21 Apr
2020
21 Apr
'20
5:27 p.m.
Hello everyone,
I used the source code to install nest simulator 2.20 from here
<https://nest-simulator.readthedocs.io/en/stable/installation/linux_install.html>
and did the following steps
(I used to do the same steps for version 2.18 without error.)
cmake -Dwith-python=3 -DCMAKE_INSTALL_PREFIX:PATH=</install/path>
</path/to/NEST/src>
make
make install
make installcheck
I got this error from "make installcheck":
Phase 1: Testing if SLI can execute scripts and report errors
-------------------------------------------------------------
Running test 'selftests/test_pass.sli'... Running Apr 21 19:46:31
SLIStartup [Error]: NEST_DATA_DIR is not usable: Apr 21 19:46:31 SLIStartup
[Error]: Directory '/usr/share/nest' does not exist. Apr 21 19:46:31
SLIStartup [Error]: I'm using the default:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/nest Apr
21 19:46:31 SLIStartup [Error]: NEST_DOC_DIR is not usable: Apr 21 19:46:31
SLIStartup [Error]: Directory '/usr/share/doc/nest' does not exist. Apr 21
19:46:31 SLIStartup [Error]: I'm using the default:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/doc/nest
/usr/bin//bin/nest /usr/share/doc/nest/selftests/test_pass.sli
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial:
20:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial:
Apr: not found
Failed: unexpected exit code 127
Running Apr 21 19:46:31 SLIStartup [Error]: NEST_DATA_DIR is not usable:
Apr 21 19:46:31 SLIStartup [Error]: Directory '/usr/share/nest' does not
exist. Apr 21 19:46:31 SLIStartup [Error]: I'm using the default:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/nest Apr
21 19:46:31 SLIStartup [Error]: NEST_DOC_DIR is not usable: Apr 21 19:46:31
SLIStartup [Error]: Directory '/usr/share/doc/nest' does not exist. Apr 21
19:46:31 SLIStartup [Error]: I'm using the default:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/doc/nest
/usr/bin//bin/nest /usr/share/doc/nest/selftests/test_pass.sli
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial:
20:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial:
Apr: not found
***
*** An unexpected exit code usually hints at a bug in the test suite!
***
*** Please report the problem at
*** https://github.com/nest/nest-simulator/issues
***
*** To help us diagnose the problem, please attach the archived content
*** of these directories to the issue:
*** -
'/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/reports'
*** -
'/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/reports/nest.CgbAi'
***
CMakeFiles/installcheck.dir/build.make:57: recipe for target
'CMakeFiles/installcheck' failed
make[3]: *** [CMakeFiles/installcheck] Error 2
CMakeFiles/Makefile2:99: recipe for target
'CMakeFiles/installcheck.dir/all' failed
make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2
CMakeFiles/Makefile2:106: recipe for target
'CMakeFiles/installcheck.dir/rule' failed
make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2
Makefile:188: recipe for target 'installcheck' failed
make: *** [installcheck] Error 2
--
regards,
Abolfazl Ziaeemehr
Department of Physics,
PhD student in Computational Physics
Institute for Advanced Studies in Basic Sciences (IASBS)
Tel: 0919 607 4296
Page: iasbs.ac.ir/~a.ziaeemehr
21 Apr
21 Apr
5:33 p.m.
Dear Abolfazl,
Could you please post the output of:
nest-config --prefix
nest-config --datadir
Could it be that there is an issue due to using a space in a filename?
Kind regards,
Charl
On Tue, Apr 21, 2020, at 17:27, Abolfazl Ziaeemehr wrote:
Hello everyone,
I used the source code to install nest simulator 2.20 from
here<https://nest-simulator.readthedocs.io/en/stable/installation/linux_install.html>
and did the following steps
(I used to do the same steps for version 2.18 without error.)
cmake -Dwith-python=3 -DCMAKE_INSTALL_PREFIX:PATH=</install/path>
</path/to/NEST/src>
make
make install
make installcheck
I got this error from "make installcheck":
Phase 1: Testing if SLI can execute scripts and report errors
-------------------------------------------------------------
Running test 'selftests/test_pass.sli'... Running Apr 21 19:46:31 SLIStartup
[Error]: NEST_DATA_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]: Directory
'/usr/share/nest' does not exist. Apr 21 19:46:31 SLIStartup [Error]: I'm
using the default: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/nest
Apr 21 19:46:31 SLIStartup [Error]: NEST_DOC_DIR is not usable: Apr 21 19:46:31 SLIStartup
[Error]: Directory '/usr/share/doc/nest' does not exist. Apr 21 19:46:31
SLIStartup [Error]: I'm using the default:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/doc/nest
/usr/bin//bin/nest /usr/share/doc/nest/selftests/test_pass.sli
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: 20:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: Apr: not
found
Failed: unexpected exit code 127
Running Apr 21 19:46:31 SLIStartup [Error]: NEST_DATA_DIR is not usable: Apr 21 19:46:31
SLIStartup [Error]: Directory '/usr/share/nest' does not exist. Apr 21 19:46:31
SLIStartup [Error]: I'm using the default:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/nest Apr 21 19:46:31
SLIStartup [Error]: NEST_DOC_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]:
Directory '/usr/share/doc/nest' does not exist. Apr 21 19:46:31 SLIStartup
[Error]: I'm using the default:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/doc/nest
/usr/bin//bin/nest /usr/share/doc/nest/selftests/test_pass.sli
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: 20:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: Apr: not
found
***
*** An unexpected exit code usually hints at a bug in the test suite!
***
*** Please report the problem at
*** https://github.com/nest/nest-simulator/issues
***
*** To help us diagnose the problem, please attach the archived content
*** of these directories to the issue:
*** - '/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/reports'
*** -
'/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/reports/nest.CgbAi'
***
CMakeFiles/installcheck.dir/build.make:57: recipe for target
'CMakeFiles/installcheck' failed
make[3]: *** [CMakeFiles/installcheck] Error 2
CMakeFiles/Makefile2:99: recipe for target 'CMakeFiles/installcheck.dir/all'
failed
make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2
CMakeFiles/Makefile2:106: recipe for target 'CMakeFiles/installcheck.dir/rule'
failed
make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2
Makefile:188: recipe for target 'installcheck' failed
make: *** [installcheck] Error 2
--
regards,
Abolfazl Ziaeemehr
Department of Physics,
PhD student in Computational Physics
Institute for Advanced Studies in Basic Sciences (IASBS)
Tel: 0919 607 4296
Page: iasbs.ac.ir/~a.ziaeemehr<http://iasbs.ac.ir/~a.ziaeemehr>
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
Attachments:
* reports.zip
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
9:14 p.m.
Dear Charl,
Could you please post the output of:
nest-config --prefix
*/usr*
nest-config --datadir
*share/nest*
I reinstalled the nest package and made sure there is no space in directory
names.
cmake -Dwith-python=3
-DCMAKE_INSTALL_PREFIX:PATH=/home/abolfazl/prog/nest-install
/home/abolfazl/prog/nest-source
regards,
Abolfazl
22 Apr
22 Apr
12:03 a.m.
Hi,
This is strange: you specified ``-DCMAKE_INSTALL_PREFIX`` as being
``/home/abolfazl/prog/nest-install``, but nest-config reports the prefix as ``/usr``. It
might be that you have two installations next to each other, one in each directory. Could
you clean all build files in all directories (and any package manager NEST installations
that might be present), and double-check the paths reported during the cmake configuration
stage, to make sure they are consistent?
Regards,
Charl
On Tue, Apr 21, 2020, at 21:14, Abolfazl Ziaeemehr wrote:
Dear Charl,
Could you please post the output of:
nest-config --prefix
*/usr*
nest-config --datadir
*share/nest*
**
I reinstalled the nest package and made sure there is no space in directory names.
cmake -Dwith-python=3 -DCMAKE_INSTALL_PREFIX:PATH=/home/abolfazl/prog/nest-install
/home/abolfazl/prog/nest-source
regards,
Abolfazl
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
8:39 a.m.
Dear Charl,
Thanks for your reply, I completely removed every build files and
directories.
and reinstalled the package.
$ ./nest-config --prefix
*/home/abolfazl/prog/nest-build*
$ ./nest-config --datadir
*share/nest*
After adding the path variable in .bashrc
Still I have these errors from make installcheck,
and I can not import nest.
FAIL: test_nn_pre_centered_synapse
(nest.tests.test_stdp_nn_synapses.STDPNNSynapsesTest)
AssertionError: 0.32057074514327416 != 0.8197400647350731 within 7 places
: stdp_nn_pre-centered_synapse test: Resulting synaptic weight 8.197401e-01
differs from expected 3.205707e-01
FAILED (SKIP=9, failures=1)
PyNEST tests: 569
Passed: 559
Skipped: 9
Failed: 1
Phase 8: Running C++ tests (experimental)
-----------------------------------------
Not running C++ tests because NEST was compiled without Boost.
NEST Testsuite Summary
----------------------
NEST Executable: /home/abolfazl/prog/nest-build/bin/nest
SLI Executable : /home/abolfazl/prog/nest-build/bin/sli
Total number of tests: 870
Passed: 859
Skipped: 10 (9 PyNEST)
Failed: 1 (1 PyNEST)
***
*** There were errors detected during the run of the NEST test suite!
***
*** Please report the problem at
*** https://github.com/nest/nest-simulator/issues
***
*** To help us diagnose the problem, please attach the archived content
*** of these directories to the issue:
*** - '/home/abolfazl/prog/nest-build/reports'
*** - '/home/abolfazl/prog/nest-build/reports/nest.RrYRt'
***
CMakeFiles/installcheck.dir/build.make:57: recipe for target
'CMakeFiles/installcheck' failed
make[3]: *** [CMakeFiles/installcheck] Error 1
CMakeFiles/Makefile2:99: recipe for target
'CMakeFiles/installcheck.dir/all' failed
make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2
CMakeFiles/Makefile2:106: recipe for target
'CMakeFiles/installcheck.dir/rule' failed
make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2
Makefile:188: recipe for target 'installcheck' failed
make: *** [installcheck] Error 2
I use cmake version 3.10.2.
regards,
Abolfazl
10:48 a.m.
Hi Abolfazl,
Great to hear we're making progress. This new error is a tough one, is has cropped up
before (https://github.com/nest/nest-simulator/issues/1435) and seems to be
installation-related. In particular, it happens when compiled without MPI support, for
reasons that are not yet clear to us. Would it be an option for you to compile with MPI
support enabled?
Thanks,
Charl
On Wed, Apr 22, 2020, at 08:39, Abolfazl Ziaeemehr wrote:
Dear Charl,
Thanks for your reply, I completely removed every build files and directories.
and reinstalled the package.
$ ./nest-config --prefix
*/home/abolfazl/prog/nest-build*
$ ./nest-config --datadir
*share/nest*
After adding the path variable in .bashrc
Still I have these errors from make installcheck,
and I can not import nest.
FAIL: test_nn_pre_centered_synapse (nest.tests.test_stdp_nn_synapses.STDPNNSynapsesTest)
AssertionError: 0.32057074514327416 != 0.8197400647350731 within 7 places :
stdp_nn_pre-centered_synapse test: Resulting synaptic weight 8.197401e-01 differs from
expected 3.205707e-01
FAILED (SKIP=9, failures=1)
PyNEST tests: 569
Passed: 559
Skipped: 9
Failed: 1
Phase 8: Running C++ tests (experimental)
-----------------------------------------
Not running C++ tests because NEST was compiled without Boost.
NEST Testsuite Summary
----------------------
NEST Executable: /home/abolfazl/prog/nest-build/bin/nest
SLI Executable : /home/abolfazl/prog/nest-build/bin/sli
Total number of tests: 870
Passed: 859
Skipped: 10 (9 PyNEST)
Failed: 1 (1 PyNEST)
***
*** There were errors detected during the run of the NEST test suite!
***
*** Please report the problem at
*** https://github.com/nest/nest-simulator/issues
***
*** To help us diagnose the problem, please attach the archived content
*** of these directories to the issue:
*** - '/home/abolfazl/prog/nest-build/reports'
*** - '/home/abolfazl/prog/nest-build/reports/nest.RrYRt'
***
CMakeFiles/installcheck.dir/build.make:57: recipe for target
'CMakeFiles/installcheck' failed
make[3]: *** [CMakeFiles/installcheck] Error 1
CMakeFiles/Makefile2:99: recipe for target 'CMakeFiles/installcheck.dir/all'
failed
make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2
CMakeFiles/Makefile2:106: recipe for target 'CMakeFiles/installcheck.dir/rule'
failed
make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2
Makefile:188: recipe for target 'installcheck' failed
make: *** [installcheck] Error 2
I use cmake version 3.10.2.
regards,
Abolfazl
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
*Attachments:*
* reports.zip
11:48 a.m.
Hi,
with mpi option enable:
*cmake -Dwith-python=3 -Dwith-mpi=ON
-DCMAKE_INSTALL_PREFIX:PATH=/home/abolfazl/prog/nest-build
/home/abolfazl/prog/nest-source*
$ make installcheck
FAIL: testWithMPI
(nest.tests.test_sp.test_mpitests.TestStructuralPlasticityMPI)
'[script]": {}'.format(failing_tests))
AssertionError: False is not true : The following tests failed when
executing with "mpirun -np 2 nosetests [script]":
['/home/abolfazl/prog/nest-build/lib/python3.6/site-packages/nest/tests/test_sp/mpitest_issue_578_sp.py']
FAIL: test_nn_pre_centered_synapse
(nest.tests.test_stdp_nn_synapses.STDPNNSynapsesTest)
AssertionError: 0.32057074514327416 != 0.8197400647350731 within 7 places
: stdp_nn_pre-centered_synapse test: Resulting synaptic weight 8.197401e-01
differs from expected 3.205707e-01
FAILED (SKIP=8, failures=2)
PyNEST tests: 569
Passed: 559
Skipped: 8
Failed: 2
Phase 8: Running C++ tests (experimental)
-----------------------------------------
Not running C++ tests because NEST was compiled without Boost.
NEST Testsuite Summary
----------------------
NEST Executable: /home/abolfazl/prog/nest-build/bin/nest
SLI Executable : /home/abolfazl/prog/nest-build/bin/sli
Total number of tests: 940
Passed: 919
Skipped: 19 (8 PyNEST)
Failed: 2 (2 PyNEST)
***
*** There were errors detected during the run of the NEST test suite!
***
*** Please report the problem at
*** https://github.com/nest/nest-simulator/issues
***
*** To help us diagnose the problem, please attach the archived content
*** of these directories to the issue:
*** - '/home/abolfazl/prog/nest-build/reports'
*** - '/home/abolfazl/prog/nest-build/reports/nest.eYBJZ'
***
CMakeFiles/installcheck.dir/build.make:57: recipe for target
'CMakeFiles/installcheck' failed
make[3]: *** [CMakeFiles/installcheck] Error 1
CMakeFiles/Makefile2:99: recipe for target
'CMakeFiles/installcheck.dir/all' failed
make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2
CMakeFiles/Makefile2:106: recipe for target
'CMakeFiles/installcheck.dir/rule' failed
make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2
Makefile:188: recipe for target 'installcheck' failed
make: *** [installcheck] Error 2
regards,
Abolfazl
24 Apr
24 Apr
7:42 p.m.
Hi,
with mpi option enable:
*cmake -Dwith-python=3 -Dwith-mpi=ON
-DCMAKE_INSTALL_PREFIX:PATH=/home/abolfazl/prog/nest-build
/home/abolfazl/prog/nest-source*
$ make installcheck
FAIL: testWithMPI (nest.tests.test_sp.test_mpitests.
TestStructuralPlasticityMPI)
'[script]": {}'.format(failing_tests))
AssertionError: False is not true : The following tests failed when
executing with "mpirun -np 2 nosetests [script]":
['/home/abolfazl/prog/nest-build/lib/python3.6/site-
packages/nest/tests/test_sp/mpitest_issue_578_sp.py']
FAIL: test_nn_pre_centered_synapse (nest.tests.test_stdp_nn_
synapses.STDPNNSynapsesTest)
AssertionError: 0.32057074514327416 != 0.8197400647350731 within 7
places : stdp_nn_pre-centered_synapse test: Resulting synaptic weight
8.197401e-01 differs from expected 3.205707e-01
FAILED (SKIP=8, failures=2)
PyNEST tests: 569
Passed: 559
Skipped: 8
Failed: 2
Phase 8: Running C++ tests (experimental)
-----------------------------------------
Not running C++ tests because NEST was compiled without Boost.
NEST Testsuite Summary
----------------------
NEST Executable: /home/abolfazl/prog/nest-build/bin/nest
SLI Executable : /home/abolfazl/prog/nest-build/bin/sli
Total number of tests: 940
Passed: 919
Skipped: 19 (8 PyNEST)
Failed: 2 (2 PyNEST)
***
*** There were errors detected during the run of the NEST test suite!
***
*** Please report the problem at
*** https://github.com/nest/nest-simulator/issues
***
*** To help us diagnose the problem, please attach the archived content
*** of these directories to the issue:
*** - '/home/abolfazl/prog/nest-build/reports'
*** - '/home/abolfazl/prog/nest-build/reports/nest.eYBJZ'
***
CMakeFiles/installcheck.dir/build.make:57: recipe for target
'CMakeFiles/installcheck' failed
make[3]: *** [CMakeFiles/installcheck] Error 1
CMakeFiles/Makefile2:99: recipe for target 'CMakeFiles/installcheck.dir/all'
failed
make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2
CMakeFiles/Makefile2:106: recipe for target 'CMakeFiles/installcheck.dir/rule'
failed
make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2
Makefile:188: recipe for target 'installcheck' failed
make: *** [installcheck] Error 2
regards,
Abolfazl
--
Abolfazl Ziaeemehr
Department of Physics,
PhD student in Computational Physics
Institute for Advanced Studies in Basic Sciences (IASBS)
Tel: 0919 607 4296
Page: iasbs.ac.ir/~a.ziaeemehr
27 Apr
27 Apr
12:12 p.m.
Hi,
One thing I didn't notice initially is the CMake version. For the next release after
NEST 2.20 we will recommend to use CMake version 3.12 or higher (and preferably 3.16+).
Could you perhaps try if this might solve your problem?
Thanks!
Charl
On Fri, Apr 24, 2020, at 19:42, Abolfazl Ziaeemehr wrote:
Department of Physics,
PhD student in Computational Physics
Institute for Advanced Studies in Basic Sciences (IASBS)
Hi,
with mpi option enable:
*cmake -Dwith-python=3 -Dwith-mpi=ON
-DCMAKE_INSTALL_PREFIX:PATH=/home/abolfazl/prog/nest-build
/home/abolfazl/prog/nest-source*
$ make installcheck
FAIL: testWithMPI (nest.tests.test_sp.test_mpitests.TestStructuralPlasticityMPI)
'[script]": {}'.format(failing_tests))
AssertionError: False is not true : The following tests failed when executing with
"mpirun -np 2 nosetests [script]":
['/home/abolfazl/prog/nest-build/lib/python3.6/site-packages/nest/tests/test_sp/mpitest_issue_578_sp.py']
FAIL: test_nn_pre_centered_synapse
(nest.tests.test_stdp_nn_synapses.STDPNNSynapsesTest)
AssertionError: 0.32057074514327416 != 0.8197400647350731 within 7 places :
stdp_nn_pre-centered_synapse test: Resulting synaptic weight 8.197401e-01 differs from
expected 3.205707e-01
FAILED (SKIP=8, failures=2)
PyNEST tests: 569
Passed: 559
Skipped: 8
Failed: 2
Phase 8: Running C++ tests (experimental)
-----------------------------------------
Not running C++ tests because NEST was compiled without Boost.
NEST Testsuite Summary
----------------------
NEST Executable: /home/abolfazl/prog/nest-build/bin/nest
SLI Executable : /home/abolfazl/prog/nest-build/bin/sli
Total number of tests: 940
Passed: 919
Skipped: 19 (8 PyNEST)
Failed: 2 (2 PyNEST)
***
*** There were errors detected during the run of the NEST test suite!
***
*** Please report the problem at
*** https://github.com/nest/nest-simulator/issues
***
*** To help us diagnose the problem, please attach the archived content
*** of these directories to the issue:
*** - '/home/abolfazl/prog/nest-build/reports'
*** - '/home/abolfazl/prog/nest-build/reports/nest.eYBJZ'
***
CMakeFiles/installcheck.dir/build.make:57: recipe for target
'CMakeFiles/installcheck' failed
make[3]: *** [CMakeFiles/installcheck] Error 1
CMakeFiles/Makefile2:99: recipe for target 'CMakeFiles/installcheck.dir/all'
failed
make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2
CMakeFiles/Makefile2:106: recipe for target 'CMakeFiles/installcheck.dir/rule'
failed
make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2
Makefile:188: recipe for target 'installcheck' failed
make: *** [installcheck] Error 2
regards,
Abolfazl
--
Abolfazl Ziaeemehr Tel: 0919 607 4296
Page: iasbs.ac.ir/~a.ziaeemehr
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
28 Apr
28 Apr
10:26 a.m.
Hi again,
I installed cmake version 3.17.1.
nest-simulator can be imported properly. However I got the following error
from make installcheck.
===========================================================================
FAIL: test_nn_pre_centered_synapse
(nest.tests.test_stdp_nn_synapses.STDPNNSynapsesTest)
AssertionError: 0.32057074514327416 != 0.8197400647350731 within 7 places
: stdp_nn_pre-centered_synapse test: Resulting synaptic weight 8.197401e-01
differs from expected 3.205707e-01
FAILED (SKIP=9, failures=1)
PyNEST tests: 569
Passed: 559
Skipped: 9
Failed: 1
Phase 8: Running C++ tests (experimental)
-----------------------------------------
Not running C++ tests because NEST was compiled without Boost.
NEST Testsuite Summary
----------------------
NEST Executable: /home/abolfazl/prog/nest-build/bin/nest
SLI Executable : /home/abolfazl/prog/nest-build/bin/sli
Total number of tests: 870
Passed: 859
Skipped: 10 (9 PyNEST)
Failed: 1 (1 PyNEST)
***
*** There were errors detected during the run of the NEST test suite!
***
*** Please report the problem at
*** https://github.com/nest/nest-simulator/issues
***
*** To help us diagnose the problem, please attach the archived content
*** of these directories to the issue:
*** - '/home/abolfazl/prog/nest-build/reports'
*** - '/home/abolfazl/prog/nest-build/reports/nest.CN7PI'
***
CMakeFiles/installcheck.dir/build.make:77: recipe for target
'CMakeFiles/installcheck' failed
make[3]: *** [CMakeFiles/installcheck] Error 1
CMakeFiles/Makefile2:607: recipe for target
'CMakeFiles/installcheck.dir/all' failed
make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2
CMakeFiles/Makefile2:614: recipe for target
'CMakeFiles/installcheck.dir/rule' failed
make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2
Makefile:208: recipe for target 'installcheck' failed
make: *** [installcheck] Error 2
===========================================================================
Thanks,
regards
Abolfazl
29 Apr
29 Apr
12:16 p.m.
Dear Abolfazl,
Thank you for the report. We have been able to reproduce the issue on a particular machine
(the Norwegian Saga supercomputer). A GitHub issue already exists for this; see
https://github.com/nest/nest-simulator/issues/1435.
Now that we have reproduced the issue, debugging should be a lot easier. Please give us
some time to hone in on the source of the problem. We will get back to you as soon as we
know more.
Regards,
Charl
On Tue, Apr 28, 2020, at 10:26, Abolfazl Ziaeemehr wrote:
Hi again,
I installed cmake version 3.17.1.
nest-simulator can be imported properly. However I got the following error from make
installcheck.
===========================================================================
FAIL: test_nn_pre_centered_synapse (nest.tests.test_stdp_nn_synapses.STDPNNSynapsesTest)
AssertionError: 0.32057074514327416 != 0.8197400647350731 within 7 places :
stdp_nn_pre-centered_synapse test: Resulting synaptic weight 8.197401e-01 differs from
expected 3.205707e-01
FAILED (SKIP=9, failures=1)
PyNEST tests: 569
Passed: 559
Skipped: 9
Failed: 1
Phase 8: Running C++ tests (experimental)
-----------------------------------------
Not running C++ tests because NEST was compiled without Boost.
NEST Testsuite Summary
----------------------
NEST Executable: /home/abolfazl/prog/nest-build/bin/nest
SLI Executable : /home/abolfazl/prog/nest-build/bin/sli
Total number of tests: 870
Passed: 859
Skipped: 10 (9 PyNEST)
Failed: 1 (1 PyNEST)
***
*** There were errors detected during the run of the NEST test suite!
***
*** Please report the problem at
*** https://github.com/nest/nest-simulator/issues
***
*** To help us diagnose the problem, please attach the archived content
*** of these directories to the issue:
*** - '/home/abolfazl/prog/nest-build/reports'
*** - '/home/abolfazl/prog/nest-build/reports/nest.CN7PI'
***
CMakeFiles/installcheck.dir/build.make:77: recipe for target
'CMakeFiles/installcheck' failed
make[3]: *** [CMakeFiles/installcheck] Error 1
CMakeFiles/Makefile2:607: recipe for target 'CMakeFiles/installcheck.dir/all'
failed
make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2
CMakeFiles/Makefile2:614: recipe for target 'CMakeFiles/installcheck.dir/rule'
failed
make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2
Makefile:208: recipe for target 'installcheck' failed
make: *** [installcheck] Error 2
===========================================================================
Thanks,
regards
Abolfazl
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21 Apr
21 Apr
5:38 p.m.
Dear Abolfazl,
Could you please post the output of:
nest-config --prefix
nest-config --datadir
Could it be that there is an issue due to using a space in a filename?
Kind regards,
Charl
On Tue, Apr 21, 2020, at 17:27, Abolfazl Ziaeemehr wrote:
Hello everyone,
I used the source code to install nest simulator 2.20 from here
<https://nest-simulator.readthedocs.io/en/stable/installation/linux_install.html>
and did the following steps
(I used to do the same steps for version 2.18 without error.)
`cmake -Dwith-python=3 -DCMAKE_INSTALL_PREFIX:PATH=</install/path>
</path/to/NEST/src>`
`make `
`make install`
`make installcheck`
I got this error from "make installcheck":
Phase 1: Testing if SLI can execute scripts and report errors
-------------------------------------------------------------
Running test 'selftests/test_pass.sli'... Running Apr 21 19:46:31 SLIStartup
[Error]: NEST_DATA_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]: Directory
'/usr/share/nest' does not exist. Apr 21 19:46:31 SLIStartup [Error]: I'm
using the default: /home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/nest
Apr 21 19:46:31 SLIStartup [Error]: NEST_DOC_DIR is not usable: Apr 21 19:46:31 SLIStartup
[Error]: Directory '/usr/share/doc/nest' does not exist. Apr 21 19:46:31
SLIStartup [Error]: I'm using the default:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/doc/nest
/usr/bin//bin/nest /usr/share/doc/nest/selftests/test_pass.sli
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: 20:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: Apr: not
found
Failed: unexpected exit code 127
Running Apr 21 19:46:31 SLIStartup [Error]: NEST_DATA_DIR is not usable: Apr 21 19:46:31
SLIStartup [Error]: Directory '/usr/share/nest' does not exist. Apr 21 19:46:31
SLIStartup [Error]: I'm using the default:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/nest Apr 21 19:46:31
SLIStartup [Error]: NEST_DOC_DIR is not usable: Apr 21 19:46:31 SLIStartup [Error]:
Directory '/usr/share/doc/nest' does not exist. Apr 21 19:46:31 SLIStartup
[Error]: I'm using the default:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/share/doc/nest
/usr/bin//bin/nest /usr/share/doc/nest/selftests/test_pass.sli
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: 20:
/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/bin/nest_serial: Apr: not
found
***
*** An unexpected exit code usually hints at a bug in the test suite!
***
*** Please report the problem at
*** https://github.com/nest/nest-simulator/issues
***
*** To help us diagnose the problem, please attach the archived content
*** of these directories to the issue:
*** - '/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/reports'
*** -
'/home/abolfazl/prog/install-dir/nest-simulator-2.20.0_build/reports/nest.CgbAi'
***
CMakeFiles/installcheck.dir/build.make:57: recipe for target
'CMakeFiles/installcheck' failed
make[3]: *** [CMakeFiles/installcheck] Error 2
CMakeFiles/Makefile2:99: recipe for target 'CMakeFiles/installcheck.dir/all'
failed
make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2
CMakeFiles/Makefile2:106: recipe for target 'CMakeFiles/installcheck.dir/rule'
failed
make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2
Makefile:188: recipe for target 'installcheck' failed
make: *** [installcheck] Error 2
--
regards,
Abolfazl Ziaeemehr
Department of Physics,
PhD student in Computational Physics
Institute for Advanced Studies in Basic Sciences (IASBS)
Tel: 0919 607 4296
Page: iasbs.ac.ir/~a.ziaeemehr
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*Attachments:*
* reports.zip
1550
days inactive
1558
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11 comments
3 participants
participants (3)
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Abolfazl Ziaeemehr -
Charl Linssen -
Charl Linssen