28 Feb
2022
28 Feb
'22
12:23 p.m.
Hi Steffen,
Good question :)
I tried installing it with conda because I'm having issues with current
installation in a virtual environment (not NEST related issue).
Following were the steps:
conda update conda
conda create -n nest_conda nomkl numpy scipy matplotlib ipython cython
nose
conda activate nest_dev
pip install junitparser
and a few other pytest packages. I am certain that it is permission issue
but I don't know how to resolve this issue "runtime library [libgomp.so.1]
in /usr/lib/gcc/x86_64-linux-gnu/9 may be hidden by files in:
/home/<user>/miniconda3/envs/nestConda/lib" without running CMAKE with sudo
On Mon, Feb 28, 2022 at 12:00 PM Steffen Graber <s.graber(a)fz-juelich.de>
wrote:
Hi Maryada
Thanks for your feedback.
Could you describe me exactly what you did to install NEST?
Best
Steffen
Am 26.02.22 um 19:25 schrieb Maryada Maryada:
Dear NEST users,
After trying multiple ideas, I am still facing the issue where my
installation is successful with an error message:
-- Configuring done
CMake Warning at cmake/UseCython.cmake:100 (add_library):
Cannot generate a safe runtime search path for target pynestkernel
because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libgomp.so.1] in /usr/lib/gcc/x86_64-linux-gnu/9 may
be hidden by files in:
/home/<user>/miniconda3/envs/nestConda/lib
Some of these libraries may not be found correctly.
Call Stack (most recent call first):
cmake/UseCython.cmake:283 (python_add_module)
pynest/CMakeLists.txt:28 (cython_add_module)
------------------------------------------------------------------------------------------------
This leads to the failure of multiple tests. The summary of the tests and
logs for the failed tests is attached.
I must mention that I tested the installation by creating a neuron and it
works fine.
It would be nice to get rid of the error, please see error_msg file to
see where it fails.
--
Thanks and Regards
*Maryada*
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--
-------------------------------------------------------------------------------------
Steffen Graber
SimLab Neuroscience
Division HPC in Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
Forschungszentrum Jülich GmbH
E-mail: s.graber(a)fz-juelich.de
Phone: +49 2461 61 85457 http://www.fz-juelich.de/ias/jsc
Institute of Neuroscience and Medicine (INM-6)
Computational and Systems Neuroscience &
Institute for Advanced Simulation (IAS-6)
Theoretical Neuroscience &
JARA Institute Brain Structure-Function Relationships (INM-10)
Forschungszentrum Jülich GmbHhttp://www.csn.fz-juelich.de
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Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht,
Prof. Dr. Frauke Melchior
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--
Thanks and Regards
*Maryada*