Hello Alessandro, A first, very useful step to diagnose your mpiblast freeze would be to run mpiblast with the --debug command-line option. That will cause a verbose debugging log to be printed. If the debug output is smaller than a few KB, please send it to the list. Otherwise, please send it directly to me...
Thanks, -Aaron alessandro albiero wrote: > 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 > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > ------------------------------------------------------------------------ > > _______________________________________________ > Mpiblast-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mpiblast-users > ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Mpiblast-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mpiblast-users
