hi sergei -

I just noticed that when I am running a SLAC analysis, when I get to the "Output Options" menu, and choose "Output is spooled to a tab separated file", the process of writing the analysis output to the file is very slow.  I had thought that by the time I get to that screen, all the values that are to be written to file have already been computed, but if I do a tail -f on the output file, HYPHY is writing approx 1 output value per second.  So even after the positive selection results are ready, printing the output file takes several times longer than the analysis that produced the results.  I've reproduced this problem on at least two computers, using the HYPHYMPI source code build for OSX, on both networked and non-networked disk space, so it's not a network lag problem.  any ideas?

thanks as always
-dan

oops -  i meant the HYPHYMP build, not the MPI build

Dear Dan,

This is indeed unusually slow; but I think there my "spool-to-file" code is really old and effectively the file handle is reopened every time a number is written out. I'll update the output function to buffer the output and write to file once (as it should be done) and post the fix.

Still; one value per second is unusually slow!

Cheers,
Sergei

Dear Dan,

I added buffered file output to SLAC. It's rolled into today's update or you can download this file Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login and place it inside TemplateBatchFiles.

Cheers,
Sergei