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.
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@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 maybe 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@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
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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Maryada Maryada -
Steffen Graber