[CP2K:1610] Re: output problems

Jun Cheng chen... at googlemail.com
Fri Dec 5 12:22:26 CET 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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> >
>
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