9 May
2024
9 May
'24
9:10 p.m.
Hello,
I have been trying NEST under the WSL in Windows and I am glad to say that it works! I
think that getting NEST working correctly under the WSL may attract more users, to both
NEST and the WSL. BTW (this is a side note), I have noticed that some Python codes
(unrelated to NEST) run a little faster (15-20%) under the WSL than in Windows itself.
Anyway, nest works perfectly on the WSL using either Spyder as IDE or JupyterLab. However,
after a while the installation breaks.
After doing any upgrade via "conda upgrade --all" (once it was NEST itself
updated), when I try to import NEST I get the error transcribed below, which ends in
"ImportError: libgsl.so.25: cannot open shared object file: No such file or
directory".
I have narrowed down the problem to this: when installing NEST, the package
"conda-forge::gsl-2.7-he838d99_0" is installed along. Then, if I do any
"conda update --all" (or I guess that if I install any other package that uses
gsl), the package gets updated "conda-forge::gsl-2.7-he838d99_0 -->
pkgs/main::gsl-2.7.1-h6e86dc7_1".
Then here:
https://nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simulator…
I found out that "If you upgrade your environment, you might have to cmake and
compile NEST anew in order for it to pick up the new version.". So I thought that a
force-reinstall of nest might do the trick, but it didn't.
Moreover, I did the following:
- start a new, clean environment
- install gsl before nest (I got main::gsl-2.7.1-h6e86dc7_1)
- then install nest-simulator.
But the error appears again.
FINALLY, I did "conda install conda-forge::gsl", it picked gsl-2.7-he838d99_0
and now NEST works again!! So it seems that the problem is specific with gsl-2.7.1
(and/or whatever version is in main?).
I don't want to end up using NEST in a frozen environment where nothing can be added
or changed, neither before nor after installing NEST. Although I found the workaround, I
guess you may find a way of this not happening at all.
Thank you and best regards
Patricio.
In [1]: import nest
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
Cell In[1], line 1
----> 1 import nest
File ~/miniconda3/lib/python3.12/site-packages/nest/__init__.py:64
61 import sys # noqa
62 import types # noqa
---> 64 from .ll_api_kernel_attributes import KernelAttribute # noqa
66 try:
67 import versionchecker # noqa: F401
File ~/miniconda3/lib/python3.12/site-packages/nest/ll_api_kernel_attributes.py:22
1 # -*- coding: utf-8 -*-
2 #
3 # ll_api_kernel_attributes.py
(...)
19 # You should have received a copy of the GNU General Public License
20 # along with NEST. If not, see <http://www.gnu.org/licenses/>.
---> 22 from .ll_api import spp, sps, sr, stack_checker
25 class KernelAttribute:
26 """
27 Descriptor that dispatches attribute access to the nest kernel.
28 """
File ~/miniconda3/lib/python3.12/site-packages/nest/ll_api.py:53
48 # Make MPI-enabled NEST import properly. The underlying problem is that the
49 # shared object pynestkernel dynamically opens other libraries that open
50 # yet other libraries.
51 sys.setdlopenflags(os.RTLD_NOW | os.RTLD_GLOBAL)
---> 53 from . import pynestkernel as kernel # noqa pylint: disable=no-name-in-module
55 __all__ = [
56 "check_stack",
57 "connect_arrays",
(...)
69 "take_array_index",
70 ]
73 engine = kernel.NESTEngine()
ImportError: libgsl.so.25: cannot open shared object file: No such file or directory