Hi Dennis, We've installed junitparser but again we do not have success: Executing NEST's testsuite... Error: PyNEST testing requested, but 'pytest' cannot be run.        Testing also requires the 'pytest-xdist' and 'pytest-timeout' extensions. CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:464: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:471: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 Even though we have installed pytest-xdist and tytest-timeout extensions.Could you help us? Best,Petia On Wednesday, June 29, 2022 at 01:52:11 PM GMT+3, Dennis Terhorst d.terhorst@fz-juelich.de wrote:

Hi,

could you check if you have junitparser in your python environment? I saw a similar inexpressive error message when that package is missing. We need to fix the detection of junitparser in `testsuite/do_tests.sh`, the error message may not be printed.

Best, Dennis

On 29.06.22 12:33, Petia Koprinkova wrote:

Hi, Could you help us with NEST 3.3. installation? The final (check) state give the following error: Executing NEST's testsuite... CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:446: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:453: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2

We have Ubuntu desctop with installed NEST 2.18 and it works. But for some reason NEST 3.3. failed. Best regards, Petia Koprinkova-Hristova _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

-- Dipl.-Phys. Dennis Terhorst Coordinator Software Development

Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany

Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst@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.-Ing. Harald Bolt, Prof. Dr. Frauke Melchior ---------------------------------------------------------------------- _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

Hi Dennis, We've just repeated all installation steps from  Installation from source without a virtual Python environment (link below) Running of make installcheck from the NEST 3.3 folder yelded the following result:

Error: PyNEST testing requested, but 'pytest' cannot be run.        Testing also requires the 'pytest-xdist' and 'pytest-timeout' extensions. CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:464: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:471: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2It seems the same as prvious one.Best,Petia

On Wednesday, June 29, 2022 at 07:22:20 PM GMT+3, Dennis Terhorst d.terhorst@fz-juelich.de wrote:

Hi Petia,

this sound's a lot like an inconsistency in the Python setup. Did you choose the venv or the prefix path ofhttps://nest-simulator.readthedocs.io/en/v3.3/installation/linux_install.htm... Are you running the `make installcheck` from the same location where the pytest-* are installed, i.e. consistently *in* the environment or *outside*?

Best, Dennis

On 29.06.22 14:37, Petia Koprinkova wrote:

Hi Dennis, We've installed junitparser but again we do not have success: Executing NEST's testsuite... Error: PyNEST testing requested, but 'pytest' cannot be run.        Testing also requires the 'pytest-xdist' and 'pytest-timeout' extensions. CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:464: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:471: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 Even though we have installed pytest-xdist and tytest-timeout extensions. Could you help us? Best, Petia On Wednesday, June 29, 2022 at 01:52:11 PM GMT+3, Dennis Terhorst d.terhorst@fz-juelich.de wrote:

Hi,

could you check if you have junitparser in your python environment? I saw a similar inexpressive error message when that package is missing. We need to fix the detection of junitparser in `testsuite/do_tests.sh`, the error message may not be printed.

Best, Dennis

On 29.06.22 12:33, Petia Koprinkova wrote:

Hi, Could you help us with NEST 3.3. installation? The final (check) state give the following error: Executing NEST's testsuite... CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:446: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:453: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2

We have Ubuntu desctop with installed NEST 2.18 and it works. But for some reason NEST 3.3. failed. Best regards, Petia Koprinkova-Hristova _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

-- Dipl.-Phys. Dennis Terhorst Coordinator Software Development

Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany

Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst@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.-Ing. Harald Bolt, Prof. Dr. Frauke Melchior ---------------------------------------------------------------------- _______________________________________________ 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

-- Dipl.-Phys. Dennis Terhorst Coordinator Software Development

Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany

Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst@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.-Ing. Harald Bolt, Prof. Dr. Frauke Melchior ---------------------------------------------------------------------- _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

Hi Steffen, We have Ubuntu 16.10 operating system. Python3 was installed following instructions on nest-simulator site (sudo apt install....). I think we still have Python2 vesrion on the same computer.We also keep the older vesrion of NEST 2.18. Thank you in advance,Best,Petia On Friday, July 1, 2022 at 01:54:58 PM GMT+3, Steffen Graber s.graber@fz-juelich.de wrote:

Hi Petia,

I'm trying to reproduce the issue, but still lack some information:

Which operating system and version do you use? Which pytest version do you have installed? (The test seems to stumble over this). Has that been installed via PyPi or the package manager? And, is python2 still on your system?

Sorry if something has already been answered in the correspondence and I have overlooked it.

Best

Steffen

Am 01.07.22 um 11:59 schrieb Petia Koprinkova:

Hi Dennis, We've just repeated all installation steps from  Installation from source without a virtual Python environment (link below) Running of make installcheck from the NEST 3.3 folder yelded the following result:

Error: PyNEST testing requested, but 'pytest' cannot be run.        Testing also requires the 'pytest-xdist' and 'pytest-timeout' extensions. CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:464: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:471: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 It seems the same as prvious one. Best, Petia

On Wednesday, June 29, 2022 at 07:22:20 PM GMT+3, Dennis Terhorst d.terhorst@fz-juelich.de wrote:

Hi Petia,

this sound's a lot like an inconsistency in the Python setup. Did you choose the venv or the prefix path of https://nest-simulator.readthedocs.io/en/v3.3/installation/linux_install.htm... Are you running the `make installcheck` from the same location where the pytest-* are installed, i.e. consistently *in* the environment or *outside*?

Best, Dennis

On 29.06.22 14:37, Petia Koprinkova wrote:

Hi Dennis, We've installed junitparser but again we do not have success: Executing NEST's testsuite... Error: PyNEST testing requested, but 'pytest' cannot be run.        Testing also requires the 'pytest-xdist' and 'pytest-timeout' extensions. CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:464: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:471: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 Even though we have installed pytest-xdist and tytest-timeout extensions. Could you help us? Best, Petia On Wednesday, June 29, 2022 at 01:52:11 PM GMT+3, Dennis Terhorst d.terhorst@fz-juelich.de wrote:

Hi,

could you check if you have junitparser in your python environment? I saw a similar inexpressive error message when that package is missing. We need to fix the detection of junitparser in `testsuite/do_tests.sh`, the error message may not be printed.

Best, Dennis

On 29.06.22 12:33, Petia Koprinkova wrote:

Hi, Could you help us with NEST 3.3. installation? The final (check) state give the following error: Executing NEST's testsuite... CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:446: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:453: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2

We have Ubuntu desctop with installed NEST 2.18 and it works. But for some reason NEST 3.3. failed. Best regards, Petia Koprinkova-Hristova _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

-- Dipl.-Phys. Dennis Terhorst Coordinator Software Development

Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany

Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst@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.-Ing. Harald Bolt, Prof. Dr. Frauke Melchior ---------------------------------------------------------------------- _______________________________________________ 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

-- Dipl.-Phys. Dennis Terhorst Coordinator Software Development

Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany

Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst@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.-Ing. Harald Bolt, Prof. Dr. Frauke Melchior ---------------------------------------------------------------------- _______________________________________________ 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.orgTo unsubscribe send an email to users-leave@nest-simulator.org -- ------------------------------------------------------------------------------------- Steffen Graber

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 GmbH http://www.csn.fz-juelich.de

SDL 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

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

Hi Steffen, We will try but next week. I am afraid that every update could cause some problems so we did not update recetly... Best,Petia On Friday, July 1, 2022 at 03:18:27 PM GMT+3, Steffen Graber s.graber@fz-juelich.de wrote:

Hi Petia

Thank you very much. I will have a look at it.

However, Ubuntu 16.10 has reached the end of its life, and it is difficult to test. Is it possible to switch to a more up-to-date Ubuntu?

Best

Steffen

Am 01.07.22 um 13:14 schrieb Petia Koprinkova:

Hi Steffen, We have Ubuntu 16.10 operating system.  Python3 was installed following instructions on nest-simulator site (sudo apt install....).  I think we still have Python2 vesrion on the same computer. We also keep the older vesrion of NEST 2.18. Thank you in advance, Best, Petia On Friday, July 1, 2022 at 01:54:58 PM GMT+3, Steffen Graber s.graber@fz-juelich.de wrote:

Hi Petia,

I'm trying to reproduce the issue, but still lack some information:

Which operating system and version do you use? Which pytest version do you have installed? (The test seems to stumble over this). Has that been installed via PyPi or the package manager? And, is python2 still on your system?

Sorry if something has already been answered in the correspondence and I have overlooked it.

Best

Steffen

Am 01.07.22 um 11:59 schrieb Petia Koprinkova:

Hi Dennis, We've just repeated all installation steps from  Installation from source without a virtual Python environment (link below) Running of make installcheck from the NEST 3.3 folder yelded the following result:

Error: PyNEST testing requested, but 'pytest' cannot be run.        Testing also requires the 'pytest-xdist' and 'pytest-timeout' extensions. CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:464: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:471: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 It seems the same as prvious one. Best, Petia

On Wednesday, June 29, 2022 at 07:22:20 PM GMT+3, Dennis Terhorst d.terhorst@fz-juelich.de wrote:

Hi Petia,

this sound's a lot like an inconsistency in the Python setup. Did you choose the venv or the prefix path of https://nest-simulator.readthedocs.io/en/v3.3/installation/linux_install.htm... Are you running the `make installcheck` from the same location where the pytest-* are installed, i.e. consistently *in* the environment or *outside*?

Best, Dennis

On 29.06.22 14:37, Petia Koprinkova wrote:

Hi Dennis, We've installed junitparser but again we do not have success: Executing NEST's testsuite... Error: PyNEST testing requested, but 'pytest' cannot be run.        Testing also requires the 'pytest-xdist' and 'pytest-timeout' extensions. CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:464: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:471: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 Even though we have installed pytest-xdist and tytest-timeout extensions. Could you help us? Best, Petia On Wednesday, June 29, 2022 at 01:52:11 PM GMT+3, Dennis Terhorst d.terhorst@fz-juelich.de wrote:

Hi,

could you check if you have junitparser in your python environment? I saw a similar inexpressive error message when that package is missing. We need to fix the detection of junitparser in `testsuite/do_tests.sh`, the error message may not be printed.

Best, Dennis

On 29.06.22 12:33, Petia Koprinkova wrote:

Hi, Could you help us with NEST 3.3. installation? The final (check) state give the following error: Executing NEST's testsuite... CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:446: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:453: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2

We have Ubuntu desctop with installed NEST 2.18 and it works. But for some reason NEST 3.3. failed. Best regards, Petia Koprinkova-Hristova _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

-- Dipl.-Phys. Dennis Terhorst Coordinator Software Development

Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany

Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst@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.-Ing. Harald Bolt, Prof. Dr. Frauke Melchior ---------------------------------------------------------------------- _______________________________________________ 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

-- Dipl.-Phys. Dennis Terhorst Coordinator Software Development

Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany

Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst@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.-Ing. Harald Bolt, Prof. Dr. Frauke Melchior ---------------------------------------------------------------------- _______________________________________________ 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.orgTo unsubscribe send an email to users-leave@nest-simulator.org -- ------------------------------------------------------------------------------------- Steffen Graber

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 GmbH http://www.csn.fz-juelich.de

SDL 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

--------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------- 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 --------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------- _______________________________________________ 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

-- ------------------------------------------------------------------------------------- Steffen Graber

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 GmbH http://www.csn.fz-juelich.de

SDL 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

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

Dear Jochen, Thank you very mich for considering my question. We will upgrade the system and hopefully we will manage to install NEST 3.3. Meanwhile I've discovered that you alredy issued NEST 3.3. for visrtual machine so we could start with it now. We aslo would like to install it on supercomputer in our institute and if we need some support I will ask you again. Best wishes,Petia On Monday, July 4, 2022 at 01:04:25 PM GMT+3, Jochen Martin Eppler j.eppler@fz-juelich.de wrote:

Dear Petia,

I understand your worries with updates, but it's really quite hard to help you with a 6 year old OS.

Can you maybe check if NEST 3.3 is working on a newer system, if you can't upgrade the machine? All NEST development happens on current systems and there's so many things that could be wrong or interacting in incompatible or bad ways and it is very likely that your problem goes away when you update.

Cheers, Jochen!

On 01.07.22 15:15, Petia Koprinkova wrote:

Hi Steffen, We will try but next week. I am afraid that every update could cause some problems so we did not update recetly... Best, Petia On Friday, July 1, 2022 at 03:18:27 PM GMT+3, Steffen Graber s.graber@fz-juelich.de wrote:

Hi Petia

Thank you very much. I will have a look at it.

However, Ubuntu 16.10 has reached the end of its life, and it is difficult to test. Is it possible to switch to a more up-to-date Ubuntu?

Best

Steffen

Am 01.07.22 um 13:14 schrieb Petia Koprinkova:

Hi Steffen, We have Ubuntu 16.10 operating system.  Python3 was installed following instructions on nest-simulator site (sudo apt install....).  I think we still have Python2 vesrion on the same computer. We also keep the older vesrion of NEST 2.18. Thank you in advance, Best, Petia On Friday, July 1, 2022 at 01:54:58 PM GMT+3, Steffen Graber s.graber@fz-juelich.de wrote:

Hi Petia,

I'm trying to reproduce the issue, but still lack some information:

Which operating system and version do you use? Which pytest version do you have installed? (The test seems to stumble over this). Has that been installed via PyPi or the package manager? And, is python2 still on your system?

Sorry if something has already been answered in the correspondence and I have overlooked it.

Best

Steffen

Am 01.07.22 um 11:59 schrieb Petia Koprinkova:

Hi Dennis, We've just repeated all installation steps from  Installation from source without a virtual Python environment (link below) Running of make installcheck from the NEST 3.3 folder yelded the following result:

Error: PyNEST testing requested, but 'pytest' cannot be run.        Testing also requires the 'pytest-xdist' and 'pytest-timeout' extensions. CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:464: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:471: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 It seems the same as prvious one. Best, Petia

On Wednesday, June 29, 2022 at 07:22:20 PM GMT+3, Dennis Terhorst d.terhorst@fz-juelich.de wrote:

Hi Petia,

this sound's a lot like an inconsistency in the Python setup. Did you choose the venv or the prefix path of https://nest-simulator.readthedocs.io/en/v3.3/installation/linux_install.htm... Are you running the `make installcheck` from the same location where the pytest-* are installed, i.e. consistently *in* the environment or *outside*?

Best, Dennis

On 29.06.22 14:37, Petia Koprinkova wrote:

Hi Dennis, We've installed junitparser but again we do not have success: Executing NEST's testsuite... Error: PyNEST testing requested, but 'pytest' cannot be run.        Testing also requires the 'pytest-xdist' and 'pytest-timeout' extensions. CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:464: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:471: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2 Even though we have installed pytest-xdist and tytest-timeout extensions. Could you help us? Best, Petia On Wednesday, June 29, 2022 at 01:52:11 PM GMT+3, Dennis Terhorst d.terhorst@fz-juelich.de wrote:

Hi,

could you check if you have junitparser in your python environment? I saw a similar inexpressive error message when that package is missing. We need to fix the detection of junitparser in `testsuite/do_tests.sh`, the error message may not be printed.

Best, Dennis

On 29.06.22 12:33, Petia Koprinkova wrote:

Hi, Could you help us with NEST 3.3. installation? The final (check) state give the following error: Executing NEST's testsuite... CMakeFiles/installcheck.dir/build.make:70: recipe for target 'CMakeFiles/installcheck' failed make[3]: *** [CMakeFiles/installcheck] Error 1 CMakeFiles/Makefile2:446: recipe for target 'CMakeFiles/installcheck.dir/all' failed make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 CMakeFiles/Makefile2:453: recipe for target 'CMakeFiles/installcheck.dir/rule' failed make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 Makefile:179: recipe for target 'installcheck' failed make: *** [installcheck] Error 2

We have Ubuntu desctop with installed NEST 2.18 and it works. But for some reason NEST 3.3. failed. Best regards, PetiaKoprinkova-Hristova _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

-- Dipl.-Phys. Dennis Terhorst Coordinator Software Development

Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany

Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst@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.-Ing. Harald Bolt, Prof. Dr. Frauke Melchior ---------------------------------------------------------------------- _______________________________________________ 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

-- Dipl.-Phys. Dennis Terhorst Coordinator Software Development

Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany

Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst@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.-Ing. Harald Bolt, Prof. Dr. Frauke Melchior ---------------------------------------------------------------------- _______________________________________________ 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 -- ------------------------------------------------------------------------------------- Steffen Graber

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 GmbH http://www.csn.fz-juelich.de

SDL 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

--------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------- 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 --------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------- _______________________________________________ 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

-- ------------------------------------------------------------------------------------- Steffen Graber

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 GmbH http://www.csn.fz-juelich.de

SDL 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

--------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------- 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 --------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------- _______________________________________________ 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.orgTo unsubscribe send an email to users-leave@nest-simulator.org -- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation _______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org