[gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1

Thank you Berk, my problem, was indeed that I didn't have any valid .cpt files. The only way that I could proceed was to extract a frame from the .xtc file and run it through grompp again to get a new .tpr. That's fine and things are running again. I just wanted to pass all of this information a

Re: [gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1

e...@mail.utoronto.ca > > To: gmx-users@gromacs.org > > Date: Fri, 29 Mar 2013 01:15:06 + > > Subject: [gmx-users] chiller failure leads to truncated .cpt and > _prev.cpt files using gromacs 4.6.1 > > > > Thank you, Berk, Justin, and Matthew, for your assistance.

RE: [gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1

[gmx-users] chiller failure leads to truncated .cpt and _prev.cpt > files using gromacs 4.6.1 > > Thank you, Berk, Justin, and Matthew, for your assistance. > > I checked with my sysadmin, who said: > > The /global/scratch FS is Lustre. It is fully POSIX and the fsync etc >

[gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1

Thank you, Berk, Justin, and Matthew, for your assistance. I checked with my sysadmin, who said: The /global/scratch FS is Lustre. It is fully POSIX and the fsync etc are fully and well implemented. However when the 'power off' command is issued there is no way OS can finish I/O in a controlled

RE: [gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1

000 > Subject: [gmx-users] chiller failure leads to truncated .cpt and _prev.cpt > files using gromacs 4.6.1 > > Dear Matthew: > > Thank you for noticing the file size. This is a very good lead. > I had not noticed that this was special. Indeed, here is the complete listing >

Re: [gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1

On 3/26/13 11:13 PM, Christopher Neale wrote: Dear Matthew: Thank you for noticing the file size. This is a very good lead. I had not noticed that this was special. Indeed, here is the complete listing for truncated/corrupt .cpt files: -rw-r- 1 cneale cneale 1048576 Mar 26 18:53 md3.cpt

[gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1

Dear Matthew: Thank you for noticing the file size. This is a very good lead. I had not noticed that this was special. Indeed, here is the complete listing for truncated/corrupt .cpt files: -rw-r- 1 cneale cneale 1048576 Mar 26 18:53 md3.cpt -rw-r- 1 cneale cneale 1048576 Mar 26 18:54 m

Re: [gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1

Dear Chris, While it's always possible that GROMACS can be improved (or debugged), this smells more like a system-level problem. The corrupt checkpoint files are precisely 1MiB or 2MiB, which suggests strongly either 1) GROMACS was in the middle of a buffer flush when it was killed (but the filesy

[gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1

Dear Users: A cluster that I use went down today with a chiller failure. I lost all 16 jobs (running gromacs 4.6.1). For 13 of these jobs, not only is the .cpt file truncated, but also the _prev.cpt file is truncated, meaning that I am going to have to go back through the files, extract a frame