17 Nov
2021
17 Nov
'21
12:24 p.m.
Here, something goes wrong with library paths, so that NEST apparently looks for the wrong
versions of GSL and readline. I won't have time to attend more to this today. The only
remaining suggestion is to try the "other" way, i.e., explicitly specifying a
installation directory. Also, it looks like you might be building and running from your
home directory. I'd suggest to build in a separate directory. Delete everything in
that build directory before making new attempts to be sure no old information is left in
CMake caches.
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Head, Department of Data Science
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>
Home http://arken.nmbu.no/~plesser
On 17/11/2021, 12:12, "Julien Ballbé"
<julien.ballbe@gmail.com<mailto:julien.ballbe@gmail.com>> wrote:
Hi,
I did as you suggested and ran
cmake /Users/julienballbe/Downloads/nest-simulator-master
It went well for the cmake, make and make install commands but when I ran the make
installcheck I got the following message (I attach the full log output):
(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien ~ % make installcheck
Executing NEST's testsuite...
dyld[12978]: Library not loaded: @rpath/libgsl.25.dylib
Referenced from: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/sli
Reason: tried:
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libgsl.25.dylib'
(no such file), '/usr/local/lib/libgsl.25.dylib' (no such file),
'/usr/lib/libgsl.25.dylib' (no such file)
2021-11-17 11:34:30.712 defaults[12980:953560]
The domain/default pair of (com.apple.CrashReporter, DialogType) does not exist
================================================================================
NEST testsuite
Date: Mer 17 nov 2021 10:34:30 UTC
Sysinfo: Darwin 21.0.1 arm64
dyld[12984]: Library not loaded: @rpath/libgsl.25.dylib
Referenced from: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/sli
Reason: tried:
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libgsl.25.dylib'
(no such file), '/usr/local/lib/libgsl.25.dylib' (no such file),
'/usr/lib/libgsl.25.dylib' (no such file)
NEST executable .... nest_serial (version )
PREFIX ............. /Users/julienballbe/miniforge3/envs/nest-simulator-dev
Python executable ..
/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/python3.9 (version 3.9.7)
PYTHONPATH .........
/Users/julienballbe/miniforge3/envs/nest-simulator-dev/lib/python3.9/site-packages
Pytest version ..... 6.2.5
timeout ..... 120 s
Running MPI tests .. no (compiled without MPI support)
TEST_BASEDIR .......
/Users/julienballbe/miniforge3/envs/nest-simulator-dev/share/nest/testsuite
REPORTDIR .......... /Users/julienballbe/reports
PATH ............... /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin
/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin
/Users/julienballbe/miniforge3/condabin
/usr/local/bin
/usr/bin
/bin
/usr/sbin
/sbin
================================================================================
dyld[12998]: Library not loaded: @rpath/libreadline.8.dylib
Referenced from: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/nest
Reason: tried:
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libreadline.8.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libreadline.8.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libreadline.8.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libreadline.8.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libreadline.8.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libreadline.8.dylib'
(no such file), '/usr/local/lib/libreadline.8.dylib' (no such file),
'/usr/lib/libreadline.8.dylib' (no such file)
Phase 1: Testing if SLI can execute scripts and report errors
-------------------------------------------------------------
Running test 'selftests/test_pass.sli'... Failed: unexpected exit code 134
==================================================
Following is the full output of the test:
==================================================
dyld[13021]: Library not loaded: @rpath/libgsl.25.dylib
Referenced from: /Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/sli
Reason: tried:
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../lib/nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../lib/nest/libgsl.25.dylib'
(no such file),
'/Users/julienballbe/miniforge3/envs/nest-simulator-dev/bin/../../../nest/libgsl.25.dylib'
(no such file), '/usr/local/lib/libgsl.25.dylib' (no such file),
'/usr/lib/libgsl.25.dylib' (no such file)
==================================================
***
*** An unexpected exit code usually hints at a bug in the test suite!
/Users/julienballbe/miniforge3/envs/nest-simulator-dev/share/nest/testsuite/run_test.sh:
line 169: ask_results: command not found
make[3]: *** [CMakeFiles/installcheck] Error 2
make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2
make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2
Is that normal?
Thank you for your help,
Best,
Julien
Le mer. 17 nov. 2021 à 11:16, Hans Ekkehard Plesser
<hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> a écrit
:
Hi,
It depends on where you want NEST installed. Personally, I prefer to place NEST in a
directory of its own, but that is mainly because as a developer I usually have a number of
NEST builds around. Thus, I would use something like
cmake -DCMAKE_INSTALL_PREFIX:PATH=/Users/julienballbe/NEST
/Users/julienballbe/Downloads/nest-simulator-master
On the other hand, you can also choose to install NEST right with your other Python
packages using just
cmake /Users/julienballbe/Downloads/nest-simulator-master
Then, NEST will be installed in the site-packages part of your nest-simulator-dev conda
environment. This makes it even easier for Python to find the nest Python module.
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Head, Department of Data Science
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>
Home http://arken.nmbu.no/~plesser
On 17/11/2021, 11:09, "Julien Ballbé"
<julien.ballbe@gmail.com<mailto:julien.ballbe@gmail.com>> wrote:
Hi,
Thank you for all your responses. I attached the full log file.
I found the CMAKE_INSTALL_PREFIX instruction on the nest installation guidelines
(https://nest-simulator.readthedocs.io/en/v3.1/installation/mac_install.html) in the
building NEST section.
Indeed, I did not see the space in the command line. That should fix it, but before I do
anything, would you recommend that :
1) I create a build directory NEST and run
(nest-simulator-dev) julienballbe@MacBook-Pro-de-Julien ~ % cmake
-DCMAKE_INSTALL_PREFIX:PATH=/Users/julienballbe/NEST
/Users/julienballbe/Downloads/nest-simulator-master
or
2) use as Robin suggested 'cmake path/to/src', in which case the command line will
be, I supposed,
cmake path/to/src /Users/julienballbe/Downloads/nest-simulator-master ?
Thank you for your help!
Best,
Julien
Le mer. 17 nov. 2021 à 10:04, Robin Gilbert De Schepper
<robingilbert.deschepper@unipv.it<mailto:robingilbert.deschepper@unipv.it>> a
écrit :
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