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 Fri Apr 22 2016 - 02:30:04 PDT
