Hi Fabian,
That error is from inside the code that reads the inpcrd file and is independent of the GPU code. I'd try running with just serial cpu (swap pmemd.cuda.MPI for pmemd and drop the mpirun) and see if you get the same error.
Then check your input options - make sure you are giving the right files for each command line switch and also make sure that the prmtop matches the inpcrd file etc.
All the best
Ross
> On Nov 12, 2015, at 08:47, Fabian gmail <fabian.glaser.gmail.com> wrote:
>
> Hi,
>
> I got a weird error when running GPU jobs:
>
> 1) From the output
>
>
> |---------------- GPU PEER TO PEER INFO -----------------
> |
> | Peer to Peer support: ENABLED
> |
> |--------------------------------------------------------
>
> | ERROR: I could not understand line 49846
> 199.3676234-169.4028942 339.9971292
>
>
>> From the qsub output
>
> [fabian.amber long_100ns_r0]$ more wt0.o277
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
>
> any idea what is happennig?
>
> Thanks!!
>
> Fabian
>
>
>
> Dr. Fabian Glaser
> Head of the Structural Bioinformatics section
>
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
>
> fglaser at technion dot ac dot il
> Tel: +972 4 8293701
> http://bku.technion.ac.il
>
>
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Received on Thu Nov 12 2015 - 09:30:04 PST
