Dear Developers,
We work for the university of Padua and we are interested in your programm.
We are developping a web-services platform for the gene annotation and we
would like to use mpiblast for making our system faster. In fact we have to
use blast but this limit the platform in term of time.
We hope to resolve this problem using a parallelized blast like mpiblast.
I try to test mpiblast but I have some problems and I ask help to you.
1) I try to use the mpiblast version 1.4.0 with ncbi tools of oct 2004. In
my pc (with debian etch) I can't compile the ncbi tools. I check in the web
and I have seen that this problem is know.... so I try to compile ncbi tools
and mpiblast in a debian Sarge. The compiling problem are resolved but
mpiblast don't work correctly.
MpiFormatBD seems to work correctly and it produces a fragmented formatted
database but mpiblast doesn't produce output.
I try to run the programm with "mpirun" in a cluster of 8 machines (all with
etch...). Mpiblast is correctly launched in every machine but after 30
minutes I have to kill the processes because they seem freezed. I don't
receive any error messages. Using a normal blastn with the same query and
database, it completes the operation in 4 seconds.
The configuration file .ncbirc is correct and it includes shared directories
all accessible.
I try to launch mpiblast with STRACE for checking where it freezes: in every
case I tried, it freezes with this output
"write(-1, "cmd=client_bnr_fence_in gid=0 gr"..., 48) = -1 EBADF (Bad file
descriptor)"
2) I try to use the rpm version. I convert all with alien but also in this
case the programm doesn't work correctly. When I try to run it, I receive
always the same error :
"Sorry, mpiBLAST must be run on 3 or more nodes
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0"
even if I try to run it on 8 nodes!!!
We try to use different version of ncbi tools (more recent, if the patch was
available...) and different version of mpiblast but we receive always the
same messages from the system.
May this be a problem of debian version ? ( we compile on sarge but the we
test the programm on etch.... but we can't downgrade all the machine....).
I hope to receive help.
Best Regards
Alessandro Albiero
c/o Bioinformatic Lab. of CRIBI, Prof. G. Valle,
University of Padova,
V.le G. Colombo 3, 35121 Padova (Pd) Italy,
tel +39 0498276165,
--
Alessandro
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