What kind of simulation were you trying to perform, what was your
command line input, and what does your MD input file look like?
Honestly, if this is not an ensemble run (e.g. REMD etc) I can pretty
much guarantee that pmemd will not scale to 171 nodes. Also, I've
personally only seen fair to poor performance from OpenMPI + Amber. In
my opinion you are better off with mvapich or Intel MPI if those are
available.
-Dan
On Sun, Mar 19, 2017 at 6:48 PM, Miguel Rivera
<miguelrivera1855.gmail.com> wrote:
> Hello fellow AMBER users
>
> Quick question. I am trying to run pmemd.MPI on lonestar5 by TACC and I am
> recieving this message. Just an FYI it is running amber14
>
> [Sun Mar 19 05:02:37 2017] [c0-0c1s0n1] Fatal error in MPI_Init: Other MPI
> error, error stack:
> MPIR_Init_thread(525):
> MPID_Init(225).......: channel initialization failed
> MPID_Init(598).......: PMI2 init failed: 1
> aborting job:
> Fatal error in MPI_Init: Other MPI error, error stack:
> MPIR_Init_thread(525):
> MPID_Init(225).......: channel initialization failed
> MPID_Init(598).......: PMI2 init failed: 1
>
> I am running on 171 nodes. Is this a flag fix or a bigger issue.
>
> Thanks!
>
> Miguel R.
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Mar 20 2017 - 06:00:04 PDT
