cd AmberTools/src && make install make[1]: Entering directory `/usr/local/amber12/AmberTools/src' AmberTools13 has no CUDA-enabled components (cd ../../src && make cuda ) make[2]: Entering directory `/usr/local/amber12/src' Starting installation of Amber12 (cuda) at Wed Jun 5 16:32:27 EDT 2013. cd pmemd && make cuda make[3]: Entering directory `/usr/local/amber12/src/pmemd' make -C src/ cuda make[4]: Entering directory `/usr/local/amber12/src/pmemd/src' make -C ./cuda make[5]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda' make[5]: `cuda.a' is up to date. make[5]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda' make -C ./cuda make[5]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda' make[5]: `cuda.a' is up to date. make[5]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda' make -C ./cuda make[5]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda' make[5]: `cuda.a' is up to date. make[5]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda' make -C ./cuda make[5]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda' make[5]: `cuda.a' is up to date. make[5]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda' make -C ./cuda make[5]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda' make[5]: `cuda.a' is up to date. make[5]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda' make -C ./cuda make[5]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda' make[5]: `cuda.a' is up to date. make[5]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda' make -C ./cuda make[5]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda' make[5]: `cuda.a' is up to date. make[5]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda' gfortran -O3 -mtune=native -DCUDA -Duse_SPFP -o pmemd.cuda gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o img.o nbips.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o dihedrals.o extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o pmemd_lib.o runfiles.o file_io.o bintraj.o binrestart.o pmemd_clib.o pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o pme_alltasks_setup.o pme_setup.o ene_frc_splines.o gb_alltasks_setup.o nextprmtop_section.o angles_ub.o dihedrals_imp.o cmap.o charmm.o charmm_gold.o findmask.o remd.o multipmemd.o remd_exchg.o amd.o gbsa.o \ ./cuda/cuda.a -L/usr/local/cuda/lib64 -L/usr/local/cuda/lib -lcurand -lcufft -lcudart -L/usr/lib64 -lstdc++ -L/usr/local/amber12/lib -L/usr/local/amber12/lib -lnetcdf bintraj.o: In function `__bintraj_mod_MOD_checkerror.part.0': bintraj.F90:(.text+0x6e): undefined reference to `__netcdf_MOD_nf90_strerror' bintraj.o: In function `__bintraj_mod_MOD_end_binary_frame': bintraj.F90:(.text+0x332): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal' bintraj.F90:(.text+0x35e): undefined reference to `__netcdf_MOD_nf90_sync' bintraj.F90:(.text+0x4ba): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal' bintraj.F90:(.text+0x4cf): undefined reference to `__netcdf_MOD_nf90_sync' bintraj.o: In function `__bintraj_mod_MOD_write_binary_cell_dat': bintraj.F90:(.text+0x671): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal' bintraj.F90:(.text+0x7a7): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal' bintraj.o: In function `__bintraj_mod_MOD_write_binary_vels_axis_flipped': bintraj.F90:(.text+0xa0e): undefined reference to `__netcdf_MOD_nf90_put_var_2d_fourbytereal' bintraj.o: In function `__bintraj_mod_MOD_write_binary_vels': bintraj.F90:(.text+0xbba): undefined reference to `__netcdf_MOD_nf90_put_var_2d_eightbytereal' bintraj.o: In function `__bintraj_mod_MOD_write_binary_crds_axis_flipped': bintraj.F90:(.text+0xe74): undefined reference to `__netcdf_MOD_nf90_put_var_2d_fourbytereal' bintraj.o: In function `__bintraj_mod_MOD_write_binary_crds': bintraj.F90:(.text+0x1066): undefined reference to `__netcdf_MOD_nf90_put_var_2d_eightbytereal' bintraj.o: In function `__bintraj_mod_MOD_close_binary_files': bintraj.F90:(.text+0x10e6): undefined reference to `__netcdf_MOD_nf90_close' bintraj.F90:(.text+0x1104): undefined reference to `__netcdf_MOD_nf90_close' bintraj.o: In function `__bintraj_mod_MOD_open_binary_files': bintraj.F90:(.text+0x11aa): undefined reference to `__netcdf_MOD_nf90_create' bintraj.F90:(.text+0x11db): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x120c): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x123d): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x126e): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x12a2): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x12d6): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x130a): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x133e): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x1372): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.o:bintraj.F90:(.text+0x13a6): more undefined references to `__netcdf_MOD_nf90_put_att_text' follow bintraj.o: In function `__bintraj_mod_MOD_open_binary_files': bintraj.F90:(.text+0x143e): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x14c7): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x14fb): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x1595): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x15c9): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x1608): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x1639): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x16c6): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x1767): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x17f1): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x1825): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x18b2): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x18e6): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x191c): undefined reference to `__netcdf_MOD_nf90_set_fill' bintraj.F90:(.text+0x193e): undefined reference to `__netcdf_MOD_nf90_enddef' bintraj.F90:(.text+0x1a7c): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text' bintraj.F90:(.text+0x1bc5): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text' bintraj.F90:(.text+0x1d34): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text' bintraj.F90:(.text+0x1d7f): undefined reference to `__netcdf_MOD_nf90_create' bintraj.F90:(.text+0x1db0): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x1de1): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x1e12): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x1e43): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x1e77): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x1eab): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x1edf): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x1f13): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x1f47): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.o:bintraj.F90:(.text+0x1f7b): more undefined references to `__netcdf_MOD_nf90_put_att_text' follow bintraj.o: In function `__bintraj_mod_MOD_open_binary_files': bintraj.F90:(.text+0x2016): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x209c): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x20d0): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x2164): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x2198): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x21c6): undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal' bintraj.F90:(.text+0x21ec): undefined reference to `__netcdf_MOD_nf90_set_fill' bintraj.F90:(.text+0x220e): undefined reference to `__netcdf_MOD_nf90_enddef' bintraj.F90:(.text+0x2344): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text' bintraj.F90:(.text+0x29ff): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x2a46): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x2a87): undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal' binrestart.o: In function `__binrestart_mod_MOD_checkerror.part.0': binrestart.F90:(.text+0x6e): undefined reference to `__netcdf_MOD_nf90_strerror' binrestart.o: In function `__binrestart_mod_MOD_write_nc_coords': binrestart.F90:(.text+0x36f): undefined reference to `__netcdf_MOD_nf90_put_var_2d_eightbytereal' binrestart.F90:(.text+0x4e1): undefined reference to `__netcdf_MOD_nf90_put_var_2d_eightbytereal' binrestart.o: In function `__binrestart_mod_MOD_getdiminfo': binrestart.F90:(.text+0x563): undefined reference to `__netcdf_MOD_nf90_inq_dimid' binrestart.F90:(.text+0x585): undefined reference to `__netcdf_MOD_nf90_inquire_dimension' binrestart.o: In function `__binrestart_mod_MOD_read_nc_refc': binrestart.F90:(.text+0x6a4): undefined reference to `__netcdf_MOD_nf90_open' binrestart.F90:(.text+0x6fb): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x757): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x7c8): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x8cc): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x92b): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0xa8f): undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal' binrestart.F90:(.text+0xb97): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0xbd5): undefined reference to `__netcdf_MOD_nf90_close' binrestart.o: In function `__binrestart_mod_MOD_read_nc_restart': binrestart.F90:(.text+0xf5e): undefined reference to `__netcdf_MOD_nf90_open' binrestart.F90:(.text+0xfb5): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x1011): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x1082): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x111b): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x1177): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x12fd): undefined reference to `__netcdf_MOD_nf90_get_var_2d_eightbytereal' binrestart.F90:(.text+0x140b): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x1458): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x1483): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x14df): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x1541): undefined reference to `__netcdf_MOD_nf90_get_var_eightbytereal' binrestart.F90:(.text+0x158e): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x15c0): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x15d8): undefined reference to `__netcdf_MOD_nf90_close' binrestart.F90:(.text+0x161b): undefined reference to `__netcdf_MOD_nf90_get_var_eightbytereal' binrestart.F90:(.text+0x1668): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x1788): undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal' binrestart.F90:(.text+0x18a8): undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal' binrestart.F90:(.text+0x19b7): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x1b29): undefined reference to `__netcdf_MOD_nf90_get_var_2d_eightbytereal' binrestart.o: In function `__binrestart_mod_MOD_read_nc_restart_atoms': binrestart.F90:(.text+0x1fbe): undefined reference to `__netcdf_MOD_nf90_open' binrestart.F90:(.text+0x201a): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x208b): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x210d): undefined reference to `__netcdf_MOD_nf90_close' binrestart.o: In function `__binrestart_mod_MOD_check_nc_restart': binrestart.F90:(.text+0x2347): undefined reference to `__netcdf_MOD_nf90_open' binrestart.F90:(.text+0x237f): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x23ab): undefined reference to `__netcdf_MOD_nf90_close' binrestart.o: In function `__binrestart_mod_MOD_read_nc_restart_box': binrestart.F90:(.text+0x23f8): undefined reference to `__netcdf_MOD_nf90_open' binrestart.F90:(.text+0x2445): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x2492): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x25d4): undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal' binrestart.F90:(.text+0x2732): undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal' binrestart.F90:(.text+0x2799): undefined reference to `__netcdf_MOD_nf90_close' binrestart.o: In function `__binrestart_mod_MOD_write_nc_restart': binrestart.F90:(.text+0x2954): undefined reference to `__netcdf_MOD_nf90_create' binrestart.F90:(.text+0x2989): undefined reference to `__netcdf_MOD_nf90_def_var_scalar' binrestart.F90:(.text+0x29ce): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x2a0d): undefined reference to `__netcdf_MOD_nf90_def_dim' binrestart.F90:(.text+0x2ab1): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' binrestart.F90:(.text+0x2af0): undefined reference to `__netcdf_MOD_nf90_def_dim' binrestart.F90:(.text+0x2b91): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' binrestart.F90:(.text+0x2bd6): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x2c8b): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' binrestart.F90:(.text+0x2cd0): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x2d0f): undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal' binrestart.F90:(.text+0x2d4c): undefined reference to `__netcdf_MOD_nf90_def_dim' binrestart.F90:(.text+0x2de0): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' binrestart.F90:(.text+0x2e1f): undefined reference to `__netcdf_MOD_nf90_def_dim' binrestart.F90:(.text+0x2e5e): undefined reference to `__netcdf_MOD_nf90_def_dim' binrestart.F90:(.text+0x2eff): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' binrestart.F90:(.text+0x2f93): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' binrestart.F90:(.text+0x2fd8): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x306c): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' binrestart.F90:(.text+0x30b1): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x30e3): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x3128): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x316d): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x31b2): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.o:binrestart.F90:(.text+0x31f7): more undefined references to `__netcdf_MOD_nf90_put_att_text' follow binrestart.o: In function `__binrestart_mod_MOD_write_nc_restart': binrestart.F90:(.text+0x3273): undefined reference to `__netcdf_MOD_nf90_set_fill' binrestart.F90:(.text+0x32a6): undefined reference to `__netcdf_MOD_nf90_enddef' binrestart.F90:(.text+0x33f5): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text' binrestart.F90:(.text+0x3543): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text' binrestart.F90:(.text+0x3690): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text' binrestart.F90:(.text+0x36ec): undefined reference to `__netcdf_MOD_nf90_put_var_eightbytereal' binrestart.F90:(.text+0x3945): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal' binrestart.F90:(.text+0x3a82): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal' binrestart.F90:(.text+0x3a95): undefined reference to `__netcdf_MOD_nf90_close' binrestart.F90:(.text+0x3db4): undefined reference to `__netcdf_MOD_nf90_open' collect2: ld returned 1 exit status make[4]: *** [pmemd.cuda] Error 1 make[4]: Leaving directory `/usr/local/amber12/src/pmemd/src' make[3]: *** [cuda] Error 2 make[3]: Leaving directory `/usr/local/amber12/src/pmemd' make[2]: *** [cuda] Error 2 make[2]: Leaving directory `/usr/local/amber12/src' make[1]: [cuda] Error 2 (ignored) make[1]: Leaving directory `/usr/local/amber12/AmberTools/src' make[1]: Entering directory `/usr/local/amber12/src' Starting installation of Amber12 (cuda) at Wed Jun 5 16:32:27 EDT 2013. cd pmemd && make cuda make[2]: Entering directory `/usr/local/amber12/src/pmemd' make -C src/ cuda make[3]: Entering directory `/usr/local/amber12/src/pmemd/src' make -C ./cuda make[4]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda' make[4]: `cuda.a' is up to date. make[4]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda' make -C ./cuda make[4]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda' make[4]: `cuda.a' is up to date. make[4]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda' make -C ./cuda make[4]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda' make[4]: `cuda.a' is up to date. make[4]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda' make -C ./cuda make[4]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda' make[4]: `cuda.a' is up to date. make[4]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda' make -C ./cuda make[4]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda' make[4]: `cuda.a' is up to date. make[4]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda' make -C ./cuda make[4]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda' make[4]: `cuda.a' is up to date. make[4]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda' make -C ./cuda make[4]: Entering directory `/usr/local/amber12/src/pmemd/src/cuda' make[4]: `cuda.a' is up to date. make[4]: Leaving directory `/usr/local/amber12/src/pmemd/src/cuda' gfortran -O3 -mtune=native -DCUDA -Duse_SPFP -o pmemd.cuda gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o inpcrd_dat.o dynamics_dat.o img.o nbips.o parallel_dat.o parallel.o gb_parallel.o pme_direct.o pme_recip_dat.o pme_slab_recip.o pme_blk_recip.o pme_slab_fft.o pme_blk_fft.o pme_fft_dat.o fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o nb_exclusions.o cit.o dynamics.o bonds.o angles.o dihedrals.o extra_pnts_nb14.o runmd.o loadbal.o shake.o prfs.o mol_list.o runmin.o constraints.o axis_optimize.o gb_ene.o veclib.o gb_force.o timers.o pmemd_lib.o runfiles.o file_io.o bintraj.o binrestart.o pmemd_clib.o pmemd.o random.o degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o pme_alltasks_setup.o pme_setup.o ene_frc_splines.o gb_alltasks_setup.o nextprmtop_section.o angles_ub.o dihedrals_imp.o cmap.o charmm.o charmm_gold.o findmask.o remd.o multipmemd.o remd_exchg.o amd.o gbsa.o \ ./cuda/cuda.a -L/usr/local/cuda/lib64 -L/usr/local/cuda/lib -lcurand -lcufft -lcudart -L/usr/lib64 -lstdc++ -L/usr/local/amber12/lib -L/usr/local/amber12/lib -lnetcdf bintraj.o: In function `__bintraj_mod_MOD_checkerror.part.0': bintraj.F90:(.text+0x6e): undefined reference to `__netcdf_MOD_nf90_strerror' bintraj.o: In function `__bintraj_mod_MOD_end_binary_frame': bintraj.F90:(.text+0x332): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal' bintraj.F90:(.text+0x35e): undefined reference to `__netcdf_MOD_nf90_sync' bintraj.F90:(.text+0x4ba): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal' bintraj.F90:(.text+0x4cf): undefined reference to `__netcdf_MOD_nf90_sync' bintraj.o: In function `__bintraj_mod_MOD_write_binary_cell_dat': bintraj.F90:(.text+0x671): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal' bintraj.F90:(.text+0x7a7): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal' bintraj.o: In function `__bintraj_mod_MOD_write_binary_vels_axis_flipped': bintraj.F90:(.text+0xa0e): undefined reference to `__netcdf_MOD_nf90_put_var_2d_fourbytereal' bintraj.o: In function `__bintraj_mod_MOD_write_binary_vels': bintraj.F90:(.text+0xbba): undefined reference to `__netcdf_MOD_nf90_put_var_2d_eightbytereal' bintraj.o: In function `__bintraj_mod_MOD_write_binary_crds_axis_flipped': bintraj.F90:(.text+0xe74): undefined reference to `__netcdf_MOD_nf90_put_var_2d_fourbytereal' bintraj.o: In function `__bintraj_mod_MOD_write_binary_crds': bintraj.F90:(.text+0x1066): undefined reference to `__netcdf_MOD_nf90_put_var_2d_eightbytereal' bintraj.o: In function `__bintraj_mod_MOD_close_binary_files': bintraj.F90:(.text+0x10e6): undefined reference to `__netcdf_MOD_nf90_close' bintraj.F90:(.text+0x1104): undefined reference to `__netcdf_MOD_nf90_close' bintraj.o: In function `__bintraj_mod_MOD_open_binary_files': bintraj.F90:(.text+0x11aa): undefined reference to `__netcdf_MOD_nf90_create' bintraj.F90:(.text+0x11db): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x120c): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x123d): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x126e): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x12a2): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x12d6): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x130a): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x133e): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x1372): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.o:bintraj.F90:(.text+0x13a6): more undefined references to `__netcdf_MOD_nf90_put_att_text' follow bintraj.o: In function `__bintraj_mod_MOD_open_binary_files': bintraj.F90:(.text+0x143e): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x14c7): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x14fb): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x1595): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x15c9): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x1608): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x1639): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x16c6): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x1767): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x17f1): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x1825): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x18b2): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x18e6): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x191c): undefined reference to `__netcdf_MOD_nf90_set_fill' bintraj.F90:(.text+0x193e): undefined reference to `__netcdf_MOD_nf90_enddef' bintraj.F90:(.text+0x1a7c): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text' bintraj.F90:(.text+0x1bc5): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text' bintraj.F90:(.text+0x1d34): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text' bintraj.F90:(.text+0x1d7f): undefined reference to `__netcdf_MOD_nf90_create' bintraj.F90:(.text+0x1db0): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x1de1): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x1e12): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x1e43): undefined reference to `__netcdf_MOD_nf90_def_dim' bintraj.F90:(.text+0x1e77): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x1eab): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x1edf): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x1f13): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x1f47): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.o:bintraj.F90:(.text+0x1f7b): more undefined references to `__netcdf_MOD_nf90_put_att_text' follow bintraj.o: In function `__bintraj_mod_MOD_open_binary_files': bintraj.F90:(.text+0x2016): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x209c): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x20d0): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x2164): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x2198): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x21c6): undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal' bintraj.F90:(.text+0x21ec): undefined reference to `__netcdf_MOD_nf90_set_fill' bintraj.F90:(.text+0x220e): undefined reference to `__netcdf_MOD_nf90_enddef' bintraj.F90:(.text+0x2344): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text' bintraj.F90:(.text+0x29ff): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' bintraj.F90:(.text+0x2a46): undefined reference to `__netcdf_MOD_nf90_put_att_text' bintraj.F90:(.text+0x2a87): undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal' binrestart.o: In function `__binrestart_mod_MOD_checkerror.part.0': binrestart.F90:(.text+0x6e): undefined reference to `__netcdf_MOD_nf90_strerror' binrestart.o: In function `__binrestart_mod_MOD_write_nc_coords': binrestart.F90:(.text+0x36f): undefined reference to `__netcdf_MOD_nf90_put_var_2d_eightbytereal' binrestart.F90:(.text+0x4e1): undefined reference to `__netcdf_MOD_nf90_put_var_2d_eightbytereal' binrestart.o: In function `__binrestart_mod_MOD_getdiminfo': binrestart.F90:(.text+0x563): undefined reference to `__netcdf_MOD_nf90_inq_dimid' binrestart.F90:(.text+0x585): undefined reference to `__netcdf_MOD_nf90_inquire_dimension' binrestart.o: In function `__binrestart_mod_MOD_read_nc_refc': binrestart.F90:(.text+0x6a4): undefined reference to `__netcdf_MOD_nf90_open' binrestart.F90:(.text+0x6fb): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x757): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x7c8): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x8cc): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x92b): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0xa8f): undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal' binrestart.F90:(.text+0xb97): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0xbd5): undefined reference to `__netcdf_MOD_nf90_close' binrestart.o: In function `__binrestart_mod_MOD_read_nc_restart': binrestart.F90:(.text+0xf5e): undefined reference to `__netcdf_MOD_nf90_open' binrestart.F90:(.text+0xfb5): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x1011): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x1082): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x111b): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x1177): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x12fd): undefined reference to `__netcdf_MOD_nf90_get_var_2d_eightbytereal' binrestart.F90:(.text+0x140b): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x1458): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x1483): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x14df): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x1541): undefined reference to `__netcdf_MOD_nf90_get_var_eightbytereal' binrestart.F90:(.text+0x158e): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x15c0): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x15d8): undefined reference to `__netcdf_MOD_nf90_close' binrestart.F90:(.text+0x161b): undefined reference to `__netcdf_MOD_nf90_get_var_eightbytereal' binrestart.F90:(.text+0x1668): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x1788): undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal' binrestart.F90:(.text+0x18a8): undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal' binrestart.F90:(.text+0x19b7): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x1b29): undefined reference to `__netcdf_MOD_nf90_get_var_2d_eightbytereal' binrestart.o: In function `__binrestart_mod_MOD_read_nc_restart_atoms': binrestart.F90:(.text+0x1fbe): undefined reference to `__netcdf_MOD_nf90_open' binrestart.F90:(.text+0x201a): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x208b): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x210d): undefined reference to `__netcdf_MOD_nf90_close' binrestart.o: In function `__binrestart_mod_MOD_check_nc_restart': binrestart.F90:(.text+0x2347): undefined reference to `__netcdf_MOD_nf90_open' binrestart.F90:(.text+0x237f): undefined reference to `__netcdf_MOD_nf90_get_att_text' binrestart.F90:(.text+0x23ab): undefined reference to `__netcdf_MOD_nf90_close' binrestart.o: In function `__binrestart_mod_MOD_read_nc_restart_box': binrestart.F90:(.text+0x23f8): undefined reference to `__netcdf_MOD_nf90_open' binrestart.F90:(.text+0x2445): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x2492): undefined reference to `__netcdf_MOD_nf90_inq_varid' binrestart.F90:(.text+0x25d4): undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal' binrestart.F90:(.text+0x2732): undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal' binrestart.F90:(.text+0x2799): undefined reference to `__netcdf_MOD_nf90_close' binrestart.o: In function `__binrestart_mod_MOD_write_nc_restart': binrestart.F90:(.text+0x2954): undefined reference to `__netcdf_MOD_nf90_create' binrestart.F90:(.text+0x2989): undefined reference to `__netcdf_MOD_nf90_def_var_scalar' binrestart.F90:(.text+0x29ce): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x2a0d): undefined reference to `__netcdf_MOD_nf90_def_dim' binrestart.F90:(.text+0x2ab1): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' binrestart.F90:(.text+0x2af0): undefined reference to `__netcdf_MOD_nf90_def_dim' binrestart.F90:(.text+0x2b91): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' binrestart.F90:(.text+0x2bd6): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x2c8b): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' binrestart.F90:(.text+0x2cd0): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x2d0f): undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal' binrestart.F90:(.text+0x2d4c): undefined reference to `__netcdf_MOD_nf90_def_dim' binrestart.F90:(.text+0x2de0): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' binrestart.F90:(.text+0x2e1f): undefined reference to `__netcdf_MOD_nf90_def_dim' binrestart.F90:(.text+0x2e5e): undefined reference to `__netcdf_MOD_nf90_def_dim' binrestart.F90:(.text+0x2eff): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' binrestart.F90:(.text+0x2f93): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' binrestart.F90:(.text+0x2fd8): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x306c): undefined reference to `__netcdf_MOD_nf90_def_var_manydims' binrestart.F90:(.text+0x30b1): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x30e3): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x3128): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x316d): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.F90:(.text+0x31b2): undefined reference to `__netcdf_MOD_nf90_put_att_text' binrestart.o:binrestart.F90:(.text+0x31f7): more undefined references to `__netcdf_MOD_nf90_put_att_text' follow binrestart.o: In function `__binrestart_mod_MOD_write_nc_restart': binrestart.F90:(.text+0x3273): undefined reference to `__netcdf_MOD_nf90_set_fill' binrestart.F90:(.text+0x32a6): undefined reference to `__netcdf_MOD_nf90_enddef' binrestart.F90:(.text+0x33f5): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text' binrestart.F90:(.text+0x3543): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text' binrestart.F90:(.text+0x3690): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text' binrestart.F90:(.text+0x36ec): undefined reference to `__netcdf_MOD_nf90_put_var_eightbytereal' binrestart.F90:(.text+0x3945): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal' binrestart.F90:(.text+0x3a82): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal' binrestart.F90:(.text+0x3a95): undefined reference to `__netcdf_MOD_nf90_close' binrestart.F90:(.text+0x3db4): undefined reference to `__netcdf_MOD_nf90_open' collect2: ld returned 1 exit status make[3]: *** [pmemd.cuda] Error 1 make[3]: Leaving directory `/usr/local/amber12/src/pmemd/src' make[2]: *** [cuda] Error 2 make[2]: Leaving directory `/usr/local/amber12/src/pmemd' make[1]: *** [cuda] Error 2 make[1]: Leaving directory `/usr/local/amber12/src' make: *** [install] Error 2