Installing and running
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The parallel blast programs are located in the directory
~/blast1.4/blastapp/net. In that directory execute:
- make clean to delete everything except the necessary
sources.
- make tags to make a tags table in file TAGS readable
by emacs.
- make to make the executables.
Two additional environment variables were introduced:
- BLASTNUMSLAVES: number of machines to use.
- BLASTNUMCHUNKS: number of chunks to cut the database into.
If these envrionment variables are not defined, the values are taken
from the equally named constants defined in blast.pvm.c.
The problem is, when a new version of blast programs arrives. Blast
programs will probably always consist of the parts:
- parse arguments
- do searching
- print results
So, try to follow our method: Let the master and the slaves do the
parsing of arguments, let the slaves do the searching, and let the
master print the results. If the new version is not very different,
then, by modifying a little bit the Perl script net_patch.pe you
might be able to generate the parallel blast programs (net_blastp.c, etc.). But probably you will have to change also
something in the module results.[ch], because the mapping,
unmapping and adding of the results is done there.
Minor updates will have perhaps to be done, when a new version of PVM
or of the operating system comes out. The blast programs depend on the
very portable ncbi and gish libraries, so most probably, recompilation of
the programs will be enough.
To run the parallel blast programs, you have to start the PVM deamon
on as many machines as possible, start the blast deamon demon_blast and execute the client blast.pvm. A simple
session looks like this:
In one xterm start pvm and demon_blast. These are started just once.
% pvmd ~/pvm3/bin/some_hosts.pvm &
% demon_blast ~/pvm3/bin/some_hosts.pvm
And in another start the parallel blast application with the same
arguments as in the serial version:
% blastp.pvm swiss ~/queries/protpart1.seq -batch
Next: The servers
Up: The parallel blast
Previous: Deamon and client
Compte de groupe
Fri Jan 20 15:43:12 MET 1995