[gmx-developers] EM with gmx4.0.2

[andrea spitaleri]

Hi there,
i tried both options and I got:

> mpirun -np 16 mdrun -s box -npme 0 -dd 4 4 1

Program mdrun, VERSION 4.0.2
Source code file: domdec.c, line: 5824

Fatal error:
The initial cell size (3.250000) is smaller than the cell size limit (6.483255), change options -dd,
-rdd or -rcon, see the log file for details

> 
> mpirun -np 16 mdrun -s box -npme 8 -dd 4 2 1

Program mdrun, VERSION 4.0.2
Source code file: domdec.c, line: 5824

Fatal error:
The initial cell size (3.250000) is smaller than the cell size limit (6.483255), change options -dd,
-rdd or -rcon, see the log file for details


still failing.

thanks for your help

andrea

> 
> 
> Carsten
> 
> 
> On Nov 19, 2008, at 1:52 PM, andrea spitaleri wrote:
> 
>> Hi there,
>> we having trouble in EM using gmx-4.0.2. Basically the problem is  
>> that the run crash immediately
>> complaining about the number of separate PME:
>>
>>> mdrun -s box -v -deffnm boxem
>> Program mdrun, VERSION 4.0.2
>> Source code file: domdec_setup.c, line: 132
>>
>> Fatal error:
>> Could not find an appropriate number of separate PME nodes. i.e. >=  
>> 0.727885*#nodes (11) and <=
>> #nodes/2 (8) and reasonable performance wis
>> e (grid_x=88, grid_y=88).
>> Use the -npme option of mdrun or change the number of processors or  
>> the PME grid dimensions, see the
>> manual for details.
>>
>> while:
>>
>>> mdrun -s box -npme 8 -v -deffnm boxem
>> gives:
>> Program mdrun, VERSION 4.0.2
>> Source code file: domdec.c, line: 5860
>>
>> Fatal error:
>> The size of the domain decomposition grid (0) does not match the  
>> number of nodes (8). The total
>> number of nodes is 16
>>
>> We are able to minimize the system using gmx-3.3.3 and then run the  
>> MD with gmx-4.0.2 without troubles.
>> our em.mdp is:
>>
>> define              =  -DFLEXIBLE
>> integrator          =  steep
>> dt                  =  0.002    ; ps
>> nsteps              =  2000
>> nstlist             =  5
>> ns_type             =  grid
>> pbc                 =  xyz
>> rlist               =  0.9
>> table-extension     =  2
>> coulombtype         =  PME
>> rcoulomb            =  0.9
>> rvdw                =  0.9
>> fourierspacing      =  0.15
>> fourier_nx          =  0
>> fourier_ny          =  0
>> fourier_nz          =  0
>> pme_order           =  4
>> ewald_rtol          =  1e-5
>> optimize_fft              =  yes
>> ;
>> ;       Energy minimizing stuff
>> ;
>> emtol               =  1000
>> emstep              =  0.01
>> lincs_iter          = 4
>>
>>
>> any help is well accepted.
>>
>> thanks in advance
>>
>> andrea
>>
>> -- 
>> -------------------------------
>> Andrea Spitaleri PhD
>> Dulbecco Telethon Institute
>> c/o DIBIT Scientific Institute
>> Biomolecular NMR, 1B4
>> Via Olgettina 58
>> 20132 Milano (Italy)
>> http://biomolecularnmr.ihsr.dom/
>> Tel: 0039-0226434348/5622/3497/4922
>> Fax: 0039-0226434153
>> -------------------------------
>> _______________________________________________
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-developers-request at gromacs.org.
> 
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11
> 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
> 
> 
> 
> 
> 
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-developers-request at gromacs.org.
> 

-- 
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
-------------------------------