AMBER Archive (2006)

Subject: AMBER: AMBER9 compilation error on IBM Cluster

From: amit_at_mbu.iisc.ernet.in
Date: Mon May 15 2006 - 06:11:50 CDT

Dear amber users,
I have compiled amber9 on SGI Altix 3700 and its working fine. Thank you
Ross for your kind help.
Amber9 compilation on IBM cluster P720 using IBM fortran and c/c++
compilers(xlf90, xlfc, xlfC). Parallel operating Enviorment(poe) is used
along with ESS Library.
I am not able to figure out the error.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
../lib/nxtsec.o ../lib/sys.a -lesslsmp -L/opt/ibmcmp/xlf/9.1/lib64
-lxlf90_r -L/opt/ibmcmp/xlsmp/1.5/lib64 -lxlsmp
-L/opt/ibmcmp/xlmass/4.1/lib64 -lmassvp4_64
-L/opt/ibmhpc/ppe.poe/lib/libmpi64 -lmpi -lm
/opt/ibmhpc/ppe.poe/bin/mpfort[122]: [: ew_handle_dips.o: unexpected
operator/operand
qmmm_module.PIMD.o(.text+0xa148): In function
`.__qmmm_module_NMOD_deallocate_qmmm':
: undefined reference to `.qm2_dftb_deallocate'
dynlib.PIMD.o(.text+0x48): In function `.corpac':
: undefined reference to `.__bintraj_NMOD_write_binary_traj'
dynlib.PIMD.o(.text+0xaac): In function `.open_dump_files_2_1':
: undefined reference to `.__bintraj_NMOD_open_binary_files'
dynlib.PIMD.o(.text+0xbcc): In function `.close_dump_files':
: undefined reference to `.__bintraj_NMOD_close_binary_files'
dynlib.PIMD.o(.text+0x1d2c): In function `.prntmd':
: undefined reference to `.amflsh'
dynlib.PIMD.o(.text+0x5894): In function `.cenmas':
: undefined reference to `.amflsh'
force.PIMD.o(.text+0x7780): In function `.force':
: undefined reference to `.__amoeba_interface_NMOD_am_nonbond_eval'
force.PIMD.o(.text+0x8098): In function `.force':
: undefined reference to `.__amoeba_interface_NMOD_am_val_eval'
force.PIMD.o(.text+0x8dec): In function `.force':
: undefined reference to `.morsify_init'
force.PIMD.o(.text+0x8e08): In function `.force':
: undefined reference to `.morsify'
force.PIMD.o(.text+0xb504): In function `.force':
: undefined reference to `.__ntrfc_evb_NMOD_evb_ntrfc'
force.PIMD.o(.text+0xcccc): In function `.force':
: undefined reference to `.out_evb'
mdread.PIMD.o(.text+0x12cc): In function `.mdread1':
: undefined reference to `.pb_read'
mdread.PIMD.o(.text+0x12f8): In function `.mdread1':
: undefined reference to `.__amoeba_mdin_NMOD_amoeba_read_mdin'
mdread.PIMD.o(.text+0x77f8): In function `.mdread2':
: undefined reference to `.pb_init'
mdread.PIMD.o(.text+0x79c0): In function `.mdread2':
: undefined reference to `.evb_input'
mdread.PIMD.o(.text+0x79c8): In function `.mdread2':
: undefined reference to `.evb_init'
mdread.PIMD.o(.text+0x79d0): In function `.mdread2':
: undefined reference to `.evb_alloc'
mdread.PIMD.o(.text+0x79d8): In function `.mdread2':
: undefined reference to `.__evb_pimd_NMOD_evb_pimd_init'
nonbond_list.PIMD.o(.text+0x3288): In function `.__nblist_NMOD_nonbond_list':
: undefined reference to `.amflsh'
rdparm.PIMD.o(.text+0x200): In function `.rdparm1':
: undefined reference to `.nxtsec'
rdparm.PIMD.o(.text+0x334): In function `.rdparm1':
: undefined reference to `.nxtsec'
rdparm.PIMD.o(.text+0xf80): In function `.rdparm1':
: undefined reference to `.nxtsec'
rdparm.PIMD.o(.text+0x1424): In function `.rdparm2':
: undefined reference to `.nxtsec'
rdparm.PIMD.o(.text+0x15a8): In function `.rdparm2':
: undefined reference to `.nxtsec'
rdparm.PIMD.o(.text+0x170c): more undefined references to `.nxtsec' follow
runmd.PIMD.o(.text+0x2764): In function `.runmd':
: undefined reference to `.amflsh'
runmd.PIMD.o(.text+0x8528): In function `.runmd':
: undefined reference to `.__amoeba_runmd_NMOD_am_runmd_scale_cell'
runmd.PIMD.o(.text+0x9574): In function `.runmd':
: undefined reference to `.__bintraj_NMOD_end_binary_frame'
runmd.PIMD.o(.text+0x95a4): In function `.runmd':
: undefined reference to `.__bintraj_NMOD_end_binary_frame'
runmd.PIMD.o(.text+0x99d4): In function `.runmd':
: undefined reference to `.amflsh'
runmd.PIMD.o(.text+0xa7ec): In function `.runmd':
: undefined reference to `.evb_dealloc'
runmd.PIMD.o(.text+0xa7f4): In function `.runmd':
: undefined reference to `.__evb_pimd_NMOD_evb_pimd_dealloc'
sander.PIMD.o(.text+0x11c): In function `.sander':
: undefined reference to `.wallclock'
sander.PIMD.o(.text+0xa54): In function `.sander':
: undefined reference to `.__amoeba_interface_NMOD_amoeba_readparm'
sander.PIMD.o(.text+0xca4): In function `.sander':
: undefined reference to `.amoeba_check_newstyle_inpcrd'
sander.PIMD.o(.text+0xcf0): In function `.sander':
: undefined reference to `.__amoeba_runmd_NMOD_am_runmd_get_coords'
sander.PIMD.o(.text+0x1b9c): In function `.sander':
: undefined reference to `.amflsh'
sander.PIMD.o(.text+0x38b4): In function `.sander':
: undefined reference to `.amflsh'
sander.PIMD.o(.text+0x4be4): In function `.sander':
: undefined reference to `.wallclock'
sander.PIMD.o(.text+0x514c): In function `.sander':
: undefined reference to `.nwallclock'
sander.PIMD.o(.text+0x51b4): In function `.sander':
: undefined reference to `.amflsh'
sander.PIMD.o(.text+0x529c): In function `.sander':
: undefined reference to `.pb_free'
sander.PIMD.o(.text+0x54c0): In function `.sander':
: undefined reference to `.__amoeba_interface_NMOD_amoeba_deallocate'
sander.PIMD.o(.text+0x5aa0): In function `.sander':
: undefined reference to `.amflsh'
ew_setup.PIMD.o(.text+0x380c): In function `.load_ewald_info':
: undefined reference to `.amoeba_check_newstyle_inpcrd'
ew_setup.PIMD.o(.text+0x3840): In function `.load_ewald_info':
: undefined reference to `.__amoeba_runmd_NMOD_am_runmd_get_ucell_info'
ew_setup.PIMD.o(.text+0x4d38): In function `.pmesh_kspace_setup':
: undefined reference to `.__fft_NMOD_fft_init'
trace.o(.text+0x17f0): In function `.__trace_NMOD_trace_exit':
: undefined reference to `.wallclock'
trace.o(.text+0x196c): In function `.__trace_NMOD_trace_enter':
: undefined reference to `.wallclock'
lmod.o(.text+0xcb0): In function `.__lmod_driver_NMOD_run_xmin':
: undefined reference to `.xmin'
lmod.o(.text+0x36b0): In function `.__lmod_driver_NMOD_run_lmod':
: undefined reference to `.lmod'
pb_force.o(.text+0xaa14): In function `.__poisson_boltzmann_NMOD_pb_fdfrc':
: undefined reference to `.pb_print'
relax_mat.o(.text+0x5940): In function `.__relax_mat_NMOD_remarc':
: undefined reference to `.dspev'
printe.o(.text+0x2bc): In function `.report_min_results':
: undefined reference to `.amflsh'
printe.o(.text+0x448): In function `.report_min_progress_2_1':
: undefined reference to `.amflsh'
printe.o(.text+0x1218): In function `.printe':
: undefined reference to `.amflsh'
runmin.o(.text+0xc30): In function `.runmin':
: undefined reference to `.ddot'
runmin.o(.text+0x15b8): In function `.runmin':
: undefined reference to `.ddot'
runmin.o(.text+0x1a4c): In function `.runmin':
: undefined reference to `.ddot'
runmin.o(.text+0x23fc): In function `.runmin':
: undefined reference to `.evb_dealloc'
runmin.o(.text+0x25ac): In function `.runmin':
: undefined reference to `.ddot'
runmin.o(.text+0x26d8): In function `.runmin':
: undefined reference to `.ddot'
runmin.o(.text+0x2710): In function `.runmin':
: undefined reference to `.ddot'
ene.PIMD.o(.text+0x66d0): In function `.rmsfit':
: undefined reference to `.dgeev'
align.o(.text+0xbd8): In function `.align1':
: undefined reference to `.dspev'
align.o(.text+0x1438): In function `.align1':
: undefined reference to `.dspev'
new_time.o(.text+0x2348): In function `.timer_start':
: undefined reference to `.wallclock'
new_time.o(.text+0x2508): In function `.timer_stop':
: undefined reference to `.wallclock'
new_time.o(.text+0x26c8): In function `.timer_stop_start':
: undefined reference to `.wallclock'
assert.o(.text+0x158): In function `.aass':
: undefined reference to `.amflsh'
constantph.o(.text+0x1360): In function `.cnstphwriterestart':
: undefined reference to `.amflsh'
qm2_energy.o(.text+0x3d00): In function `.qm2_energy':
: undefined reference to `.qm2_dftb_energy'
qm2_get_qm_forces.o(.text+0x9c): In function `.qm2_get_qm_forces':
: undefined reference to `.qm2_dftb_forces'
qm2_get_qmmm_forces.o(.text+0x84): In function `.qm2_get_qmmm_forces':
: undefined reference to `.qm2_dftb_get_qmmm_forces'
qm2_load_params_and_allocate.o(.text+0x161d4): In function
`.qm2_load_params_and_allocate':
: undefined reference to `.qm2_dftb_load_params'
make[1]: *** [sander.PIMD.MPI] Error 1
make[1]: Leaving directory `/cluster/utemp/mburantu/amber9/src/sander'
make: *** [parallel] Error 2
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

config.h is attached for any further details.

Thanks in advance.

amit


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