Using a CUDA archive helped. qr.refine is now running.
qr.refine model.pdb data.mtz engine=aimnet2
I can see that a new file supersphere.pdb was created. But then I
got this error:
Setting aimnet2 specific defaults:
Default Aimnet2 model: aimnet2-qr
/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/aimnet2calc/__init__.py:17:
UserWarning: PySisiphus is not installed. AIMNet2Pysis will not be
available.
warnings.warn('PySisiphus is not installed. AIMNet2Pysis will not
be available.')
Found model file:
/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/aimnet2calc/assets/aimnet2-qr/aimnet2-qr_b97md4_qzvp_2.jpt
Sorry: Number of bonds with excessive lengths: 1
Cheers,
Martin
On 16/10/2024 16:27, Martin Malý wrote:
Dear Nigel,
Sorry, I downloaded something different: Linux [ download
command-line installer for development builds and modifications
(contains "modules" directory) ]
I will try to use that archive(s) that you suggested to me.
Thank you!
Martin
On 16/10/2024 15:59, Nigel Moriarty
wrote:
Martin
The best person to help is traveling today but I can get
started. Did you download the correct installer from the
link shown below?
Cheers
Nigel
---
Nigel W.
Moriarty
Building 33R0349, Molecular Biophysics and
Integrated Bioimaging
Lawrence
Berkeley National Laboratory
Berkeley, CA
94720-8235
Email : NWMoriarty@LBL.gov
I'm trying to install AQuaRef. However, I'm struggling with
running
`bash config/update_phenix.sh aimnet2` which is part of
`bash
build_into_phenix.sh aimnet2`. This script wants to install
the python
package torch-cluster. However, I'm getting the error:
/opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/python_headers.h:12:10:
fatal error: Python.h: No such file or directory
12 | #include <Python.h>
| ^~~~~~~~~~
compilation terminated.
error: command '/usr/bin/gcc' failed with exit code 1
[end of output]
I'm getting the same error when I tried to install only this
package
using the command `qrefine.python -m pip install
torch-cluster`.
I have a laptop with Ubuntu 22.04. I have all the usual
development
packages installed (build-essential, linux-headers, gcc,
g++, ...).
According Python, I have libpython3-dev, libpython3.10-dev,
python3-dev,
python3.10-dev. I can see that qrefine.python has a version
of 3.9, so I
also installed libpython3.9-dev, python3.9-dev and
python3.9-distutils
from ppa:deadsnakes/ppa but it did not help. I am also
attaching a full
log from the torch-cluster installation. It seems that the
package torch
has been installed successfully in prior.
Do you have please an idea what is wrong and how to fix it?