Got it. Thanks. Jun <div class="gmail_quote">On Fri, Dec 5, 2008 at 11:01 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;"> 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: <a href="http://cp2k.berlios.de/manual/CP2K_INPUT/GLOBAL.html#desc_WALLTIME" target="_blank">http://cp2k.berlios.de/manual/CP2K_INPUT/GLOBAL.html#desc_WALLTIME</a> so.. don't see neither the importance of your second problem, since it is not a problem! Teo <div class="Ih2E3d"> 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 </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: > > > 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 > <<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a> <mailto:<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>> > > <mailto:<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a> > <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 > >> <<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a> <mailto:<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>> </div></div>> <mailto:<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a> <mailto:<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>>>> <div><div></div><div class="Wj3C7c">> 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>