Hi everybody
Another option is to install it in a container.
if you search the list for mails with the subject "running pmemd.cuda in
Almalinux10" you will find the dockerfile. It is working flawlessly for
us. We are in an x86_64 with a 5090, but I don't think it requires lots
of changes to make compile it in a Grace ARM CPU.
Regarding the cuda-toolkit-12.8 installation It's been some months and
perhaps I remember wrong, but I'm quite sure I tried to manually install
just the cuda-toolkit-12.8 in my Almalinux10 server and it fail to
compile at some point. So depending on which OS Pedro is running some
problems other than the driver could arise.
I hope this helps as well
OCS
Oscar Conchillo Solé
Computational Biology Group
Data Center Manager, Sysadmin and Bioinformatics
Institut de Biotecnologia i Biomedicina (UAB)
Department of Genetics and Microbiology (UAB)
mail:Oscar.Conchillo.uab.cat
telf: 0034 93581 4431
On 5/5/26 09:20, Stephan Schott via AMBER wrote:
> Hi again,
>
> One thing is the CUDA toolkit, and another the GPU driver. AFAIK, CUDA 12.8 should be compatible with all current driver versions. You can install that by yourself without admin privileges, as long as you place the files in your home dir, or e.g. somewhere you'd like to share with your colleagues.
>
> So, long story short, you can get a suitable toolkit "run" installer for 12.8 for your distro from the NVIDIA archive, and get the toolkit to a folder you want by changing the installer options (you can disable everything except for the CUDA toolkit, and change the corresponding path; you can skip all driver and /usr or whatever path installations, you just need nvcc and the libraries). Then export CUDA_HOME=YOUR_CUDA_ROOT and prepend ${CUDA_HOME}/bin to your PATH and ${CUDA_HOME}/lib64 to your LD_LIBRARY_PATH.
>
> Hope that helps,
>
> Stephan Schott Verdugo
> Biochemist
>
>
> Computational Biophysical Chemistry
> Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
> Forschungszentrum Jülich GmbH
> Wilhelm-Johnen-Straße, 52425 Jülich
> Germany
>
> ---------------------------------------------------------------------------------------------
> ---------------------------------------------------------------------------------------------
> Forschungszentrum Jülich GmbH
> 52425 Jülich
> Sitz der Gesellschaft: Jülich
> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
> Dr. Stephanie Bauer (stellvertretende Vorsitzende),
> Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
> ---------------------------------------------------------------------------------------------
> ---------------------------------------------------------------------------------------------
>
>
> El mar, 5 may 2026 a la(s) 8:30 a.m., Pedro Ojeda May (pedro.ojeda-may.umu.se<mailto:pedro.ojeda-may.umu.se>) escribió:
> Hi,
>
> Thank you for the prompt response. I think the CUDA drivers would need to be <=12.8 to work with GH GPUs, not the CUDA modules, right?
> CUDA drivers are installed by the administrators, and they try to have the latest version only. Several CUDA modules with different versions
> are in general available on our clusters.
>
> /Pedro
>
>
> From: Stephan Schott <s.schott-verdugo.fz-juelich.de<mailto:s.schott-verdugo.fz-juelich.de>>
> Date: Tuesday, 5 May 2026 at 07:59
> To: Pedro Ojeda May <pedro.ojeda-may.umu.se<mailto:pedro.ojeda-may.umu.se>>; AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
> Subject: Re: [AMBER] Installing Amber on Grace Hopper GPUs with CUDA 13
>
> Hi,
>
> Not for the moment. Amber 26 just got released and we still don't have cuda 13 support. But Grace Hoppers work with cuda 12.8 as well. Any reason not to try that?
>
> Best regards,
>
> Stephan Schott Verdugo
> Biochemist
>
>
> Computational Biophysical Chemistry
> Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
> Forschungszentrum Jülich GmbH
> Wilhelm-Johnen-Straße, 52425 Jülich
> Germany
>
> ---------------------------------------------------------------------------------------------
> ---------------------------------------------------------------------------------------------
> Forschungszentrum Jülich GmbH
> 52425 Jülich
> Sitz der Gesellschaft: Jülich
> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
> Dr. Stephanie Bauer (stellvertretende Vorsitzende),
> Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
> ---------------------------------------------------------------------------------------------
> ---------------------------------------------------------------------------------------------
>
> Pedro Ojeda May via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>> schrieb am Di., 5. Mai 2026, 07:22:
> Hi,
>
> I have downloaded the following codes for Ambertools and Pmemd (for my private use):
>
> ambertools25.tar
> pmemd24.tar.bz2
>
> I tried to install them on a Cray cluster that supports CUDA 13 for Grace Hopper GPUs. I could fix some lines related to using versions
> of CUDA < 12.9. But then other errors appeared related to sm_70, sm_… and “thrust” and “cub” dependencies. Is there any code version
> (or patch) that supports this type of GPU and CUDA 13 and greater?
>
> /Pedro
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> ------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------
> Forschungszentrum Jülich GmbH
> 52425 Jülich
> Sitz der Gesellschaft: Jülich
> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
> Dr. Stephanie Bauer (stellv. Vorsitzende),
> Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
> ------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------
> Forschungszentrum Jülich GmbH
> 52425 Jülich
> Sitz der Gesellschaft: Jülich
> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
> Dr. Stephanie Bauer (stellv. Vorsitzende),
> Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
> ------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------
> Forschungszentrum Jülich GmbH
> 52425 Jülich
> Sitz der Gesellschaft: Jülich
> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
> Dr. Stephanie Bauer (stellv. Vorsitzende),
> Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
> ------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------
> Forschungszentrum Jülich GmbH
> 52425 Jülich
> Sitz der Gesellschaft: Jülich
> Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
> Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
> Dr. Stephanie Bauer (stellv. Vorsitzende),
> Prof. Dr. Ir. Pieter Jansens, Prof. Dr. Laurens Kuipers
> ------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 05 2026 - 02:00:02 PDT
