[SCore-users-jp] RE: [SCore-users] How to specify a input data file with scrun?

[yoneya ＠ nanolc.jst.go.jp]

Dear Dr. Costescu

Thanks for your comments.

> From the docs at www.gromacs.org, I find that mdrun can read the input 
> from a file specified with the "-s" command line option. Why aren't you 
> specifying it like this ? Then you don't need to redirect stdin.

The option I'd tried,
mdrun_d -deffnm data,
works same as,
mdrun_d -s data.tpr, since -deffnm specify the generic name for
I/O files not only *.tpr but the other *.gro files etc.

> If you want to send a file from stdin to the process, then I don't 
> understand exactly why you are copying it first to the nodes.

As far as I knonw, GROMACS does not read the input data from stdin
but just open and read the specified input data file.
As in your comment, only the primary execution node needs to read
the input file (also as far as I know).
However, since I do not know which node will become the primary node,
I tried to copy the input data file to all the nodes in the group.
If there are misunderstanding above, please point out that.
It will be great help to solve my problems.

Thanks again.

Makoto Yoneya
Yokoyama Nano-LC project
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