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-- Shahid. On Mon, Apr 25, 2016 at 2:00 PM, Karolina Markowska <markowska.kar.gmail.com > wrote: > Ok, this sounds like something that might work. > Could you give me an advice, how to run a job with this mdinfo trick? > > Best regards. > > > > 2016-04-25 0:46 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>: > > > One way to hack around it would be to have the code output a new file > > each time: mdinfo.1, mdinfo.2 or what have you (numbered by step). Then > > you'd never collide, though you'd have to delete a bunch of small files, > > and worst case might exceed the number of files a directory can hold. > > > > Bill > > > > On 4/24/16 12:16 PM, Karolina Markowska wrote: > > > I can do "cat mdinfo" and in most cases everything runs just fine. > > > But if I make "cat mdinfo" in the exact moment when the contents of > > mdinfo > > > changes, I get the resource unavailable error and the simulation > crashes. > > > Also if I use "tail mdinfo" and pmemd changes the mdinfo file, > everything > > > crashes. And this is probably related with the queueing system because > > when > > > I run the simulation without submitting it into the queue - everything > is > > > OK. > > > If I don't look into mdinfo file during whole simulation, everything > runs > > > OK. > > > > > > 2016-04-23 20:55 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>: > > > > > >> contents of mdinfo > > >> > > >> On 4/23/16 11:53 AM, Bill Ross wrote: > > >>> So with pmemd, you can run for an arbitrary amount of time, and then > > the > > >>> moment you 'cat mdinfo' the simulation crashes on resource > unavailable, > > >>> and the contents of pmemd are different each time, and if you don't > > look > > >>> at the file, the job runs to completion? > > >>> > > >>> Bill > > >>> > > >>> On 4/22/16 2:24 AM, Karolina Markowska wrote: > > >>>> I'm using Ubuntu 14.04, and the file system is ext4. We're using > > quota. > > >>>> > > >>>> I don't have any problem with the "ls -l mdinfo". I'm the owner of > > this > > >>>> file, I (theoretically) can read it or change it. The file is > present > > >> with > > >>>> a non-zero length and I can read it using "cat mdinfo" command. > > >>>> -rw-r----- 1 karolinam user 1257 kwi 21 14:57 mdinfo > > >>>> > > >>>> It looks OK, I guess: > > >>>> > > >>>> NSTEP = 950000 TIME(PS) = 52980.000 TEMP(K) = 298.41 > > PRESS > > >> = > > >>>> 0.0 > > >>>> Etot = -140475.4219 EKtot = 36982.3438 EPtot = > > >>>> -177457.7657 > > >>>> BOND = 1208.0342 ANGLE = 3085.0042 DIHED = > > >>>> 5565.0947 > > >>>> 1-4 NB = 1290.0424 1-4 EEL = 12081.5006 VDWAALS = > > >>>> 21022.0260 > > >>>> EELEC = -221794.1217 EHBOND = 0.0000 RESTRAINT = > > >>>> 0.0000 > > >>>> EAMD_BOOST = 84.6540 > > >>>> > > >> > > > ------------------------------------------------------------------------------ > > >>>> | Current Timing Info > > >>>> | ------------------- > > >>>> | Total steps : 25000000 | Completed : 950000 | Remaining : > > >> 24050000 > > >>>> | > > >>>> | Average timings for last 20000 steps: > > >>>> | Elapsed(s) = 93.93 Per Step(ms) = 4.70 > > >>>> | ns/day = 36.79 seconds/ns = 2348.27 > > >>>> | > > >>>> | Average timings for all steps: > > >>>> | Elapsed(s) = 4461.87 Per Step(ms) = 4.70 > > >>>> | ns/day = 36.79 seconds/ns = 2348.36 > > >>>> | > > >>>> | > > >>>> | Estimated time remaining: 31.4 hours. > > >>>> > > >> > > > ------------------------------------------------------------------------------ > > >>>> This issue does not depend on the type of MD simulation I run - it > > >> happens > > >>>> during classical MD and aMD. > > >>>> I rerun the same job using the CPU, typed "tail -f mdinfo" and > nothing > > >>>> happened. The simulation is running. > > >>>> Could it be a problem with pmemd.cuda? > > >>>> I've ran a simulation on a cluster without PBS (on CPU and GPU) > and... > > >>>> everything worked. I don't get it. > > >>>> > > >>>> Best regards. > > >>>> > > >>>> > > >>>> 2016-04-21 14:14 GMT+02:00 David A Case <david.case.rutgers.edu>: > > >>>> > > >>>>> On Thu, Apr 21, 2016, Karolina Markowska wrote: > > >>>>>> I have a strange problem. I'm running different aMD simulations > > tests > > >>>>> and I > > >>>>>> want to compare the timings. I know I can find that kind of > > >> informations > > >>>>> in > > >>>>>> the mdinfo file, but here comes the problem: several times when I > > >> opened > > >>>>>> mdinfo file (using just "cat mdinfo"), the simulation crashed and > > I've > > >>>>> got > > >>>>>> an error: > > >>>>>> At line 810 of file runfiles.F90 (unit = 7, file = 'mdinfo') > > >>>>>> Fortran runtime error: Resource temporarily unavailable > > >>>>> I don't remember any reports like this, and the amber developers > > >> (including > > >>>>> me) do this all the time. > > >>>>> > > >>>>> What is your operating system; do you know what sort of file system > > is > > >>>>> being > > >>>>> used on the drive where the mdinfo file is? > > >>>>> > > >>>>> Do you run into problems with commands like "ls -l mdinfo"? Is a > > >> mdinfo > > >>>>> file > > >>>>> present (with non-zero length) when you execute the "cat mdinfo" > > >> command? > > >>>>> Can you try to narrow down the problem? Does is depend on using aMD > > vs. > > >>>>> regular MD? Using GPUs vs CPUs? Submitted to a queuing system vs. > > >>>>> running interactively? > > >>>>> > > >>>>> ....thx...dac > > >>>>> > > >>>>> > > >>>>> _______________________________________________ > > >>>>> AMBER mailing list > > >>>>> AMBER.ambermd.org > > >>>>> http://lists.ambermd.org/mailman/listinfo/amber > > >>>>> > > >>>> _______________________________________________ > > >>>> AMBER mailing list > > >>>> AMBER.ambermd.org > > >>>> http://lists.ambermd.org/mailman/listinfo/amber > > >>> _______________________________________________ > > >>> AMBER mailing list > > >>> AMBER.ambermd.org > > >>> http://lists.ambermd.org/mailman/listinfo/amber > > >> > > >> _______________________________________________ > > >> AMBER mailing list > > >> AMBER.ambermd.org > > >> http://lists.ambermd.org/mailman/listinfo/amber > > >> > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Apr 25 2016 - 06:00:05 PDT