Re: [AMBER-Developers] [ FW: Building AMBER 20 on POWER systems]

From: Ruzhu Chen <>
Date: Wed, 15 Jul 2020 13:42:57 -0400

I created an Amber20 branch for supporting Power9 with IBM XL compiler on
gitlab. The branch includes a compile script "" for simply
configure and compile for Power system.

To clone: git clone -b amber20power9

Please try to compile it on Power9 if you have access and let me know if
there is any issue.

Ruzhu Chen, PhD (845) 433-8426(T/L 293-8426)
Email:, Mobile: (845) 337-7238
Sr. Technical Solution Architect, HPC / Genomics & Life Sciences
IBM Systems, 2455 South Road, Poughkeepsie, NY 12601

From: "Neale, Christopher Andrew" <>
To: "" <>
Date: 07/14/2020 03:44 PM
Subject: Re: [AMBER-Developers] [EXTERNAL] [ FW:
            Building AMBER 20 on POWER systems]

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,


From: David A Case <>
Sent: Tuesday, July 14, 2020 1:25:49 PM
Subject: [EXTERNAL] [AMBER-Developers] [ 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.


----- Forwarded message from Jonathan Lefman <> -----

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?
>From: Filippo Spiga <<>>
>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?
>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, 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.


----- End forwarded message -----
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Received on Wed Jul 15 2020 - 11:00:03 PDT
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