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 <div class="gmail_quote">On Fri, Dec 5, 2008 at 10:44 AM, Teodoro Laino <<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>> wrote: <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> 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 <div class="Ih2E3d"> Jun Cheng wrote: > Hi Teo, > </div><div class="Ih2E3d">> 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 <<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a> </div><div><div></div><div class="Wj3C7c">> <mailto:<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>>> 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: > <a href="http://cp2k.berlios.de/manual/CP2K_INPUT/GLOBAL.html#desc_FLUSH_SHOULD_FLUSH" target="_blank">http://cp2k.berlios.de/manual/CP2K_INPUT/GLOBAL.html#desc_FLUSH_SHOULD_FLUSH</a> > > 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: > <a href="http://cp2k.berlios.de/manual/CP2K_INPUT/FORCE_EVAL/MIXED/PRINT/DIPOLE.html" target="_blank">http://cp2k.berlios.de/manual/CP2K_INPUT/FORCE_EVAL/MIXED/PRINT/DIPOLE.html</a> > > ..... > &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 </div></div><div><div></div><div class="Wj3C7c">>> <<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a> <mailto:<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>>> 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. >> > >> > > >> > >> >> >> >> >> >> >> > > > > > > > </div></div></blockquote></div>