurses. However, I always ran into compilation errors. That is how I found https://github.com/nest/nest-simulator/issues/210

Here, the same problems occured. The interesting post is the 2nd to last one. I adapted the suggested solution to my system to have the following lines:

conda env create -f environment.yaml
export ANACONDA3_DIR=~/anaconda3/envs/multiarea_model
conda activate $ANACONDA3_DIR
export NEST_INSTALL_DIR=/absolute/path/to/nest/nest/master_anaconda3.bld/ins
export NEST_BUILD_DIR=/absolute/path/to/nest/master_anaconda3.bld
export NEST_SRC_DIR=/absolute/path/to/nest/nest-simulator
mkdir $NEST_BUILD_DIR && mkdir $NEST_INSTALL_DIR
cd $NEST_BUILD_DIR
CC=${ANACONDA3_DIR}/bin/gcc CXX=${ANACONDA3_DIR}/bin/g++ cmake3  -Dwith-python=3 -DPYTHON_INCLUDE_DIR=${ANACONDA3_DIR}/include/python3.6m -DPYTHON_LIBRARY=${ANACONDA3_DIR}/lib/python3.6 -DCMAKE_INSTALL_PREFIX:PATH=NEST_INSTALL_DIR $NEST_SRC_DIR -Dwith-gsl=${ANACONDA3_DIR} -DREADLINE_ROOT_DIR=${ANACONDA3_DIR} -DLTDL_ROOT_DIR=${ANACONDA3_DIR}`

However, when I execute this (on Blaustein), I get the following error by cmake:

-- The CXX compiler identification is unknown -- The C compiler identification is unknown -- Check for working CXX compiler: /home/max.schmidt/anaconda3/envs/multiarea_model/bin/g++ -- Check for working CXX compiler: /home/max.schmidt/anaconda3/envs/multiarea_model/bin/g++ -- broken CMake Error at /usr/share/cmake3/Modules/CMakeTestCXXCompiler.cmake:54 (message): The C++ compiler "/home/max.schmidt/anaconda3/envs/multiarea_model/bin/g++" is not able to compile a simple test program.

It fails with the following output:

Change Dir: /home/max.schmidt/nest/master_anaconda3.bld/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_6fc79/fast"

/usr/bin/gmake -f CMakeFiles/cmTC_6fc79.dir/build.make CMakeFiles/cmTC_6fc79.dir/build

gmake[1]: Entering directory `/mnt/beegfs/home/max.schmidt/nest/master_anaconda3.bld/CMakeFiles/CMakeTmp'

Building CXX object CMakeFiles/cmTC_6fc79.dir/testCXXCompiler.cxx.o

/home/max.schmidt/anaconda3/envs/multiarea_model/bin/g++ -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -o CMakeFiles/cmTC_6fc79.dir/testCXXCompiler.cxx.o -c /home/max.schmidt/nest/master_anaconda3.bld/CMakeFiles/CMakeTmp/testCXXCompiler.cxx

g++: error: unrecognized command line option ‘-std=c++17’

g++: error: unrecognized command line option ‘-fstack-protector-strong’

g++: error: unrecognized command line option ‘-fno-plt’

gmake[1]: *** [CMakeFiles/cmTC_6fc79.dir/testCXXCompiler.cxx.o] Error 1

gmake[1]: Leaving directory `/mnt/beegfs/home/max.schmidt/nest/master_anaconda3.bld/CMakeFiles/CMakeTmp'

gmake: *** [cmTC_6fc79/fast] Error 2

CMake will not be able to correctly generate this project. Call Stack (most recent call first): CMakeLists.txt:25 (project)

-- Configuring incomplete, errors occurred!

To me, this looks as if the g++ version of my conda environment is too old. The version is 4.8.5 (obtained via g++ -v) and indeed it lacks the command line option from the error message. However, the system compiler, which I had used for NEST installations so far, has version "gcc version 4.8.3 20140911 (Red Hat 4.8.3-9) (GCC)" and it also doesn't recognize the command line option -std=c++17.

So, is this really a problem of the compiler version?

Created by: mschmidt87

See #210 of the NEST repository for follow-up discussion.

Created by: AlexVanMeegen

See also this repository for a systematic approach to find the point of failure.

Created by: AlexVanMeegen

Looks like it was caused by an issue in the siegert_neuron, #1059 of the NEST repository fixes it for me.

@mschmidt87, could you have a look if this works for you?

closed