error at the convergence step about seekr2 HOT 7 CLOSED

Are you sure that the correct conda environment and python version are being used to run converge.py? Try:

$ python3.8
>>> import openmm

from seekr2.

Hi,
Strangely I get an import error trying this.
Nonetheless, openmm is installed in miniconda3 directory as seen below and seekr2 commands did infact ran the GPU MD and CPU BD simulations since all anchor_0 ... folders have dcd and other files

Please do suggest what is wrong with my seerk2 installation on this workstation.
thank you for your continued suggestions and support. Best regards.
Vaibhav

(base) [niperg@kaberi ~]$ python3.8
Python 3.8.13 (default, Mar 28 2022, 11:38:47)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.

import openmm
Traceback (most recent call last):
File "", line 1, in
ModuleNotFoundError: No module named 'openmm'
quit()

(base) [niperg@kaberi ~]$ find . -name openmm
find: ‘./.cache/gnome-control-center’: Permission denied
find: ‘./.config/gnome-control-center’: Permission denied
./.local/share/Trash/files/openmm-master/olla/include/openmm
./.local/share/Trash/files/openmm-master/openmmapi/include/openmm
./.local/share/Trash/files/openmm-master/platforms/common/include/openmm
./.local/share/Trash/files/openmm-master/plugins/amoeba/openmmapi/include/openmm
./.local/share/Trash/files/openmm-master/plugins/amoeba/serialization/include/openmm
./.local/share/Trash/files/openmm-master/plugins/drude/openmmapi/include/openmm
./.local/share/Trash/files/openmm-master/plugins/drude/serialization/include/openmm
./.local/share/Trash/files/openmm-master/plugins/rpmd/openmmapi/include/openmm
./.local/share/Trash/files/openmm-master/serialization/include/openmm
./.local/share/Trash/files/openmm-master/wrappers/python/openmm
./.local/share/Trash/files/openmm-master/wrappers/python/simtk/openmm
./Downloads/seekr2/seekr_tut/openmm
./Downloads/seekr2/seekr_tut/openmm/olla/include/openmm
./Downloads/seekr2/seekr_tut/openmm/openmmapi/include/openmm
./Downloads/seekr2/seekr_tut/openmm/platforms/common/include/openmm
./Downloads/seekr2/seekr_tut/openmm/plugins/amoeba/openmmapi/include/openmm
./Downloads/seekr2/seekr_tut/openmm/plugins/amoeba/serialization/include/openmm
./Downloads/seekr2/seekr_tut/openmm/plugins/drude/openmmapi/include/openmm
./Downloads/seekr2/seekr_tut/openmm/plugins/drude/serialization/include/openmm
./Downloads/seekr2/seekr_tut/openmm/plugins/rpmd/openmmapi/include/openmm
./Downloads/seekr2/seekr_tut/openmm/serialization/include/openmm
./Downloads/seekr2/seekr_tut/openmm/wrappers/python/openmm
./Downloads/seekr2/seekr_tut/openmm/wrappers/python/simtk/openmm
./Downloads/seekr2/seekr_tut/openmm/build/python/openmm
./Downloads/seekr2/seekr_tut/openmm/build/python/simtk/openmm
./miniconda3/pkgs/openmm-7.7.0-py38hb15d7a2_1/share/openmm
./miniconda3/pkgs/openmm-7.7.0-py38hb15d7a2_1/lib/python3.8/site-packages/simtk/openmm
./miniconda3/pkgs/openmm-7.7.0-py38hb15d7a2_1/lib/python3.8/site-packages/openmm
./miniconda3/pkgs/openmm-7.7.0-py38hb15d7a2_1/include/openmm
./miniconda3/pkgs/parmed-3.4.3-py310hd8f1fbe_2/lib/python3.10/site-packages/parmed/openmm
./miniconda3/lib/python3.8/site-packages/ParmEd-3.4.3-py3.8-linux-x86_64.egg/parmed/openmm
./miniconda3/lib/python3.8/site-packages/parmed/openmm
./miniconda3/share/openmm
./miniconda3/include/openmm
./miniconda3/envs/myambertools/lib/python3.10/site-packages/parmed/openmm

(base) [niperg@kaberi ~]$ pwd
/home/niperg
(base) [niperg@kaberi ~]$

from seekr2.

I'm currently on vacation, but the most likely possible reason for this problem is because a different conda environment, machine, or user is running converge.py than ran run.py.

from seekr2.

Hi @vaibhavadixit, did this error get resolved?

from seekr2.

Unfortunately, no.
I tried to install everything from scratch in a new environment but each time I'm getting a new error during the seekr2 test step.
Often it complains about seekrtools_plugin missing even after the seekr2_openmm_plugin is already installed and I can find a seekrtools_plugin inside the seekr2_openmm_plugin directory.
I did even try using the full procdure given here, but in vain.
In short, I'm finding installation very confusing.

I'm thinking of moving to Ubuntu on the workstation which you mentioned last time has fewer issues with seekr2.
Please suggest.
Thank you.

from seekr2.

There is no plugin for seekrtools, so are you sure that it complains that "seekrtools_plugin" is missing? Did you try installing both seekr2 and seekrtools using "python setup.py install"?

Try skipping past the test step, and see what specific errors you encounter.

from seekr2.

Closing this issue for now...

from seekr2.