On Tue, Dec 21, 2004 at 06:28:23PM +0000, Vohra S wrote: > There is a problem regarding the running of the modeller.While running > the script file on the prompt an error is shown and the log file is not > created. I typed the following command on the prompt > > mod7 seq_search.top >seq.log01 > where mod7 is the alias directed to the executable file > > The error at the UNIX prompt is as follows > /usr28/users/gpsaro/modeller7v7/bin/mod7v7[35]: ulimit: exceeds allowable > limit

This warning is normal on SGI; see the 7v7 release notes: http://salilab.org/modeller/release.html#issues

> The log file created is empty > Please can you help me with this

You won't see anything in seq.log01, because Modeller writes its log output to seq_search.log, not to standard output, by default.

Sequence search takes a long time, as it is doing rigorous dynamic programming alignments (unlike BLAST, which uses various approximations). The basic tutorial includes an example of this: http://salilab.org/modeller/tutorial/basic.html

That particular input file (seq_search.top) takes over an hour to run on a modern PC, so it will probably take several hours on an SGI. Depending on how your OS buffers file output, you may not see anything in the seq_search.log file until the job has finished. If you really want to see lots of output, and as quickly as possible, set the OUTPUT_CONTROL variable on the first line of your script:

SET OUTPUT_CONTROL = 1 1 1 1 1

...and run Modeller using standard input and output (which is typically line buffered rather than block buffered): mod7 - < seq_search.top

Ben Webb, Modeller Caretaker