make problem on ubuntu 12.10

Asked by Pan

Hi,

My system is ubuntu 12.10. I followed the installing step in "
Installing the latest revision of ESyS-Particle on Ubuntu and variants"(https://answers.launchpad.net/esys-particle/+faq/1613)

1. sudo apt-get install libtool automake build-essential bzr
2. sudo apt-get install mpi-default-bin mpi-default-dev libboost-all-dev
3. Manually install the povray binaries, sudo ./install -no-arch-check
4. sudo apt-get install libvtk5-dev python-epydoc
5. Compile and install ESyS-Particle:
    1) sh autogen.sh
     This step returned :
      bzr: ERROR: Not a branch: "/home/user/ESyS-Particle-2.2.2/".
      using existing bzrversion.h

     2) ./configure CC=mpicc CXX=mpic++
     3) make

after a while, I got the error message:

.......
.......
l/type/.libs/libTmlType.so -lpython2.7 -pthread
../../Model/.libs/libModel.so: undefined reference to `MPI_Op_commutative'
../../Model/.libs/libModel.so: undefined reference to `MPI_Reduce_local'
collect2: error: ld returned 1 exit status
make[3]: *** [dump2pov] Error 1
make[3]: Leaving directory `/home/user/ESyS-Particle-2.2.2/Tools/dump2pov'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/user/ESyS-Particle-2.2.2/Tools'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/user/ESyS-Particle-2.2.2'
make: *** [all] Error 2

I am new to Linux and I don't know how to solve the problem.

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Dion Weatherley (d-weatherley) said :
#1

Hi Pan,

The error during the 'sh autogen.sh' step is of no concern. It will not prevent ESyS-Particle from installing correctly.

Could you please post a few more lines of output prior to the extract you originally posted? I need to see the rest of the (multi-line) command ending with "l/type/.libs/libTmlType.so -lpython2.7 -pthread"

Cheers,

Dion

Revision history for this message
Pan (jianwen-pan) said :
#2

Hi Dion,

Thank you so much for your reply.

More output information is as follows:

libtool: link: (cd ".libs" && rm -f "libParallel.so" && ln -s "libParallel.so.0.0.0" "libParallel.so")
libtool: link: ar cru .libs/libParallel.a ASubLattice.o LatticeMaster.o mpia2abuf.o mpibarrier.o mpibuf.o mpicmdbuf.o mpisgbuf.o mpisgvbuf.o mpivbuf.o SubLatticeControler.o SubLattice.o CheckPointer.o CheckPointController.o CheckPointParams.o MpiInfo.o GeometryReader.o CheckPointInfo.o CheckPointLoader.o LatticeParam.o BroadCast_cmd.o BMesh2D_cmd.o GetRef_cmd.o
libtool: link: ranlib .libs/libParallel.a
libtool: link: ( cd ".libs" && rm -f "libParallel.la" && ln -s "../libParallel.la" "libParallel.la" )
make[2]: Leaving directory `/home/user/Software/ESyS-Particle-2.2.2/Parallel'
Making all in Tools
make[2]: Entering directory `/home/user/Software/ESyS-Particle-2.2.2/Tools'
Making all in dump2geo
make[3]: Entering directory `/home/user/Software/ESyS-Particle-2.2.2/Tools/dump2geo'
mpic++ -DHAVE_CONFIG_H -I. -I../.. "-I../.." -I../../Foundation -I../../Geometry -g -O2 -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cpp
mv -f .deps/main.Tpo .deps/main.Po
mpic++ -DHAVE_CONFIG_H -I. -I../.. "-I../.." -I../../Foundation -I../../Geometry -g -O2 -MT frame_geo.o -MD -MP -MF .deps/frame_geo.Tpo -c -o frame_geo.o frame_geo.cpp
mv -f .deps/frame_geo.Tpo .deps/frame_geo.Po
/bin/bash ../../libtool --tag=CXX --mode=link mpic++ -g -O2 -release 2.2.2 -L/usr/lib -o dump2geo main.o frame_geo.o ../../Foundation/libFoundation.la ../../Geometry/libGgGeometry.la ../../Parallel/libParallel.la -lpython2.7
libtool: link: warning: `-release' is ignored for programs
libtool: link: mpic++ -g -O2 -o .libs/dump2geo main.o frame_geo.o -L/usr/lib ../../Foundation/.libs/libFoundation.so ../../Geometry/.libs/libGgGeometry.so ../../Parallel/.libs/libParallel.so -lpython2.7 -pthread
make[3]: Leaving directory `/home/user/Software/ESyS-Particle-2.2.2/Tools/dump2geo'
Making all in dump2pov
make[3]: Entering directory `/home/user/Software/ESyS-Particle-2.2.2/Tools/dump2pov'
mpic++ -DHAVE_CONFIG_H -I. -I../.. "-I../.." -I../../Foundation -I../../Geometry -g -O2 -MT colormap.o -MD -MP -MF .deps/colormap.Tpo -c -o colormap.o colormap.cpp
mv -f .deps/colormap.Tpo .deps/colormap.Po
mpic++ -DHAVE_CONFIG_H -I. -I../.. "-I../.." -I../../Foundation -I../../Geometry -g -O2 -MT colormap3.o -MD -MP -MF .deps/colormap3.Tpo -c -o colormap3.o colormap3.cpp
mv -f .deps/colormap3.Tpo .deps/colormap3.Po
mpic++ -DHAVE_CONFIG_H -I. -I../.. "-I../.." -I../../Foundation -I../../Geometry -g -O2 -MT frame.o -MD -MP -MF .deps/frame.Tpo -c -o frame.o frame.cpp
mv -f .deps/frame.Tpo .deps/frame.Po
mpic++ -DHAVE_CONFIG_H -I. -I../.. "-I../.." -I../../Foundation -I../../Geometry -g -O2 -MT mesh.o -MD -MP -MF .deps/mesh.Tpo -c -o mesh.o mesh.cpp
mv -f .deps/mesh.Tpo .deps/mesh.Po
mpic++ -DHAVE_CONFIG_H -I. -I../.. "-I../.." -I../../Foundation -I../../Geometry -g -O2 -MT geocolormap.o -MD -MP -MF .deps/geocolormap.Tpo -c -o geocolormap.o geocolormap.cpp
mv -f .deps/geocolormap.Tpo .deps/geocolormap.Po
mpic++ -DHAVE_CONFIG_H -I. -I../.. "-I../.." -I../../Foundation -I../../Geometry -g -O2 -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cpp
mv -f .deps/main.Tpo .deps/main.Po
mpic++ -DHAVE_CONFIG_H -I. -I../.. "-I../.." -I../../Foundation -I../../Geometry -g -O2 -MT campos.o -MD -MP -MF .deps/campos.Tpo -c -o campos.o campos.cpp
mv -f .deps/campos.Tpo .deps/campos.Po
/bin/bash ../../libtool --tag=CXX --mode=link mpic++ -g -O2 -release 2.2.2 -L/usr/lib -o dump2pov colormap.o colormap3.o frame.o mesh.o geocolormap.o main.o campos.o ../../Foundation/libFoundation.la ../../Geometry/libGgGeometry.la ../../Model/libModel.la ../../Parallel/libParallel.la ../../tml/message/libTmlMessage.la ../../tml/type/libTmlType.la -lpython2.7
libtool: link: warning: `-release' is ignored for programs
libtool: link: mpic++ -g -O2 -o .libs/dump2pov colormap.o colormap3.o frame.o mesh.o geocolormap.o main.o campos.o -L/usr/lib ../../Foundation/.libs/libFoundation.so ../../Geometry/.libs/libGgGeometry.so ../../Model/.libs/libModel.so ../../Parallel/.libs/libParallel.so ../../tml/message/.libs/libTmlMessage.so ../../tml/type/.libs/libTmlType.so -lpython2.7 -pthread
../../Model/.libs/libModel.so: undefined reference to `MPI_Op_commutative'
../../Model/.libs/libModel.so: undefined reference to `MPI_Reduce_local'
collect2: error: ld returned 1 exit status
make[3]: *** [dump2pov] Error 1
make[3]: Leaving directory `/home/user/Software/ESyS-Particle-2.2.2/Tools/dump2pov'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/user/Software/ESyS-Particle-2.2.2/Tools'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/user/Software/ESyS-Particle-2.2.2'
make: *** [all] Error 2

Cheers,

Pan

Revision history for this message
Pan (jianwen-pan) said :
#3

Hi Dion,

I reinstalled a fresh ubuntu 12.04 OS, and now it works. Thanks again.

Regards,

Pan