[CP2K:1608] Re: output problems
Jun Cheng
chen... at googlemail.com
Fri Dec 5 10:58:14 UTC 2008
Thanks for rapid reply.
If decreasing the size of IO buffer, will it affect the speed?
With respect to the second way, jobs normally don't stop automatically
because I am doing MD except the walltime is reached. So, cp2k may not have
time to release the buffer.
Jun
On Fri, Dec 5, 2008 at 10:44 AM, Teodoro Laino <teodor... at gmail.com>wrote:
>
> Yes, I can give at least two possibilities:
> 1) change the default of the machine on which you are running (you can
> increase/decrease the size of the IO buffer, on almost
> all machine starting from commodore64. I would suggest to get in touch
> with your system administrator for that.)
> 2) wait that the job is finished. At that point the buffer is released
> and you will have your file with all the bytes at the proper place.
>
> Teo
>
> Jun Cheng wrote:
> > Hi Teo,
> >
> > Thanks a lot for the help. It works well except the third individual
> > output file is still empty even with applying FLUSH_SHOULD_FLUSH TRUE.
> > It is probably because the third force_eva section is just a classic
> > restraint to a bond to prevent it from breaking during MD runs. So its
> > output may be too small to reach the size of the IO buffer in a
> > noticeable time. In fact, I did similar runs before and never got this
> > output in 12 hours (the walltime limit). Is there a way to overcome
> > this problem?
> >
> > Cheers,
> > Jun
> >
> >
> > On Thu, Dec 4, 2008 at 8:51 PM, Laino Teodoro <teodor... at gmail.com
> > <mailto:teodor... at gmail.com>> wrote:
> >
> > Dear Jun,
> >
> > 1) you don't see nothing in the individual .out files because the
> > IO is buffered.
> > Depending on the size of the IO buffer on the machine that you are
> > using it may take a WHILE
> > to see something in the output file.
> > If you want to flush you can play with this keyword:
> >
> http://cp2k.berlios.de/manual/CP2K_INPUT/GLOBAL.html#desc_FLUSH_SHOULD_FLUSH
> >
> > 2) Switching to medium you are activating some print_key, in this
> > case DIPOLE, which for the
> > specific force_eval you are using (MIXED) requires that DIPOLE has
> > to be defined in all
> > force_eval underneath. To skip this problem you can disable by
> > hand the print_key DIPOLE:
> >
> http://cp2k.berlios.de/manual/CP2K_INPUT/FORCE_EVAL/MIXED/PRINT/DIPOLE.html
> >
> > .....
> > &DIPOLE OFF
> > &END
> > .....
> >
> > This will solve your issue.
> > Teo
> >
> > On 4 Dec 2008, at 19:15, Jun Cheng wrote:
> >
> >> Hi Teo,
> >>
> >> I am very sorry about this.
> >> The file (test.tgz) is uploaded in group files.
> >> Thanks.
> >>
> >> Jun
> >>
> >> On Thu, Dec 4, 2008 at 6:00 PM, Teodoro Laino
> >> <teodor... at gmail.com <mailto:teodor... at gmail.com>> wrote:
> >>
> >>
> >> and where is your input file?
> >> What you describe has not too much sense..anyway..
> >> Provide your input file and all files necessary to
> >> investigate the
> >> problem (i.e. run it).
> >> This is a general rule when asking for help, and I'm
> >> surprised to see
> >> that one has always to remind that.
> >> Teo
> >>
> >> Jun wrote:
> >> > Hi all,
> >> >
> >> > I updated my cp2k yesterday, and did some tests on mixed multi
> >> > force_eva calcuations. I've got some problems on the outputs:
> >> > (i) When I used print_level low, the job got running.
> >> Everything
> >> > looked fine except for the empty output files corresponding
> >> to the
> >> > individual force_eva.(the overall output file, *ener file
> >> and *xyz
> >> > were fine).
> >> > (ii) Then, I tried print_low medium. I got the individual
> >> output
> >> > files, but the job stopped after initialization. The error
> >> message
> >> > is:
> >> > =============================================================
> >> > THERMOSTAT| Thermostat Info for PARTICLES
> >> > THERMOSTAT| Type of thermostat
> >> Nose-
> >> > Hoover-Chains
> >> > THERMOSTAT| Nose-Hoover-Chain
> >> > length 3
> >> > THERMOSTAT| Nose-Hoover-Chain time constant
> >> > [ fs] 1000.00
> >> > THERMOSTAT| Order of Yoshida
> >> > integrator 3
> >> > THERMOSTAT| Number of multiple time
> >> > steps 2
> >> > THERMOSTAT| Initial Potential
> >> > Energy 0.000000
> >> > THERMOSTAT| Initial Kinetic
> >> > Energy 0.000523
> >> > THERMOSTAT| End of Thermostat Info for PARTICLES
> >> >
> >> > ********************** begin of velocity initialization
> >> > ***********************
> >> > Initial
> >> > Temperature
> >> 330.00
> >> > K
> >> > COM velocity: 0.000000000000 0.000000000000
> >> > 0.000000000000
> >> > *********************** end of velocity initialization
> >> > ************************
> >> >
> >> >
> >> > *** 17:07:15 WARNING in force_env_methods:mixed_energy_forces
> >> > err=-300 ***
> >> > *** ASSERTION (cond) failed at line 1203 Error
> >> (0.259964E-11)
> >> > in ***
> >> > *** computing numerical derivatives larger then
> >> > (0.100000E-11) . ***
> >> > *
> >> > *** 17:07:15 ERRORL2 in cp_result_methods:get_result_r1
> >> > processor 0 ***
> >> > *** err=-300 Trying to access result ([DIPOLE]) which
> >> was never
> >> > stored! ***
> >> > *** /home/e89/e89/jc590/work/cp2k/makefiles/../src/
> >> > cp_result_methods.F ***
> >> > *** line
> >> > 164
> >> ***
> >> > *
> >> >
> >> > ===== Routine Calling Stack =====
> >> >
> >> > 2 qs_mol_dyn_low
> >> > 1 CP2K
> >> > CP2K| Trying to access result ([DIPOLE]) which was never
> >> stored! /
> >> >
> >>
> home/e89/e89/jc590/work/cp2k/makefiles/../src/cp_result_methods.F
> >> > line 164
> >> > CP2K| Abnormal program termination, stopped by process
> >> number 0
> >> > CP2K| Trying to access result ([DIPOLE]) which was never
> >> stored! /
> >> >
> >>
> home/e89/e89/jc590/work/cp2k/makefiles/../src/cp_result_methods.F
> >> > line 164
> >> > CP2K| Trying to access result ([DIPOLE]) which was never
> >> stored! /
> >> >
> >>
> home/e89/e89/jc590/work/cp2k/makefiles/../src/cp_result_methods.F
> >> > line 164
> >> > CP2K| Abnormal program termination, stopped by process
> >> number 65
> >> > CP2K| Abnormal program termination, stopped by process
> >> number 64
> >> > CP2K| Trying to access result ([DIPOLE]) which was never
> >> stored! /
> >> >
> >>
> home/e89/e89/jc590/work/cp2k/makefiles/../src/cp_result_methods.F
> >> > line 164
> >> > CP2K| Abnormal program termination, stopped by process
> >> number 14
> >> >
> >>
> ===================================================================
> >> >
> >> > Does anyone know what is the problem? Any reply will be
> >> appreciated.
> >> >
> >> > Cheers,
> >> > Jun
> >> >
> >> > P.S. I will upload my inputs if necessary.
> >> >
> >> > >
> >> >
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >
> >
> >
> >
> >
> > >
>
>
> >
>
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