+----[ Joe Landman <landman@scalableinformatics.com> (28.Jan.2004 03:36): | | Hi Fernan Hi Joe, and thanks for your reply. | Fernan Aguero wrote: | | >All the tests I've performed (from reading the docs) pass. | >However, all the jobs run on the slave. The master just sits | >down quietly waiting for the slave to finish with one | >segment, before feeding the next. I suppose that this | > | > | | Are you using mpirun with the -nolocal option? The -nolocal option | prevents running threads on the starting node. Also, what does your | machines file look like? Are you using a machines file or just "-np 2" ? | +----] No, I'm not using the -nolocal option. I am using a machines file. The machines file is in /usr/local/mpich/share/machines.freebsd and has just two entries, using FQDNs. Both machines are in the same network, of course. Should I list the master as 'localhost' instead? When I tested my mpich installation using the examples provided, I verified that using -np 2 would run the process in the two hosts: [fernan@pi] mpirun -np 2 cpi Process 1 on rho.iib.unsam.edu.ar Process 0 on pi.iib.unsam.edu.ar pi is approximately 3.1416009869231241, Error is 0.0000083333333309 wall clock time = 0.004861 I the formatted a database using mpiformatdb. Since the db is small enough I just splitted in two segments. [fernan@pi] mpiformatdb -N 2 -i sp_tr_nrdb/sprot.fasta -p T -o T Reading input file | Done, read 1060238 lines Trying to break sprot.fasta (52 MB) into 2 fragments of 26 MB Executing: formatdb -i sp_tr_nrdb/sprot.fasta -p T -o T -v 26 -n /databases/sprot.fasta Created 2 fragments. My .mpiblastrc is the same in both hosts, and contains the following: /databases /usr/local/databases In the master host all databases are in /usr/local/databases, which is exported to the other host (rho). In the master host /databases is just a symbolic link to /usr/local/databases. In rho, /databases is the mount point of the shared data, and /usr/local/databases is the local storage for mpiblast to use. All these directories are readable and writable by me. The NCBI data directory is also in the shared area, under a 'blastmat' directory, and the .ncbirc is the same in both hosts and contains the following: [NCBI] Data=/databases/blastmat Now I run a query using mpiblast: [fernan@pi] mpirun -np 2 /usr/local/bin/mpiblast --debug -i query_1.fa -d sprot.fasta -p blastp -o query.mpiblast I follow the run on two separate xterms, running 'top' on each host. In the master host I don't notice any increment in the CPU usage activity. In fact I don't even see mpirun listed while running :| On the 'slave' host I notice mpiblast running, with a CPU usage of 96-97% during the whole run. This is also reflected in the mpiblast output that I get using --debug (attached to this message). Also if I use mpirun -v I see: running /usr/local/bin/mpiblast on 2 386BSD ch_p4 processors Created /usr/local/databases/PI63127 Any ideas? Thanks again, Fernan -- F e r n a n A g u e r o http://genoma.unsam.edu.ar/~fernan