Hi Peng, sorry for the terribly slow reply, i've been trying to finish a dissertation... It's not clear to me why you're experiencing that compile error, as the "unindexBioseqs()" function is something of my own creation and thus isn't subject to the whims of the NCBI development team. The "wrong number of arguments" error is the sort of thing that should really only happen if the source code has been modified somehow. or perhaps the compiler can't find blast_hooks.h and gets confused?
In any case, are you willing to try a build from a more recent source code snapshot? You could try compiling this: http://mpiblast.sourceforge.net/mpiblast-latest.tar.gz with an NCBI toolkit as recent as Dec. 2005 The build procedure is slightly different for the cvs source snapshots. You'll need to run: aclocal && autoheader && automake -a && autoconf before running configure, because we don't keep the automake system in our cvs. -Aaron Peng Gu wrote: > Hi all, > > I got a problem when trying to compile the mpiblast-1.4.0 on my Fedora > Core 5 Linux machine. > > What I did: > > mkdir /nfs1/src/mpiBLAST > cd /nfs1/src/mpiBLAST > wget http://mpiblast.lanl.gov/downloads/files/mpiBLAST-1.4.0.tgz > tar -zxvf mpiBLAST-1.4.0.tgz > wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/20050605/ncbi.tar.gz > tar -zxvf ncbi.tar.gz > patch -p0 < patch -p0 < mpiblast-1.4.0/ncbi_Jun2005_evalue.patch > ncbi/make/makedis.csh > > Everything listed above goes smoothly. And here is my problem: > > cd mpiblast-1.4.0 > ./configure --prefix=/nfs1/bin/mpiBLAST > --with-ncbi=/nfs1/src/mpiBLAST/ncbi --with-mpi=/nfs1/bin/mpich2-install > > The output was: > checking build system type... i686-pc-linux > checking host system type... i686-pc-linux > checking target system type... i686-pc-linux > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > checking for MPI... /nfs1/bin/mpich2-install/bin > checking for mpicc... /nfs1/bin/mpich2-install/bin/mpicc > checking for mpicxx... /nfs1/bin/mpich2-install/bin/mpicxx > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether /nfs1/bin/mpich2-install/bin/mpicc accepts -g... yes > checking for /nfs1/bin/mpich2-install/bin/mpicc option to accept ANSI > C... none needed > checking for style of include used by make... GNU > checking dependency style of /nfs1/bin/mpich2-install/bin/mpicc... gcc3 > checking whether we are using the GNU C++ compiler... yes > checking whether /nfs1/bin/mpich2-install/bin/mpicxx accepts -g... yes > checking dependency style of /nfs1/bin/mpich2-install/bin/mpicxx... gcc3 > checking for ranlib... ranlib > checking for a BSD-compatible install... /usr/bin/install -c > checking whether ln -s works... yes > checking how to run the C preprocessor... > /nfs1/bin/mpich2-install/bin/mpicc -E > checking for egrep... grep -E > checking for ANSI C header files... yes > checking for special C compiler options needed for large files... no > checking for _FILE_OFFSET_BITS value needed for large files... 64 > checking for _LARGE_FILES value needed for large files... no > checking for getopt_long... yes > checking for getopt... yes > checking for NCBI library... /nfs1/src/mpiBLAST/ncbi > checking for /nfs1/src/mpiBLAST/ncbi/demo/formatdb.c... yes > checking for /nfs1/src/mpiBLAST/ncbi/build/ncbithr.o... yes > checking for MPI_Alloc_mem... checking for MPE timing option... false > checking for an ANSI C-conforming const... yes > checking for inline... __inline__ > checking whether time.h and sys/time.h may both be included... yes > checking whether /nfs1/bin/mpich2-install/bin/mpicc needs > -traditional... no > configure: creating ./config.status > config.status: creating Makefile > config.status: creating src/Makefile > config.status: creating src/config.h > config.status: src/config.h is unchanged > config.status: executing depfiles commands > > > And then when I type "make", I get the following errors: > > Making all in src > make[1]: Entering directory `/mnt/nfs1/src/mpiBLAST/mpiblast-1.4.0/src' > make all-am > make[2]: Entering directory `/mnt/nfs1/src/mpiBLAST/mpiblast-1.4.0/src' > if /nfs1/bin/mpich2-install/bin/mpicxx -DHAVE_CONFIG_H -I. -I. -I. > -I../include/ -I/nfs1/src/mpiBLAST/ncbi/include/ -DUSING_MPI > -DINSTALL_PREFIX="\"/nfs1/bin/mpiBLAST\"" -g -O2 -MT > mpiblast-blastjob.o -MD -MP -MF ".deps/mpiblast-blastjob.Tpo" -c -o > mpiblast-blastjob.o `test -f 'blastjob.cpp' || echo './'`blastjob.cpp; \ > then mv -f ".deps/mpiblast-blastjob.Tpo" ".deps/mpiblast- > blastjob.Po"; else rm -f ".deps/mpiblast-blastjob.Tpo"; exit 1; fi > if /nfs1/bin/mpich2-install/bin/mpicxx -DHAVE_CONFIG_H -I. -I. -I. > -I../include/ -I/nfs1/src/mpiBLAST/ncbi/include/ -DUSING_MPI > -DINSTALL_PREFIX="\"/nfs1/bin/mpiBLAST\"" -g -O2 -MT > mpiblast-db_spec.o -MD -MP -MF ".deps/mpiblast-db_spec.Tpo" -c -o > mpiblast-db_spec.o `test -f 'db_spec.cpp' || echo './'`db_spec.cpp; \ > then mv -f ".deps/mpiblast-db_spec.Tpo" ".deps/mpiblast-db_spec.Po"; > else rm -f ".deps/mpiblast-db_spec.Tpo"; exit 1; fi > if /nfs1/bin/mpich2-install/bin/mpicc -DHAVE_CONFIG_H -I. -I. -I. > -I../include/ -I/nfs1/src/mpiBLAST/ncbi/include/ -DUSING_MPI > -DINSTALL_PREFIX="\"/nfs1/bin/mpiBLAST\"" -g -O2 -MT > mpiblast-blast_hooks.o -MD -MP -MF ".deps/mpiblast-blast_hooks.Tpo" -c > -o mpiblast-blast_hooks.o `test -f 'blast_hooks.c' || echo > './'`blast_hooks.c; \ > then mv -f ".deps/mpiblast-blast_hooks.Tpo" > ".deps/mpiblast-blast_hooks.Po"; els > e rm -f ".deps/mpiblast-blast_hooks.Tpo"; exit 1; fi > blast_hooks.c:739: warning: no previous prototype for ?getQuery? > blast_hooks.c:762: warning: no previous prototype for ?getFakeBioseq? > blast_hooks.c:940: warning: no previous prototype for ?performBLAST? > blast_hooks.c:1005: warning: no previous prototype for > ?createBinASNResults? > blast_hooks.c: In function ?writeSearchStatistics?: > blast_hooks.c:1236: warning: unused variable ?anp? > blast_hooks.c:1234: warning: unused variable ?atp? > blast_hooks.c: At top level: > blast_hooks.c:1250: warning: no previous prototype for ?processReturnData? > blast_hooks.c:1294: warning: no previous prototype for ?cleanupTheMess? > blast_hooks.c:1455: warning: no previous prototype for > ?MpiBlastPrintReference? > blast_hooks.c:1479: warning: no previous prototype for > ?indexSubjectBioseqs? > blast_hooks.c:1493: warning: no previous prototype for > ?unindexSubjectBioseqs? > blast_hooks.c: In function ?outputResults?: > blast_hooks.c:1782: error: too many arguments to function > ?unindexSubjectBioseqs? > make[2]: *** [mpiblast-blast_hooks.o] Error 1 > make[2]: Leaving directory `/mnt/nfs1/src/mpiBLAST/mpiblast-1.4.0/src' > make[1]: *** [all] Error 2 > make[1]: Leaving directory `/mnt/nfs1/src/mpiBLAST/mpiblast-1.4.0 /src' > make: *** [all-recursive] Error 1 > > Can anybody tell me what has gone wrong? Thanks in advance for your > asistance. > > Regards, > Peng > ------------------------------------------------------------------------ > > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > ------------------------------------------------------------------------ > > _______________________________________________ > Mpiblast-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mpiblast-users > Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Mpiblast-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mpiblast-users
