[phenixbb] advice for speeding up cif_as_mtz

Nathaniel Echols nechols at lbl.gov
Mon Sep 10 12:20:27 PDT 2012

On Mon, Sep 10, 2012 at 7:38 AM, Eric Williams <ericwilliams at pobox.com> wrote:
> I'm currently running cif_as_mtz and model_vs_data on the whole PDB as part
> of my dissertation. Time has become a critical concern, and cif_as_mtz
> (dev-1141) is running very, very slowly (1-4 minutes per entry).
> Here's how I'm calling it:
> phenix.cif_as_mtz <sf_cif_fn> --ignore-bad-sigmas --merge
> --remove-systematic-absences --map-to-asu --symmetry=<pdb_model_fn>
> --output-file-name=<sf_mtz_fn>
> I'm hoping that perhaps someone could help me determine which command line
> argument(s) could be removed to provide maximum speed-up.

Are you running this on NFS-mounted disks by any chance?

None of these should be especially time-consuming - the only big
bottleneck in the program is "--use-model".  I just tried running the
command above on a reasonably large structure (1zy8) and it was very
quick (< 15s).  On the off chance that something big changed in the
last couple of weeks, can you update to the latest nightly build and
see if it's still running slowly?  If so, send us some IDs that take a
particularly long time and we'll see if we can reproduce the problem.


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