[OMPI users] OpenMPI 2.1.0 build error: yes/lib: No such file or director

[Prentice Bisbal]

I'm getting the following error when I build OpenMPI 2.1.0 with GCC 5.4.0:

/bin/sh ../../../../libtool --tag=CC --mode=link gcc -O3 -DNDEBUG
-finline-functions -fno-strict-aliasing -pthread -module -avoid-version
-Lyes/lib -o libmca_fs_lustre.la fs_lustre.lo fs_lustre_component.lo
fs_lustre_file_open.lo fs_lustre_file_close.lo fs_lustre_file_delete.lo
fs_lustre_file_sync.lo fs_lustre_file_set_size.lo
fs_lustre_file_get_size.lo -llustreapi -lrt -lm -lutil
../../../../libtool: line 7489: cd: yes/lib: No such file or directory
libtool: error: cannot determine absolute directory name of 'yes/lib'
make[2]: *** [libmca_fs_lustre.la] Error 1
make[2]: Leaving directory `/local/pbisbal/openmpi-2.1.0/ompi/mca/fs/lustre'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/local/pbisbal/openmpi-2.1.0/ompi'
make: *** [all-recursive] Error 1

Obviously, the problem is this argument to libtool in the above command:

-Lyes/lib

I've worked around this by going into ompi/mca/fs/lustre, running that
same libtool command but changing "-Lyes/lib" to "-L/lib", and then
resuming my build from the top level, I figured I'd report this error
here, to see if this a problem caused by me, or a bug in the configure
script.

When I do 'make check', I get another error caused by the same bad argument:

/bin/sh ../../libtool --tag=CC --mode=link gcc -O3 -DNDEBUG
-finline-functions -fno-strict-aliasing -pthread
-L/usr/pppl/slurm/15.08.8/lib -Lyes/lib -Wl,-rpath
-Wl,/usr/pppl/slurm/15.08.8/lib -Wl,-rpath -Wl,yes/lib -Wl,-rpath
-Wl,/usr/pppl/gcc/5.4-pkgs/openmpi-2.1.0/lib -Wl,--enable-new-dtags -o
external32 external32.o ../../ompi/libmpi.la ../../opal/libopen-pal.la
-lrt -lm -lutil
../../libtool: line 7489: cd: yes/lib: No such file or directory
libtool: error: cannot determine absolute directory name of 'yes/lib'
make[3]: *** [external32] Error 1
make[3]: Leaving directory `/local/pbisbal/openmpi-2.1.0/test/datatype'
make[2]: *** [check-am] Error 2
make[2]: Leaving directory `/local/pbisbal/openmpi-2.1.0/test/datatype'
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory `/local/pbisbal/openmpi-2.1.0/test'
make: *** [check-recursive] Error 1

For reference, here is my configure command:

./configure \
--prefix=/usr/pppl/gcc/5.4-pkgs/openmpi-2.1.0 \
--disable-silent-rules \
--enable-mpi-fortran \
--enable-mpi-cxx \
--enable-shared \
--enable-static \
--enable-mpi-thread-multiple \
--with-cuda=/usr/pppl/cuda/cudatoolkit/6.5.14 \
--with-pmix \
--with-verbs \
--with-hwloc \
--with-pmi=/usr/pppl/slurm/15.08.8 \
--with-slurm \
--with-lustre \
--with-psm \
CC=gcc \
CXX=g++ \
FC=gfortran \
2>&1 | tee configure.log

[Edgar Gabriel]

Can you try to just skip the --with-lustre option ? The option really is
there to provide an alternative path, if the lustre libraries are not
installed in the default directories ( e.g.
--with-lustre=/opt/lustre/....). There is obviously a bug that the
system did not recognize the missing argument. However, if the lustre
libraries and headers are installed in the default location (i.e.
/usr/), the configure logic will pick it up and compile it even if you
do not provide the --with-lustre argument.

Thanks

Edgar

Post by Prentice Bisbal
/bin/sh ../../../../libtool --tag=CC --mode=link gcc -O3 -DNDEBUG
-finline-functions -fno-strict-aliasing -pthread -module -avoid-version
-Lyes/lib -o libmca_fs_lustre.la fs_lustre.lo fs_lustre_component.lo
fs_lustre_file_open.lo fs_lustre_file_close.lo fs_lustre_file_delete.lo
fs_lustre_file_sync.lo fs_lustre_file_set_size.lo
fs_lustre_file_get_size.lo -llustreapi -lrt -lm -lutil
../../../../libtool: line 7489: cd: yes/lib: No such file or directory
libtool: error: cannot determine absolute directory name of 'yes/lib'
make[2]: *** [libmca_fs_lustre.la] Error 1
make[2]: Leaving directory `/local/pbisbal/openmpi-2.1.0/ompi/mca/fs/lustre'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/local/pbisbal/openmpi-2.1.0/ompi'
make: *** [all-recursive] Error 1
-Lyes/lib
I've worked around this by going into ompi/mca/fs/lustre, running that
same libtool command but changing "-Lyes/lib" to "-L/lib", and then
resuming my build from the top level, I figured I'd report this error
here, to see if this a problem caused by me, or a bug in the configure
script.
/bin/sh ../../libtool --tag=CC --mode=link gcc -O3 -DNDEBUG
-finline-functions -fno-strict-aliasing -pthread
-L/usr/pppl/slurm/15.08.8/lib -Lyes/lib -Wl,-rpath
-Wl,/usr/pppl/slurm/15.08.8/lib -Wl,-rpath -Wl,yes/lib -Wl,-rpath
-Wl,/usr/pppl/gcc/5.4-pkgs/openmpi-2.1.0/lib -Wl,--enable-new-dtags -o
external32 external32.o ../../ompi/libmpi.la ../../opal/libopen-pal.la
-lrt -lm -lutil
../../libtool: line 7489: cd: yes/lib: No such file or directory
libtool: error: cannot determine absolute directory name of 'yes/lib'
make[3]: *** [external32] Error 1
make[3]: Leaving directory `/local/pbisbal/openmpi-2.1.0/test/datatype'
make[2]: *** [check-am] Error 2
make[2]: Leaving directory `/local/pbisbal/openmpi-2.1.0/test/datatype'
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory `/local/pbisbal/openmpi-2.1.0/test'
make: *** [check-recursive] Error 1
./configure \
--prefix=/usr/pppl/gcc/5.4-pkgs/openmpi-2.1.0 \
--disable-silent-rules \
--enable-mpi-fortran \
--enable-mpi-cxx \
--enable-shared \
--enable-static \
--enable-mpi-thread-multiple \
--with-cuda=/usr/pppl/cuda/cudatoolkit/6.5.14 \
--with-pmix \
--with-verbs \
--with-hwloc \
--with-pmi=/usr/pppl/slurm/15.08.8 \
--with-slurm \
--with-lustre \
--with-psm \
CC=gcc \
CXX=g++ \
FC=gfortran \
2>&1 | tee configure.log

[Prentice Bisbal]

Edgar,

Thank you for the suggestion. That fixed this problem.

Prentice

Post by Edgar Gabriel
Can you try to just skip the --with-lustre option ? The option really
is there to provide an alternative path, if the lustre libraries are
not installed in the default directories ( e.g.
--with-lustre=/opt/lustre/....). There is obviously a bug that the
system did not recognize the missing argument. However, if the lustre
libraries and headers are installed in the default location (i.e.
/usr/), the configure logic will pick it up and compile it even if you
do not provide the --with-lustre argument.
Thanks
Edgar

Post by Prentice Bisbal
/bin/sh ../../../../libtool --tag=CC --mode=link gcc -O3 -DNDEBUG
-finline-functions -fno-strict-aliasing -pthread -module -avoid-version
-Lyes/lib -o libmca_fs_lustre.la fs_lustre.lo fs_lustre_component.lo
fs_lustre_file_open.lo fs_lustre_file_close.lo fs_lustre_file_delete.lo
fs_lustre_file_sync.lo fs_lustre_file_set_size.lo
fs_lustre_file_get_size.lo -llustreapi -lrt -lm -lutil
../../../../libtool: line 7489: cd: yes/lib: No such file or directory
libtool: error: cannot determine absolute directory name of 'yes/lib'
make[2]: *** [libmca_fs_lustre.la] Error 1
make[2]: Leaving directory
`/local/pbisbal/openmpi-2.1.0/ompi/mca/fs/lustre'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/local/pbisbal/openmpi-2.1.0/ompi'
make: *** [all-recursive] Error 1
-Lyes/lib
I've worked around this by going into ompi/mca/fs/lustre, running that
same libtool command but changing "-Lyes/lib" to "-L/lib", and then
resuming my build from the top level, I figured I'd report this error
here, to see if this a problem caused by me, or a bug in the configure
script.
/bin/sh ../../libtool --tag=CC --mode=link gcc -O3 -DNDEBUG
-finline-functions -fno-strict-aliasing -pthread
-L/usr/pppl/slurm/15.08.8/lib -Lyes/lib -Wl,-rpath
-Wl,/usr/pppl/slurm/15.08.8/lib -Wl,-rpath -Wl,yes/lib -Wl,-rpath
-Wl,/usr/pppl/gcc/5.4-pkgs/openmpi-2.1.0/lib -Wl,--enable-new-dtags -o
external32 external32.o ../../ompi/libmpi.la ../../opal/libopen-pal.la
-lrt -lm -lutil
../../libtool: line 7489: cd: yes/lib: No such file or directory
libtool: error: cannot determine absolute directory name of 'yes/lib'
make[3]: *** [external32] Error 1
make[3]: Leaving directory `/local/pbisbal/openmpi-2.1.0/test/datatype'
make[2]: *** [check-am] Error 2
make[2]: Leaving directory `/local/pbisbal/openmpi-2.1.0/test/datatype'
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory `/local/pbisbal/openmpi-2.1.0/test'
make: *** [check-recursive] Error 1
./configure \
--prefix=/usr/pppl/gcc/5.4-pkgs/openmpi-2.1.0 \
--disable-silent-rules \
--enable-mpi-fortran \
--enable-mpi-cxx \
--enable-shared \
--enable-static \
--enable-mpi-thread-multiple \
--with-cuda=/usr/pppl/cuda/cudatoolkit/6.5.14 \
--with-pmix \
--with-verbs \
--with-hwloc \
--with-pmi=/usr/pppl/slurm/15.08.8 \
--with-slurm \
--with-lustre \
--with-psm \
CC=gcc \
CXX=g++ \
FC=gfortran \
2>&1 | tee configure.log

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