From: Abhishek Tyagi (atyagiaa_at_connect.ust.hk)
Date: Wed Mar 18 2015 - 10:13:07 CDT
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
>>>>>>
>
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