[phenixbb] Re: AQuaRef - issues with torch-cluster installation

16 Oct 2024


      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 http://CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464 
https://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_______________________________________________
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