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 <[email protected]> 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
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