From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Jan 04 2019 - 11:16:08 CST
Hi Giacomo:
writing to disk was not so frequent as at the time you are referring to:
outputEnergies 2000 # multiple of fullElectFrequency or viceversa
restartfreq 2000
DCDfreq 5000
Nonetheless I have now increased it
outputEnergies 2000 # multiple of fullElectFrequency or viceversa
restartfreq 3000
DCDfreq 5000
and the simulation came to end without problems.
Thanks for your advice
francesco
On Thu, Jan 3, 2019 at 8:58 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> Hi Francesco, a workaround was introduced in 2.10 into the file writing
> routines of NAMD to support the file system on Blue Waters. This created a
> few related problems, but all were fixed eventually. Since you state that
> you used the nightly build, I don't think you're affected by any of those
> old bugs.
>
> A search for that error message in this mailing list returns several
> messages from you (e.g. last April), when writing the NAMD restart file.
> Brian wrote the following then:
>
> *How frequently are you writing to disk? It looks like you are writing a
> restart file every 500 steps, which is incredibly frequent and stresses
> both NAMD performance and the disk. Even writing energies to output that
> frequently can measurably slow down a simulation.*
>
> So obviously the writing frequency is the first that I would check.
> Remember that on a busy network file systems, some operations will not be
> completed within seconds (e.g. renaming files to .BAK).
>
> Giacomo
>
> On Thu, Jan 3, 2019 at 2:21 PM Victor Kwan <vkwan8_at_uwo.ca> wrote:
>
>> Does it occur over and over again? Could be I/O issue with your scratch
>> disk.
>>
>> On Mon, Dec 31, 2018 at 2:47 AM Francesco Pietra <chiendarret_at_gmail.com>
>> wrote:
>> >
>> > Hi all:
>> > During npt equilibration with restraints (single node of a cluster with
>> 36 core and four tesla gpus, namd night build) the simulation crashed with
>> >
>> > colvars: Writing the state file "./npt_restr-02.restart.colvars.state".
>> > FATAL ERROR: Unable to open text file
>> ./npt_restr-02.restart.colvars.state: File
>> > exists
>> >
>> > These are three distance colvars for both ligands.
>> >
>> > This problem did not occur with npt_restr-01. Also, it did not occur
>> with npt_restr-02 in a series of related simulations (same receptor and
>> ligand, with the latter in a different pose).
>> >
>> > I understand that I am providing little info, but I was unable to find
>> any error in the input, or previous, files.
>> >
>> > Thanks for any suggestion
>> > francesco pietra
>> >
>>
>>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>
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