[gmx-users] About getting running time from a Gromacs Run

[jesmin jahan]

Hi Mark,

Thanks for your reply. I will try to follow your instructions.

Thanks,
Jesmin

On Thu, Aug 9, 2012 at 9:06 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 10/08/2012 3:06 AM, jesmin jahan wrote:
>>
>> Dear Gromacs Users,
>>
>> I am a new user of Gromacs  and I am using gromacs to calculate
>> GB-polarization energy .
>>
>> I have a couple of questions about it. It would be great if someone
>> can answer them. Thanks in advance.
>>
>> Questions:
>>
>> 1: I got an output like this in log file from a protein simulation:
>>
>>   R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>>
>>   Computing:         Nodes     Number     G-Cycles    Seconds     %
>> -----------------------------------------------------------------------
>>   Comm. coord.          24          1        0.235        0.1     1.0
>>   Force                 24          1       17.369        5.2    71.9
>>   Wait + Comm. F        24          1        0.258        0.1     1.1
>>   Write traj.           24          1        0.296        0.1     1.2
>>   Update                24          1        0.005        0.0     0.0
>>   Comm. energies        24          2        7.252        2.2    30.0
>> -----------------------------------------------------------------------
>>   Total                 24                  24.157        7.3   100.0
>> -----------------------------------------------------------------------
>>
>> NOTE: 30 % of the run time was spent communicating energies,
>>        you might want to use the -gcom option of mdrun
>>
>>
>> Parallel run - timing based on wallclock.
>>
>>                 NODE (s)   Real (s)      (%)
>>         Time:      0.303      0.303 100.0
>>                 (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
>> Performance:      0.000     54.029      0.285     84.257
>>
>> Now my question is: What is the time to calculate the GB-polarization
>> Energy that is shown in log? Or How to get the time?
>
>
> It's a side-effect of the "Force" component of the timing breakdown.
>
>
>> 2. I have a protein with 1.5 million atoms. I tried to run it with
>> gromacs on 16 machines each with 12 cores. It generated a segmentation
>> fault. Is there any size limit to run in gromacs?
>
>
> No, but if you run yourself out of memory results are unpredictable. Consult
> your .log and stdout files for clues what is going on.
>
>
>> 3. Can I only calculate the GB-polarization energy without calculating
>> any Forces? How?
>
>
> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
>
>
>> 4. What are the good tools to get the GB- energy values along with the
>> time to calculate the GB-energy?
>
>
> As above.
>
> Mark
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-- 
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.