Thanks Aaron, Indeed I got it compiled before (and now again, without my last reported "CC/CPP" exports, and with or without non-specific "export CC=mpicc" and "export CXX=mpicxx" suggested by Zhao Xu). The problem was, when I run the mpiblast with: /opt/openmpi.gcc/bin/mpirun -np 16 -machinefile ./machines /home/local/bin/mpiblast -p blastp -i ./bait.fasta -d ecoli.aa I got following error that I don't have a clue as where to look for the cause: 1 0.095628 Bailing out with signal 11 [node001:13406] MPI_ABORT invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 0 0 0.101815 Bailing out with signal 15 [node001:13405] MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 0 15 0.157852 Bailing out with signal 15 [node001:13420] MPI_ABORT invoked on rank 15 in communicator MPI_COMM_WORLD with errorcode 0 2 0.105103 Bailing out with signal 15 [node001:13407] MPI_ABORT invoked on rank 2 in communicator MPI_COMM_WORLD with errorcode 0 3 0.109706 Bailing out with signal 15 [node001:13408] MPI_ABORT invoked on rank 3 in communicator MPI_COMM_WORLD with errorcode 0 4 0.114032 Bailing out with signal 15 [node001:13409] MPI_ABORT invoked on rank 4 in communicator MPI_COMM_WORLD with errorcode 0 5 0.117891 Bailing out with signal 15 [node001:13410] MPI_ABORT invoked on rank 5 in communicator MPI_COMM_WORLD with errorcode 0 6 0.122292 Bailing out with signal 15 [node001:13411] MPI_ABORT invoked on rank 6 in communicator MPI_COMM_WORLD with errorcode 0 7 0.125675 Bailing out with signal 15 [node001:13412] MPI_ABORT invoked on rank 7 in communicator MPI_COMM_WORLD with errorcode 0 8 0.129363 Bailing out with signal 15 [node001:13413] MPI_ABORT invoked on rank 8 in communicator MPI_COMM_WORLD with errorcode 0 9 0.134528 Bailing out with signal 15 [node001:13414] MPI_ABORT invoked on rank 9 in communicator MPI_COMM_WORLD with errorcode 0 10 0.138087 Bailing out with signal 15 [node001:13415] MPI_ABORT invoked on rank 10 in communicator MPI_COMM_WORLD with errorcode 0 11 0.141622 Bailing out with signal 15 [node001:13416] MPI_ABORT invoked on rank 11 in communicator MPI_COMM_WORLD with errorcode 0 12 0.145868 Bailing out with signal 15 [node001:13417] MPI_ABORT invoked on rank 12 in communicator MPI_COMM_WORLD with errorcode 0 13 0.149375 Bailing out with signal 15 [node001:13418] MPI_ABORT invoked on rank 13 in communicator MPI_COMM_WORLD with errorcode 0 14 0.152966 Bailing out with signal 15 [node001:13419] MPI_ABORT invoked on rank 14 in communicator MPI_COMM_WORLD with errorcode 0 [As related information, the mpirun is working fine when tested with a small "hello" program that showed responses from all nodes]. -- Zhiliang On Sun, 9 Sep 2007, Aaron Darling wrote: > Date: Sun, 09 Sep 2007 08:04:14 +1000 > From: Aaron Darling <darling at cs.wisc.edu> > Reply-To: HPC in Bioinformatics <bioclusters at bioinformatics.org> > To: HPC in Bioinformatics <bioclusters at bioinformatics.org> > Subject: Re: [Bioclusters] Re: new on using clusters: problem running mpiblast > (2) > > Hi Zhiliang > > For reasons that are beyond me, the version of autoconf that we used to > package mpiBLAST 1.4.0 does not approve of setting CC and/or CXX to > mpicc or mpicxx. Doing so results in the autoconf error you have > observed. For that reason we added the --with-mpi=/path/to/mpi > configure option. It should be sufficient to use that option alone to > set the preferred compiler path. If not, then it's a bug in the > mpiblast configure system. > > In response to your other query, I personally have not used mpiblast > with OpenMPI but I believe others have. The 1.4.0 release was tested > against mpich1/2 and LAM. > > Regards, > -Aaron > > Zhiliang Hu wrote: >> Hi Zhao - Thanks for providing more clues to solve my problem! >> >> I have actually gone through all these steps to match up the right >> number of formated sequence database segments, the number of processes >> to use, having the excutables and sequence database on shared nsf file >> paths mounted to all nodes, use the correct paths in ~/.ncbirc, and >> try out with fewest but necessary options, and so on. >> >> While the previous trials were using a mpiblast seemingly compiled >> correctly, when I tried to make sure the compile/run are using the >> same mpi sets, I tried to re-compile as >> >>> export CC=/opt/openmpi.gcc/bin/mpicc >>> export CPP=/opt/openmpi.gcc/bin/mpicxx >>> ./configure --with-ncbi=/home/share/src/ncbi --prefix=/opt/local >> --with-mpi=/opt/openmpi.gcc >> >> -- this time the compilation failed with errors: >> http://www.animalgenome.org/~hu/share/tmp/config.log >> http://www.animalgenome.org/~hu/share/tmp/config2.log >> >> The trials were with OpenMPI-1.2.1 and 1.2.3 --are these version >> compatibility problems? Is there a known MPI version that worked with >> MPIblast 1.4.0? >> >> Zhiliang >> >> >> On Thu, 6 Sep 2007, Zhao Xu wrote: >> >>> Date: Thu, 6 Sep 2007 09:08:54 +0800 >>> From: Zhao Xu <xuzh.fdu at gmail.com> >>> Reply-To: HPC in Bioinformatics <bioclusters at bioinformatics.org> >>> To: bioclusters at bioinformatics.org >>> Subject: [Bioclusters] Re: new on using clusters: problem running >>> mpiblast (2) >>> >>> Hi Zhiliang, >>> Firstly, I suggest that you run mpiBlast with the default parameters, >>> only >>> use it with -p -i -d and -o. If the default parameter works fine, you >>> should check the system environments: is there any memory limitation? >>> write >>> access? etc. >>> >>> If the default parameter can not work either, I think you should check: >>> 1. How many segements did you format the database? Is the number 12? >>> Make >>> sure you run mpiBlast with two more processes. >>> 2. Can every nodes read in the input sequences? >>> 3. Check your ~/.ncbirc, make sure each node has ~/.ncbirc and each >>> node can >>> access the directorys written in ~/.ncbirc. >>> >>> Regards, >>> XU Zhao