[Bioclusters] MPIblast installation problem
Samir Pandurangi
bioclusters@bioinformatics.org
Thu, 3 Jul 2003 16:37:25 -0700
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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=3D\"\" -DPACKAGE_TARNAME=3D\"\" =
-DPACKAGE_VERSION=3D\"\" -DPACKAGE_STRING=3D\"\" =
-DPACKAGE_BUGREPORT=3D\"\" -DPACKAGE=3D\"mpiBLAST\" =
-DVERSION=3D\"1.1.1\" -DSTDC_HEADERS=3D1 -D_FILE_OFFSET_BITS=3D64 =
-DTIME_WITH_SYS_TIME=3D1 -I. -I. -I../include/ =
-I/home/samir/apps/NCBItoolbox/ncbi/include/ -O2 =
-DINSTALL_PREFIX=3D"\"/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=3D\"\" -DPACKAGE_TARNAME=3D\"\" =
-DPACKAGE_VERSION=3D\"\" -DPACKAGE_STRING=3D\"\" =
-DPACKAGE_BUGREPORT=3D\"\" -DPACKAGE=3D\"mpiBLAST\" =
-DVERSION=3D\"1.1.1\" -DSTDC_HEADERS=3D1 -D_FILE_OFFSET_BITS=3D64 =
-DTIME_WITH_SYS_TIME=3D1 -I. -I. -I../include/ =
-I/home/samir/apps/NCBItoolbox/ncbi/include/ -O2 =
-DINSTALL_PREFIX=3D"\"/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*=20
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
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<DIV><FONT face=3DArial size=3D2>Hello all, I'm having a problem with =
MPIblast=20
installation on unix and I'm wondering if someone can help me =
out:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Here is the process, starting from a =
directory=20
called apps:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>1. I create a directory called=20
apps/MPI</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>2. In MPI, I unzip and untar the free =
version of=20
MPI called mpich available at <A=20
href=3D"http://www-unix.mcs.anl.gov/mpi/">http://www-unix.mcs.anl.gov/mpi=
/</A></FONT></DIV>
<DIV><FONT face=3DArial size=3D2> --I did a configure =
and make for=20
this. Nothing special.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>3. I downloaded the NCBItoolbox, =
ncbi.tar.Z, from=20
<A href=3D"ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/"><FONT=20
face=3D"Times New Roman"=20
size=3D3>ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/</FONT></A></FONT></DI=
V>
<DIV><FONT face=3DArial size=3D2>4. I untarred and unzipped this into =
directory=20
apps/NCBItoolbox</FONT></DIV>
<DIV><FONT face=3DArial size=3D2> --to install, i followed the =
readme=20
instructions</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>5. I downloaded MPIblast into=20
apps/MPIblast</FONT></DIV>
<DIV><FONT face=3DArial size=3D2> --to install, i followed the =
instructions=20
on <A=20
href=3D"http://mpiblast.lanl.gov/README-1.1.0.html">http://mpiblast.lanl.=
gov/README-1.1.0.html</A>.=20
specifically, i set the path of where MPIblast will be installed at=20
apps/myMPIblast and specified the path of the NCBI toolbox (as options =
while=20
running configure).</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>6. When I tried to make, I get this=20
error:</FONT></DIV>
<DIV><FONT face=3DArial=20
size=3D2>------------------------------------------</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>[117] trna> make<BR>Making all in =
src<BR>if=20
mpiCC -DPACKAGE_NAME=3D\"\" -DPACKAGE_TARNAME=3D\"\" =
-DPACKAGE_VERSION=3D\"\"=20
-DPACKAGE_STRING=3D\"\" -DPACKAGE_BUGREPORT=3D\"\" =
-DPACKAGE=3D\"mpiBLAST\"=20
-DVERSION=3D\"1.1.1\" -DSTDC_HEADERS=3D1 -D_FILE_OFFSET_BITS=3D64=20
-DTIME_WITH_SYS_TIME=3D1 -I. -I. -I../include/=20
-I/home/samir/apps/NCBItoolbox/ncbi/include/ -O2 =
-DINSTALL_PREFIX=3D"\"/home/samir/apps/myMPIblast\"" -g -O2 -MT =
mpiblast.o -MD -MP=20
-MF ".deps/mpiblast.Tpo" \<BR> -c -o mpiblast.o `test -f =
'mpiblast.cpp' ||=20
echo './'`mpiblast.cpp; \<BR>then mv ".deps/mpiblast.Tpo" =
".deps/mpiblast.Po";=20
\<BR>else rm -f ".deps/mpiblast.Tpo"; exit 1; \<BR>fi<BR>bash: mpiCC: =
command=20
not found<BR>*** Error code 1<BR>make: Fatal error: Command failed for =
target=20
`mpiblast.o'<BR>Current working directory=20
/home/samir/apps/MPIblast/mpiBLAST-1.1.1/src<BR>*** Error code =
1<BR>make: Fatal=20
error: Command failed for target=20
`all-recursive'<BR>------------------------------------------------------=
---------</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>When I tried to set the path of mpiCC =
in my=20
environment PATH, i get this error:</FONT></DIV>
<DIV><FONT face=3DArial =
size=3D2>^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>[147] trna> make<BR>Making all in =
src<BR>if=20
mpiCC -DPACKAGE_NAME=3D\"\" -DPACKAGE_TARNAME=3D\"\" =
-DPACKAGE_VERSION=3D\"\"=20
-DPACKAGE_STRING=3D\"\" -DPACKAGE_BUGREPORT=3D\"\" =
-DPACKAGE=3D\"mpiBLAST\"=20
-DVERSION=3D\"1.1.1\" -DSTDC_HEADERS=3D1 -D_FILE_OFFSET_BITS=3D64=20
-DTIME_WITH_SYS_TIME=3D1 -I. -I. -I../include/=20
-I/home/samir/apps/NCBItoolbox/ncbi/include/ -O2 =
-DINSTALL_PREFIX=3D"\"/home/samir/apps/myMPIblast\"" -g -O2 -MT =
mpiblast.o -MD -MP=20
-MF ".deps/mpiblast.Tpo" \<BR> -c -o mpiblast.o `test -f =
'mpiblast.cpp' ||=20
echo './'`mpiblast.cpp; \<BR>then mv ".deps/mpiblast.Tpo" =
".deps/mpiblast.Po";=20
\<BR>else rm -f ".deps/mpiblast.Tpo"; exit 1; \<BR>fi<BR>In file =
included from=20
/usr/local/include/c++/3.2/cstdlib:52,<BR> &=
nbsp; =20
from=20
/usr/local/include/c++/3.2/bits/stl_algobase.h:67,<BR> &=
nbsp; &n=
bsp;=20
from=20
/usr/local/include/c++/3.2/algorithm:66,<BR>  =
; =20
from mpiblast.cpp:68:<BR>/usr/include/stdlib.h:189: declaration of C =
function=20
`int getopt(int, char* <BR> const*, const char*)' conflicts=20
with<BR>getopt.h:147: previous declaration `int getopt()' here<BR>*** =
Error code=20
1<BR>make: Fatal error: Command failed for target =
`mpiblast.o'<BR>Current=20
working directory /home/samir/apps/MPIblast/mpiBLAST-1.1.1/src<BR>*** =
Error code=20
1<BR>make: Fatal error: Command failed for target=20
`all-recursive'<BR>^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^</FONT></=
DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>any ideas?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>--</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>sp</DIV></FONT></BODY></HTML>
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