Hello Hans,

Thank you for a detailed description of your setup and steps.

I checked them with mine and although I do not have all the brew packages that you have in your complete list, I have the ones you mentioned in brew leaves.

I tried to install nest with Apple’s Clang with the option -Dwith-mpi=OFF. I got the below errors during cmake.

-- 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:466 (message): 
 CMake can not find OpenMP. 
Call Stack (most recent call first): 
 CMakeLists.txt:146 (nest_process_with_openmp)

I saw another thread with the same issue and found that I had open-mpi installed via homebrew as mentioned there. The thread also mentions libomp package. I installed that and the errors were gone. The make install command was successful. After this, when I imported nest into python, I got the below errors

OMP: Error #15: Initializing libomp.dylib, but found libiomp5.dylib already initialized.
OMP: Hint This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://openmp.llvm.org/
Abort trap: 6

I did the workaround as suggested in the message by setting KMP_DUPLICATE_LIB_OK=TRUE. This setting indeed got rid of the above error and the import was successful, but as mentioned, the behaviour could be unpredictable. 

I couldn’t find any other way to work around the initial OpenMP_C and OpenMP_CXX errors other than installing libomp package. Do you know if there is any other way to resolve that error?

Thanks,
Pooja


On 18. Jan 2021, at 07:36, Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.no> wrote:

 
Hi Pooja,
 
Over the weekend, I did a brief test on a Mac with Big Sur an built NEST successfully. Below is a detailed description of my setup and steps I have taken. I hope this helps.
 
Best,
Hans Ekkehard
 
System: Mac Book Air with INTEL CPU, Big Sur 11.1
 
Apple Command Line Tools
% xcode-select --print-path
/Library/Developer/CommandLineTools
 
Homebrew packages (explicitly installed; see below for full list)
 
                % brew leaves
boost
cmake
git
gsl
imagemagick
open-mpi
scipy
wget
 
Conda packages (base installation is miniconda3; this shows only explicitly installed packages, full list below)
 
% conda create -n nest_dev nomkl numpy scipy matplotlib ipython cython nose  
% conda activate nest_dev
% pip install junitparser
% conda export --from-history
 
name: nest_dev
channels:
  - defaults
dependencies:
  - nomkl
  - numpy
  - nose
  - matplotlib
  - cython
  - ipython
  - scipy
                
Additionally via pip: junitparser
 
CMake invocation and report
 
% cmake -DCMAKE_INSTALL_PREFIX:PATH=`pwd`/install -Dwith-mpi=ON ../src
 
-- NEST version: master@0e6cd2819
 
--------------------------------------------------------------------------------
NEST Configuration Summary
--------------------------------------------------------------------------------
 
Build type          : 
Target System       : Darwin
Cross Compiling     : FALSE
C compiler          : AppleClang 12.0.0.12000032 (/Library/Developer/CommandLineTools/usr/bin/cc)
C compiler flags    :  -O2 -Wall -Xclang -fopenmp    
C++ compiler        : AppleClang 12.0.0.12000032 (/Library/Developer/CommandLineTools/usr/bin/c++)
C++ compiler flags  :  -std=c++11 -O2 -Wall -Xclang -fopenmp  
Build dynamic       : ON
 
Built-in modules    : models
User modules        : None
Python bindings     : Yes (Python 3.8.5: /Users/hep/opt/miniconda3/envs/nest_dev/bin/python3)
       Includes     : /Users/hep/opt/miniconda3/envs/nest_dev/include/python3.8
       Libraries    : /Users/hep/opt/miniconda3/envs/nest_dev/lib/libpython3.8.dylib
 
Cython bindings     : Yes (Cython 0.29.21: /Users/hep/opt/miniconda3/envs/nest_dev/bin/cython)
MPI4PY header     : NO 
Use threading       : Yes (OpenMP: -Xclang -fopenmp)
Use GSL             : Yes (GSL 2.6)
    Includes        : /usr/local/Cellar/gsl/2.6/include
    Libraries       : /usr/local/Cellar/gsl/2.6/lib/libgsl.dylib;/usr/local/Cellar/gsl/2.6/lib/libgslcblas.dylib
 
Use Readline        : No
Use libltdl         : Yes (LTDL 2.4.6)
    Includes        : /usr/local/include
    Libraries       : /usr/local/lib/libltdl.dylib
 
Use doxygen         : No
Use MPI             : Yes (MPI: /usr/local/bin/mpicxx)
    FLAGS           : 
    Includes        : /usr/local/Cellar/open-mpi/4.0.5/include
    Link Flags      : -L/usr/local/Cellar/libevent/2.1.12/lib
    Libraries       : /usr/local/Cellar/open-mpi/4.0.5/lib/libmpi.dylib
 
Use MUSIC           : No
Use libneurosim     : No
Use Boost           : Yes (Boost 1.75.0)
    Includes        : /usr/local/include
    Libraries       : 
 
Use recording backend Arbor   : No
Use SIONlib         : No
 
————————————————————————————————————————
 
Results from testsuite
 
                % make -j4 install
                % make installcheck
 
----------------------------------------------------------------------
NEST Testsuite Results
----------------------------------------------------------------------
Phase                    Tests   Skipped  Failures    Errors      Time
----------------------------------------------------------------------
01 basetests                 6         0         0         0      12.0
02 selftests                 8         4         0         0      24.0
03 unittests               185         1         0         0     208.0
04 regressiontests          94         7         0         0     142.0
05 mpitests                 79         0         0         0     258.0
07 pynesttests             796        11         0         0     144.2
08 cpptests                 29         0         0         0       0.0
----------------------------------------------------------------------
Total                     1197        23         0         0     788.2
----------------------------------------------------------------------
 
 
Complete list of Brew packages
 
% brew list
 
aom 2.0.1
boost 1.75.0_1
cmake 3.19.3
docbook 5.1_1
docbook-xsl 1.79.2_1
freetype 2.10.4
gcc 10.2.0_2
gdbm 1.18.1_1
gettext 0.21
ghostscript 9.53.3_1
git 2.30.0
glib 2.66.4_1
gmp 6.2.1
gnu-getopt 2.36.1
gsl 2.6
hwloc 2.4.0
icu4c 67.1
ilmbase 2.5.4
imagemagick 7.0.10-57
isl 0.23
jpeg 9d
libde265 1.0.8
libevent 2.1.12
libffi 3.3_2
libheif 1.10.0
libidn2 2.3.0
liblqr 0.4.2_1
libmpc 1.2.1
libomp 11.0.1
libpng 1.6.37
libtiff 4.2.0
libtool 2.4.6_2
libunistring 0.9.10
little-cms2 2.11
mpfr 4.1.0
numpy 1.19.5
open-mpi 4.0.5
openblas 0.3.13
openexr 2.5.4
openjpeg 2.3.1
openssl@1.1 1.1.1i
pcre 8.44
pcre2 10.36
pybind11 2.6.1_1
python@3.8 3.8.7
python@3.9 3.9.1_6
readline 8.1
scipy 1.6.0
shared-mime-info 2.1
sqlite 3.34.0
tcl-tk 8.6.11
webp 1.1.0
wget 1.21
x265 3.4_2
xmlto 0.0.28
xz 5.2.5
 
 
Complete list of Conda packages in nest_dev
 
% conda activate nest_dev
% conda env export
name: nest_dev
channels:
  - defaults
dependencies:
  - appnope=0.1.2=py38hecd8cb5_1001
  - backcall=0.2.0=py_0
  - blas=1.0=openblas
  - ca-certificates=2020.12.8=hecd8cb5_0
  - certifi=2020.12.5=py38hecd8cb5_0
  - cycler=0.10.0=py38_0
  - cython=0.29.21=py38h23ab428_0
  - decorator=4.4.2=py_0
  - freetype=2.10.4=ha233b18_0
  - ipython=7.19.0=py38h01d92e1_1
  - ipython_genutils=0.2.0=pyhd3eb1b0_1
  - jedi=0.17.2=py38hecd8cb5_1
  - jpeg=9b=he5867d9_2
  - kiwisolver=1.3.0=py38h23ab428_0
  - lcms2=2.11=h92f6f08_0
  - libcxx=10.0.0=1
  - libedit=3.1.20191231=h1de35cc_1
  - libffi=3.3=hb1e8313_2
  - libgfortran=3.0.1=h93005f0_2
  - libopenblas=0.3.10=h0794777_0
  - libpng=1.6.37=ha441bb4_0
  - libtiff=4.1.0=hcb84e12_1
  - lz4-c=1.9.2=h79c402e_3
  - matplotlib=3.3.2=hecd8cb5_0
  - matplotlib-base=3.3.2=py38h181983e_0
  - ncurses=6.2=h0a44026_1
  - nomkl=3.0=0
  - nose=1.3.7=pyhd3eb1b0_1006
  - numpy=1.19.2=py38h63973fd_0
  - numpy-base=1.19.2=py38h68fea81_0
  - olefile=0.46=py_0
  - openssl=1.1.1i=h9ed2024_0
  - parso=0.7.0=py_0
  - pexpect=4.8.0=pyhd3eb1b0_3
  - pickleshare=0.7.5=pyhd3eb1b0_1003
  - pillow=8.1.0=py38h5270095_0
  - pip=20.3.3=py38hecd8cb5_0
  - prompt-toolkit=3.0.8=py_0
  - ptyprocess=0.7.0=pyhd3eb1b0_2
  - pygments=2.7.4=pyhd3eb1b0_0
  - pyparsing=2.4.7=py_0
  - python=3.8.5=h26836e1_1
  - python-dateutil=2.8.1=py_0
  - readline=8.0=h1de35cc_0
  - scipy=1.5.2=py38h4420a3a_0
  - setuptools=51.1.2=py38hecd8cb5_4
  - six=1.15.0=py38hecd8cb5_0
  - sqlite=3.33.0=hffcf06c_0
  - tk=8.6.10=hb0a8c7a_0
  - tornado=6.1=py38h9ed2024_0
  - traitlets=5.0.5=py_0
  - wcwidth=0.2.5=py_0
  - wheel=0.36.2=pyhd3eb1b0_0
  - xz=5.2.5=h1de35cc_0
  - zlib=1.2.11=h1de35cc_3
  - zstd=1.4.5=h41d2c2f_0
  - pip:
    - future==0.18.2
    - junitparser==1.6.2
 
 
 
 
 
 
-- 
 
Prof. Dr. Hans Ekkehard Plesser
Head, Department of Data Science
 
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
 
Phone +47 6723 1560
 
 
On 15/01/2021, 15:48, "Babu, Pooja" <p.babu@fz-juelich.de> wrote:
 
Hello everyone, 
 
I have a Mac with Big Sur and I tried installing NEST with a Conda environment as mentioned here by pulling in the latest code from Github. My commands look like this
 
conda create -n nestml_dev nomkl numpy scipy matplotlib ipython cython nose pytest
conda activate nestml_dev
 
<Pull the latest code from github>
mkdir nest-simulator-build
cd nest-simulator-build
 
cmake -DCMAKE_INSTALL_PREFIX:PATH=<nest_path> -DCMAKE_C_COMPILER=gcc-10 -DCMAKE_CXX_COMPILER=g++-10 <nest_src>
make -j4
make install
 
After this, if I try to import nest in python or run nest from the command line, I get the following error
 
OMP: Error #13: Assertion failure at kmp_csupport.cpp(590).
OMP: Hint Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.
Abort trap: 6
 
Has anyone else seen this error? Any pointers on this would be helpful.
 
Thank you,
Pooja


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