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

Email hans.ekkehard.plesser@nmbu.no

Home http://arken.nmbu.no/~plesser

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

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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