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