Re: [AMBER] REMD error

From: Marcela Madrid <>
Date: Tue, 2 Jul 2019 09:57:43 -0400

hi Dave,

thanks for your answer. It is not just a problem with the test examples.
It is a problem whenever we try to run REMD on the GPUs on Bridges at the PSC.
The reason why I am looking at it is a user wants to run it. REMD on the CPUs works fine (with the corresponding executable of course),
it is just a problem with the GPUs. So it occurred to me to see if it passes the tests and we have the same error
messages. The user has her input files in the directory where she runs.

I think it is either a problem with the configuration of the GPU nodes on Bridges or a bug.
Each Bridges node has 24 cores and 2 P100 GPUs. I have asked for 1 node, ntasks-per-node=2 and the 2 GPUs
but I get the error message about not finding the input files.
Amber on GPUs was compiled with
./configure -cuda -mpi gnu
Attempting to compile with intel compilers instead of gnu gave error messages.

O3 -ccbin icpc -o cuda_mg_wrapper.o -c
In file included from /opt/packages/cuda/9.2/bin/../targets/x86_64-linux/include/host_config.h(50),
                 from /opt/packages/cuda/9.2/bin/../targets/x86_64-linux/include/cuda_runtime.h(78),
/opt/packages/cuda/9.2/bin/../targets/x86_64-linux/include/crt/host_config.h(79): error: #error directive: -- unsupported ICC configuration! Only
ICC 15.0, ICC 16.0, and ICC 17.0 on Linux x86_64 are supported!
  #error -- unsupported ICC configuration! Only ICC 15.0, ICC 16.0, and ICC 17.0 on Linux x86_64 are supported!

We do not have such old versions of the compilers. Any hints will be appreciated
as to how to run REMD on the GPUS. Thanks so much,


> On Jul 2, 2019, at 9:01 AM, David A Case <> wrote:
> On Mon, Jul 01, 2019, Marcela Madrid wrote:
>>> Two replica GB REMD test.
>>> Unit 5 Error on OPEN:
> OK: query for the REMD experts: in AMBERHOME/test/cuda/remd there are
> two directories: rem_2rep_gb and rem_gb_2rep. The files are
> in the former, but the tests actually get run in the latter directory.
> Same general problem for rem_2rep_pme: the needed files are
> in rem_wat_2 (or maybe in rem_wat).
> I'm probably missing something here, but cleaning up (or at least
> commenting) the cuda/remd test folder seems worthwhile: there are
> folders that seem never to be used, and input files that seem to be in
> the wrong place.
> Marcela: I'd ignore these failures for now; something should get posted
> here that either fixes the problem, or figures out a problem with your
> inputs. (My money is on the former.)
> ...dac
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Received on Tue Jul 02 2019 - 07:00:03 PDT
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