[Bioclusters] MPIblast installation problem

Samir Pandurangi bioclusters@bioinformatics.org
Thu, 3 Jul 2003 17:20:26 -0700


thanks for the info, the unix server I'm using:
SunOS trna 5.8 Generic_108528-21 sun4u sparc SUNW,Sun-Fire-880
does that shed any light on the solution? thanks.
--
sp

----- Original Message ----- 
From: "Aaron Darling" <darling@cs.wisc.edu>
To: <bioclusters@bioinformatics.org>
Sent: Thursday, July 03, 2003 5:07 PM
Subject: Re: [Bioclusters] MPIblast installation problem


> Samir, could you tell us what type of Unix you are using?
>
> The problem seems to be that your unix installation already has a
> getopt() implementation, but probably does not have a getopt_long().
> Because the build system can't find GNU getopt_long header file it tries
> to use the GNU getopt source code that is included with the mpiBLAST
> distribution.
>
> One possible workaround would be removing the getopt() function from
> getopt.h, getopt.c and getopt1.c in the mpiBLAST-1.1.1/src directory,
> though I can't guarantee that this will work without knowing the details
> of your system.
>
> A long term solution will probably be conditionally defining the mpiBLAST
> supplied getopt() depending on whether a system supplied getopt() exists.
>
> Hope that helps,
> -Aaron
>
> On Thu, 3 Jul 2003, Samir Pandurangi wrote:
>
> > Hello all, I'm having a problem with MPIblast installation on unix and
I'm wondering if someone can help me out:
> > Here is the process, starting from a directory called apps:
> > 1. I create a directory called apps/MPI
> > 2. In MPI, I unzip and untar the free version of MPI called mpich
available at http://www-unix.mcs.anl.gov/mpi/
> >     --I did a configure and make for this. Nothing special.
> > 3. I downloaded the NCBItoolbox, ncbi.tar.Z, from
ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/
> > 4. I untarred and unzipped this into directory apps/NCBItoolbox
> >  --to install, i followed the readme instructions
> > 5. I downloaded MPIblast into apps/MPIblast
> >  --to install, i followed the instructions on
http://mpiblast.lanl.gov/README-1.1.0.html. specifically, i set the path of
where MPIblast will be installed at apps/myMPIblast and specified the path
of the NCBI toolbox (as options while running configure).
> > 6. When I tried to make, I get this error:
> > ------------------------------------------
> > [117] trna> make
> > Making all in src
> > if
mpiCC -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPA
CKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"mpiBLAST\" -DVERSION=
\"1.1.1\" -DSTDC_HEADERS=1 -D_FILE_OFFSET_BITS=64 -DTIME_WITH_SYS_TIME=1 -I.
 -I. -I../include/ -I/home/samir/apps/NCBItoolbox/ncbi/include/     -O2 -DIN
STALL_PREFIX="\"/home/samir/apps/myMPIblast\"" -g -O2 -MT
mpiblast.o -MD -MP -MF ".deps/mpiblast.Tpo" \
> >   -c -o mpiblast.o `test -f 'mpiblast.cpp' || echo './'`mpiblast.cpp; \
> > then mv ".deps/mpiblast.Tpo" ".deps/mpiblast.Po"; \
> > else rm -f ".deps/mpiblast.Tpo"; exit 1; \
> > fi
> > bash: mpiCC: command not found
> > *** Error code 1
> > make: Fatal error: Command failed for target `mpiblast.o'
> > Current working directory /home/samir/apps/MPIblast/mpiBLAST-1.1.1/src
> > *** Error code 1
> > make: Fatal error: Command failed for target `all-recursive'
> > ---------------------------------------------------------------
> >
> >
> > When I tried to set the path of mpiCC in my environment PATH, i get this
error:
> > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> > [147] trna> make
> > Making all in src
> > if
mpiCC -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPA
CKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"mpiBLAST\" -DVERSION=
\"1.1.1\" -DSTDC_HEADERS=1 -D_FILE_OFFSET_BITS=64 -DTIME_WITH_SYS_TIME=1 -I.
 -I. -I../include/ -I/home/samir/apps/NCBItoolbox/ncbi/include/     -O2 -DIN
STALL_PREFIX="\"/home/samir/apps/myMPIblast\"" -g -O2 -MT
mpiblast.o -MD -MP -MF ".deps/mpiblast.Tpo" \
> >   -c -o mpiblast.o `test -f 'mpiblast.cpp' || echo './'`mpiblast.cpp; \
> > then mv ".deps/mpiblast.Tpo" ".deps/mpiblast.Po"; \
> > else rm -f ".deps/mpiblast.Tpo"; exit 1; \
> > fi
> > In file included from /usr/local/include/c++/3.2/cstdlib:52,
> >                  from /usr/local/include/c++/3.2/bits/stl_algobase.h:67,
> >                  from /usr/local/include/c++/3.2/algorithm:66,
> >                  from mpiblast.cpp:68:
> > /usr/include/stdlib.h:189: declaration of C function `int getopt(int,
char*
> >    const*, const char*)' conflicts with
> > getopt.h:147: previous declaration `int getopt()' here
> > *** Error code 1
> > make: Fatal error: Command failed for target `mpiblast.o'
> > Current working directory /home/samir/apps/MPIblast/mpiBLAST-1.1.1/src
> > *** Error code 1
> > make: Fatal error: Command failed for target `all-recursive'
> > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> >
> > any ideas?
> > --
> > sp
>
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