Errors after apparent successful install

[Mark Potter]

I see the vt error but it doesn't stop the install from completing. i'm at a loss on this one...

[root@linhead maappython]# ./test_eventtree.py

Traceback (most recent call last):

  File "./test_eventtree.py", line 3, in <module>

    from mpi4py import MPI

ImportError: /apps/python/3.3.4/lib/python3.3/site-packages/mpi4py/MPI.cpython-33m.so: undefined symbol: ompi_mpi_logic

[root@linhead maappython]#

[root@linhead mpi4py-1.3.1]# python setup.py install

running install

running build

running build_src

running build_py

running build_clib

MPI configuration: [mpi] from 'mpi.cfg'

MPI C compiler:    /apps/openmpi/1.6.5/bin/mpicc

MPI C++ compiler:  /apps/openmpi/1.6.5/bin/mpicxx

MPI F77 compiler:  /apps/openmpi/1.6.5/bin/mpif77

MPI F90 compiler:  /apps/openmpi/1.6.5/bin/mpif90

checking for library 'vt-mpi' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -lvt-mpi -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

building 'vt' dylib library

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -c src/pmpi-vt.c -o build/temp.linux-x86_64-3.3/src/pmpi-vt.o

/apps/openmpi/1.6.5/bin/mpicc -shared build/temp.linux-x86_64-3.3/src/pmpi-vt.o -o build/lib.linux-x86_64-3.3/mpi4py/lib-pmpi/libvt.so -Wl,-whole-archive -lvt-mpi -Wl,-no-whole-archive -lotf -lz -ldl

/usr/bin/ld: cannot find -lotf

collect2: error: ld returned 1 exit status

warning: build_clib: building library "vt" failed

warning: build_clib: command '/apps/openmpi/1.6.5/bin/mpicc' failed with exit status 1

running build_ext

MPI configuration: [mpi] from 'mpi.cfg'

MPI C compiler:    /apps/openmpi/1.6.5/bin/mpicc

MPI C++ compiler:  /apps/openmpi/1.6.5/bin/mpicxx

MPI F77 compiler:  /apps/openmpi/1.6.5/bin/mpif77

MPI F90 compiler:  /apps/openmpi/1.6.5/bin/mpif90

running build_exe

MPI configuration: [mpi] from 'mpi.cfg'

MPI C compiler:    /apps/openmpi/1.6.5/bin/mpicc

MPI C++ compiler:  /apps/openmpi/1.6.5/bin/mpicxx

MPI F77 compiler:  /apps/openmpi/1.6.5/bin/mpif77

MPI F90 compiler:  /apps/openmpi/1.6.5/bin/mpif90

running install_lib

writing byte-compilation script '/tmp/tmpjidpqe.py'

/apps/python/3.3.4/bin/python -O /tmp/tmpjidpqe.py

removing /tmp/tmpjidpqe.py

running install_egg_info

Removing /apps/python/3.3.4/lib/python3.3/site-packages/mpi4py-1.3.1-py3.3.egg-info

Writing /apps/python/3.3.4/lib/python3.3/site-packages/mpi4py-1.3.1-py3.3.egg-info

[root@linhead mpi4py-1.3.1]#

[Lisandro Dalcin]

On 27 February 2014 00:19, Mark Potter <romeosi...@gmail.com> wrote:
> I see the vt error but it doesn't stop the install from completing. i'm at a
> loss on this one...
>

Ignore the vt error, that's an optional component.

Can you try to start fresh (rm -rf build), send me full output of the
build and install command, and the output of "ldd
/apps/python/3.3.4/lib/python3.3/site-packages/mpi4py/MPI.cpython-33m.so"
?


--
Lisandro Dalcin
---------------
CIMEC (UNL/CONICET)
Predio CONICET-Santa Fe
Colectora RN 168 Km 472, Paraje El Pozo
3000 Santa Fe, Argentina
Tel: +54-342-4511594 (ext 1016)
Tel/Fax: +54-342-4511169

[Mark Potter]

Build:

[root@linhead mpi4py-1.3.1]# python setup.py build >> build.out 2>&1

[root@linhead mpi4py-1.3.1]# cat build.out

running build

running build_src

running build_py

creating build

creating build/lib.linux-x86_64-3.3

creating build/lib.linux-x86_64-3.3/mpi4py

copying src/rc.py -> build/lib.linux-x86_64-3.3/mpi4py

copying src/__init__.py -> build/lib.linux-x86_64-3.3/mpi4py

creating build/lib.linux-x86_64-3.3/mpi4py/include

creating build/lib.linux-x86_64-3.3/mpi4py/include/mpi4py

copying src/include/mpi4py/mpi4py.h -> build/lib.linux-x86_64-3.3/mpi4py/include/mpi4py

copying src/include/mpi4py/mpi4py.MPI.h -> build/lib.linux-x86_64-3.3/mpi4py/include/mpi4py

copying src/include/mpi4py/mpi4py.MPI_api.h -> build/lib.linux-x86_64-3.3/mpi4py/include/mpi4py

copying src/include/mpi4py/__init__.pxd -> build/lib.linux-x86_64-3.3/mpi4py/include/mpi4py

copying src/include/mpi4py/MPI.pxd -> build/lib.linux-x86_64-3.3/mpi4py/include/mpi4py

copying src/include/mpi4py/mpi_c.pxd -> build/lib.linux-x86_64-3.3/mpi4py/include/mpi4py

copying src/include/mpi4py/__init__.pyx -> build/lib.linux-x86_64-3.3/mpi4py/include/mpi4py

copying src/include/mpi4py/mpi.pxi -> build/lib.linux-x86_64-3.3/mpi4py/include/mpi4py

copying src/include/mpi4py/mpi4py.i -> build/lib.linux-x86_64-3.3/mpi4py/include/mpi4py

copying src/MPI.pxd -> build/lib.linux-x86_64-3.3/mpi4py

copying src/mpi_c.pxd -> build/lib.linux-x86_64-3.3/mpi4py

running build_clib

MPI configuration: [mpi] from 'mpi.cfg'

MPI C compiler:    /apps/openmpi/1.6.5/bin/mpicc

MPI C++ compiler:  /apps/openmpi/1.6.5/bin/mpicxx

MPI F77 compiler:  /apps/openmpi/1.6.5/bin/mpif77

MPI F90 compiler:  /apps/openmpi/1.6.5/bin/mpif90

checking for library 'pthread' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -lpthread -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

checking for library 'mpe' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -lmpe -lpthread -o _configtest

/usr/bin/ld: cannot find -lmpe

collect2: error: ld returned 1 exit status

failure.

removing: _configtest.c _configtest.o

checking for library 'lmpe' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -llmpe -lpthread -o _configtest

/usr/bin/ld: cannot find -llmpe

collect2: error: ld returned 1 exit status

failure.

removing: _configtest.c _configtest.o

building 'mpe' dylib library

creating build/temp.linux-x86_64-3.3

creating build/temp.linux-x86_64-3.3/src

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -c src/pmpi-mpe.c -o build/temp.linux-x86_64-3.3/src/pmpi-mpe.o

creating build/lib.linux-x86_64-3.3/mpi4py/lib-pmpi

/apps/openmpi/1.6.5/bin/mpicc -shared build/temp.linux-x86_64-3.3/src/pmpi-mpe.o -o build/lib.linux-x86_64-3.3/mpi4py/lib-pmpi/libmpe.so

checking for library 'vt-mpi' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -lvt-mpi -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

building 'vt' dylib library

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -c src/pmpi-vt.c -o build/temp.linux-x86_64-3.3/src/pmpi-vt.o

/apps/openmpi/1.6.5/bin/mpicc -shared build/temp.linux-x86_64-3.3/src/pmpi-vt.o -o build/lib.linux-x86_64-3.3/mpi4py/lib-pmpi/libvt.so -Wl,-whole-archive -lvt-mpi -Wl,-        no-whole-archive -lotf -lz -ldl

/usr/bin/ld: cannot find -lotf

collect2: error: ld returned 1 exit status

warning: build_clib: building library "vt" failed

warning: build_clib: command '/apps/openmpi/1.6.5/bin/mpicc' failed with exit status 1

checking for library 'vt-mpi' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -lvt-mpi -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

building 'vt-mpi' dylib library

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -c src/pmpi-vt-mpi.c -o build/temp.linux-x86_64-3.3/src/pmpi-vt-mpi.o

/apps/openmpi/1.6.5/bin/mpicc -shared build/temp.linux-x86_64-3.3/src/pmpi-vt-mpi.o -lvt-mpi -o build/lib.linux-x86_64-3.3/mpi4py/lib-pmpi/libvt-mpi.so

checking for library 'vt-hyb' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -lvt-hyb -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

building 'vt-hyb' dylib library

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -c src/pmpi-vt-hyb.c -o build/temp.linux-x86_64-3.3/src/pmpi-vt-hyb.o

/apps/openmpi/1.6.5/bin/mpicc -shared build/temp.linux-x86_64-3.3/src/pmpi-vt-hyb.o -lvt-hyb -o build/lib.linux-x86_64-3.3/mpi4py/lib-pmpi/libvt-hyb.so

running build_ext

MPI configuration: [mpi] from 'mpi.cfg'

MPI C compiler:    /apps/openmpi/1.6.5/bin/mpicc

MPI C++ compiler:  /apps/openmpi/1.6.5/bin/mpicxx

MPI F77 compiler:  /apps/openmpi/1.6.5/bin/mpif77

MPI F90 compiler:  /apps/openmpi/1.6.5/bin/mpif90

checking for MPI compile and link ...

checking for header 'mpi.h' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c _configtest.c -o _configtest.o

success!

removing: _configtest.c _configtest.o

success!

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c _configtest.c -o _configtest.o

success!

removing: _configtest.c _configtest.o

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -Lbuild/temp.linux-x86_64-3.3 -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

checking for missing MPI functions/symbols ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c _configtest.c -o _configtest.o

success!

removing: _configtest.c _configtest.o

checking for function 'MPI_Type_create_f90_integer' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -Lbuild/temp.linux-x86_64-3.3 -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

checking for function 'MPI_Type_create_f90_real' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -Lbuild/temp.linux-x86_64-3.3 -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

checking for function 'MPI_Type_create_f90_complex' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -Lbuild/temp.linux-x86_64-3.3 -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

building 'mpi4py.MPI' extension

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c src/MPI.c -o build/temp.linux-x86_64-3.        3/src/MPI.o

/apps/openmpi/1.6.5/bin/mpicc -shared build/temp.linux-x86_64-3.3/src/MPI.o -Lbuild/temp.linux-x86_64-3.3 -o build/lib.linux-x86_64-3.3/mpi4py/MPI.cpython-33m.so

writing build/lib.linux-x86_64-3.3/mpi4py/mpi.cfg

checking for MPE availability ...

checking for library 'pthread' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -Lbuild/temp.linux-x86_64-3.3 -lpthread -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

checking for library 'mpe' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -Lbuild/temp.linux-x86_64-3.3 -lmpe -lpthread -o _configtest

/usr/bin/ld: cannot find -lmpe

collect2: error: ld returned 1 exit status

failure.

removing: _configtest.c _configtest.o

checking for library 'lmpe' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -Lbuild/temp.linux-x86_64-3.3 -llmpe -lpthread -o _configtest

/usr/bin/ld: cannot find -llmpe

collect2: error: ld returned 1 exit status

failure.

removing: _configtest.c _configtest.o

checking for header 'mpe.h' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c _configtest.c -o _configtest.o

_configtest.c:3:17: fatal error: mpe.h: No such file or directory

 #include <mpe.h>

                 ^

compilation terminated.

failure.

removing: _configtest.c _configtest.o

failure.

building 'mpi4py.MPE' extension

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c src/MPE.c -o build/temp.linux-x86_64-3.        3/src/MPE.o

/apps/openmpi/1.6.5/bin/mpicc -shared build/temp.linux-x86_64-3.3/src/MPE.o -Lbuild/temp.linux-x86_64-3.3 -o build/lib.linux-x86_64-3.3/mpi4py/MPE.cpython-33m.so

checking for dlopen() availability ...

checking for header 'dlfcn.h' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c _configtest.c -o _configtest.o

success!

removing: _configtest.c _configtest.o

success!

checking for library 'dl' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -Lbuild/temp.linux-x86_64-3.3 -ldl -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

checking for function 'dlopen' ...

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c _configtest.c -o _configtest.o

/apps/openmpi/1.6.5/bin/mpicc _configtest.o -Lbuild/temp.linux-x86_64-3.3 -ldl -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

building 'mpi4py.dl' extension

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/apps/python/3.3.4/include/python3.3m -c src/dy        nload.c -o build/temp.linux-x86_64-3.3/src/dynload.o

/apps/openmpi/1.6.5/bin/mpicc -shared build/temp.linux-x86_64-3.3/src/dynload.o -Lbuild/temp.linux-x86_64-3.3 -ldl -o build/lib.linux-x86_64-3.3/mpi4py/dl.cpython-33m.s        o

running build_exe

MPI configuration: [mpi] from 'mpi.cfg'

MPI C compiler:    /apps/openmpi/1.6.5/bin/mpicc

MPI C++ compiler:  /apps/openmpi/1.6.5/bin/mpicxx

MPI F77 compiler:  /apps/openmpi/1.6.5/bin/mpif77

MPI F90 compiler:  /apps/openmpi/1.6.5/bin/mpif90

building 'python-mpi' executable

/apps/openmpi/1.6.5/bin/mpicc -fPIC -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/apps/python/3.3.4/include/python3.3m -c src/python.c -o build/temp.linux-x86_64        -3.3/src/python.o

creating build/lib.linux-x86_64-3.3/mpi4py/bin

/apps/openmpi/1.6.5/bin/mpicc -Wl,-export-dynamic build/temp.linux-x86_64-3.3/src/python.o -L/apps/python/3.3.4/lib -L/apps/python/3.3.4/lib/python3.3/config-3.3m -Lbui        ld/temp.linux-x86_64-3.3 -lpython3.3m -o build/lib.linux-x86_64-3.3/mpi4py/bin/python-mpi -lpthread -ldl -lutil -lm

[root@linhead mpi4py-1.3.1]#

Install:

writing byte-compilation script '/tmp/tmpzy2yzz.py'

/apps/python/3.3.4/bin/python -O /tmp/tmpzy2yzz.py

removing /tmp/tmpzy2yzz.py

running install_egg_info

Removing /apps/python/3.3.4/lib/python3.3/site-packages/mpi4py-1.3.1-py3.3.egg-info

Writing /apps/python/3.3.4/lib/python3.3/site-packages/mpi4py-1.3.1-py3.3.egg-info

LDD:

[root@linhead mpi4py-1.3.1]# ldd /apps/python/3.3.4/lib/python3.3/site-packages/mpi4py/MPI.cpython-33m.so

        linux-vdso.so.1 =>  (0x00007fff17aec000)

        libmpi.so.1 => /apps/openmpi/1.6.5/lib/libmpi.so.1 (0x00007f874ac2b000)

        libdl.so.2 => /lib64/libdl.so.2 (0x00007f874aa01000)

        libm.so.6 => /lib64/libm.so.6 (0x00007f874a77d000)

        librt.so.1 => /lib64/librt.so.1 (0x00007f874a575000)

        libnsl.so.1 => /lib64/libnsl.so.1 (0x00007f874a35b000)

        libutil.so.1 => /lib64/libutil.so.1 (0x00007f874a158000)

        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f8749f3b000)

        libc.so.6 => /lib64/libc.so.6 (0x00007f8749ba7000)

        /lib64/ld-linux-x86-64.so.2 (0x0000003d4c200000)

[root@linhead mpi4py-1.3.1]#

[Mark Potter]

Thanks for the assist. Apparently I was having a forest for the trees moment, removing the build dir and starting fresh seems to have worked. No mpi4py errors on the test run this morning.