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@1.1mailto:openssl@1.1 1.1.1i pcre 8.44 pcre2 10.36 pybind11 2.6.1_1 python@3.8mailto:python@3.8 3.8.7 python@3.9mailto: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 Email hans.ekkehard.plesser@nmbu.nomailto:hans.ekkehard.plesser@nmbu.no Home http://arken.nmbu.no/~plesser
On 15/01/2021, 15:48, "Babu, Pooja" <p.babu@fz-juelich.demailto: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 herehttps://www.nest-initiative.org/mailinglist/hyperkitty/list/users@nest-simulator.org/thread/QKRQZOQ6DXPKV7QB7CSE3DVZ22HFAU52/ 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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