[MOAB-dev] build MOAB error

[Vijay S. Mahadevan]

First, make sure mpicxx points to the mpich3.0.4 installation.

Your logs show that HDF5 was configured without issues.
HDF5_LIBS='-lhdf5    -lz -ldl -lm'. But your linker line above for
makeops doesn't seem to include HDF5_LIBS correctly. The LDFLAGS are
correct though. Can you send us moab.make generated during your
configuration ?

Vijay

On Tue, Jul 21, 2015 at 10:17 AM, Xu Wu <xuwu2 at illinois.edu> wrote:
> Greetings,
>
> I tried to build MOAB on a Ubuntu machine but I saw the following error:
> I am using Ubuntu 14.04, with mpich-3.0.4, HDF5-1.8.14 and netcdf-4.3.2.
> Previously I used successfully build MOAB with same configuration commands
> (Only difference is that I used openMPI before), but I do not know why
> doesn't it work this time.
>
>     ../configure \
> --prefix=/home/xu/research/softwares/Projects_warthog/warthog/moab/install \
> --with-hdf5=/home/xu/research/softwares/Projects_warthog/Dependencies/hdf5-1.8.14
> \
> --with-netcdf=/home/xu/research/softwares/Projects_warthog/Dependencies/netcdf-4.3.2
> \
>     --with-mpi  \
>     --enable-shared CC=mpicc CXX=mpicxx FC=mpif90 F77=mpif77
>
>
>
>
>
> I also attached the configuration log. (There are a few error messages, but
> I saw same messages before and I could still build MOAB, so I think they
> should not be the reason).
>
> Thank you.
>
>
> -Xu
>
>
> libtool: link: mpicxx -Wall -pipe -pedantic -Wno-long-long -Wextra
> -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow
> -Wunused-parameter -O2 -DNDEBUG -o .libs/hexmodops makeops.o
> -L/home/xu/research/softwares/Projects_warthog/Dependencies/netcdf-4.3.2/lib
> /home/xu/research/softwares/Projects_warthog/Dependencies/netcdf-4.3.2/lib/libnetcdf.so
> -L/home/xu/research/softwares/Projects_warthog/Dependencies/hdf5-1.8.14/lib
> ../src/.libs/libMOAB.so ../itaps/imesh/.libs/libiMesh.so -lz -ldl -lm
> -Wl,-rpath
> -Wl,/home/xu/research/softwares/Projects_warthog/Dependencies/netcdf-4.3.2/lib
> -Wl,-rpath
> -Wl,/home/xu/research/softwares/Projects_warthog/warthog/moab/install/lib
> ../src/.libs/libMOAB.so: undefined reference to `H5Pcreate'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tget_size'
> ../src/.libs/libMOAB.so: undefined reference to `H5Fopen'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_INT_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5check_version'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tconvert'
> ../src/.libs/libMOAB.so: undefined reference to `H5Awrite'
> ../src/.libs/libMOAB.so: undefined reference to `H5Aclose'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tset_tag'
> ../src/.libs/libMOAB.so: undefined reference to `H5Gunlink'
> ../src/.libs/libMOAB.so: undefined reference to `H5Acreate2'
> ../src/.libs/libMOAB.so: undefined reference to `H5Dget_space'
> ../src/.libs/libMOAB.so: undefined reference to `H5Gcreate2'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tenum_nameof'
> ../src/.libs/libMOAB.so: undefined reference to `H5Aiterate2'
> ../src/.libs/libMOAB.so: undefined reference to `H5Eget_auto2'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_LLONG_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_B16_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tenum_insert'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_SHORT_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Dread'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tarray_create2'
> ../src/.libs/libMOAB.so: undefined reference to `H5Dfill'
> ../src/.libs/libMOAB.so: undefined reference to `H5Fget_obj_ids'
> ../src/.libs/libMOAB.so: undefined reference to `H5Gget_objname_by_idx'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_UCHAR_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tequal'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tcommit2'
> ../src/.libs/libMOAB.so: undefined reference to `H5Sget_simple_extent_ndims'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_HSSIZE_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tset_size'
> ../src/.libs/libMOAB.so: undefined reference to `H5Fis_hdf5'
> ../src/.libs/libMOAB.so: undefined reference to `H5Topen2'
> ../src/.libs/libMOAB.so: undefined reference to `H5Fget_obj_count'
> ../src/.libs/libMOAB.so: undefined reference to `H5Aget_type'
> ../src/.libs/libMOAB.so: undefined reference to `H5Fcreate'
> ../src/.libs/libMOAB.so: undefined reference to `H5Pclose'
> ../src/.libs/libMOAB.so: undefined reference to `H5Screate_simple'
> ../src/.libs/libMOAB.so: undefined reference to `H5Sselect_hyperslab'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_DOUBLE_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Sget_simple_extent_dims'
> ../src/.libs/libMOAB.so: undefined reference to `H5P_CLS_DATASET_XFER_ID_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_C_S1_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Dopen2'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_B32_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tcopy'
> ../src/.libs/libMOAB.so: undefined reference to `H5Dget_type'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_ULLONG_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tget_sign'
> ../src/.libs/libMOAB.so: undefined reference to `H5Screate'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_UINT_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Giterate'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tget_super'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_FLOAT_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Eset_auto2'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_LONG_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Aopen_name'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tget_array_dims2'
> ../src/.libs/libMOAB.so: undefined reference to `H5Aread'
> ../src/.libs/libMOAB.so: undefined reference to `H5Pset_dxpl_mpio'
> ../src/.libs/libMOAB.so: undefined reference to `H5Iget_type'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_LDOUBLE_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Sclose'
> ../src/.libs/libMOAB.so: undefined reference to `H5Gset_comment'
> ../src/.libs/libMOAB.so: undefined reference to `H5open'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tclose'
> ../src/.libs/libMOAB.so: undefined reference to `H5Sselect_none'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_SCHAR_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Gopen2'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tenum_create'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_B64_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_USHORT_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_B8_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Dwrite'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tset_precision'
> ../src/.libs/libMOAB.so: undefined reference to `H5Dclose'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tget_class'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tcreate'
> ../src/.libs/libMOAB.so: undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5T_NATIVE_ULONG_g'
> ../src/.libs/libMOAB.so: undefined reference to `H5Fclose'
> ../src/.libs/libMOAB.so: undefined reference to `H5Gget_num_objs'
> ../src/.libs/libMOAB.so: undefined reference to `H5Tget_precision'
> ../src/.libs/libMOAB.so: undefined reference to `H5Gclose'
> ../src/.libs/libMOAB.so: undefined reference to `H5Dcreate2'
> ../src/.libs/libMOAB.so: undefined reference to `H5Pset_fapl_mpio'
> ../src/.libs/libMOAB.so: undefined reference to `H5Scopy'
> collect2: error: ld returned 1 exit status
> make[2]: *** [hexmodops] Error 1
> make[2]: Leaving directory
> `/home/xu/research/softwares/Projects_warthog/warthog/moab/build/tools'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory
> `/home/xu/research/softwares/Projects_warthog/warthog/moab/build/tools'
> make: *** [all-recursive] Error 1
>