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

From: Derek M Shore <des2037.med.cornell.edu>
Date: Tue, 23 Nov 2021 00:53:53 +0000

Thanks very much for your suggestions, Prof. Case!

I think your suggestions that there is a problem with DetectBinaryFile() makes a lot of sense; the reason is because the majority of my errors are related to mdgx, and most have the same initial error:
>ReadRst >> Attempted to read inpcrd as a NetCDF
>ReadRst >> restart file, but failed.

Here is a list of all the test that fail with this error:
cd mdgx/1p7e && ./Test.1p7e
cd mdgx/MLE && ./Test.mle
cd mdgx/Settle && ./Test.settle
cd mdgx/CMAP && ./Test.cmap
cd mdgx/MCBarostat && ./Test.mcb
cd mdgx/TIP4P && ./Test.tip4p
cd mdgx/ForceCalc && ./Test.frcc
cd mdgx/AddEP && ./Test.addep
cd mdgx/Triclinic && ./Test.triclinic
cd mdgx/Peptides && ./Test.peptides
cd mdgx/Topology && ./Test.prmtop_vs
cd mdgx/Topology && ./Test.tip4p
cd mdgx/Topology && ./Test.tip5p
cd mdgx/Topology && ./Test.methanol

(many of the above test scripts have multiple parts/failures)

I am attaching the first inpcrd (for Test.1p7e); it's not a binary file, and it looks normal to me. Just for fun, I tried loading a inpcrd & prmtop created by CHARMM-GUI for a completely different system (changing mdgx.in as needed), and I got the same error. (the point was to see if mdgx could handle an arbitrary inpcrd/prmtop, and it could not.

Any advice or suggestions on how to resolve is most appreciated. Please let me know if I can provide any additional info that could be helpful.

Best,
Derek

Derek M. Shore, Ph.D.
Scientific Computing Technology Engineer
Institute for Computational Biomedicine
Department of Physiology and Biophysics

Weill Cornell Medicine
Department of Physiology and Biophysics
1300 York Avenue, Room LC501A
New York, NY 10065
T: 212-746-6386
des2037.med.cornell.edu
 
 

´╗┐On 11/20/21, 9:03 AM, "David A Case" <david.case.rutgers.edu> wrote:

    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
    AMBER.ambermd.org
    https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=X5Sc7H5NSWV3agvbxBXvARVirdVlt5y-nKiETDcG3R8&m=falYyFfqOlpxG-cP5tpVOJ7PZYcZ5dOFs05fU6fr2QePx8L5-Y5BZPaTT2I7V9aD&s=K4IXuCOT6BVfLkDTOj0iL-jNKt-mNfqCyb5pwrrnI_8&e=


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Nov 22 2021 - 17:00:02 PST
Custom Search