Hi Ankit, mpiBLAST needs to process the query file before it can start BLASTing. This is unfortunatly currently a serial process, and so with large query files the master node may spend a long time before the workers start doing thier thing. If you try it with a small query file first you should see the workers start up right away. Give the masternode some time. You can look in the mailing list archives for other query-file size related discussions. -Lucas
On Wednesday, April 12, 2006 at 23:55 -0700, ankit patel wrote: > Hi Lucas, > > By using mpirun with -v command i got the output that > on all machine mpiblast was running but when i was > going on all machines than i found that mpiblast was > running on only my master machine. On other machines > mpiblast process was not running. > > In attachment i am sending you lamboot -d , lamhalt -d > (when running lamd), lamnodes, mpirun and mpiblast > command output with -v option and all files in local > directory as mentioned in MPIBLAST_LOCAL variable on > all machines. > > --- Lucas Carey <[EMAIL PROTECTED]> wrote: > > > Hi Ankit, > > This is probably a problem with the way lam is > > setup. > > what is the output of > > lamhalt -d (if its already running) > > lamboot -d > > lamnodes > > lamhalt -d > > > > If lam is setup correctly then mpiblast should run > > on all nodes. > > To get a list of the nodes that mpiblast is being > > run on: > > mpirun -v -np 24 .... mpiblast .... > > > > -Lucas > > > > > > On Wednesday, April 12, 2006 at 03:01 -0700, ankit > > patel wrote: > > > > > > Hi Lucas, > > > Thanks for your help. Now i can run my > > program mpiblast. But still i > > > have question why mpiblast is not run on all > > machines? I have 12 Sun > > > fire v20z machines and each has two > > processors. But when i am running > > > my my job for 24 processors than it > > execute randomaly not on all > > > machines. It used hardely 8-9 processors at one > > time. > > > I used lam-mpi 7.0. Is there any problem > > with lam environment for > > > mpiblast? > > > Lucas Carey <[EMAIL PROTECTED]> wrote: > > > > > > Hi Ankit, > > > Could you post the conents of your .ncbicr > > file? > > > Also, you can try passing them as environment > > variables: > > > mpirun -np 24 -x > > > > > > MPIBLAST_SHARED=/where/ever,MPIBLAST_LOCAL=/local/storage > > mpirun > > > -Lucas > > > On Sunday, April 09, 2006 at 23:39 -0700, > > ankit patel wrote: > > > > i think i have a problem to set the > > environment > > > > variable for mpiblast. MPIBLAST_SHARED and > > > > MPIBLAST_LOCAL. I am already set in .ncbirc > > file > > > > created by me at home directory as well as > > in ncbi > > > > directory but i failed to get output. so > > can u tell me > > > > when i have to make .ncbirc file and what i > > have to > > > > write in it. > > > > > > > > With Best Regards, > > > > > > > > Ankit Patel > > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by xPML, a > > groundbreaking scripting language > > that extends applications into web and mobile media. > > Attend the live webcast > > and join the prime developer group breaking into > > this new coding territory! > > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 > > _______________________________________________ > > Mpiblast-users mailing list > > [email protected] > > > https://lists.sourceforge.net/lists/listinfo/mpiblast-users > > > > With Best Regards, > > Ankit Patel > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 _______________________________________________ Mpiblast-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mpiblast-users
