On Thu, 21 Apr 2016 08:14:54 -0400
David A Case <david.case.rutgers.edu> wrote:
> 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.
There is a very old one: http://archive.ambermd.org/200407/0259.html
but apparently involving NFS so not really surprising.
> 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"?
This only reads information from the directory node but the error
message suggests to me, as far as I understand, that a read() returned
with EAGAIN because the corresponding write has not finished yet. But
then again I can't say that I know too much about non-blocking I/O.
> 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?
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Received on Thu Apr 21 2016 - 06:00:04 PDT
