OpenMPI 1.5rc5 fails in opal/tools/wrappers for PGI 10.3 (see http://www.open-mpi.org/community/lists/devel/2010/08/8312.php)
:
Making all in tools/wrappers
make[2]: Entering directory `/usr/local/src/openmpi-1.5rc5/opal/
tools/wrappers'
CC opal_wrapper.o
CCLD opal_wrapper
../../../opal/.libs/libopen-pal.so: undefined reference to
`pthread_create'
../../../opal/.libs/libopen-pal.so: undefined reference to `assert'
../../../opal/.libs/libopen-pal.so: undefined reference to
`pthread_mutex_trylock'
../../../opal/.libs/libopen-pal.so: undefined reference to
`pthread_atfork'
../../../opal/.libs/libopen-pal.so: undefined reference to
`pthread_join'
make[2]: *** [opal_wrapper] Error 2
make[2]: Leaving directory `/usr/local/src/openmpi-1.5rc5/opal/tools/
wrappers'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/usr/local/src/openmpi-1.5rc5/opal'
make: *** [all-recursive] Error 1
OpenMPI 1.4.2 does not have this problem. After the make for OpenMPI
1.4.2, I rm'd opal_wrapper and compared the make commands that are
issued for 1.4.2:
[root@hydra wrappers]# cd opal/tools/wrappers
[root@hydra wrappers]# ls
CMakeLists.txt generic_wrapper.1in Makefile
Makefile.in opalcc-wrapper-data.txt.in opalc++-wrapper-
data.txt.in opal_wrapper.1 opal_wrapper.c
generic_wrapper.1 help-opal-wrapper.txt Makefile.am opalcc-
wrapper-data.txt opalc++-wrapper-data.txt
opal_wrapper opal_wrapper.1in opal_wrapper.o
[root@hydra wrappers]# rm opal_wrapper
rm: remove regular file `opal_wrapper'? y
[root@hydra wrappers]# make -n
rm -f opal_wrapper
/bin/sh ../../../libtool --tag=CC --mode=link pgcc -m64 -DNDEBUG -
g -O3 -tp amd64 -DNO_PGI_OFFSET -export-dynamic -o opal_wrapper
opal_wrapper.o ../../../opal/libopen-pal.la -lnsl -lutil -lpthread
I see that -lpthread is missing in the 1.5rc5 build:
[root@hydra wrappers]# cd opal/tools/wrappers
[root@hydra wrappers]# ls
CMakeLists.txt help-opal-wrapper.txt Makefile.am opalcc-
wrapper-data.txt opalc++-wrapper-data.txt opal.pc
opal_wrapper.1in opal_wrapper.o
generic_wrapper.1in Makefile Makefile.in opalcc-
wrapper-data.txt.in opalc++-wrapper-data.txt.in opal.pc.in
opal_wrapper.c
[root@hydra wrappers]# make -n
rm -f opal_wrapper
echo " CCLD " opal_wrapper;/bin/sh ../../../libtool --silent --
tag=CC --mode=link pgcc -m64 -DNDEBUG -g -O3 -tp amd64 -
DNO_PGI_OFFSET -export-dynamic -o opal_wrapper
opal_wrapper.o ../../../opal/libopen-pal.la -lnsl -lutil
echo Creating opal_wrapper.1 man page...
sed -e 's/#PACKAGE_NAME#/Open MPI/g' \
-e 's/#PACKAGE_VERSION#/1.5rc5/g' \
-e 's/#OMPI_DATE#/Aug 17, 2010/g' \
> opal_wrapper.1 < opal_wrapper.1in
That account for all the missing pthread_* references. However, when
I manually issue the link command and supply -lpthread, assert is
still undefined:
[root@hydra wrappers]# /bin/sh ../../../libtool --silent --tag=CC
--mode=link pgcc -m64 -DNDEBUG -g -O3 -tp amd64 -DNO_PGI_OFFSET -
export-dynamic -o opal_wrapper opal_wrapper.o ../../../opal/libopen-
pal.la -lnsl -lutil -lpthread
../../../opal/.libs/libopen-pal.so: undefined reference to `assert'
I get the same result when I cut-and-paste the 1.4.2 link command:
[root@hydra wrappers]# /bin/sh ../../../libtool --tag=CC --
mode=link pgcc -m64 -DNDEBUG -g -O3 -tp amd64 -DNO_PGI_OFFSET -
export-dynamic -o opal_wrapper opal_wrapper.o ../../../opal/
libopen-pal.la -lnsl -lutil -lpthread
libtool: link: pgcc -m64 -DNDEBUG -g -O3 -tp amd64 -DNO_PGI_OFFSET -
o .libs/opal_wrapper opal_wrapper.o -Wl,--export-dynamic ../../../
opal/.libs/libopen-pal.so -ldl -lnsl -lutil -lpthread -Wl,-rpath -
Wl,/opt/pgi/linux86-64/10.3/openmpi/lib
../../../opal/.libs/libopen-pal.so: undefined reference to `assert'
I re-ran the make without my patches, and the assert() reference
disappeared:
[root@hydra openmpi-1.5rc5]# tail make.log
CCLD opal_wrapper
../../../opal/.libs/libopen-pal.so: undefined reference to
`pthread_create'
../../../opal/.libs/libopen-pal.so: undefined reference to
`pthread_mutex_trylock'
../../../opal/.libs/libopen-pal.so: undefined reference to
`pthread_atfork'
../../../opal/.libs/libopen-pal.so: undefined reference to
`pthread_join'
make[2]: *** [opal_wrapper] Error 2
make[2]: Leaving directory `/usr/local/src/openmpi-1.5rc5/opal/tools/
wrappers'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/usr/local/src/openmpi-1.5rc5/opal'
make: *** [all-recursive] Error 1
I don't know why -- -DNDEBUG should have eliminated any declarations
from <assert.h>.
Manually adding -lpthreads makes the link error go away:
[root@hydra openmpi-1.5rc5]# cd opal/tools/wrappers
[root@hydra wrappers]# /bin/sh ../../../libtool --silent --tag=CC
--mode=link pgcc -m64 -DNDEBUG -g -O3 -tp amd64 -DNO_PGI_OFFSET -
export-dynamic -o opal_wrapper opal_wrapper.o ../../../opal/libopen-
pal.la -lnsl -lutil -lpthread
It looks like the changes in the opal/tools/wrappers/Makefile
(configure/automake?) from 1.4.2 to 1.5rc5 are not supplying the
pthreads library correctly to the link step.
Larry Baker
US Geological Survey
650-329-5608
ba...@usgs.gov
On Aug 17, 2010, at 2:18 PM, Jeff Squyres wrote:
We still have one known possible regression:
https://svn.open-mpi.org/trac/ompi/ticket/2530
But we posted rc5 anyway (there's a bunch of stuff that has been
pending for a while that is now in). Please test!
http://www.open-mpi.org/software/ompi/v1.5/
--
Jeff Squyres
jsquy...@cisco.com
For corporate legal information go to:
http://www.cisco.com/web/about/doing_business/legal/cri/
_______________________________________________
devel mailing list
de...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/devel
