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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Received on Sat Apr 23 2016 - 12:00:08 PDT
