[gmx-users] Long trajectory split

Sun Feb 23 18:48:11 CET 2014

Justin, the other runs with the very same binary do not produce the same
problem.

Mark, I just omitted the _mpi of the line here, but is was compiled as _mpi.

My log file top:

*Gromacs version:    VERSION 4.6.1Precision:          singleMemory
model:       64 bitMPI library:        MPIOpenMP support:     disabledGPU
support:        disabledinvsqrt routine:    gmx_software_invsqrt(x)CPU
acceleration:   SSE4.1FFT library:        fftw-3.3.2-sse2Large file
support: enabledRDTSCP usage:       enabledBuilt on:           Sex Nov 29
16:08:45 BRST 2013Built by:           root at jupiter [CMAKE]Build
OS/arch:      Linux 2.6.32.13-0.4-default x86_64Build CPU vendor:
GenuineIntelBuild CPU brand:    Intel(R) Xeon(R) CPU           X5650  @
2.67GHzBuild CPU family:   6   Model: 44   Stepping: 2Build CPU features:
apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pdcm pdpe1gb
popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3(...)*

*Initializing Domain Decomposition on 24 nodesDynamic load balancing:
autoWill sort the charge groups at every domain (re)decompositionInitial
maximum inter charge-group distances:    two-body bonded interactions:
0.621 nm, LJ-14, atoms 3801 3812  multi-body bonded interactions: 0.621 nm,
G96Angle, atoms 3802 3812Minimum cell size due to bonded interactions:
0.683 nmMaximum distance for 5 constraints, at 120 deg. angles, all-trans:
0.820 nmEstimated maximum distance required for P-LINCS: 0.820 nmThis
distance will limit the DD cell size, you can override this with -rconGuess
for relative PME load: 0.26Will use 18 particle-particle and 6 PME only
nodesThis is a guess, check the performance at the end of the log fileUsing
6 separate PME nodesScaling the initial minimum size with 1/0.8 (option
-dds) = 1.25Optimizing the DD grid for 18 cells with a minimum initial size
of 1.025 nmThe maximum allowed number of cells is: X 8 Y 8 Z 8Domain
decomposition grid 3 x 2 x 3, separate PME nodes 6PME domain decomposition:
3 x 2 x 1Interleaving PP and PME nodesThis is a particle-particle only
nodeDomain decomposition nodeid 0, coordinates 0 0 0"*

2014-02-23 18:08 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 2/23/14, 11:32 AM, Marcelo Depólo wrote:
>
>> Maybe I should explain it better.
>>
>> I am using "*mpirun -np 24 mdrun -s prt.tpr -e prt.edr -o prt.trr*",
>> pretty
>>
>> much a standard line. This job in a batch creates the outputs and, after
>> some (random) time, a back up is done and new files are written, but the
>> job itself do not finish.
>>
>>
> It would help if you can post the .log file from one of the runs to see
> the information regarding mdrun's parallel capabilities.  This still sounds
> like a case of an incorrectly compiled binary.  Do other runs with the same
> binary produce the same problem?
>
> -Justin
>
>
>
>> 2014-02-23 17:12 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>>>
>>> On 2/23/14, 11:00 AM, Marcelo Depólo wrote:
>>>
>>>  But it is not quite happening simultaneously, Justin.
>>>>
>>>> It is producing one after another and, consequently, backing up the
>>>> files.
>>>>
>>>>
>>>>  You'll have to provide the exact commands you're issuing.  Likely
>>> you're
>>> leaving the output names to the default, which causes them to be backed
>>> up
>>> rather than overwritten.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
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>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
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-- 
Marcelo Depólo Polêto
Uppsala Universitet - Sweden
Science without Borders - CAPES
Phone: +46 76 581 67 49