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 >> _______________________________________________ >> Bioclusters maillist - Bioclusters at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bioclusters >> > _______________________________________________ > Bioclusters maillist - Bioclusters at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters