[phenixbb] differences between command line and GUI?

Thomas C. Terwilliger terwilliger at lanl.gov
Mon Mar 28 07:21:11 PDT 2011

Hi Kendall,

I am guessing that this is an autobuild job, and that the machines used in
the cluster are different than the machines used from the GUI.  If this is
the case, then I am not too surprised, as autobuild makes many decisions
that are either/or (place a chain here or not) rather than continuous
(move this atom here) so that tiny numerical differences can lead to
significant differences in the final model.

Now if you run from the GUI or command line and all machines are the
same...then it should be the same, because the GUI is creating a
parameters file and then running that command file.

Autobuild also uses a random seed to generate trial positions for new
chains, so if you re-run your job with i_ran_seed=xxxx, varying xxxx, you
will get different results as well.

I hope that helps!
-Tom T

>> Dear PHENIX developers,
>> I ran a job through the GUI, and then what I thought was the same job on
>> our cluster. The job from the cluster has Rfree that is 0.7% higher. I'm
>> totally at a loss to figure out what is causing this. It is the same
>> version of PHENIX (1.7-650). I then took the .eff file from the GUI job
>> and used that as the params file for the command line job but still get
>> the big difference in R free. Any suggestions?
>> Best regards,
>> Kendall Nettles
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