[MOAB-dev] build MOAB error

[Xu Wu]

Hi Vijay,

The issue has been fixed.

I checked my previous HDF5(1.8.14) lib folder, and found no shared 
libraries. HDF5 configure has both shared and static enabled by default, 
but I do not know why they are not installed
   --enable-shared[=PKGS]  build shared libraries [default=yes]
   --enable-static[=PKGS]  build static libraries [default=yes]

Then I reinstall HDF5 by explicitly enabling shared libraries, and MOAB 
now can be built correctly.
I do not know if this is the reason, but it did fix the issue.
Thanks,


-Xu


On 07/21/2015 11:08 AM, Vijay S. Mahadevan wrote:
> 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
>>

-- 

Department of Nuclear, Plasma, and Radiological Engineering
University of Illinois Urbana-Champaign
224 Talbot Laboratory
104 South Wright Street
Urbana, IL 61801