[MOAB-dev] build MOAB error

Tue Jul 21 11:33:16 CDT 2015

The linkage for HDF5 during configuration worked and so that must have
picked up the static library directly. So technically, it shouldn't
have been a problem. I cant comment more without looking at things in
closer detail.

But good that its fixed though. Let us know if there are any other issues.

Vijay

On Tue, Jul 21, 2015 at 11:29 AM, Xu Wu <xuwu2 at illinois.edu> wrote:
> 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
>