NEST compilation issues in connection with conda environment about multi-area-model HOT 4 CLOSED

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
nest/nest-simulator#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?

from multi-area-model.

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

from multi-area-model.

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

from multi-area-model.

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?

from multi-area-model.