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
> >>>
> >>>
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> >>>
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Received on Sun Apr 24 2016 - 12:30:03 PDT
