On Fri, Jul 26, 2013 at 4:22 PM, ANDREI LEITaO <andleitao.iqsc.usp.br>wrote:
>
> AMBERHOME is set in bashrc.
> I made 'make clean' before running ./configure gnu
>
>
> There is a problem using netCDF and I got this error:
>
> ------------------------------ ------------
> make[3]: Leaving directory `/usr/local/bin/amber12/src/ lib'
> cd ../lib && make nxtsec.o
> make[3]: Entering directory `/usr/local/bin/amber12/src/ lib'
> make[3]: `nxtsec.o' is up to date.
> make[3]: Leaving directory `/usr/local/bin/amber12/src/ lib'
> cd ../../AmberTools/src/blas && make install
> make[3]: Entering directory `/usr/local/bin/amber12/ AmberTools/src/blas'
> make[3]: Nothing to be done for `install'.
> make[3]: Leaving directory `/usr/local/bin/amber12/ AmberTools/src/blas'
> cd ../../AmberTools/src/lapack && make install
> make[3]: Entering directory `/usr/local/bin/amber12/ AmberTools/src/lapack'
> make[3]: Nothing to be done for `install'.
> make[3]: Leaving directory `/usr/local/bin/amber12/ AmberTools/src/lapack'
> cd ../../AmberTools/src/arpack && make install
> make[3]: Entering directory `/usr/local/bin/amber12/ AmberTools/src/arpack'
> make[3]: Nothing to be done for `install'.
> make[3]: Leaving directory `/usr/local/bin/amber12/ AmberTools/src/arpack'
> if [ -n "" ]; then \
> cd ../../AmberTools/src/rism && make librism; \
> fi
> gfortran -DBINTRAJ -ffree-form -I../../AmberTools/src/pbsa
> -I../../AmberTools/src/sqm -I../../AmberTools/src/rism -I../../include
> -I/usr/local/bin/amber12/ include -I/usr/local/bin/amber12/ include -o
> sander file_io_dat.o constants.o state.o memory_module.o stack.o
> nose_hoover.o nose_hoover_vars.o nose_hoover_init.o trace.o rmsgrd.o lmod.o
> rand2.o lmodC.o xminC.o decomp.o icosasurf.o egb.o remd.o findmask.o
> relax_mat.o nmr.o multitmd.o multisander.o sander.o trajene.o cshf.o
> nmrcal.o mtmdcall.o pearsn.o printe.o runmin.o rdparm.o sander_lib.o
> mdread.o locmem.o runmd.o getcor.o degcnt.o decnvh.o fastwt.o parallel.o
> shake.o ene.o mdwrit.o minrit.o set.o dynlib.o mdfil.o nmlsrc.o ew_force.o
> ew_setup.o ew_box.o ew_bspline.o ew_fft.o nonbond_list.o short_ene.o
> ew_recip.o pcshift.o align.o csa.o rfree.o rgroup.o amopen.o debug.o
> ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o mexit.o new_time.o
> extra_pts.o thermo_int.o matinv.o assert.o mmtsb.o mmtsb_client.o erfcfun.o
> constantph.o prn_dipoles.o ips.o sglds.o iwrap2.o emap.o amoeba_valence.o
> amoeba_multipoles.o amoeba_recip.o amoeba_interface.o amoeba_direct.o
> amoeba_mdin.o amoeba_adjust.o amoeba_self.o amoeba_vdw.o amoeba_induced.o
> amoeba_runmd.o bintraj.o binrestart.o spatial_recip.o spatial_fft.o parms.o
> softcore.o mbar.o linear_response.o molecule.o xref.o dssp.o charmm.o
> crg_reloc.o amd.o qm_mm.o qm_ewald.o qmmm_vsolv.o qm2_extern_module.o
> qm2_extern_adf_module.o qm2_read_adf_results.o KFReader.o ArrayList.o
> qm2_extern_gms_module.o qm2_extern_tc_module.o qm2_extern_gau_module.o
> qm2_extern_orc_module.o qm2_extern_nw_module.o qmmm_adaptive_module.o
> prn_qmmm_dipole.o \
> pimd_vars.o pimd_force.o pimd_init.o cmd_vars.o cmd_matrix.o lscivr_vars.o
> lsc_init.o lsc_xp.o force.o -L/usr/local/bin/amber12/lib -lsqm \
> ncsu-abmd-hooks.o ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o
> ncsu-colvar.o ncsu-colvar-math.o ncsu-colvar-type.o ncsu-colvar-utils.o
> ncsu-constants.o ncsu-cv-ANGLE.o ncsu-cv-COM_ANGLE.o ncsu-cv-COM_DISTANCE.o
> ncsu-cv-COM_TORSION.o ncsu-cv-COS_OF_DIHEDRAL.o ncsu-cv-DISTANCE.o
> ncsu-cv-HANDEDNESS.o ncsu-cv-LCOD.o ncsu-cv-MULTI_RMSD.o
> ncsu-cv-N_OF_BONDS.o ncsu-cv-N_OF_STRUCTURES.o ncsu-cv-R_OF_GYRATION.o
> ncsu-cv-TORSION.o ncsu-lexer.o ncsu-parser.o ncsu-pmd-hooks.o ncsu-rmsd.o
> ncsu-sander-hooks.o ncsu-sander-proxy.o ncsu-cv-PCA.o ncsu-read-pca.o
> ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o mt19937.o \
> -lFpbsa ../../AmberTools/src/lib/ nxtsec.o \
> ../../AmberTools/src/lib/sys.a -L/usr/local/bin/amber12/lib -lnetcdf \
> -larpack -llapack -lblas \
>
> trajene.o: In function `__trajenemod_MOD_trajene':
> trajene.F90:(.text+0x402): undefined reference to
> `__netcdf_MOD_nf90_get_var_1d_ eightbytereal'
> trajene.F90:(.text+0x759): undefined reference to
> `__netcdf_MOD_nf90_get_var_1d_ eightbytereal'
> trajene.F90:(.text+0xd33): undefined reference to `__netcdf_MOD_nf90_open'
> trajene.F90:(.text+0xe50): undefined reference to
> `__netcdf_MOD_nf90_strerror'
> trajene.F90:(.text+0xfbb): undefined reference to
> `__netcdf_MOD_nf90_inq_dimid'
> trajene.F90:(.text+0xfdd): undefined reference to
> `__netcdf_MOD_nf90_inquire_ dimension'
> trajene.F90:(.text+0x108b): undefined reference to
> `__netcdf_MOD_nf90_inq_dimid'
> trajene.F90:(.text+0x10ad): undefined reference to
> `__netcdf_MOD_nf90_inquire_ dimension'
> trajene.F90:(.text+0x11f9): undefined reference to
> `__netcdf_MOD_nf90_close'
> trajene.F90:(.text+0x135b): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> trajene.F90:(.text+0x1391): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> trajene.F90:(.text+0x13b0): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> bintraj.o: In function `__bintraj_MOD_checkncerror. part.0':
> bintraj.F90:(.text+0x6e): undefined reference to
> `__netcdf_MOD_nf90_strerror'
> bintraj.o: In function `__bintraj_MOD_end_nc_define':
> bintraj.F90:(.text+0x186): undefined reference to
> `__netcdf_MOD_nf90_set_fill'
> bintraj.F90:(.text+0x1b9): undefined reference to
> `__netcdf_MOD_nf90_enddef'
> bintraj.F90:(.text+0x2d4): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ text'
> bintraj.o: In function `__bintraj_MOD_open_nc_file':
> bintraj.F90:(.text+0x37c): undefined reference to
> `__netcdf_MOD_nf90_create'
> bintraj.F90:(.text+0x3bf): undefined reference to
> `__netcdf_MOD_nf90_def_dim'
> bintraj.F90:(.text+0x3f8): undefined reference to
> `__netcdf_MOD_nf90_def_dim'
> bintraj.F90:(.text+0x42f): undefined reference to
> `__netcdf_MOD_nf90_def_dim'
> bintraj.F90:(.text+0x468): undefined reference to
> `__netcdf_MOD_nf90_def_dim'
> bintraj.F90:(.text+0x4a5): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> bintraj.F90:(.text+0x4ea): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> bintraj.F90:(.text+0x52f): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> bintraj.F90:(.text+0x574): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> bintraj.F90:(.text+0x5b9): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> bintraj.o:bintraj.F90:(.text+ 0x5fe): more undefined references to
> `__netcdf_MOD_nf90_put_att_ text' follow
> bintraj.o: In function `__bintraj_MOD_open_nc_file':
> bintraj.F90:(.text+0x69f): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> bintraj.F90:(.text+0x72f): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> bintraj.F90:(.text+0x76c): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> bintraj.F90:(.text+0x7e3): undefined reference to `__netcdf_MOD_nf90_open'
> bintraj.F90:(.text+0x88b): undefined reference to
> `__netcdf_MOD_nf90_inq_dimid'
> bintraj.F90:(.text+0x8bd): undefined reference to
> `__netcdf_MOD_nf90_inquire_ dimension'
> bintraj.F90:(.text+0x8e8): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> bintraj.o: In function `__bintraj_MOD_end_binary_ frame':
> bintraj.F90:(.text+0xb2a): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ eightbytereal'
> bintraj.F90:(.text+0xb56): undefined reference to `__netcdf_MOD_nf90_sync'
> bintraj.F90:(.text+0xcca): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ eightbytereal'
> bintraj.F90:(.text+0xcf6): undefined reference to `__netcdf_MOD_nf90_sync'
> bintraj.o: In function `__bintraj_MOD_write_binary_ traj':
> bintraj.F90:(.text+0xf4b): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ eightbytereal'
> bintraj.F90:(.text+0x10f2): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ eightbytereal'
> bintraj.F90:(.text+0x1291): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ eightbytereal'
> bintraj.F90:(.text+0x13e7): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ eightbytereal'
> bintraj.o: In function `__bintraj_MOD_close_binary_ files':
> bintraj.F90:(.text+0x1454): undefined reference to
> `__netcdf_MOD_nf90_close'
> bintraj.F90:(.text+0x1470): undefined reference to
> `__netcdf_MOD_nf90_close'
> bintraj.o: In function `__bintraj_MOD_open_binary_ files':
> bintraj.F90:(.text+0x15f4): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> bintraj.F90:(.text+0x1628): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> bintraj.F90:(.text+0x1672): undefined reference to
> `__netcdf_MOD_nf90_def_dim'
> bintraj.F90:(.text+0x16b3): undefined reference to
> `__netcdf_MOD_nf90_def_dim'
> bintraj.F90:(.text+0x1744): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> bintraj.F90:(.text+0x17d5): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> bintraj.F90:(.text+0x1866): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> bintraj.F90:(.text+0x18ad): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> bintraj.F90:(.text+0x193e): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> bintraj.F90:(.text+0x1985): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> bintraj.F90:(.text+0x1b39): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> bintraj.F90:(.text+0x1b6d): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> bintraj.F90:(.text+0x1b9b): undefined reference to
> `__netcdf_MOD_nf90_put_att_ one_fourbytereal'
> bintraj.F90:(.text+0x1be5): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> bintraj.F90:(.text+0x1c20): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> bintraj.F90:(.text+0x1e01): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ text'
> bintraj.F90:(.text+0x1f52): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ text'
> bintraj.F90:(.text+0x1f9d): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> bintraj.F90:(.text+0x1fe5): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> binrestart.o: In function `__binrestart_MOD_getdiminfo':
> binrestart.F90:(.text+0x38): undefined reference to
> `__netcdf_MOD_nf90_inq_dimid'
> binrestart.F90:(.text+0x75): undefined reference to
> `__netcdf_MOD_nf90_inquire_ dimension'
> binrestart.o: In function `__binrestart_MOD_read_nc_ restart':
> binrestart.F90:(.text+0x1b0): undefined reference to
> `__netcdf_MOD_nf90_open'
> binrestart.F90:(.text+0x204): undefined reference to
> `__netcdf_MOD_nf90_get_att_ text'
> binrestart.F90:(.text+0x257): undefined reference to
> `__netcdf_MOD_nf90_get_att_ text'
> binrestart.F90:(.text+0x2c4): undefined reference to
> `__netcdf_MOD_nf90_get_att_ text'
> binrestart.F90:(.text+0x486): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> binrestart.F90:(.text+0x4d0): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> binrestart.F90:(.text+0x529): undefined reference to
> `__netcdf_MOD_nf90_get_att_ text'
> binrestart.F90:(.text+0x689): undefined reference to
> `__netcdf_MOD_nf90_get_var_1d_ eightbytereal'
> binrestart.F90:(.text+0x6de): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> binrestart.F90:(.text+0x731): undefined reference to
> `__netcdf_MOD_nf90_get_att_ text'
> binrestart.F90:(.text+0x78f): undefined reference to
> `__netcdf_MOD_nf90_get_var_ eightbytereal'
> binrestart.F90:(.text+0x7da): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> binrestart.F90:(.text+0x7f2): undefined reference to
> `__netcdf_MOD_nf90_close'
> binrestart.F90:(.text+0x823): undefined reference to
> `__netcdf_MOD_nf90_get_var_ eightbytereal'
> binrestart.F90:(.text+0x944): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> binrestart.F90:(.text+0x999): undefined reference to
> `__netcdf_MOD_nf90_get_att_ text'
> binrestart.F90:(.text+0xaee): undefined reference to
> `__netcdf_MOD_nf90_get_var_1d_ eightbytereal'
> binrestart.o: In function `__binrestart_MOD_check_nc_ restart':
> binrestart.F90:(.text+0xf37): undefined reference to
> `__netcdf_MOD_nf90_open'
> binrestart.F90:(.text+0xf6f): undefined reference to
> `__netcdf_MOD_nf90_get_att_ text'
> binrestart.F90:(.text+0xf9b): undefined reference to
> `__netcdf_MOD_nf90_close'
> binrestart.o: In function `__binrestart_MOD_read_nc_ restart_box':
> binrestart.F90:(.text+0xfe8): undefined reference to
> `__netcdf_MOD_nf90_open'
> binrestart.F90:(.text+0x102c): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> binrestart.F90:(.text+0x1070): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> binrestart.F90:(.text+0x11a9): undefined reference to
> `__netcdf_MOD_nf90_get_var_1d_ eightbytereal'
> binrestart.F90:(.text+0x1304): undefined reference to
> `__netcdf_MOD_nf90_get_var_1d_ eightbytereal'
> binrestart.F90:(.text+0x136f): undefined reference to
> `__netcdf_MOD_nf90_close'
> binrestart.o: In function `__binrestart_MOD_write_nc_ restart':
> binrestart.F90:(.text+0x14c5): undefined reference to
> `__netcdf_MOD_nf90_create'
> binrestart.F90:(.text+0x1525): undefined reference to
> `__netcdf_MOD_nf90_def_var_ scalar'
> binrestart.F90:(.text+0x1569): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> binrestart.F90:(.text+0x159f): undefined reference to
> `__netcdf_MOD_nf90_def_dim'
> binrestart.F90:(.text+0x1632): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> binrestart.F90:(.text+0x1666): undefined reference to
> `__netcdf_MOD_nf90_def_dim'
> binrestart.F90:(.text+0x16fe): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> binrestart.F90:(.text+0x173a): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> binrestart.F90:(.text+0x17ea): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> binrestart.F90:(.text+0x1826): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> binrestart.F90:(.text+0x185c): undefined reference to
> `__netcdf_MOD_nf90_put_att_ one_fourbytereal'
> binrestart.F90:(.text+0x18a1): undefined reference to
> `__netcdf_MOD_nf90_def_dim'
> binrestart.F90:(.text+0x192c): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> binrestart.F90:(.text+0x1962): undefined reference to
> `__netcdf_MOD_nf90_def_dim'
> binrestart.F90:(.text+0x1998): undefined reference to
> `__netcdf_MOD_nf90_def_dim'
> binrestart.F90:(.text+0x1a30): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> binrestart.F90:(.text+0x1abb): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> binrestart.F90:(.text+0x1af7): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> binrestart.F90:(.text+0x1b82): undefined reference to
> `__netcdf_MOD_nf90_def_var_ manydims'
> binrestart.F90:(.text+0x1bbe): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> binrestart.F90:(.text+0x1bfa): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> binrestart.F90:(.text+0x1c36): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> binrestart.F90:(.text+0x1c72): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> binrestart.F90:(.text+0x1cae): undefined reference to
> `__netcdf_MOD_nf90_put_att_ text'
> binrestart.o:binrestart.F90:(. text+0x1cea): more undefined references to
> `__netcdf_MOD_nf90_put_att_ text' follow
> binrestart.o: In function `__binrestart_MOD_write_nc_ restart':
> binrestart.F90:(.text+0x1d54): undefined reference to
> `__netcdf_MOD_nf90_set_fill'
> binrestart.F90:(.text+0x1d7e): undefined reference to
> `__netcdf_MOD_nf90_enddef'
> binrestart.F90:(.text+0x1ed0): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ text'
> binrestart.F90:(.text+0x2019): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ text'
> binrestart.F90:(.text+0x2174): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ text'
> binrestart.F90:(.text+0x21a8): undefined reference to
> `__netcdf_MOD_nf90_put_var_ eightbytereal'
> binrestart.F90:(.text+0x22d7): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ eightbytereal'
> binrestart.F90:(.text+0x240d): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ eightbytereal'
> binrestart.F90:(.text+0x2563): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ eightbytereal'
> binrestart.F90:(.text+0x26a2): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ eightbytereal'
> binrestart.F90:(.text+0x26c3): undefined reference to
> `__netcdf_MOD_nf90_close'
> binrestart.F90:(.text+0x2711): undefined reference to
> `__netcdf_MOD_nf90_open'
> ncsu-umbrella.o: In function `check_rc.1950':
> ncsu-umbrella.F90:(.text+0x2e) : undefined reference to
> `__netcdf_MOD_nf90_strerror'
> ncsu-umbrella.o: In function `check_rc.1760':
> ncsu-umbrella.F90:(.text+ 0x1ee): undefined reference to
> `__netcdf_MOD_nf90_strerror'
> ncsu-umbrella.o: In function `__ncsu_umbrella_MOD_umbrella_ save':
> ncsu-umbrella.F90:(.text+ 0x5f0): undefined reference to
> `__netcdf_MOD_nf90_create'
> ncsu-umbrella.F90:(.text+ 0x651): undefined reference to
> `__netcdf_MOD_nf90_put_att_ one_fourbyteint'
> ncsu-umbrella.F90:(.text+ 0x6b7): undefined reference to
> `__netcdf_MOD_nf90_put_att_ fourbyteint'
> ncsu-umbrella.F90:(.text+ 0x719): undefined reference to
> `__netcdf_MOD_nf90_put_att_ fourbyteint'
> ncsu-umbrella.F90:(.text+ 0x77f): undefined reference to
> `__netcdf_MOD_nf90_put_att_ eightbytereal'
> ncsu-umbrella.F90:(.text+ 0x7e5): undefined reference to
> `__netcdf_MOD_nf90_put_att_ eightbytereal'
> ncsu-umbrella.F90:(.text+ 0x814): undefined reference to
> `__netcdf_MOD_nf90_def_dim'
> ncsu-umbrella.F90:(.text+ 0x848): undefined reference to
> `__netcdf_MOD_nf90_def_var_ onedim'
> ncsu-umbrella.F90:(.text+ 0x86b): undefined reference to
> `__netcdf_MOD_nf90_enddef'
> ncsu-umbrella.F90:(.text+ 0x89e): undefined reference to
> `__netcdf_MOD_nf90_put_var_1d_ eightbytereal'
> ncsu-umbrella.F90:(.text+ 0x8b8): undefined reference to
> `__netcdf_MOD_nf90_close'
> ncsu-umbrella.o: In function `__ncsu_umbrella_MOD_umbrella_ load':
> ncsu-umbrella.F90:(.text+ 0x9a9): undefined reference to
> `__netcdf_MOD_nf90_open'
> ncsu-umbrella.F90:(.text+ 0x9e4): undefined reference to
> `__netcdf_MOD_nf90_get_att_ one_fourbyteint'
> ncsu-umbrella.F90:(.text+ 0xa85): undefined reference to
> `__netcdf_MOD_nf90_get_att_ fourbyteint'
> ncsu-umbrella.F90:(.text+ 0xb08): undefined reference to
> `__netcdf_MOD_nf90_get_att_ fourbyteint'
> ncsu-umbrella.F90:(.text+ 0xb8f): undefined reference to
> `__netcdf_MOD_nf90_get_att_ eightbytereal'
> ncsu-umbrella.F90:(.text+ 0xc16): undefined reference to
> `__netcdf_MOD_nf90_get_att_ eightbytereal'
> ncsu-umbrella.F90:(.text+ 0xc7d): undefined reference to
> `__netcdf_MOD_nf90_inq_dimid'
> ncsu-umbrella.F90:(.text+ 0xcb5): undefined reference to
> `__netcdf_MOD_nf90_inquire_ dimension'
> ncsu-umbrella.F90:(.text+ 0xdab): undefined reference to
> `__netcdf_MOD_nf90_inq_varid'
> ncsu-umbrella.F90:(.text+ 0xe48): undefined reference to
> `__netcdf_MOD_nf90_get_var_1d_ eightbytereal'
> ncsu-umbrella.F90:(.text+ 0xe6b): undefined reference to
> `__netcdf_MOD_nf90_close'
> collect2: ld returned 1 exit status
> make[2]: *** [sander] Error 1
> make[2]: Leaving directory `/usr/local/bin/amber12/src/ sander'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory `/usr/local/bin/amber12/src'
> make: *** [install] Error 2
>
My guess is that you have some system NetCDF installation lying around that
does not have the F90 symbols included (or they're included in a
libnetcdff.so file).
A workaround for the time being is to modify the config.h file that is
created by configure and replace the phrase
-L/usr/local/bin/amber12/lib -lnetcdf
with
/usr/local/bin/amber12/lib/libnetcdf.a
Then run "make" as per usual. This will force "make" to use the Amber
NetCDF libraries. This has already been fixed in the developer's version,
but I'll turn it into a bugfix shortly with a handful of other small fixes.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jul 26 2013 - 18:00:02 PDT
