[BiO BB] parallel clustalw

[Deeþàn Chakravarthÿ]

Hi All,
  Am trying to compile parallel version of clustalw on Cent OS 4.  I 
downloaded  the package from

ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/ParClustal0.2.tar.gz


I have ncbi tool kit installed in my machine.  When I run make I get the 
following error.

: undefined reference to `seek_si_sj_to_calculate'
slaves.o(.text+0x687): In function `main_processes_slaves':
: undefined reference to `subpairalign'
collect2: ld returned 1 exit status
make: *** [clustalx] Error 1

I had attached the complete output of make, uname and gcc version below.


$ uname -a
Linux panther5.nus.edu.sg 2.6.9-42.0.10.ELsmp #1 SMP Tue Feb 27 10:11:19 
EST 2007 i686 i686 i386 GNU/Linux


]$ gcc -v
Reading specs from /usr/lib/gcc/i386-redhat-linux/3.4.6/specs
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man 
--infodir=/usr/share/info --enable-shared --enable-threads=posix 
--disable-checking --with-system-zlib --enable-__cxa_atexit 
--disable-libunwind-exceptions --enable-java-awt=gtk 
--host=i386-redhat-linux
Thread model: posix
gcc version 3.4.6 20060404 (Red Hat 3.4.6-8)



$ make
cc -c -O -I/usr/include/openmpi/ init.c
cc -c -O -I/usr/include/openmpi/ interface.c
cc -c -O -I/usr/include/openmpi/ readseq.c
cc -c -O -I/usr/include/openmpi/ writeseq.c
cc -c -O -I/usr/include/openmpi/ showpair.c
cc -c -O -I/usr/include/openmpi/ malign.c
cc -c -O -I/usr/include/openmpi/ util.c
cc -c -O -I/usr/include/openmpi/ trees.c
cc -c -O -I/usr/include/openmpi/ gcgcheck.c
cc -c -O -I/usr/include/openmpi/ prfalign.c
cc  -c -O -I/usr/include/openmpi/ pairalign.c
cc -c -O -I/usr/include/openmpi/ calcgapcoeff.c
cc -c -O -I/usr/include/openmpi/ calcprf1.c
cc -c -O -I/usr/include/openmpi/ calcprf2.c
cc -c -O -I/usr/include/openmpi/ readtree.c
cc -c -O -I/usr/include/openmpi/ seqweight.c
cc -c -O -I/usr/include/openmpi/ readmat.c
cc -c -O -I/usr/include/openmpi/ alnscore.c
cc -c -O -I/usr/include/openmpi/ random.c
cc -c -O -I/usr/include/openmpi/ motifs.c
cc -c -O -I/usr/include/openmpi/ bionj.c
cc  -c -O -I/usr/include/openmpi/ slaves.c
cc -c -O -I/usr/include/openmpi/ -DWIN_MOTIF 
-I/home/griduser/clustalw/toolbox/ncbi/include  xutils.c
cc -c -O -I/usr/include/openmpi/ -DWIN_MOTIF 
-I/home/griduser/clustalw/toolbox/ncbi/include  xmenu.c
cc -c -O -I/usr/include/openmpi/ -DWIN_MOTIF 
-I/home/griduser/clustalw/toolbox/ncbi/include  xcolor.c
cc -c -O -I/usr/include/openmpi/ -DWIN_MOTIF 
-I/home/griduser/clustalw/toolbox/ncbi/include  xdisplay.c
cc -c -O -I/usr/include/openmpi/ -DWIN_MOTIF 
-I/home/griduser/clustalw/toolbox/ncbi/include  xscore.c
cc -c -O -I/usr/include/openmpi/ -DWIN_MOTIF 
-I/home/griduser/clustalw/toolbox/ncbi/include  clustalx.c
cc -o clustalx init.o interface.o readseq.o writeseq.o showpair.o 
malign.o util.o trees.o gcgcheck.o prfalign.o pairalign.o calcgapcoeff.o 
calcprf1.o calcprf2.o readtree.o seqweight.o readmat.o alnscore.o 
random.o motifs.o bionj.o slaves.o xutils.o xmenu.o xcolor.o xdisplay.o 
xscore.o clustalx.o -O -lm -lmpi -lrt -pthread 
-L/home/griduser/clustalw/toolbox/ncbi/lib -L/usr/lib/openmpi/ 
-L/usr/X11R6/lib  -lvibrant -lncbi -lpthread -lXm -lXmu -lXt -lX11 -lm
/home/griduser/clustalw/toolbox/ncbi/lib/libncbi.a(ncbifile.o)(.text+0x945): 
In function `Nlm_TmpNam':
: warning: the use of `tempnam' is dangerous, better use `mkstemp'
writeseq.o(.text+0x284): In function `open_output_file':
: warning: the `gets' function is dangerous and should not be used.
slaves.o(.text+0x5f0): In function `main_processes_slaves':
: undefined reference to `seek_si_sj_to_calculate'
slaves.o(.text+0x687): In function `main_processes_slaves':
: undefined reference to `subpairalign'
collect2: ld returned 1 exit status
make: *** [clustalx] Error 1



Thanks
Deepan