Hi,

I have attached log files from cmake, make, make install and make installcheck. Yeah, it seems like I can ignore the install egg info since I can import nest after building. However the make installcheck fails. Any idea why?

/Mikael

Den ons 27 juli 2022 kl 11:41 skrev Robin Gilbert De Schepper < robingilbert.deschepper@unipv.it>:

Hi,

I believe the output you see, even though it looks pretty error-y, is related to the not-so-important `install_egg_info` step that produces some Python metadata. AFAIK, this error output can be ignored and installation will continue. Do you have your full cmake and make install output? Perhaps there are other errors there?

On Wed, 27 Jul 2022, 10:19 Mikael Lindahl, mickelindahl@gmail.com wrote:

...

Hi,

I am trying to build NEST on debian 11 with cmake 3.16.9 and conda python=3.9. I have attached my installation script asswell as the full logs for make and install steps. ( I run the script with using source to conda activate will play nice)

During "make install" I get the following message error

-- Set runtime path of "/home/mikael/git/bgmodel/nest/dist/install/nest-simulator-3.3/lib/python3.9/site-packages/nest/pynestkernel.so" to "$ORIGIN/../lib/nest:$ORIGIN/../../lib/nest:$ORIGIN/../../../nest:/home/mikael/opt/anaconda3/envs/nest-3.3/lib" running install_egg_info /home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running egg_info creating nest_simulator.egg-info writing nest_simulator.egg-info/PKG-INFO writing dependency_links to nest_simulator.egg-info/dependency_links.txt writing requirements to nest_simulator.egg-info/requires.txt writing top-level names to nest_simulator.egg-info/top_level.txt writing manifest file 'nest_simulator.egg-info/SOURCES.txt' reading manifest file 'nest_simulator.egg-info/SOURCES.txt' writing manifest file 'nest_simulator.egg-info/SOURCES.txt' Copying nest_simulator.egg-info to /home/mikael/git/bgmodel/nest/dist/install/nest-simulator-3.3/lib/python3.9/site-packages/nest_simulator-3.3-py3.9.egg-info Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 477, in get_distribution dist = get_provider(dist) File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 353, in get_provider return working_set.find(moduleOrReq) or require(str(moduleOrReq))[0] File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 897, in require needed = self.resolve(parse_requirements(requirements)) File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 783, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'nest-simulator' distribution was not found and is required by the application

And for make installcheck i get this error

Scanning dependencies of target installcheck Executing NEST's testsuite... make[3]: *** [CMakeFiles/installcheck.dir/build.make:61: CMakeFiles/installcheck] Error 1 make[2]: *** [CMakeFiles/Makefile2:524: CMakeFiles/installcheck.dir/all] Error 2 make[1]: *** [CMakeFiles/Makefile2:531: CMakeFiles/installcheck.dir/rule] Error 2 make: *** [Makefile:178: installcheck] Error 2 It took 160 seconds

Anyone who knows how to solve this?

/Mikael

-- Mikael Lindahl Phd Phone: +46735119429 Email: m lindahlm@csc.kth.seickelindahl@gmail.com _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

---

NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

Hi Håkon,

Tried using environment.yml and now the test suite ran! However, 11 tests failed. Should I be worried about this? Have attached cmake, make, make install and make installcheck logs.

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html - generated xml file: /home/mikael/git/bgmodel/nest/dist/build/nest-simulator-3.3/reports/07_pynesttests.xml - =========================== short test summary info ============================ ERROR ../../install/nest-simulator-3.3/share/nest/testsuite/pytests/test_connect_all_to_all.py ERROR ../../install/nest-simulator-3.3/share/nest/testsuite/pytests/test_connect_fixed_indegree.py ERROR ../../install/nest-simulator-3.3/share/nest/testsuite/pytests/test_connect_fixed_outdegree.py ERROR ../../install/nest-simulator-3.3/share/nest/testsuite/pytests/test_connect_fixed_total_number.py ERROR ../../install/nest-simulator-3.3/share/nest/testsuite/pytests/test_connect_one_to_one.py ERROR ../../install/nest-simulator-3.3/share/nest/testsuite/pytests/test_connect_pairwise_bernoulli.py ERROR ../../install/nest-simulator-3.3/share/nest/testsuite/pytests/test_connect_symmetric_pairwise_bernoulli.py ERROR ../../install/nest-simulator-3.3/share/nest/testsuite/pytests/test_poisson_generator_rate_change.py ERROR ../../install/nest-simulator-3.3/share/nest/testsuite/pytests/test_regression_issue-1034.py ERROR ../../install/nest-simulator-3.3/share/nest/testsuite/pytests/test_sp/test_growth_curves.py ERROR ../../install/nest-simulator-3.3/share/nest/testsuite/pytests/test_spatial/test_spatial_distributions.py =========== 474 passed, 41 skipped, 68 warnings, 11 errors in 46.65s =========== make[3]: *** [CMakeFiles/installcheck.dir/build.make:71: CMakeFiles/installcheck] Error 1 make[2]: *** [CMakeFiles/Makefile2:465: CMakeFiles/installcheck.dir/all] Error 2 make[1]: *** [CMakeFiles/Makefile2:472: CMakeFiles/installcheck.dir/rule] Error 2 make: *** [Makefile:179: installcheck] Error 2

/Mikael

Den mån 1 aug. 2022 kl 12:01 skrev Håkon Mørk hakon.mork@nmbu.no:

Hi Mikael,

Looks like you are missing one or more Python packages. Either "pytest" itself, or one of the extensions "pytest-xdist" or "pytest-timeout".

It is suggested to use the Conda environment file, "environment.yml", which is included with the NEST source. It contains all Python packages you need to build, test, and work with NEST.

Best, Håkon

---

*From:* Mikael Lindahl mickelindahl@gmail.com *Sent:* 29 July 2022 13:08 *To:* NEST User Mailing List users@nest-simulator.org *Subject:* [NEST Users] Re: Fwd: Building nest 3.3

Some people who received this message don't often get email from mickelindahl@gmail.com. Learn why this is important https://aka.ms/LearnAboutSenderIdentification Hi,

I have attached log files from cmake, make, make install and make installcheck. Yeah, it seems like I can ignore the install egg info since I can import nest after building. However the make installcheck fails. Any idea why?

/Mikael

Den ons 27 juli 2022 kl 11:41 skrev Robin Gilbert De Schepper < robingilbert.deschepper@unipv.it>:

Hi,

I believe the output you see, even though it looks pretty error-y, is related to the not-so-important `install_egg_info` step that produces some Python metadata. AFAIK, this error output can be ignored and installation will continue. Do you have your full cmake and make install output? Perhaps there are other errors there?

On Wed, 27 Jul 2022, 10:19 Mikael Lindahl, mickelindahl@gmail.com wrote:

Hi,

I am trying to build NEST on debian 11 with cmake 3.16.9 and conda python=3.9. I have attached my installation script asswell as the full logs for make and install steps. ( I run the script with using source to conda activate will play nice)

During "make install" I get the following message error

-- Set runtime path of "/home/mikael/git/bgmodel/nest/dist/install/nest-simulator-3.3/lib/python3.9/site-packages/nest/pynestkernel.so" to "$ORIGIN/../lib/nest:$ORIGIN/../../lib/nest:$ORIGIN/../../../nest:/home/mikael/opt/anaconda3/envs/nest-3.3/lib" running install_egg_info /home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running egg_info creating nest_simulator.egg-info writing nest_simulator.egg-info/PKG-INFO writing dependency_links to nest_simulator.egg-info/dependency_links.txt writing requirements to nest_simulator.egg-info/requires.txt writing top-level names to nest_simulator.egg-info/top_level.txt writing manifest file 'nest_simulator.egg-info/SOURCES.txt' reading manifest file 'nest_simulator.egg-info/SOURCES.txt' writing manifest file 'nest_simulator.egg-info/SOURCES.txt' Copying nest_simulator.egg-info to /home/mikael/git/bgmodel/nest/dist/install/nest-simulator-3.3/lib/python3.9/site-packages/nest_simulator-3.3-py3.9.egg-info Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 477, in get_distribution dist = get_provider(dist) File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 353, in get_provider return working_set.find(moduleOrReq) or require(str(moduleOrReq))[0] File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 897, in require needed = self.resolve(parse_requirements(requirements)) File "/home/mikael/opt/anaconda3/envs/nest-3.3/lib/python3.9/site-packages/pkg_resources/__init__.py", line 783, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'nest-simulator' distribution was not found and is required by the application

And for make installcheck i get this error

Scanning dependencies of target installcheck Executing NEST's testsuite... make[3]: *** [CMakeFiles/installcheck.dir/build.make:61: CMakeFiles/installcheck] Error 1 make[2]: *** [CMakeFiles/Makefile2:524: CMakeFiles/installcheck.dir/all] Error 2 make[1]: *** [CMakeFiles/Makefile2:531: CMakeFiles/installcheck.dir/rule] Error 2 make: *** [Makefile:178: installcheck] Error 2 It took 160 seconds

Anyone who knows how to solve this?

/Mikael

-- Mikael Lindahl Phd Phone: +46735119429 Email: m lindahlm@csc.kth.seickelindahl@gmail.com _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

---

NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

-- Mikael Lindahl Phd Phone: +46735119429 Email: m lindahlm@csc.kth.seickelindahl@gmail.com _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org