Hi Aaron, The mpiBLAST and NCBI tool box Dec 2005 works. Thanks a lot for your help. Peng
On 7/8/06, Aaron Darling <[EMAIL PROTECTED]> wrote: > 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 > ------------------------------------------------------------------------- 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
