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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Received on Sat Apr 23 2016 - 12:00:07 PDT
