Re: [AMBER] Summit compile and "Attempted to read inpcrd as a NetCDF restart file, but failed"

From: David A Case <>
Date: Sat, 20 Nov 2021 09:03:06 -0500

On Fri, Nov 19, 2021, Derek M Shore wrote:
>I am trying to compile/test Amber20 (tools + GPU-accelerated MD), on Summit
>at ORNL (IBM POWER9, NVIDIA V100s). The compile seems to run without a
>problem. When I `make test.serial`, most of the tests pass, but I see
>several errors similar to this one:
>*/amber20/AmberTools/test/mdgx/1p7e$ ./Test.1p7e
>ReadRst >> Attempted to read inpcrd as a NetCDF
>ReadRst >> restart file, but failed.

Do the errors all happen with mdgx? If so, you may be able to ignore
them for the time being, if you are not planning to use mdgx.

The inpcrd file in the test you cite is indeed a formatted restart file, and
not a NetCDF file. So the problem may be with mdgx, and not with NetCDF.
(This is just speculation: it depends on whether you see the same error with
pememd.) Maybe Dave Cerutti has some insight into how mdgx decides how to
try to open a restart file, but it's odd that this fails only on Summit.

My WAG is that the DetectBinaryFile() may not be working on the Summit file
system. To help, you could (a) comment out the final line of the
/amber20/AmberTools/test/mdgx/1p7e/Test.1p7e script, and (b) post (as an
attachment!) the inpcrd file that the test creates.

Thanks for the report....dac

AMBER mailing list
Received on Sat Nov 20 2021 - 06:30:02 PST
Custom Search