Sorry for the late reply. I just learned that amber 14 and 16 that they
have has been broken on there end for months! So I am trying to fix it to
get it to work I'll post the results if I get any. I was trying to run
entropy, decomp,
mmpb gb sa, all the CPU heavy and ram heavy calculations.
On Mon, Mar 20, 2017 at 6:30 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 07 2017 - 12:30:02 PDT
