[Bioclusters] Re: new on using clusters: problem running mpiblast (2)

Aaron Darling darling at cs.wisc.edu
Sat Sep 8 18:04:14 EDT 2007

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.


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

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