[Mpiblast-users] mpiBLAST compiling error

Thu, 29 Jun 2006 21:21:18 -0700

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
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