[phenixbb] Re: AQuaRef - error - Number of bonds with excessive lengths: 1

Martin This appears to be a bug. We will investigate more. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : [email protected] Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Wed, Oct 16, 2024 at 9:38 AM Martin Malý wrote:

Dear Nigel,

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 : [email protected] Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

On Wed, Oct 16, 2024 at 7:51 AM Martin Malý wrote:

...

Dear colleagues,

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 | ^~~~~~~~~~ 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?

Thank you. Martin_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

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