Here's what we know about Amber 18 on Summit. Sorry if this is all old news, but sending anyway in case it is useful for anyone.
### compilation:
Our straightforward attempt at Amber18 compilation on Summit ran into “configure: error: Fortran could not compile .f90 files”, which was solved for us by Graham Lopez at NCCS, who gave the following advice:
0) module load gcc python/3 netcdf netcdf-fortran bzip2
1) edit Ambertools/src/configure2 and change line 2729 to "./configure \"
2) ./configure --with-python /sw/summit/python/3.6/anaconda3/5.3.0/bin/python -nosse -nofftw3 gnu
3) make install
### runtime:
We also got some run-time help from Verónica Vergara at NCCS, who helped us understand the following:
amber18 with GPUs on Summit needs:
#BSUB -alloc_flags "gpudefault"
Also, if not using MPI version, then one jsrun option that works is this:
jsrun --smpiargs "none"
### performance:
performance with GPUs was surprisingly good. Fast GPUs didn't appear to suffer from the slow CPUs.
Thank you,
Chris.
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Tuesday, July 14, 2020 1:25:49 PM
To: amber-developers.ambermd.org
Subject: [EXTERNAL] [AMBER-Developers] [jlefman.nvidia.com: FW: Building AMBER 20 on POWER systems]
Hi everyone: see query below about people that know anything about
power9 and Amber. Apologies if you get this twice.
...thx...dac
----- Forwarded message from Jonathan Lefman <jlefman.nvidia.com> -----
On Tue, Jul 14, 2020, Jonathan Lefman wrote:
>
>I think the group in Italy wants to run Amber20 on a Power9 GPU
>system. Do you think we should introduce them to you so you can help them
>meet the person from IBM who made the patch for Amber20? I'm not sure if
>Ruzhu ever connected with you on maintaining their Power9 patch in the
>Amber repo. What do you recommend?
>
>Jon
>
>From: Filippo Spiga <fspiga.nvidia.com<mailto:fspiga.nvidia.com>>
>
>CINECA in Italy deployed a bit Marconi 100. They have users looking at
>building AMBER 20 with XLC and Spectrum MPI. I am aware of a patch that
>makes this possible, who is the best person within the AMBER development
>group to provide such patch to AMBER licensee?
>
>-
>FILIPPO SPIGA
>EMEA HPC Developer Relations
>
I'm cc-ing your message to the Amber developer's group. I think(?)
people have managed to get all of Amber working on a power9/GPU system
called "Summit" at Oak Ridge, but I don't know anything about the status
of that. I don't recall any patches being posted to our development
platform on this subject. Ruzhu Chen has an account at
gitlab.ambermd.org, but I don't think has made merge requests.
I could be mis-remembering here. Developers: anyone have info to share
about power9?
I'm just an intermediary here, and have no real answers to share.
...thx...dac
----- End forwarded message -----
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Received on Tue Jul 14 2020 - 13:00:03 PDT
