Hi, following on from my previous message on BLAST parallelisation I have managed to persuade our cluster manager to install MPI support for us and now I can use mpiBLAST after all. I have a few questions regarding its configuration which I cannot seem to get any info about elsewhere. Our Linux cluster is a shared facility of currently 118 cpus on 59 dual processor machines which gets used heavily by particle physicists running jobs that often take days or even weeks. Traffic is spasmodic but most times it is fairly heavy. We have three nodes reserved for jobs of less than one hour's wall time. I am part of the bio group and we have a share of 20% of the total compute time on this cluster. Jobs get submitted and queued via the OpenPBS batch system. The queue priority is worked out by a formula which among other things takes into account recent usage (if you had lots of jobs recently you get penalised) and job size (if your job is small it gets a higher priority). Questions: 1. How many database fragments should I generate? 2. How will the spasmodic traffic on the cluster affect the performance of mpiBLAST? 3. How are jobs partitioned for queuing with PBS (given an input file with one sequence and a different scenario where the input file contains multiple query sequences)? 4. When I issue the mpirun command and I specify the number of nodes to be used, what does that do? Will this actually work on a cluster like this where I don't have any control over the scheduling process? cheers Micha -- -------------------------------------------------- Dr Micha M Bayer Grid Developer, BRIDGES Project National e-Science Centre, Glasgow Hub 246c Kelvin Building University of Glasgow Glasgow G12 8QQ Scotland, UK Email: michab@dcs.gla.ac.uk Project home page: http://www.brc.dcs.gla.ac.uk/projects/bridges/ Personal Homepage: http://www.brc.dcs.gla.ac.uk/~michab/ Tel.: +44 (0)141 330 2958