Dear David,
I tried with --progress but untill 48 cores it was showing the error
"FATAL: allocation failure in ivector()" .
The memory information is as follows:
1. Master Node: 94 GB
2. CPU Node: 94 GB (X6)
3. GPU Node: 64 GB (X3)
As per your suggestion I have attached my PDB file with this mail.
Thanks,
Priti
On Mon, Jul 23, 2018 at 9:20 PM David A Case <david.case.rutgers.edu> wrote:
> On Mon, Jul 23, 2018, PRITI ROY wrote:
> >
> > I tried my system( 5550 atoms and TIP3P) with 48 to 144 cores with many
> > type of combinations and ended up with no output for long run time
> > (~3days). I think this problem is not due to memory problem or this
> > calculation may stuck in infinite loop (might be I am wrong).
>
> Try *much* smaller numbers of MPI threads. Use the --progress flag to
> follow what is happening. The key point of your hardware is the amount
> of memory, which you don't list.
>
> If you are able to share your PDB file, you might post it, and we can
> see if we see problems in running this through rism3d.snglpnt. 5000
> atoms should not require extraordinary amounts of time, such as days.
>
> ....hope this helps...dac
>
>
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- application/x-aportisdoc attachment: A.pdb
Received on Wed Jul 25 2018 - 22:30:02 PDT
