[gmx-users] X particles communicated to PME node Y are more ...

[Justin Lemkul]

On 3/7/13 1:17 PM, Miguel Ángel Mompeán García wrote:
> 2013/3/4 Justin Lemkul <jalemkul at vt.edu>
>
>> Dear Justin,
>>
>
> With 4.5.5 the jobs have completed. I am going to repeat them with 4.6.1
> If you find something weird in the mdp file or require further explanations
> on the points do mention I will do my best to provide the necessary info.
> Right below are the comments:
>
>
>
>> In that case, it's probably something worth pursuing.  Having the new
>> version fail when an older version works is curious.  Can you please
>> provide all of the following details:
>>
>> 1. Compilers used to build Gromacs
>>
>      2. Hardware description
>
> These lines are from the CMakeOutput.log file:
>
> The system is: Linux - 2.6.32-5-amd64 - x86_64            (*****)
> Compiling the C compiler identification source file "CMakeCCompilerId.c"
> succeeded.
> Compiler: /usr/bin/gcc
>
> cc -v:      gcc version 4.4.5
>
> 3. mdrun command
>> 4. Complete .mdp file
>
>
> grompp -f minimize.mdp -c Mut3.gro -o em.tpr -p topol.top
> mdrun -v -deffnm em
>
>
> The minimize.mdp file:
>
> integrator      = steep
> emtol           = 1000.0
> emstep          = 0.01
> nsteps          = 50000
> nstlist         = 1
> ns_type         = grid
> rlist           = 1.0
> coulombtype     = PME
> rcoulomb        = 1.0
> rvdw            = 1.0
> pbc             = xyz
>
>

Does the .tpr file run on a machine with different hardware or compilers?  The 
GCC version is outdated, though in principle should work fine.  If the failure 
consistently happens on your machine (and especially if it happens on other 
machines), please file a bug report on redmine.gromacs.org and include a .tpr 
file and all of the information posted above.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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