[MOAB-dev] build error on mcs machines

Thu Feb 24 10:01:32 CST 2011

Our system have 2 different versions of "mpicc/mpicxx" under "/usr" and "/usr/lib/mpich" as follows.

I used the following configuration to build MOAB.
(--prefix=/homes/hongjun/lib/MOAB-new --with-mpi
--with-cgm=/homes/hongjun/lib/CGM --enable-debug
--disable-optimize
--enable-igeom --enable-imesh --enable-dagmc)
So, I think there is no other dependencies built with a different mpicc/mpicxx.

-----------------------------------------
grind:~> /usr/bin/mpicxx -v
mpicxx for MPICH2 version 1.2.1p1
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.4.3-4ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared --enable-multiarch --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4 --program-suffix=-4.4 --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-plugin --enable-objc-gc --disable-werror --with-arch-32=i486 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5)
-----------------------------------------

-----------------------------------------
grind:~> /usr/lib/mpich/bin/mpicxx -v
mpiCC for 1.2.7 (release) of : 2005/11/04 11:54:51
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.4.3-4ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared --enable-multiarch --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4 --program-suffix=-4.4 --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-plugin --enable-objc-gc --disable-werror --with-arch-32=i486 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
-----------------------------------------

----- Original Message -----
> From: "Jason Kraftcheck" <kraftche at cae.wisc.edu>
> To: "Hong-Jun Kim" <hongjun at mcs.anl.gov>
> Cc: moab-dev at mcs.anl.gov
> Sent: Thursday, February 24, 2011 9:18:32 AM
> Subject: Re: [MOAB-dev] build error on mcs machines
> On 02/23/2011 04:10 PM, Hong-Jun Kim wrote:
> > Yes, the library in "-L/usr/lib/mpich/lib/" and "mpicxx" being used
> > (/usr/bin/mpicxx) are different versions.
> >
> 
> Are you certain? Is there a different libmpich in /usr/lib? What about
> the
> other stuff: Is mpicc consistant with mpicxx? Where any of the other
> dependencies (e.g. hdf5) built with a different mpicc/mpicxx?
> 
> - jason
> 
> > I attached my "config.log" file and all configuration checks look
> > being
> > done with the "/usr/bin/mpicxx". So, I have no idea why
> > "-L/usr/lib/mpich/lib/" is in the build command line. Do you know
> > why
> > libtool put "-L/usr/lib/mpich/lib/"? Thanks.
> >
> > Hong-Jun
> >
> >
> > ----- Original Message -----
> >> From: "Jason Kraftcheck" <kraftche at cae.wisc.edu> To: "Hong-Jun Kim"
> >> <hongjun at mcs.anl.gov> Cc: moab-dev at mcs.anl.gov Sent: Wednesday,
> >> February 23, 2011 3:19:39 PM Subject: Re: [MOAB-dev] build error on
> >> mcs
> >> machines On 02/23/2011 03:12 PM, Hong-Jun Kim wrote:
> >>> Hi, all
> >>>
> >>> In ANL, we have had troubles to build parallel MOAB with our own
> >>> hdf5
> >>> and mpich libraries, then I removed options for this and used the
> >>> mpich installed in system as follows.
> >>>
> >>
> >> Verify that the -L/usr/lib/mpich/lib/ from the link line is correct
> >> for
> >> the mpicxx being used to compile.
> >>
> >> Verify that 'mpicxx' is the one you think it is (i.e. 'which
> >> mpicxx').
> >>
> >> Verify that 'mpicc' is consistent with 'mpicxx' (i.e. 'which
> >> mpicc').
> >>
> >> Verify that none of the external libraries being linked (-lnetcdf
> >> /usr/lib/libhdf5.so) where built with some other version of MPI.
> >>
> >> - jason
> >>
> >>
> >>> ------------------------------------------ ./configure
> >>> --prefix=/homes/hongjun/lib/MOAB-new --with-mpi
> >>> --with-cgm=/homes/hongjun/lib/CGM --enable-debug
> >>> --disable-optimize
> >>> --enable-igeom --enable-imesh --enable-dagmc
> >>> ------------------------------------------
> >>>
> >>> However, I still have undefined reference errors as follows about
> >>> some mpi functions. Actually, I have no idea why this kind of
> >>> errors
> >>> are coming. Does anybody have any idea about this? Thanks.
> >>>
> >>> Hong-Jun
> >>>
> >>> -----------------------------------------------------------
> >>> make[3]:
> >>> Entering directory
> >>> `/nfs/mcs-homes138/hongjun/source/moab-new/tools'
> >>> /bin/sh ../libtool --tag=CXX --mode=link mpicxx -Wall -pipe
> >>> -pedantic
> >>> -Wno-long-long -g -R/homes/hongjun/lib/CGM/lib
> >>> -L/homes/hongjun/lib/CGM/lib
> >>> -L/homes/fathom/3rdparty/occ/OpenCASCADE6.3.0/gcc/lib -o mbconvert
> >>> convert.o ../src/libMOAB.la -lm libtool: link: mpicxx -Wall -pipe
> >>> -pedantic -Wno-long-long -g -o mbconvert convert.o
> >>> -L/homes/hongjun/lib/CGM/lib
> >>> -L/homes/fathom/3rdparty/occ/OpenCASCADE6.3.0/gcc/lib
> >>> ../src/.libs/libMOAB.a -lnetcdf /usr/lib/libhdf5.so
> >>> -L/usr/lib/mpich/lib/ -lz /homes/hongjun/lib/CGM/lib/libcgm.a
> >>> /home/fathom/3rdparty/occ/OpenCASCADE6.3.0/gcc/lib/libTKSTL.so
> >>> (more
> >>> occ libraries....) -ldl -lm -Wl,-rpath
> >>> -Wl,/home/fathom/3rdparty/occ/OpenCASCADE6.3.0/gcc/lib -Wl,-rpath
> >>> -Wl,/home/fathom/3rdparty/occ/OpenCASCADE6.3.0/gcc/lib -Wl,-rpath
> >>> -Wl,/homes/hongjun/lib/CGM/lib /usr/lib/libmpichcxx.so: undefined
> >>> reference to `MPI_Win_unlock' /usr/lib/libmpichcxx.so: undefined
> >>> reference to `PMPI_Type_set_name' /usr/lib/libmpichcxx.so:
> >>> undefined
> >>> reference to `MPI_Grequest_complete' /usr/lib/libmpichcxx.so:
> >>> undefined reference to `MPI_Put' /usr/lib/libmpichcxx.so:
> >>> undefined
> >>> reference to `MPI_Comm_get_attr' /usr/lib/libmpichcxx.so:
> >>> undefined
> >>> reference to `MPI_File_call_errhandler' /usr/lib/libmpichcxx.so:
> >>> undefined reference to `MPI_Pack_external_size'
> >>> /usr/lib/libmpichcxx.so: undefined reference to `MPI_Win_start'
> >>> /usr/lib/libmpichcxx.so: undefined reference to
> >>> `MPI_Win_set_errhandler'
> >>> -----------------------------------------------------------
> >>>
> >>> ----- Original Message -----
> >>>> From: "Iulian Grindeanu" <iulian at mcs.anl.gov> To:
> >>>> moab-dev at mcs.anl.gov Sent: Monday, February 21, 2011 3:53:06 PM
> >>>> Subject: [MOAB-dev] build error on mcs machines Hello, I was
> >>>> wondering if anybody has a good build on MCS machines now. I am
> >>>> getting errors I did not have last week, and I do not know the
> >>>> cause
> >>>>
> >>>> It seems to be related to hdf5 library and dependency on netcdf.
> >>>> Hong Jun and I have the same problems, for parallel or serial
> >>>> builds. It is fine on my laptop, where I have only one hdf5
> >>>> version.
> >>>>
> >>>> Does anybody have a suggestion?
> >>>>
> >>>> Iulian
> >>>>
> >>>>
> >>>> Making all in . make[3]: Entering directory
> >>>> `/nfs/mcs-homes129/iulian/serial/MOAB/tools' CXXLD mbconvert
> >>>> /usr/bin/ld: warning: libstdc++.so.5, needed by
> >>>> /home/fathom/3rdparty/cubit/Cubit64/cubit-10.2-amd64/bin/libcubiti19.so,
> >>>>
> >>>>
> may conflict with libstdc++.so.6
> >>>> /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so:
> >>>>
> >>>>
> undefined reference to `H5DSget_num_scales'
> >>>> /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so:
> >>>>
> >>>>
> undefined reference to `H5DSset_scale'
> >>>> /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so:
> >>>>
> >>>>
> undefined reference to `H5DSget_scale_name'
> >>>> /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so:
> >>>>
> >>>>
> undefined reference to `H5DSis_scale'
> >>>> /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so:
> >>>>
> >>>>
> undefined reference to `H5DSdetach_scale'
> >>>> /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so:
> >>>>
> >>>>
> undefined reference to `H5DSiterate_scales'
> >>>> /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so:
> >>>>
> >>>>
> undefined reference to `H5DSattach_scale'
> >>
> >>
> >> -- "A foolish consistency is the hobgoblin of little minds" - Ralph
> >> Waldo Emerson
> 
> 
> --
> "A foolish consistency is the hobgoblin of little minds" - Ralph Waldo
> Emerson