[CP2K:1610] Re: output problems
Jun Cheng
chen... at googlemail.com
Fri Dec 5 11:22:26 UTC 2008
Got it. Thanks.
Jun
On Fri, Dec 5, 2008 at 11:01 AM, Teodoro Laino <teodor... at gmail.com>wrote:
>
> Regarding the first question, depends a lot on the machine on which you
> are running. Check with your system administrator!
>
> About the second question: you can tell CP2K after a certain amount of
> execution time:
> http://cp2k.berlios.de/manual/CP2K_INPUT/GLOBAL.html#desc_WALLTIME
>
> so.. don't see neither the importance of your second problem, since it
> is not a problem!
> Teo
>
> Jun Cheng wrote:
> > 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 <mailto: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>
> > > <mailto: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>
> > <mailto: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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