Hi Mark and Alexey,
Thank you for taking the time to write the responses. Following is the info
about the cluster
[chou...@hpc-login2 ~]$ uname -a
Linux hpc-login2 2.6.18-164.el5 #1 SMP Thu Sep 3 03:28:30 EDT 2009 x86_64
x86_64 x86_64 GNU/Linux
[chou...@hpc2000 ~]$ mpiexec --version
Version 0.82
Hi
Looks like your system simply runs out of memory. So power cycling nodes isnt
needed. If your cluster runs linux then it already has OOM Killer that will
kill processes that runs out of memory. Also having swap on nodes is a good
idea even with huge amount of memory.
Memory usage for mpi pr
<mailto:mark.abra...@anu.edu.au>>> wrote:
>>>
>>>- Original Message -----
>>>From: Amit Choubey
mailto:kgp.a...@gmail.com>
;>>>>>> i could
>>>>>>>> > get a rough estimation.
>>>>>>>> >
>>>>>>>> > Thank you.
>>>>>>>> >
>>>>>>>> > amit
>>>>>>>>
>
>>>>>>> > On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham <
>>>>>>> mark.abra...@anu.edu.au>
>>>>>>> > wrote:
>>>>>>> >>
>>>>>>> >> On 3/03/2010 12:53 PM, Amit Choubey wr
; On 3/03/2010 12:53 PM, Amit Choubey wrote:
>>>>>> >>>
>>>>>> >>> Hi Mark,
>>>>>> >>>
>>>>>> >>>I quoted the memory usage requirements from a presentation by
>>>>>> Berk
t;>>>> Berk
>>>>> >>>Hess, Following is the link to it
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>>>> http://www.csc.fi/english/research/sciences/chemis
t;>>Hess, Following is the link to it
>>>> >>>
>>>> >>>
>>>> >>>
>>>> >>>
>>>> http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf
>>>> >>>
;> >>> thing.
>>> >>>
>>> >>>My system only contains SPC water. I want Berendsen T coupling and
>>> >>>Coulomb interaction with Reaction Field.
>>> >>>
>>> >>>I just want a
;
>> >>> I just want a rough estimate of how big of a system of water can be
>> >>>simulated on our super computers.
>> >>
>> >> Try increasingly large systems until it runs out of memory. There's
>> your
>> >> answer.
>&g
big of a system of water can be
> >>>simulated on our super computers.
> >>
> >> Try increasingly large systems until it runs out of memory. There's your
> >> answer.
> >>
> >> Mark
> >>
> >>> On Fri, Feb 26, 2010 at 3:56
tems until it runs out of memory. There's your
>> answer.
>>
>> Mark
>>
>> On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham >> <mailto:mark.abra...@anu.edu.au>> wrote:
>>>
>>>- Original Message -
>>>From:
a rough estimate of how big of a system of water can be
>>> simulated on our super computers.
>>
>> Try increasingly large systems until it runs out of memory. There's your
>> answer.
>>
>> Mark
>>
>>> On Fri, Feb 26, 2010 at 3:56 PM, Ma
te:
>>
>> ----- Original Message -
>>From: Amit Choubey mailto:kgp.a...@gmail.com>>
>>Date: Saturday, February 27, 2010 10:17
>>Subject: Re: [gmx-users] gromacs memory usage
>>To: Discussion list for GROMACS users ><mailto:gmx
.@gmail.com>>
Date: Saturday, February 27, 2010 10:17
Subject: Re: [gmx-users] gromacs memory usage
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
> Hi Mark,
> We have few nodes with 64 GB memory and many other with 16 GB of
memory. I am atte
r super computers.
>
> Thank you,
>
> Amit
>
On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham wrote:
> - Original Message -
> From: Amit Choubey
> Date: Saturday, February 27, 2010 10:17
> Subject: Re: [gmx-users] gromacs memory usage
> To: Discussion list for G
- Original Message -
From: Amit Choubey
Date: Saturday, February 27, 2010 10:17
Subject: Re: [gmx-users] gromacs memory usage
To: Discussion list for GROMACS users
> Hi Mark,
> We have few nodes with 64 GB memory and many other with 16 GB of memory. I am
> attempting a simu
. Is this
true?
Thank you,
amit
On Fri, Feb 26, 2010 at 2:57 PM, Mark Abraham wrote:)
> - Original Message -
> From: Amit Choubey
> Date: Friday, February 26, 2010 20:05
> Subject: [gmx-users] gromacs memory usage
> To: Discussion list for GROMACS users
>
> > Hi,
- Original Message -
From: Amit Choubey
Date: Friday, February 26, 2010 20:05
Subject: [gmx-users] gromacs memory usage
To: Discussion list for GROMACS users
> Hi,
> I am having trouble with running gromacs with a large system. I am trying to
> use several processors for th
Hi,
I am having trouble with running gromacs with a large system. I am trying to
use several processors for the md. The error is a memory allocation error
and it might be due to low RAM or large no of particles. I want to know the
detailed memory usage of mdrun ie say for N atoms how much memory d
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