[Dock-fans] Interactive vs batchmode execution

Scott Brozell sbrozell at scripps.edu
Fri Apr 4 14:49:26 PDT 2008


On Fri, 4 Apr 2008, Francesco Pietra wrote:

> I performed successfully several parallel docking procedures with dock6.2. Then, to
> investigate why it runs out of memory with a larger ligand, the interactive mode was
> used.
> Although that memory investigation is still incomplete, I wanted to carry out
> further the work on smaller ligands. Now the command for batch mode, either serial
> $ dock6 -i anchor_and_grow.in -o anchor_and_grow.out
> or parallel
> $ mpirun -np 1 dock6.mpi -i anchor_and_grow.in -o anchor_and_grow.out
> initiates the interactive mode. The in file is fine, it is just the one that was OK
> before, while the program tries to write the new .in-o file. I checked with various
> previous directories. Why that and how to return to batch mode?

The sole determiner of interactive versus batch is the use of -o
without -o then interactive, with -o then batch.
Parallel Dock cannot be run interactively:
Error: DOCK must be run with the -o outfile option under MPI

Thus, your problem description is unclear; is this just a typo:
.in-o file
   ^ there should be a space here.

If not then send verbatim and verbose details.

> I did nothing in between, except for installing the debian package "sysstat".
> Incidentally, which is the easiest way of taking a record of the output of "top"
> command? In case of failure, the initial output obviously disappears.

I used cut-n-paste.  top can be run in batch and the output redirected:
top -b > pot


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