[CP2K:4711] Problem on FERMI (BlueGeneQ)

Teodoro Laino teodor... at gmail.com
Wed Oct 23 11:42:54 CEST 2013


In this case, I would try restarting a simple job.. 
can you restart just a water QM run?

On Oct 23, 2013, at 10:09 AM, Jacopo Sgrignani <sgr... at gmail.com> wrote:

> Hi
> the out and error files are attached. However the error file only
> concerns the wall clock limit of the machine.
> 
> Also the submission script is attached.
> 
> Thanks
> 
> Jacopo
> 
> 2013/10/22, Teodoro Laino <teodor... at gmail.com>:
>> no log files? no error files?
>> it's difficult to provide any help..
>> 
>> On Oct 22, 2013, at 4:37 PM, jacopos <sgr... at gmail.com> wrote:
>> 
>>> Dear All
>>> I'm trying to run QM/MM calculation on FERMI the BlueGeneQ at CINECA
>>> (Italy),
>>> after several tests I'm not able to restart my calculation (they regularly
>>> start).
>>> In particular if I add these lines
>>> 
>>> 
>>> &EXT_RESTART
>>> EXTERNAL_FILE md2.restart
>>> &END EXT_RESTART
>>> 
>>> in my input file, the calculation usually ands  at the beginning  of the
>>> FIST calculation without errors.
>>> 
>>> 
>>> CELL_TOP| Volume [angstrom^3]:
>>> 669564.040
>>> CELL_TOP| Vector a [angstrom    87.140     0.000     0.000    |a| =
>>> 87.140
>>> CELL_TOP| Vector b [angstrom     0.000    97.870     0.000    |b| =
>>> 97.870
>>> CELL_TOP| Vector c [angstrom     0.000    -0.000    78.510    |c| =
>>> 78.510
>>> CELL_TOP| Angle (b,c), alpha [degree]:
>>> 90.000
>>> CELL_TOP| Angle (a,c), beta  [degree]:
>>> 90.000
>>> CELL_TOP| Angle (a,b), gamma [degree]:
>>> 90.000
>>> CELL_TOP| Orthorhombic:
>>>  YES
>>> 
>>> *** 16:17:35 WARNING in atoms_input:read_atoms_input :: Overwriting  ***
>>> *** coordinates. Active coordinates read from &COORD section. Active ***
>>> *** coordinates READ from &COORD section atoms_input.F line 129      ***
>>> 
>>> 
>>> AMBER_INFO| Reading Amber Topology File: cp2k.prmtop
>>> AMBER_INFO| Amber PrmTop V.8 or greater.
>>> AMBER_INFO| %VERSION  VERSION_STAMP = V0001.000  DATE = 02/22/11
>>> 10:48:46
>>> AMBER_INFO| Information from AMBER topology file:
>>> 
>>> 
>>> NATOM  =   64055 NTYPES =      19 NBONH =   60298 MBONA  =    3846
>>> NTHETH =    8585 MTHETA =    5232 NPHIH =   16075 MPHIA  =   10244
>>> NHPARM =       0 NPARM  =       0 NNB   =  117079 NRES   =   19302
>>> NBONA  =    3846 NTHETA =    5232 NPHIA =   10244 NUMBND =      71
>>> NUMANG =     149 NPTRA  =      53 NATYP =      48 NPHB   =       1
>>> 
>>> Do you have advices to overcome this problem?
>>> 
>>> Thanks
>>> 
>>> Jacopo
>>> 
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