[Bioclusters] MPIblast installation problem
landman
bioclusters@bioinformatics.org
Fri, 4 Jul 2003 00:40:27 -0500
Hi Samir:
You might want to try using the gcc option
--nostdinc
thought the caveat would be for that one particular file, that it may break
everything else in that file. You would have to map out the include path by
hand on the command line using -I/path/ statements.
Then again, it might just work...
Joe
On Thu, 3 Jul 2003 17:20:26 -0700, Samir Pandurangi wrote
> 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
> >
> > _______________________________________________
> > Bioclusters maillist - Bioclusters@bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bioclusters
>
> _______________________________________________
> Bioclusters maillist - Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
--
Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web : http://scalableinformatics.com
phone: +1 734 612 4615