[AMBER] Compilation with MVAPICH2-GDR

From: Yasser Almeida via AMBER <amber.ambermd.org>
Date: Mon, 4 Aug 2025 11:05:49 +0200

Hello,

I am compiling AMBER24 (pmemd24) in a HPC cluster with GPU nodes. I have
nodes with 2xA30 and 8xH100 GPUs. I compiled AMBER with MPI and works
fine. In the manual, section 2.2.8 says:

As of Amber 24, significantly improved performance of pmemd.cuda.MPI is
available through the MVAPICH MPI library’s MVAPICH2-GDR GPU to GPU
direct communication facility[20]. The improvement is 84% for the
explicit solvent subset of the Amber benchmark suite. Users must
manually activate this feature: Edit run cmake and add -DMVAPICH2GDR GPU
DIRECT COMM=TRUE to the Linux section. And you must use MVAPICH2-GDR
version 2.3.7 or later as your MPI. If you employ this feature then, in
addition to citing Amber, please also cite reference [20] and note
whether this capability enabled larger simulations.

Where it says "GPU to GPU direct communication", does this refers to GPU
to GPU direct communication between GPUs of different nodes and/or
within a single node?

Thanks in advance and best regards,

Yasser

--
Yasser Almeida-Hernández, PhD
Computational Bioengineering
Fakultät Bio- und Chemieingenieurwesen
Technische Universität Dortmund
Otto-Hahn-Str. 6. Raum C1-02-R408
44227 Dortmund
Phone: +49 0231 7556856
Email: yasser.almeida.tu-dortmund.de
Wichtiger Hinweis: Die Information in dieser E-Mail ist vertraulich. Sie ist ausschließlich für den Adressaten bestimmt. Sollten Sie nicht der für diese E-Mail bestimmte Adressat sein, unterrichten Sie bitte den Absender und vernichten Sie diese Mail. Vielen Dank.
Unbeschadet der Korrespondenz per E-Mail, sind unsere Erklärungen ausschließlich final rechtsverbindlich, wenn sie in herkömmlicher Schriftform (mit eigenhändiger Unterschrift) oder durch Übermittlung eines solchen Schriftstücks per Telefax erfolgen.
Important note: The information included in this e-mail is confidential. It is solely intended for the recipient. If you are not the intended recipient of this e-mail please contact the sender and delete this message. Thank you. Without prejudice of e-mail correspondence, our statements are only legally binding when they are made in the conventional written form (with personal signature) or when such documents are sent by fax.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Aug 04 2025 - 02:30:02 PDT