18 Jan
2021
18 Jan
'21
9:48 p.m.
Hi Pooja,
Concerning libomp: As the full brew package list shows, I had that installed. I wonder a
bit why I have it and you did not get it automatically even though you have the same brew
leaves I have. It may be that I had the libomp leftover as dependency of another package
that I uninstalled in the meantime or that brew leaves is not entirely reliable. But that
problem is solved.
The complaint about libiomp5 in my experience relates to NumPy built with the Intel MKL,
which is default for conda. Usually, one can avoid this by creating a conda environment
where nomkl is the first package specified/installed. You can check this either by running
conda list and check if nomkl or a number of mkl* packages are installed, or by importing
numpy into Python and then running numpy.__config__.show(). If that mentions mkl_rt
libraries, you have NumPy with MKL in your environment, if it shows only openblas you
don’t.
Best,
Hans Ekkehard
--
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 18/01/2021, 20:30, "Babu, Pooja"
<p.babu@fz-juelich.de<mailto:p.babu@fz-juelich.de>> wrote:
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<https://www.nest-simulator.org/mailinglist/hyperkitty/list/users@…
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<mailto: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<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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