[Bioclusters] MPIblast installation problem

[Aaron Darling]

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=\"\" -DPACKAGE_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 -DINSTALL_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=\"\" -DPACKAGE_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 -DINSTALL_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