From: Atanu Maity (atanuchem48_at_gmail.com)
Date: Wed Mar 18 2015 - 23:32:32 CDT
I also faced the same problem once. I tried a trick to solve it which is -
merge individual dcd using catdcd and then merge all of the merged dcds in
to a single dcd. That worked fine for my system. You can try this ---
catdcd -o Production_merge.dcd Production.dcd
catdcd -o Prodution_1_merge.dcd Prodution_1.dcd
catdcd -o Production_100_merge.dcd Production_100.dcd
catdcd -o full-100.dcd Production_merge.dcd Prodution_1_merge.dcd
Production_100_merge.dcd
On Wed, Mar 18, 2015 at 8:43 PM, Abhishek Tyagi <atyagiaa_at_connect.ust.hk>
wrote:
> size of dcd files are as follows:
> 1. 21.3 gb
> 2. 59.7 gb
> 3 81.1 gb
>
> the operating system is linux based gpu cluster with 4 nvidia and 32 cpu
>
> > On 18 Mar, 2015, at 11:06 pm, Josh Vermaas <vermaas2_at_illinois.edu>
> wrote:
> >
> > Alright, next dumb question, what is you operating system, and what are
> the file sizes reported by the OS? Some file systems/OS combinations don't
> like files over a certain size, and that might be what is going on here.
> >
> > -Josh
> >
> > On 3/18/15 8:51 AM, Abhishek Tyagi wrote:
> >> Dear Josh,
> >>
> >> the log file is as follows:
> >>
> >>
> >> TIMING: 99999000 CPU: 1.22372e+06, 0.024316/step Wall: 1.22372e+06,
> 0.024316/step, 0.00675445 hours remaining, 713.925781 MB of memory in use.
> >> ENERGY: 99999000 1559.9895 2857.4765 2476.5506
> 24.8891 -644729.0421 83417.3582 369.5601 0.0000
> 82181.4611 -471841.7569 299.0941 -554023.2180
> -471677.3357 300.1053 -20758.0248 94.6445
> 1367630.1184 10.8342 10.8706
> >>
> >> PRESSURE: 100000000 -21209.7 411.919 -465.102 280.973 -21472.1 16.9422
> -366.092 174.739 -20903.4
> >> GPRESSURE: 100000000 -169.389 407.024 -547.253 305.837 -307.554
> -33.7555 -401.648 127.4 -514.401
> >> PRESSAVG: 100000000 -10.4791 9.51392 -51.2958 84.5688 1.1351 55.0474
> -96.1522 -13.0117 -59.8567
> >> GPRESSAVG: 100000000 -10.6852 9.1878 -51.6702 84.2353 1.02011 54.9018
> -96.312 -12.7367 -59.6655
> >> TIMING: 100000000 CPU: 1.22375e+06, 0.0244166/step Wall: 1.22375e+06,
> 0.0244166/step, 0 hours remaining, 713.929688 MB of memory in use.
> >> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY MISC
> KINETIC TOTAL TEMP POTENTIAL TOTAL3
> TEMPAVG PRESSURE GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
> >>
> >> ENERGY: 100000000 1578.6460 2839.1712 2494.6513
> 28.1142 -644220.4090 82951.3469 391.2504 0.0000
> 82455.8013 -471481.4278 300.0925 -553937.2291
> -471313.5083 300.3080 -21195.0447 -330.4479
> 1367630.1184 -23.0669 -23.1102
> >>
> >> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 100000000
> >> WRITING COORDINATES TO DCD FILE Production_100.dcd AT STEP 100000000
> >> WRITING COORDINATES TO RESTART FILE AT STEP 100000000
> >> FINISHED WRITING RESTART COORDINATES
> >> WRITING VELOCITIES TO RESTART FILE AT STEP 100000000
> >> FINISHED WRITING RESTART VELOCITIES
> >> WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 100000000
> >> CLOSING EXTENDED SYSTEM TRAJECTORY FILE
> >> WRITING COORDINATES TO OUTPUT FILE AT STEP 100000000
> >> CLOSING COORDINATE DCD FILE Production_100.dcd
> >> WRITING VELOCITIES TO OUTPUT FILE AT STEP 100000000
> >> ====================================================
> >>
> >> WallClock: 1223748.000000 CPUTime: 1223748.000000 Memory: 713.941406
> MB
> >> Program finished.
> >>
> >>
> >>> On 18 Mar, 2015, at 10:36 pm, Josh Vermaas <vermaas2_at_illinois.edu>
> wrote:
> >>>
> >>> Hi Abhi,
> >>>
> >>> Did you check if the NAMD job terminated normally? Oftentimes during
> an abnormal termination (such as when you hit the wallclock limit), the dcd
> generated is too short for what the header claims. Since the header is
> written at the beginning of the simulation, the dcd header will claim a
> framecount based on the number of steps you are planning to run. What are
> the filesizes for the dcds in question? Is the sum of the sizes for
> Production.dcd and Production_1.dcd equal to that of Production_100.dcd?
> Catdcd is telling you no, so if I were to bet, I'd assume that the last
> simulation terminated abnormally (check the logfile!).
> >>>
> >>> -Josh
> >>>
> >>> On 3/18/15 8:29 AM, Abhishek Tyagi wrote:
> >>>> Thankyou for your reply,
> >>>>
> >>>> I have again checked it, I am a bit confused, could you suggest what
> else could be done in this
> >>>>
> >>>> Thanks
> >>>>
> >>>> ABhi
> >>>>
> >>>>> On 18 Mar, 2015, at 10:27 pm, btreece_at_andrew.cmu.edu wrote:
> >>>>>
> >>>>> Hi Abhi,
> >>>>>
> >>>>> After reading your output, it appears there is an issue with
> >>>>> Production_100.dcd. The other two wrote 50001 frames and the header
> for
> >>>>> Production_100.dcd claimed to have the other 50000, but only 23701
> were
> >>>>> able to be read. I know you said you checked it, but I would inspect
> that
> >>>>> file more closely. Perhaps you missed something?
> >>>>>
> >>>>> Bradley
> >>>>>
> >>>>>> Dear Experts,
> >>>>>>
> >>>>>> I am using NAMD 2.10 on gpu cluster, initially I had performed MD
> for
> >>>>>> 50ns, when I restarted from 50 to 100ns, the MD finishes
> successfully.
> >>>>>> Finally, I was trying to use catdcd to merge these files in to one
> big dcd
> >>>>>> file as follows:
> >>>>>> This is first time I am experiencing this error.
> >>>>>>
> >>>>>>
> >>>>>> catdcd -o full-100.dcd Production.dcd Prodution_1.dcd
> Production_100.dcd
> >>>>>> CatDCD 4.0
> >>>>>> dcdplugin) detected standard 32-bit DCD file of native endianness
> >>>>>> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> >>>>>> Opening file 'full-100.dcd' for writing.
> >>>>>> dcdplugin) detected standard 32-bit DCD file of native endianness
> >>>>>> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> >>>>>> Opened file 'Production.dcd' for reading.
> >>>>>> Read 13157 frames from file Production.dcd, wrote 13157.
> >>>>>> dcdplugin) detected standard 32-bit DCD file of native endianness
> >>>>>> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> >>>>>> Opened file 'Prodution_1.dcd' for reading.
> >>>>>> Read 36844 frames from file Prodution_1.dcd, wrote 36844.
> >>>>>> dcdplugin) detected standard 32-bit DCD file of native endianness
> >>>>>> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> >>>>>> dcdplugin) Warning: DCD header claims 50000 frames, file size
> indicates
> >>>>>> there are actually 23071 frames
> >>>>>> Opened file 'Production_100.dcd' for reading.
> >>>>>> Read 23071 frames from file Production_100.dcd, wrote 23071.
> >>>>>> Total frames: 73072
> >>>>>> Frames written: 73072
> >>>>>> CatDCD exited normally.
> >>>>>>
> >>>>>>
> >>>>>> ?What is doubtful here is the number of frames should be 100000 but
> these
> >>>>>> are 73000, I checked these trajectories in vmd and i cant see any
> problem
> >>>>>> their.
> >>>>>>
> >>>>>> Could you please tell me what is happened to this MD.
> >>>>>>
> >>>>>>
> >>>>>> Thanks in advance
> >>>>>>
> >>>>>>
> >>>>>> Abhi
> >>>>>>
> >
>
>
>
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:44 CST