[CP2K:1609] Re: output problems

Teodoro Laino teodor... at gmail.com
Fri Dec 5 12:01:40 CET 2008


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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