Hi Harry,
Might not be the problem but does this machine have its ccp4 scratch
space ($CCP4_SCR) mounted from another machine by nfs across a network?
Refmac writes a lot of temporary files to CCP4_SCR and if this is across
a busy network it can really slow Refmac's progress.
Ronan
Harry M. Greenblatt wrote:
BS"D
Dear All,
One our our linux boxes (kernel 2.4.20) has begun recently to run
refmac at worse than snail's pace. This is a 3.2 GHz Xeon dual CPU
Dell machine from 4 years ago. All other things seem fine, including
other CCP programs. But refmac jobs (for various proteins) that take
a minute or two on other machines can sit for many tens of minutes
making very slow progress (but yes, they are getting somewhere).
Using top, one can see that the machine is completely idle, and the
refmac job has used up a few seconds of CPU time, even after ten
minutes, although its priority is normal. In top, under the status
column, it has a status of "D", which, according to the documentation,
is "uninterruptible sleep". Running refmac on another computer, I see
that is does enter the "D" state a few times during the run, but never
stays that way very long. Any ideas?
Thanks
Harry
-------------------------------------------------------------------------
Harry M. Greenblatt
Staff Scientist
Dept of Structural Biology [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
Weizmann Institute of Science Phone: 972-8-934-3625
Rehovot, 76100 Facsimile: 972-8-934-4159
Israel
