Oh, because dragonegg doesn't support OpenMP yet. Is there a compiler flag
to disable OpenMP in pmemd?
On Sat, Mar 5, 2016 at 2:18 AM, Jason Swails <jason.swails.gmail.com> wrote:
> mpif90 -fplugin=/usr/lib64/dragonegg.so -fplugin=/usr/lib64/dragonegg.so
> -fPIC -O3 -mtune=native -o /home/swails/build_amber/amber/bin/pmemd.MPI
> gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o mdin_ctrl_dat.o
> mdin_emil_dat.o mdin_ewald_dat.o mdin_debugf_dat.o prmtop_dat.o
> inpcrd_dat.o dynamics_dat.o emil.o img.o nbips.o offload_allocation.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 gb_ene_hybrid.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 AmberNetcdf.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 gamd.o ti.o gbsa.o barostats.o scaledMD.o
> constantph.o energy_records.o constantph_dat.o relaxmd.o sgld.o emap.o
> get_efield_energy.o -L/home/swails/build_amber/amber/lib \
> /home/swails/build_amber/amber/lib/libnetcdff.a
> /home/swails/build_amber/amber/lib/libnetcdf.a
> /home/swails/build_amber/amber/lib/libemil.a -lstdc++ -lmpi_cxx
> gb_parallel.o: In function `__gb_parallel_mod_MOD_gb_parallel_setup':
> gb_parallel.F90:(.text+0x9f3): undefined reference to
> `omp_get_num_threads_'
> gb_ene_hybrid.o: In function
> `__gb_ene_hybrid_mod_MOD_gb_ene_hyb_force_timode':
> gb_ene_hybrid.F90:(.text+0x2b69): undefined reference to
> `omp_get_thread_num_'
> gb_ene_hybrid.F90:(.text+0x401c): undefined reference to
> `omp_get_thread_num_'
> gb_ene_hybrid.o: In function `__gb_ene_hybrid_mod_MOD_gb_ene_hyb_force':
> gb_ene_hybrid.F90:(.text+0x7928): undefined reference to
> `omp_get_thread_num_'
> gb_ene_hybrid.F90:(.text+0x8c6c): undefined reference to
> `omp_get_thread_num_'
> gb_ene_hybrid.o: In function `__gb_ene_hybrid_mod_MOD_gb_ene_hyb_energy':
> gb_ene_hybrid.F90:(.text+0xc579): undefined reference to
> `omp_get_thread_num_'
> gb_ene_hybrid.o:gb_ene_hybrid.F90:(.text+0xd76c): more undefined
> references to `omp_get_thread_num_' follow
> gb_ene_hybrid.o: In function
> `__gb_ene_hybrid_mod_MOD_final_gb_setup_hybrid':
> gb_ene_hybrid.F90:(.text+0x194eb): undefined reference to
> `omp_get_num_threads_'
> bonds.o: In function `__bonds_mod_MOD_get_bond_energy_gb':
> bonds.F90:(.text+0x3d0): undefined reference to `omp_set_lock_'
> bonds.F90:(.text+0x44f): undefined reference to `omp_unset_lock_'
> bonds.F90:(.text+0x470): undefined reference to `omp_set_lock_'
> bonds.F90:(.text+0x4c3): undefined reference to `omp_unset_lock_'
> bonds.o: In function `__bonds_mod_MOD_bonds_setup':
> bonds.F90:(.text+0x117f): undefined reference to `omp_init_lock_'
> angles.o: In function `__angles_mod_MOD_get_angle_energy_gb':
> angles.F90:(.text+0x5ec): undefined reference to `omp_set_lock_'
> angles.F90:(.text+0x662): undefined reference to `omp_unset_lock_'
> angles.F90:(.text+0x683): undefined reference to `omp_set_lock_'
> angles.F90:(.text+0x6ec): undefined reference to `omp_unset_lock_'
> angles.F90:(.text+0x70d): undefined reference to `omp_set_lock_'
> angles.F90:(.text+0x764): undefined reference to `omp_unset_lock_'
> angles.o: In function `__angles_mod_MOD_angles_setup':
> angles.F90:(.text+0x112f): undefined reference to `omp_init_lock_'
> dihedrals.o: In function `__dihedrals_mod_MOD_get_dihed_energy_gb':
> dihedrals.F90:(.text+0x2847): undefined reference to `omp_set_lock_'
> dihedrals.F90:(.text+0x28c1): undefined reference to `omp_unset_lock_'
> dihedrals.F90:(.text+0x28e5): undefined reference to `omp_set_lock_'
> dihedrals.F90:(.text+0x2948): undefined reference to `omp_unset_lock_'
> dihedrals.F90:(.text+0x296c): undefined reference to `omp_set_lock_'
> dihedrals.F90:(.text+0x29c6): undefined reference to `omp_unset_lock_'
> dihedrals.F90:(.text+0x29ea): undefined reference to `omp_set_lock_'
> dihedrals.F90:(.text+0x2a44): undefined reference to `omp_unset_lock_'
> dihedrals.o: In function `__dihedrals_mod_MOD_dihedrals_setup':
> dihedrals.F90:(.text+0x398f): undefined reference to `omp_init_lock_'
> extra_pnts_nb14.o: In function
> `__extra_pnts_nb14_mod_MOD_get_nb14_energy_gb':
> extra_pnts_nb14.F90:(.text+0x21aa): undefined reference to `omp_set_lock_'
> extra_pnts_nb14.F90:(.text+0x23f7): undefined reference to
> `omp_unset_lock_'
> extra_pnts_nb14.F90:(.text+0x241d): undefined reference to `omp_set_lock_'
> extra_pnts_nb14.F90:(.text+0x24ce): undefined reference to
> `omp_unset_lock_'
> extra_pnts_nb14.o: In function `__extra_pnts_nb14_mod_MOD_nb14_setup':
> extra_pnts_nb14.F90:(.text+0x859f): undefined reference to `omp_init_lock_'
> shake.o: In function `__shake_mod_MOD_shake_gb':
> shake.F90:(.text+0x1c1): undefined reference to `omp_get_thread_num_'
> pmemd.o: In function `main':
> pmemd.F90:(.text+0x7a6): undefined reference to `omp_get_max_threads_'
> pme_alltasks_setup.o: In function
> `__pme_alltasks_setup_mod_MOD_pme_alltasks_setup':
> pme_alltasks_setup.F90:(.text+0x1f): undefined reference to
> `omp_set_num_threads_'
> collect2: error: ld returned 1 exit status
> Makefile:103: recipe for target
> '/home/swails/build_amber/amber/bin/pmemd.MPI' failed
> make[3]: *** [/home/swails/build_amber/amber/bin/pmemd.MPI] Error 1
> make[3]: Leaving directory '/home/swails/build_amber/amber/src/pmemd/src'
> Makefile:22: recipe for target 'parallel' failed
> make[2]: *** [parallel] Error 2
> make[2]: Leaving directory '/home/swails/build_amber/amber/src/pmemd'
> Makefile:28: recipe for target 'parallel' failed
> make[1]: *** [parallel] Error 2
> make[1]: Leaving directory '/home/swails/build_amber/amber/src'
> Makefile:7: recipe for target 'install' failed
> make: *** [install] Error 2
>
>
> Looks like it needs -lgomp for gfortran, but I'm not sure what the Intel
> version of the OpenMP library is called. Was this actually tested? Should
> we really be mixing OpenMP and MPI by default when users don't request
> -openmp?
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 04 2016 - 23:30:08 PST
