From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jan 03 2019 - 13:57:50 CST
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
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).
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
> On Mon, Dec 31, 2018 at 2:47 AM Francesco Pietra <chiendarret_at_gmail.com>
> > 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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