Hi Priti,
Can you also supply a prmtop file? If you are not using water, you should also provide the XVV.
Tyler
> On Jul 25, 2018, at 10:13 PM, PRITI ROY <priitii.roy.gmail.com> wrote:
>
> 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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Received on Wed Aug 01 2018 - 16:00:02 PDT
