> Hi Jeremy, > > I have two questions for you. > (1)After you did mpiformatdb -N 44, how many fragments > did you get? Did you get 45 fragments or 44? > (2)When you run mpiBlast, how many cpus or nodes you > specify? (I mean, what is your number for xx in mpirun > -np xx). I actually ended up with 46 segments. mpiformatdb split it up into 10 meg segments, and protein nr is 459 megabytes, so the last 46th segment (nr.45) is about 6 megabytes. I run mpiblast as follows: time mpirun -np 46 mpiblast -p blastp -d nr -i nr-protein.fasta -o nrprotein-np46.out The master node actually has 4 segments of the db. When I run mpirun in verbose mode, it tells me I am starting 4 jobs on n0, then 2 jobs from n1 to n20. Also I have an update on the user situation. If you chmod -R 777 the local storage directory, when another user runs mpiblast, he/she will not experience the lag because of the segments being copied. This is the only way around sharing local storage with a number of users. If your really paranoid about security, you could always make an 'mpiblast' users group and assign blast users to this group. I have tested this with 3 user accounts, each one did NOT copy segments to local storage, and the timed tests where very similar, anywhere from 5.4 to 5.9 seconds. -- Jeremy Mann jeremy@biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility http://www.bioinformatics.uthscsa.edu Phone: (210) 567-2672 -- Jeremy Mann jeremy@biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility http://www.bioinformatics.uthscsa.edu Phone: (210) 567-2672