Hi,
I have Amber12 and Ambertools13 on my workstation and I installed the basic version without any problem using the information provided in this site:
http://jswails.wikidot.com/installing-amber12-and-ambertools-12#toc12
I had to specify the netCDF file to run the installation.
./configure --with-netcdf /usr/local/bin/amber12/AmberTools/ gnu
make install and make test #run OK.
However, when I try to install the CUDA version using the same netcdf path, I get the following problem:
./configure --with-netcdf /usr/local/bin/amber12/AmberTools/ -cuda gnu #(no problem at this step)
make install
----------------------------
make[5]: Leaving directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[5]: Entering directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make[5]: `cuda.a' is up to date.
make[5]: Leaving directory `/usr/local/bin/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-5.0/lib64 -L/usr/local/cuda-5.0/lib -lcurand -lcufft -lcudart -L/usr/lib64 -lstdc++ -L/usr/local/bin/amber12/lib -L/usr/local/bin/amber12/AmberTools//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+0x11a9): undefined reference to `__netcdf_MOD_nf90_create'
bintraj.F90:(.text+0x11da): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x120b): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x123c): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x126d): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x12a1): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x12d5): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1309): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x133d): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1371): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.o:bintraj.F90:(.text+0x13a5): more undefined references to `__netcdf_MOD_nf90_put_att_text' follow
bintraj.o: In function `__bintraj_mod_MOD_open_binary_files':
bintraj.F90:(.text+0x143d): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x14c6): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x14fa): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1594): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x15c8): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1607): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x1638): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x16c5): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x1766): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x17f0): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x1824): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x18b1): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x18e5): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x191b): undefined reference to `__netcdf_MOD_nf90_set_fill'
bintraj.F90:(.text+0x193d): undefined reference to `__netcdf_MOD_nf90_enddef'
bintraj.F90:(.text+0x1a7b): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text'
bintraj.F90:(.text+0x1bc4): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text'
bintraj.F90:(.text+0x1d33): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text'
bintraj.F90:(.text+0x1d7e): undefined reference to `__netcdf_MOD_nf90_create'
bintraj.F90:(.text+0x1daf): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x1de0): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x1e11): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x1e42): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x1e76): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1eaa): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1ede): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1f12): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1f46): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.o:bintraj.F90:(.text+0x1f7a): more undefined references to `__netcdf_MOD_nf90_put_att_text' follow
bintraj.o: In function `__bintraj_mod_MOD_open_binary_files':
bintraj.F90:(.text+0x2015): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x209b): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x20cf): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x2163): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x2197): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x21c5): undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal'
bintraj.F90:(.text+0x21eb): undefined reference to `__netcdf_MOD_nf90_set_fill'
bintraj.F90:(.text+0x220d): undefined reference to `__netcdf_MOD_nf90_enddef'
bintraj.F90:(.text+0x2343): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text'
bintraj.F90:(.text+0x2a17): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x2a5e): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x2a9f): 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/bin/amber12/src/pmemd/src'
make[3]: *** [cuda] Error 2
make[3]: Leaving directory `/usr/local/bin/amber12/src/pmemd'
make[2]: *** [cuda] Error 2
make[2]: Leaving directory `/usr/local/bin/amber12/src'
make[1]: [cuda] Error 2 (ignored)
make[1]: Leaving directory `/usr/local/bin/amber12/AmberTools/src'
make[1]: Entering directory `/usr/local/bin/amber12/src'
Starting installation of Amber12 (cuda) at Sun Jul 21 18:55:38 BRT 2013.
cd pmemd && make cuda
make[2]: Entering directory `/usr/local/bin/amber12/src/pmemd'
make -C src/ cuda
make[3]: Entering directory `/usr/local/bin/amber12/src/pmemd/src'
make -C ./cuda
make[4]: Entering directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make -C ./cuda
make[4]: Entering directory `/usr/local/bin/amber12/src/pmemd/src/cuda'
make[4]: `cuda.a' is up to date.
make[4]: Leaving directory `/usr/local/bin/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-5.0/lib64 -L/usr/local/cuda-5.0/lib -lcurand -lcufft -lcudart -L/usr/lib64 -lstdc++ -L/usr/local/bin/amber12/lib -L/usr/local/bin/amber12/AmberTools//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+0x11a9): undefined reference to `__netcdf_MOD_nf90_create'
bintraj.F90:(.text+0x11da): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x120b): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x123c): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x126d): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x12a1): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x12d5): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1309): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x133d): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1371): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.o:bintraj.F90:(.text+0x13a5): more undefined references to `__netcdf_MOD_nf90_put_att_text' follow
bintraj.o: In function `__bintraj_mod_MOD_open_binary_files':
bintraj.F90:(.text+0x143d): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x14c6): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x14fa): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1594): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x15c8): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1607): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x1638): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x16c5): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x1766): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x17f0): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x1824): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x18b1): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x18e5): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x191b): undefined reference to `__netcdf_MOD_nf90_set_fill'
bintraj.F90:(.text+0x193d): undefined reference to `__netcdf_MOD_nf90_enddef'
bintraj.F90:(.text+0x1a7b): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text'
bintraj.F90:(.text+0x1bc4): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text'
bintraj.F90:(.text+0x1d33): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text'
bintraj.F90:(.text+0x1d7e): undefined reference to `__netcdf_MOD_nf90_create'
bintraj.F90:(.text+0x1daf): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x1de0): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x1e11): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x1e42): undefined reference to `__netcdf_MOD_nf90_def_dim'
bintraj.F90:(.text+0x1e76): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1eaa): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1ede): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1f12): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x1f46): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.o:bintraj.F90:(.text+0x1f7a): more undefined references to `__netcdf_MOD_nf90_put_att_text' follow
bintraj.o: In function `__bintraj_mod_MOD_open_binary_files':
bintraj.F90:(.text+0x2015): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x209b): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x20cf): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x2163): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x2197): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x21c5): undefined reference to `__netcdf_MOD_nf90_put_att_one_fourbytereal'
bintraj.F90:(.text+0x21eb): undefined reference to `__netcdf_MOD_nf90_set_fill'
bintraj.F90:(.text+0x220d): undefined reference to `__netcdf_MOD_nf90_enddef'
bintraj.F90:(.text+0x2343): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text'
bintraj.F90:(.text+0x2a17): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
bintraj.F90:(.text+0x2a5e): undefined reference to `__netcdf_MOD_nf90_put_att_text'
bintraj.F90:(.text+0x2a9f): 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/bin/amber12/src/pmemd/src'
make[2]: *** [cuda] Error 2
make[2]: Leaving directory `/usr/local/bin/amber12/src/pmemd'
make[1]: *** [cuda] Error 2
make[1]: Leaving directory `/usr/local/bin/amber12/src'
make: *** [install] Error 2
------------------------
I checked on the amber mailing list to see if I could find a way to fix the netcdf issue without success.
Specs of the system:
Linux 3.6.11-4.fc16.x86_64 #1 x86_64 x86_64 GNU/Linux
GTX680 graphics card
cuda-5.0
NVIDIA driver version 319.23
Kind regards,
Andrei
Prof. Dr. Andrei Leitão
Grupo de Química Medicinal (NEQUIMED)
Instituto de Química de São Carlos - USP
Av. Trabalhador São-carlense, 400
Tel:(16)3373-9943
Medicinal Chemistry Group (NEQUIMED)
Institute of Chemistry of Sao Carlos - USP - Brazil
Phone:+55(16)3373-9943
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jul 21 2013 - 16:00:02 PDT
