18 Jan
2021
18 Jan
'21
7:36 a.m.
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<mailto:openssl@1.1> 1.1.1i
pcre 8.44
pcre2 10.36
pybind11 2.6.1_1
python@3.8<mailto:python@3.8> 3.8.7
python@3.9<mailto: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<mailto:hans.ekkehard.plesser@nmbu.no>
Home http://arken.nmbu.no/~plesser
On 15/01/2021, 15:48, "Babu, Pooja"
<p.babu@fz-juelich.de<mailto: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<https://www.nest-initiative.org/mailinglist/hyperkitty/list/users@n…
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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