So for the new Intel optimizations in PMEMD, openmp is currently required (I believe this is especially important for the GB portion). When we were looking through the configure2 file it looked like the dragonegg compiler didn't support openmp, which would make it incompatible with the new pmemd code. Its been thoroughly tested with intel, gnu, and mpich though.
-Charlie
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Friday, March 04, 2016 11:22 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] pmemd.MPI build broken
Looks like OpenMP+MPI is forced on us... this is a pretty hefty change...
I'll just skip pmemd testing until this gets fixed.
On Sat, Mar 5, 2016 at 2:19 AM, Jason Swails <jason.swails.gmail.com> wrote:
> 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?
>>
>
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Received on Sat Mar 05 2016 - 00:00:04 PST
