********>bugfix.11: Author: George Giambasu, Ross Walker and Thomas Steinbrecher Date: 11/10/2008 Programs: sander Description: In softcore calculations where only one of the TI pairs contains softcore atoms the Center of Mass is not updated correctly across the MPI threads leading to calculations failures. Originally reported and debugged by George Giambasu (York group, UMN). Apply the following patch from $AMBERHOME: patch -p0 -N ------------------------------------------------------------------------------ --- src/sander/softcore.f 2008-11-10 14:47:20.000000000 -0800 +++ src/sander/softcore.f 2008-11-10 14:57:19.000000000 -0800 @@ -25,6 +25,7 @@ character(len=256), save :: scmask integer,save :: nsoftcore, natom_partner, nsoftcore_partner, extra_atoms, nmixed ! numbers of softcore atoms integer, dimension(:),allocatable,save :: nsc, nsc_partner ! keeps track of which atoms are softcore atoms + integer, dimension(:),allocatable,save :: molecule_type, molecule_type_partner ! keeps track of which molecules are partially softcore integer, dimension(:),allocatable,save :: frcmask_sc, frcmask, frcmask_partner ! for efficient force mixing integer :: ier_alloc, ierr integer,save :: logdvdl, dvdl_pnt, dvdl_norest @@ -353,7 +354,7 @@ ! Go over all common coordinates and check for deviations ! deviating by more than 0.1 A leads to termination - write(6,'(a)') ' Checking for mismatched coordinates' + write(6,'(a)') ' Checking for mismatched coordinates.' nadj=0 do i=1,3*nmixed @@ -363,7 +364,7 @@ frcmask(i),' differs from partner coordinate ', & frcmask_partner(i),' !' call sander_bomb('sc_check_and_adjust', & - 'Atom coordinate disagreement','Check input files') + 'Atom coordinate disagreement','Check input files.') else nadj = nadj + 1 if (isProcessV1) then @@ -376,9 +377,9 @@ ' differs from partner coordinate ', & frcmask_partner(i),' !' if (isProcessV1) then - write (6,'(a)') ' Deviation is small, using partner coordinate' + write (6,'(a)') ' Deviation is small, using partner coordinate.' else - write (6,'(a)') ' Deviation is small, changing partner coordinate' + write (6,'(a)') ' Deviation is small, changing partner coordinate.' end if else write (6,'(a)') ' ... making more adjustments ...' @@ -390,13 +391,123 @@ end if end do if (nadj>9) then - write (6,'(a,i5,a)') ' A total of ',nadj,' small coordinate adjustments were made, check results carefully' + write (6,'(a,i5,a)') ' A total of ',nadj,' small coordinate adjustments were made, check results carefully.' end if end subroutine sc_check_and_adjust_crd !=================================================================================================== + subroutine sc_check_perturbed_molecules(nummols, molsiz) + + integer nummols,molsiz(*) + + integer nummols_partner + integer i, iatom, num, imol, temp + + ! Check for every molecule if it is *partially* softcore + ! on either this or the partner side + + ! First communicate the number of molecules + + !write (6,*) 'Debugging info for pscale:' + + call mpi_sendrecv( nummols, 1, MPI_INTEGER, partner, 5, & + nummols_partner, 1, MPI_INTEGER, partner, 5, & + commmaster, ist, ierr ) + + ! Prepare the molecule type array + allocate (molecule_type(nummols),stat=ier_alloc) + if (ier_alloc /= 0) call sander_bomb('sc_check_perturbed_molecules[softcore.f]','cant allocate molecule_type','') + + allocate (molecule_type_partner(nummols_partner),stat=ier_alloc) + if (ier_alloc /= 0) call sander_bomb('sc_check_perturbed_molecules[softcore.f]','cant allocate molecule_type_partner','') + + !write (6,*) nummols, 'Molecules on this side, ', nummols_partner, ' on the partner side' + + ! check which molecules are partially softcore + i=0 + do imol = 1, nummols + temp=0 + num = molsiz(imol) + do iatom = 1, num + i = i + 1 + temp = temp + nsc(i) + end do + if (temp == 0) then + ! no atoms in this molecule are softcore + ! its C.O.M. needs not be communicated later + ! unless the partner molecule is partially softcore + molecule_type(imol)=0 + else + if (temp == num) then + ! all atoms in this molecule are softcore + ! its C.O.M. needs not be communicated later + molecule_type(imol) = 2 + else + ! some atoms in this molecule are softcore + ! its C.O.M. need to be communicated later + molecule_type(imol) = 1 + end if + end if + end do + + ! exchange the molecule type arrays + + call mpi_sendrecv( molecule_type, nummols, MPI_INTEGER, partner, 5, & + molecule_type_partner, nummols_partner, MPI_INTEGER, partner, 5, & + commmaster, ist, ierr ) + + ! now go through the arrays and check which non-soft core + ! molecule on this side has a partially soft core molecule + ! on the partner side + + i=0 + do imol = 1, nummols + if (molecule_type(imol) == 2) then + ! this molecule is completely softcore on this side + ! nothing corresponds to it on the partner -> do nothing + else + i=i+1 + if (molecule_type_partner(i) == 2) then + ! skip all complete softcore partner molecules + do + i = i + 1 + if (molecule_type_partner(i) /= 2) then + exit + end if + end do + end if + if (molecule_type(imol) == 0 .and. molecule_type_partner(i) == 1) then + ! This molecule has no softcore atoms but its partner molecule has + ! therefore prepare for sending its C.O.M. later + molecule_type(imol) = 1 + write (6,'(a,i5,a)') ' Molecule ',imol,' is nonsoftcore, but its partner is partially softcore, therefore its C.O.M. will be exchanged.' + end if + end if + end do + + !write (6,'(a)') 'Final molecule types:' + + imol=0 + do i = 1, nummols + if (molecule_type(i) == 2) then + write (6,'(a,i5,a)') ' Molecule ',i,' is completely softcore and skipped for C.O.M..' + end if + if (molecule_type(i) == 1) then + write (6,'(a,i5,a)') ' Molecule ',i,' is partially softcore on this side or the corresponding partner molecule is.' + end if + if (molecule_type(i) == 0) then + imol = imol + 1 + end if + end do + !write (6, '(i5,a)') imol,'Molecules are nonsoftcore on both sides' + + return + + end subroutine sc_check_perturbed_molecules +!=================================================================================================== + subroutine sc_pscale(natom,x,amass,nummols,molsiz,oldrecip,ucell) ! This subroutine is copied from ew_pscale, but includes master-to-master ! communication to get average center of masses for perturbed molecules @@ -442,10 +553,7 @@ ymol = ymol / massmol zmol = zmol / massmol - if (sc_temp == 0 .or. sc_temp == num) then - ! none or all atoms in this molecule are softcore - ! C.O.M. calculated above is correct, do nothing - else + if (molecule_type(imol) == 1) then ! calculate the average C.O.M. of the V0 and V1 versions of the molecule call mpi_sendrecv( xmol, 1, MPI_DOUBLE_PRECISION, partner, 5, & xmol_partner, 1, MPI_DOUBLE_PRECISION, partner, 5, & --- src/sander/depend 2008-11-10 15:08:32.000000000 -0800 +++ src/sander/depend 2008-11-10 15:08:36.000000000 -0800 @@ -799,8 +799,10 @@ evb_umb.o: \ dprec.h\ + constants.o\ evb_vars.o\ - evb_pimd_init.o + evb_pimd_init.o\ + md.h evb_umb.o: evb_umb.f @@ -809,8 +811,10 @@ evb_umb.LES.o: \ dprec.h\ + constants.o\ evb_vars.o\ - evb_pimd_init.LES.o + evb_pimd_init.LES.o\ + md.h evb_umb.LES.o: evb_umb.f $(FPP) -DLES evb_umb.f > _evb_umb.f @@ -819,6 +823,7 @@ evb_umb_primitive.o: \ assert.h\ dprec.h\ + constants.o\ evb_vars.o\ pimd_vars.o\ evb_pimd_init.o\ @@ -834,6 +839,7 @@ evb_umb_primitive.LES.o: \ assert.h\ dprec.h\ + constants.o\ evb_vars.o\ pimd_vars.o\ evb_pimd_init.LES.o\ @@ -3070,6 +3076,7 @@ copyright.h\ dprec.h\ def_time.h\ + assert.h\ qmmm_module.o\ constants.o @@ -3640,10 +3647,12 @@ evb_mathf.o schlegel_diis.o: \ + assert.h\ dprec.h\ evb_vars.o schlegel_full.o: \ + assert.h\ dprec.h\ evb_vars.o @@ -3653,6 +3662,7 @@ evb_mathf.o schlegel_gmres.o: \ + assert.h\ dprec.h\ evb_vars.o\ files.h\ --- src/sander/sander.f 2008-11-10 14:45:09.000000000 -0800 +++ src/sander/sander.f 2008-11-10 15:27:46.000000000 -0800 @@ -55,7 +55,7 @@ #ifdef MPI /* SOFT CORE */ use softcore, only: setup_sc, cleanup_sc, ifsc, extra_atoms, sc_sync_x, & - summarize_ti_changes + summarize_ti_changes, sc_check_perturbed_molecules #endif #if defined(MPI) @@ -734,6 +734,10 @@ end if call setup_sc(natom, nres, ih(m04), ih(m06), & ix(i02), ih(m02), x(lcrd), ntypes, clambda, nstlim) + if (ntp > 0 .and. master) then + ! check which molecules are perturbed in NPT runs + call sc_check_perturbed_molecules(nspm, ix(i70)) + end if ! -- ti decomp if (idecomp > 0) then if (sanderrank == 0) call build_dec_mask(natom) --- test/softcore/complex/out.0.save 2008-11-10 15:36:04.000000000 -0800 +++ test/softcore/complex/out.0.save 2008-11-10 15:36:12.000000000 -0800 @@ -3,7 +3,7 @@ Amber 10 SANDER 2008 ------------------------------------------------------- -| Run on 12/21/2007 at 17:35:26 +| Run on 11/10/2008 at 15:32:27 [-O]verwriting output File Assignments: @@ -35,13 +35,13 @@ icfe=1, clambda = 0.6, ifsc=1, scmask=':BNZ@H6', crgmask=':BNZ@H6', - / + / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: MPI +| Flags: MPI USE_MPI_IN_PLACE getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read @@ -148,7 +148,8 @@ Softcore Mask :BNZ@H6; matches 1 atoms this run corresponds to V0, its softcore atoms interact fully for lambda=0 this process: 29881 atoms, partner process: 29882 atoms - Checking for mismatched coordinates + Checking for mismatched coordinates. + Molecule 2 is partially softcore on this side or the corresponding partner molecule is. Checking for SHAKE constraints on bonds crossing into the SC region Removing shake constraints from C6 BNZ 163 -- H6 BNZ 163 @@ -421,42 +422,43 @@ 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.07 ( 0.18% of Total) -| Build the list 3.70 (97.64% of List ) -| Other 0.09 ( 2.36% of List ) -| List time 3.79 ( 9.87% of Nonbo) -| Short_ene time 27.00 (99.06% of Direc) -| Other 0.26 ( 0.94% of Direc) -| Direct Ewald time 27.26 (78.77% of Ewald) -| Adjust Ewald time 0.20 ( 0.59% of Ewald) -| Fill Bspline coeffs 0.46 ( 6.46% of Recip) -| Fill charge grid 1.44 (20.36% of Recip) -| Scalar sum 0.88 (12.38% of Recip) -| Grad sum 1.61 (22.71% of Recip) +| Read coords time 0.04 ( 0.17% of Total) +| Build the list 2.49 (98.35% of List ) +| Other 0.04 ( 1.65% of List ) +| List time 2.53 (11.38% of Nonbo) +| Short_ene time 15.42 (98.69% of Direc) +| Other 0.20 ( 1.31% of Direc) +| Direct Ewald time 15.63 (79.25% of Ewald) +| Adjust Ewald time 0.15 ( 0.75% of Ewald) +| Fill Bspline coeffs 0.29 ( 7.48% of Recip) +| Fill charge grid 0.57 (14.61% of Recip) +| Scalar sum 0.70 (18.04% of Recip) +| Grad sum 0.88 (22.53% of Recip) | FFT back comm time 0.00 ( 0.01% of FFT t) -| Other 2.70 (100.0% of FFT t) -| FFT time 2.70 (38.08% of Recip) +| Other 1.45 (100.0% of FFT t) +| FFT time 1.45 (37.33% of Recip) | Other 0.00 ( 0.01% of Recip) -| Recip Ewald time 7.09 (20.48% of Ewald) -| Force Adjust 0.04 ( 0.11% of Ewald) -| Virial junk 0.02 ( 0.05% of Ewald) -| Ewald time 34.60 (90.13% of Nonbo) -| Nonbond force 38.40 (99.24% of Force) -| Bond/Angle/Dihedral 0.26 ( 0.67% of Force) -| Other 0.03 ( 0.09% of Force) -| Force time 38.69 (95.95% of Runmd) -| Shake time 0.23 ( 0.58% of Runmd) -| Verlet update time 1.11 ( 2.75% of Runmd) -| Ekcmr time 0.06 ( 0.16% of Runmd) +| Recip Ewald time 3.89 (19.72% of Ewald) +| Force Adjust 0.01 ( 0.04% of Ewald) +| Virial junk 0.02 ( 0.11% of Ewald) +| Other 0.02 ( 0.12% of Ewald) +| Ewald time 19.72 (88.62% of Nonbo) +| Nonbond force 22.25 (98.74% of Force) +| Bond/Angle/Dihedral 0.27 ( 1.19% of Force) +| Other 0.02 ( 0.07% of Force) +| Force time 22.54 (89.09% of Runmd) +| Shake time 0.12 ( 0.46% of Runmd) +| Verlet update time 1.21 ( 4.80% of Runmd) +| Ekcmr time 0.02 ( 0.09% of Runmd) | CRD distribute time 0.00 ( 0.01% of Runmd) -| Other 0.22 ( 0.55% of Runmd) -| Runmd Time 40.33 (98.54% of Total) -| Other 0.52 ( 1.28% of Total) -| Total time 40.92 (100.0% of ALL ) +| Other 1.40 ( 5.55% of Runmd) +| Runmd Time 25.30 (97.70% of Total) +| Other 0.55 ( 2.12% of Total) +| Total time 25.89 (100.0% of ALL ) | Highest rstack allocated: 1551741 | Highest istack allocated: 29881 -| Job began at 17:35:26.756 on 12/21/2007 -| Setup done at 17:35:27.354 on 12/21/2007 -| Run done at 17:36:07.680 on 12/21/2007 +| Job began at 15:32:27.938 on 11/10/2008 +| Setup done at 15:32:28.532 on 11/10/2008 +| Run done at 15:32:53.829 on 11/10/2008 | wallclock() was called 2772 times --- test/softcore/complex_rst/out.0.save 2008-11-10 15:37:09.000000000 -0800 +++ test/softcore/complex_rst/out.0.save 2008-11-10 15:37:21.000000000 -0800 @@ -3,7 +3,7 @@ Amber 10 SANDER 2008 ------------------------------------------------------- -| Run on 12/21/2007 at 17:45:19 +| Run on 11/10/2008 at 15:33:17 [-O]verwriting output File Assignments: @@ -37,17 +37,17 @@ ntp = 1, pres0 = 1.0, taup = 2.0, nmropt=1, dvdl_norest=1, - / + / &wt TYPE="END", - / + / DISANG=disang -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: MPI +| Flags: MPI USE_MPI_IN_PLACE getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read @@ -199,7 +199,8 @@ Softcore Mask :BNZ; matches 12 atoms this run corresponds to V0, its softcore atoms interact fully for lambda=0 this process: 26836 atoms, partner process: 26824 atoms - Checking for mismatched coordinates + Checking for mismatched coordinates. + Molecule 2 is completely softcore and skipped for C.O.M.. Checking for SHAKE constraints on bonds crossing into the SC region Sum of charges from parm topology file = -0.00000019 @@ -493,7 +494,7 @@ EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = -0.7352 EAMBER (non-restraint) = 6.2680 DV/DL = 4.7976 - Ewald error estimate: 0.3377E-15 + Ewald error estimate: -0.8586E-15 ------------------------------------------------------------------------------ @@ -520,42 +521,43 @@ 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.07 ( 0.17% of Total) -| Build the list 4.16 (98.11% of List ) -| Other 0.08 ( 1.89% of List ) -| List time 4.24 (11.29% of Nonbo) -| Short_ene time 24.69 (99.06% of Direc) -| Other 0.23 ( 0.94% of Direc) -| Direct Ewald time 24.92 (74.74% of Ewald) -| Adjust Ewald time 0.19 ( 0.57% of Ewald) -| Fill Bspline coeffs 0.41 ( 5.05% of Recip) -| Fill charge grid 1.54 (18.82% of Recip) -| Scalar sum 1.70 (20.85% of Recip) -| Grad sum 1.62 (19.75% of Recip) -| FFT back comm time 0.00 ( 0.02% of FFT t) -| Other 2.90 (100.0% of FFT t) -| FFT time 2.91 (35.52% of Recip) +| Read coords time 0.04 ( 0.16% of Total) +| Build the list 2.90 (98.88% of List ) +| Other 0.03 ( 1.12% of List ) +| List time 2.93 (12.91% of Nonbo) +| Short_ene time 14.74 (98.66% of Direc) +| Other 0.20 ( 1.34% of Direc) +| Direct Ewald time 14.94 (75.59% of Ewald) +| Adjust Ewald time 0.13 ( 0.67% of Ewald) +| Fill Bspline coeffs 0.22 ( 4.81% of Recip) +| Fill charge grid 0.69 (14.78% of Recip) +| Scalar sum 1.11 (23.94% of Recip) +| Grad sum 0.88 (18.91% of Recip) +| FFT back comm time 0.00 ( 0.01% of FFT t) +| Other 1.74 (100.0% of FFT t) +| FFT time 1.74 (37.56% of Recip) | Other 0.00 ( 0.01% of Recip) -| Recip Ewald time 8.18 (24.53% of Ewald) -| Force Adjust 0.04 ( 0.11% of Ewald) -| Virial junk 0.02 ( 0.05% of Ewald) -| Ewald time 33.34 (88.71% of Nonbo) -| Nonbond force 37.59 (99.24% of Force) -| Bond/Angle/Dihedral 0.26 ( 0.68% of Force) -| Other 0.03 ( 0.09% of Force) -| Force time 37.88 (96.40% of Runmd) -| Shake time 0.19 ( 0.48% of Runmd) -| Verlet update time 0.99 ( 2.51% of Runmd) -| Ekcmr time 0.05 ( 0.12% of Runmd) +| Recip Ewald time 4.65 (23.51% of Ewald) +| Force Adjust 0.01 ( 0.03% of Ewald) +| Virial junk 0.02 ( 0.10% of Ewald) +| Other 0.02 ( 0.10% of Ewald) +| Ewald time 19.76 (87.09% of Nonbo) +| Nonbond force 22.69 (99.27% of Force) +| Bond/Angle/Dihedral 0.15 ( 0.67% of Force) +| Other 0.01 ( 0.05% of Force) +| Force time 22.86 (92.31% of Runmd) +| Shake time 0.10 ( 0.39% of Runmd) +| Verlet update time 0.60 ( 2.42% of Runmd) +| Ekcmr time 0.02 ( 0.06% of Runmd) | CRD distribute time 0.00 ( 0.01% of Runmd) -| Other 0.19 ( 0.48% of Runmd) -| Runmd Time 39.29 (98.81% of Total) -| Other 0.40 ( 1.02% of Total) -| Total time 39.76 (100.0% of ALL ) +| Other 1.19 ( 4.80% of Runmd) +| Runmd Time 24.76 (98.49% of Total) +| Other 0.34 ( 1.35% of Total) +| Total time 25.14 (100.0% of ALL ) | Highest rstack allocated: 1523862 | Highest istack allocated: 26836 -| Job began at 17:45:19.728 on 12/21/2007 -| Setup done at 17:45:20.201 on 12/21/2007 -| Run done at 17:45:59.491 on 12/21/2007 +| Job began at 15:33:17.598 on 11/10/2008 +| Setup done at 15:33:17.977 on 11/10/2008 +| Run done at 15:33:42.737 on 11/10/2008 | wallclock() was called 2772 times --- test/softcore/complex_rst/out.1.save 2008-11-10 15:37:41.000000000 -0800 +++ test/softcore/complex_rst/out.1.save 2008-11-10 15:37:47.000000000 -0800 @@ -3,7 +3,7 @@ Amber 10 SANDER 2008 ------------------------------------------------------- -| Run on 12/21/2007 at 17:45:19 +| Run on 11/10/2008 at 15:33:17 [-O]verwriting output File Assignments: @@ -36,13 +36,13 @@ temp0 = 300, ntt = 3, gamma_ln = 5, ntp = 1, pres0 = 1.0, taup = 2.0, dvdl_norest=1, - / + / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: MPI +| Flags: MPI USE_MPI_IN_PLACE getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read @@ -146,7 +146,7 @@ Softcore Mask matches 0 atoms this run corresponds to V1, its softcore atoms interact fully for lambda=1 this process: 26824 atoms, partner process: 26836 atoms - Checking for mismatched coordinates + Checking for mismatched coordinates. Checking for SHAKE constraints on bonds crossing into the SC region Sum of charges from parm topology file = -0.00000019 @@ -345,7 +345,7 @@ EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = -0.7352 EAMBER (non-restraint) = 6.2680 DV/DL = 4.7976 - Ewald error estimate: 0.3377E-15 + Ewald error estimate: -0.8586E-15 ------------------------------------------------------------------------------ TI atoms summary @@ -357,42 +357,43 @@ 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.07 ( 0.17% of Total) -| Build the list 4.12 (98.09% of List ) -| Other 0.08 ( 1.91% of List ) -| List time 4.20 (11.21% of Nonbo) -| Short_ene time 24.64 (99.06% of Direc) -| Other 0.23 ( 0.94% of Direc) -| Direct Ewald time 24.87 (74.73% of Ewald) -| Adjust Ewald time 0.19 ( 0.57% of Ewald) -| Fill Bspline coeffs 0.40 ( 4.87% of Recip) -| Fill charge grid 1.55 (19.02% of Recip) -| Scalar sum 1.70 (20.86% of Recip) -| Grad sum 1.61 (19.75% of Recip) +| Read coords time 0.04 ( 0.16% of Total) +| Build the list 2.82 (98.83% of List ) +| Other 0.03 ( 1.17% of List ) +| List time 2.86 (12.91% of Nonbo) +| Short_ene time 14.38 (98.79% of Direc) +| Other 0.18 ( 1.21% of Direc) +| Direct Ewald time 14.56 (75.55% of Ewald) +| Adjust Ewald time 0.14 ( 0.70% of Ewald) +| Fill Bspline coeffs 0.27 ( 5.92% of Recip) +| Fill charge grid 0.63 (13.98% of Recip) +| Scalar sum 1.12 (24.92% of Recip) +| Grad sum 0.87 (19.34% of Recip) | FFT back comm time 0.00 ( 0.01% of FFT t) -| Other 2.90 (100.0% of FFT t) -| FFT time 2.90 (35.49% of Recip) +| Other 1.61 (100.0% of FFT t) +| FFT time 1.61 (35.83% of Recip) | Other 0.00 ( 0.01% of Recip) -| Recip Ewald time 8.17 (24.54% of Ewald) -| Force Adjust 0.04 ( 0.11% of Ewald) -| Virial junk 0.02 ( 0.05% of Ewald) -| Ewald time 33.28 (88.78% of Nonbo) -| Nonbond force 37.49 (99.24% of Force) -| Bond/Angle/Dihedral 0.25 ( 0.67% of Force) -| Other 0.03 ( 0.08% of Force) -| Force time 37.77 (96.14% of Runmd) -| Shake time 0.18 ( 0.46% of Runmd) -| Verlet update time 0.99 ( 2.51% of Runmd) -| Ekcmr time 0.05 ( 0.13% of Runmd) -| CRD distribute time 0.01 ( 0.02% of Runmd) -| Other 0.29 ( 0.74% of Runmd) -| Runmd Time 39.29 (98.81% of Total) -| Other 0.41 ( 1.02% of Total) -| Total time 39.76 (100.0% of ALL ) +| Recip Ewald time 4.50 (23.36% of Ewald) +| Force Adjust 0.01 ( 0.03% of Ewald) +| Virial junk 0.02 ( 0.10% of Ewald) +| Other 0.05 ( 0.25% of Ewald) +| Ewald time 19.27 (87.09% of Nonbo) +| Nonbond force 22.13 (99.24% of Force) +| Bond/Angle/Dihedral 0.16 ( 0.72% of Force) +| Other 0.01 ( 0.04% of Force) +| Force time 22.30 (89.70% of Runmd) +| Shake time 0.10 ( 0.41% of Runmd) +| Verlet update time 0.62 ( 2.48% of Runmd) +| Ekcmr time 0.01 ( 0.06% of Runmd) +| CRD distribute time 0.01 ( 0.06% of Runmd) +| Other 1.81 ( 7.29% of Runmd) +| Runmd Time 24.86 (98.87% of Total) +| Other 0.24 ( 0.96% of Total) +| Total time 25.14 (100.0% of ALL ) | Highest rstack allocated: 1523538 | Highest istack allocated: 26824 -| Job began at 17:45:19.728 on 12/21/2007 -| Setup done at 17:45:20.202 on 12/21/2007 -| Run done at 17:45:59.489 on 12/21/2007 +| Job began at 15:33:17.598 on 11/10/2008 +| Setup done at 15:33:17.882 on 11/10/2008 +| Run done at 15:33:42.737 on 11/10/2008 | wallclock() was called 2772 times --- test/softcore/dynlmb/out.0.save 2008-11-10 15:38:21.000000000 -0800 +++ test/softcore/dynlmb/out.0.save 2008-11-10 15:38:28.000000000 -0800 @@ -3,7 +3,7 @@ Amber 10 SANDER 2008 ------------------------------------------------------- -| Run on 12/21/2007 at 17:36:24 +| Run on 11/10/2008 at 15:33:11 [-O]verwriting output File Assignments: @@ -36,13 +36,13 @@ icfe=1, clambda = 0.10000, ifsc=1, scmask=':1', logdvdl=1, dynlmb = 0.1, - / + / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: MPI +| Flags: MPI USE_MPI_IN_PLACE getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read @@ -146,7 +146,8 @@ Softcore Mask :1; matches 15 atoms this run corresponds to V0, its softcore atoms interact fully for lambda=0 this process: 2715 atoms, partner process: 2700 atoms - Checking for mismatched coordinates + Checking for mismatched coordinates. + Molecule 1 is completely softcore and skipped for C.O.M.. Checking for SHAKE constraints on bonds crossing into the SC region Sum of charges from parm topology file = 0.00000000 @@ -1042,45 +1043,44 @@ 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.12% of Total) -| Build the list 0.44 (94.98% of List ) -| Other 0.02 ( 5.02% of List ) -| List time 0.46 ( 8.69% of Nonbo) -| Short_ene time 4.16 (99.17% of Direc) -| Other 0.03 ( 0.83% of Direc) -| Direct Ewald time 4.20 (86.32% of Ewald) -| Adjust Ewald time 0.02 ( 0.51% of Ewald) +| Read coords time 0.00 ( 0.10% of Total) +| Build the list 0.31 (95.19% of List ) +| Other 0.02 ( 4.81% of List ) +| List time 0.32 ( 9.71% of Nonbo) +| Short_ene time 2.33 (98.81% of Direc) +| Other 0.03 ( 1.19% of Direc) +| Direct Ewald time 2.36 (78.67% of Ewald) +| Adjust Ewald time 0.02 ( 0.56% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.04 ( 7.08% of Recip) -| Fill charge grid 0.10 (15.74% of Recip) -| Scalar sum 0.12 (18.80% of Recip) -| Grad sum 0.15 (23.96% of Recip) -| FFT back comm time 0.00 ( 0.09% of FFT t) -| Other 0.22 (100.0% of FFT t) -| FFT time 0.22 (34.33% of Recip) -| Other 0.00 ( 0.09% of Recip) -| Recip Ewald time 0.63 (13.03% of Ewald) -| Force Adjust 0.00 ( 0.04% of Ewald) -| Virial junk 0.00 ( 0.06% of Ewald) +| Fill Bspline coeffs 0.05 ( 7.56% of Recip) +| Fill charge grid 0.07 (11.52% of Recip) +| Scalar sum 0.23 (37.96% of Recip) +| Grad sum 0.11 (17.65% of Recip) +| FFT back comm time 0.00 ( 0.04% of FFT t) +| Other 0.16 (100.0% of FFT t) +| FFT time 0.16 (25.22% of Recip) +| Other 0.00 ( 0.08% of Recip) +| Recip Ewald time 0.62 (20.56% of Ewald) +| Force Adjust 0.00 ( 0.05% of Ewald) +| Virial junk 0.00 ( 0.12% of Ewald) | Other 0.00 ( 0.02% of Ewald) -| Ewald time 4.86 (91.30% of Nonbo) -| Other 0.00 ( 0.01% of Nonbo) -| Nonbond force 5.32 (99.71% of Force) -| Bond/Angle/Dihedral 0.01 ( 0.26% of Force) -| Other 0.00 ( 0.03% of Force) -| Force time 5.34 (95.22% of Runmd) -| Shake time 0.03 ( 0.50% of Runmd) -| Verlet update time 0.21 ( 3.77% of Runmd) +| Ewald time 3.00 (90.29% of Nonbo) +| Nonbond force 3.32 (99.64% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.33% of Force) +| Other 0.00 ( 0.04% of Force) +| Force time 3.33 (84.06% of Runmd) +| Shake time 0.02 ( 0.46% of Runmd) +| Verlet update time 0.10 ( 2.49% of Runmd) | Ekcmr time 0.00 ( 0.07% of Runmd) -| CRD distribute time 0.00 ( 0.01% of Runmd) -| Other 0.02 ( 0.43% of Runmd) -| Runmd Time 5.61 (99.17% of Total) -| Other 0.04 ( 0.71% of Total) -| Total time 5.66 (100.0% of ALL ) +| CRD distribute time 0.00 ( 0.04% of Runmd) +| Other 0.51 (12.88% of Runmd) +| Runmd Time 3.96 (99.21% of Total) +| Other 0.03 ( 0.69% of Total) +| Total time 4.00 (100.0% of ALL ) | Highest rstack allocated: 136713 | Highest istack allocated: 2715 -| Job began at 17:36:24.804 on 12/21/2007 -| Setup done at 17:36:24.851 on 12/21/2007 -| Run done at 17:36:30.460 on 12/21/2007 +| Job began at 15:33:11.739 on 11/10/2008 +| Setup done at 15:33:11.770 on 11/10/2008 +| Run done at 15:33:15.735 on 11/10/2008 | wallclock() was called 4978 times --- test/softcore/dynlmb/out.1.save 2008-11-10 15:38:42.000000000 -0800 +++ test/softcore/dynlmb/out.1.save 2008-11-10 15:38:48.000000000 -0800 @@ -3,7 +3,7 @@ Amber 10 SANDER 2008 ------------------------------------------------------- -| Run on 12/21/2007 at 17:36:24 +| Run on 11/10/2008 at 15:33:11 [-O]verwriting output File Assignments: @@ -36,13 +36,13 @@ icfe=1, clambda = 0.10000, ifsc=1, scmask='', logdvdl=1, dynlmb = 0.1, - / + / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: MPI +| Flags: MPI USE_MPI_IN_PLACE getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read @@ -146,7 +146,7 @@ Softcore Mask matches 0 atoms this run corresponds to V1, its softcore atoms interact fully for lambda=1 this process: 2700 atoms, partner process: 2715 atoms - Checking for mismatched coordinates + Checking for mismatched coordinates. Checking for SHAKE constraints on bonds crossing into the SC region Sum of charges from parm topology file = 0.00000000 @@ -852,45 +852,44 @@ 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.12% of Total) -| Build the list 0.43 (94.97% of List ) -| Other 0.02 ( 5.03% of List ) -| List time 0.46 ( 8.71% of Nonbo) -| Short_ene time 4.08 (99.20% of Direc) -| Other 0.03 ( 0.80% of Direc) -| Direct Ewald time 4.11 (86.14% of Ewald) -| Adjust Ewald time 0.02 ( 0.51% of Ewald) +| Read coords time 0.00 ( 0.10% of Total) +| Build the list 0.30 (94.99% of List ) +| Other 0.02 ( 5.01% of List ) +| List time 0.32 ( 9.81% of Nonbo) +| Short_ene time 2.30 (98.79% of Direc) +| Other 0.03 ( 1.21% of Direc) +| Direct Ewald time 2.33 (79.19% of Ewald) +| Adjust Ewald time 0.02 ( 0.56% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.04 ( 6.78% of Recip) -| Fill charge grid 0.10 (16.17% of Recip) -| Scalar sum 0.12 (18.80% of Recip) -| Grad sum 0.15 (23.83% of Recip) -| FFT back comm time 0.00 ( 0.09% of FFT t) -| Other 0.22 (100.0% of FFT t) -| FFT time 0.22 (34.33% of Recip) -| Other 0.00 ( 0.10% of Recip) -| Recip Ewald time 0.63 (13.23% of Ewald) -| Force Adjust 0.00 ( 0.04% of Ewald) -| Virial junk 0.00 ( 0.06% of Ewald) -| Other 0.00 ( 0.02% of Ewald) -| Ewald time 4.78 (91.28% of Nonbo) -| Other 0.00 ( 0.01% of Nonbo) -| Nonbond force 5.23 (99.76% of Force) -| Bond/Angle/Dihedral 0.01 ( 0.21% of Force) -| Other 0.00 ( 0.03% of Force) -| Force time 5.24 (93.54% of Runmd) -| Shake time 0.03 ( 0.45% of Runmd) -| Verlet update time 0.21 ( 3.69% of Runmd) +| Fill Bspline coeffs 0.04 ( 7.32% of Recip) +| Fill charge grid 0.07 (12.05% of Recip) +| Scalar sum 0.21 (35.94% of Recip) +| Grad sum 0.11 (18.17% of Recip) +| FFT back comm time 0.00 ( 0.05% of FFT t) +| Other 0.16 (100.0% of FFT t) +| FFT time 0.16 (26.44% of Recip) +| Other 0.00 ( 0.09% of Recip) +| Recip Ewald time 0.59 (20.06% of Ewald) +| Force Adjust 0.00 ( 0.05% of Ewald) +| Virial junk 0.00 ( 0.12% of Ewald) +| Other 0.00 ( 0.01% of Ewald) +| Ewald time 2.94 (90.18% of Nonbo) +| Nonbond force 3.26 (99.72% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.24% of Force) +| Other 0.00 ( 0.04% of Force) +| Force time 3.27 (82.47% of Runmd) +| Shake time 0.02 ( 0.41% of Runmd) +| Verlet update time 0.10 ( 2.49% of Runmd) | Ekcmr time 0.00 ( 0.07% of Runmd) -| CRD distribute time 0.00 ( 0.02% of Runmd) -| Other 0.13 ( 2.24% of Runmd) -| Runmd Time 5.61 (99.17% of Total) -| Other 0.04 ( 0.71% of Total) -| Total time 5.65 (100.0% of ALL ) +| CRD distribute time 0.03 ( 0.83% of Runmd) +| Other 0.54 (13.73% of Runmd) +| Runmd Time 3.97 (99.26% of Total) +| Other 0.03 ( 0.64% of Total) +| Total time 4.00 (100.0% of ALL ) | Highest rstack allocated: 136308 | Highest istack allocated: 2700 -| Job began at 17:36:24.804 on 12/21/2007 -| Setup done at 17:36:24.851 on 12/21/2007 -| Run done at 17:36:30.457 on 12/21/2007 +| Job began at 15:33:11.739 on 11/10/2008 +| Setup done at 15:33:11.768 on 11/10/2008 +| Run done at 15:33:15.735 on 11/10/2008 | wallclock() was called 4978 times --- test/softcore/min/out.0.save 2008-11-10 15:39:06.000000000 -0800 +++ test/softcore/min/out.0.save 2008-11-10 15:39:25.000000000 -0800 @@ -3,7 +3,7 @@ Amber 10 SANDER 2008 ------------------------------------------------------- -| Run on 10/20/2007 at 15:10:09 +| Run on 11/10/2008 at 15:32:22 [-O]verwriting output File Assignments: @@ -33,13 +33,13 @@ ntp = 1, pres0 = 1.0, taup = 2.0, icfe=1, clambda = 0.50000, ifsc=1, scmask=':1', - / + / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: MPI +| Flags: MPI USE_MPI_IN_PLACE getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read @@ -57,13 +57,13 @@ | Memory Use Allocated -| Real 257540 +| Real 254825 | Hollerith 17193 -| Integer 82352 +| Integer 79637 | Max Pairs 1204555 | nblistReal 32580 | nblist Int 112310 -| Total 7799 kbytes +| Total 7767 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals @@ -118,6 +118,9 @@ Ewald Coefficient = 0.30768 Interpolation order = 4 +| MPI Timing options: +| profile_mpi = 0 + -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- @@ -132,7 +135,8 @@ Softcore Mask :1; matches 15 atoms this run corresponds to V0, its softcore atoms interact fully for lambda=0 this process: 2715 atoms, partner process: 2700 atoms - Checking for mismatched coordinates + Checking for mismatched coordinates. + Molecule 1 is completely softcore and skipped for C.O.M.. Checking for SHAKE constraints on bonds crossing into the SC region Sum of charges from parm topology file = 0.00000000 @@ -365,39 +369,40 @@ 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.06% of Total) -| Build the list 0.08 (65.71% of List ) -| Other 0.04 (34.29% of List ) -| List time 0.12 ( 1.17% of Nonbo) -| Short_ene time 8.40 (99.26% of Direc) -| Other 0.06 ( 0.74% of Direc) -| Direct Ewald time 8.46 (83.69% of Ewald) -| Adjust Ewald time 0.04 ( 0.37% of Ewald) +| Read coords time 0.00 ( 0.05% of Total) +| Build the list 0.04 (70.10% of List ) +| Other 0.02 (29.90% of List ) +| List time 0.06 ( 1.64% of Nonbo) +| Short_ene time 2.65 (98.85% of Direc) +| Other 0.03 ( 1.15% of Direc) +| Direct Ewald time 2.69 (78.38% of Ewald) +| Adjust Ewald time 0.02 ( 0.54% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.07 ( 4.47% of Recip) -| Fill charge grid 0.18 (11.05% of Recip) -| Scalar sum 0.21 (12.99% of Recip) -| Grad sum 0.22 (13.98% of Recip) -| FFT back comm time 0.00 ( 0.01% of FFT t) -| Other 0.92 (100.0% of FFT t) -| FFT time 0.92 (57.32% of Recip) -| Other 0.00 ( 0.18% of Recip) -| Recip Ewald time 1.60 (15.85% of Ewald) -| Force Adjust 0.00 ( 0.02% of Ewald) -| Virial junk 0.01 ( 0.06% of Ewald) -| Other 0.00 ( 0.01% of Ewald) -| Ewald time 10.11 (98.82% of Nonbo) -| Nonbond force 10.23 (99.72% of Force) -| Bond/Angle/Dihedral 0.03 ( 0.26% of Force) -| Other 0.00 ( 0.02% of Force) -| Force time 10.26 (100.0% of Runmd) -| Runmd Time 10.26 (74.16% of Total) -| Other 3.57 (25.78% of Total) -| Total time 13.84 (100.0% of ALL ) +| Fill Bspline coeffs 0.05 ( 7.06% of Recip) +| Fill charge grid 0.09 (12.14% of Recip) +| Scalar sum 0.28 (39.56% of Recip) +| Grad sum 0.12 (16.92% of Recip) +| FFT back comm time 0.00 ( 0.05% of FFT t) +| Other 0.17 (100.0% of FFT t) +| FFT time 0.17 (24.24% of Recip) +| Other 0.00 ( 0.08% of Recip) +| Recip Ewald time 0.72 (20.95% of Ewald) +| Force Adjust 0.00 ( 0.03% of Ewald) +| Virial junk 0.00 ( 0.06% of Ewald) +| Other 0.00 ( 0.02% of Ewald) +| Ewald time 3.43 (98.36% of Nonbo) +| Other 0.00 ( 0.01% of Nonbo) +| Nonbond force 3.48 (99.59% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.36% of Force) +| Other 0.00 ( 0.05% of Force) +| Force time 3.50 (100.0% of Runmd) +| Runmd Time 3.50 (81.68% of Total) +| Other 0.78 (18.27% of Total) +| Total time 4.28 (100.0% of ALL ) | Highest rstack allocated: 136713 | Highest istack allocated: 2715 -| Job began at 15:10:09.678 on 10/20/2007 -| Setup done at 15:10:09.790 on 10/20/2007 -| Run done at 15:10:23.514 on 10/20/2007 +| Job began at 15:32:22.409 on 11/10/2008 +| Setup done at 15:32:22.438 on 11/10/2008 +| Run done at 15:32:26.691 on 11/10/2008 | wallclock() was called 4410 times --- test/softcore/min/out.1.save.orig 2008-11-10 15:39:11.000000000 -0800 +++ test/softcore/min/out.1.save 2008-11-10 15:39:19.000000000 -0800 @@ -3,7 +3,7 @@ Amber 10 SANDER 2008 ------------------------------------------------------- -| Run on 10/20/2007 at 15:10:09 +| Run on 11/10/2008 at 15:32:22 [-O]verwriting output File Assignments: @@ -33,13 +33,13 @@ ntp = 1, pres0 = 1.0, taup = 2.0, icfe=1, clambda = 0.50000, ifsc=1, scmask='', - / + / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: MPI +| Flags: MPI USE_MPI_IN_PLACE getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read @@ -57,13 +57,13 @@ | Memory Use Allocated -| Real 256544 +| Real 253844 | Hollerith 17102 -| Integer 81208 +| Integer 78508 | Max Pairs 1197900 | nblistReal 32400 | nblist Int 111764 -| Total 7757 kbytes +| Total 7725 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals @@ -118,6 +118,9 @@ Ewald Coefficient = 0.30768 Interpolation order = 4 +| MPI Timing options: +| profile_mpi = 0 + -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- @@ -132,7 +135,7 @@ Softcore Mask matches 0 atoms this run corresponds to V1, its softcore atoms interact fully for lambda=1 this process: 2700 atoms, partner process: 2715 atoms - Checking for mismatched coordinates + Checking for mismatched coordinates. Checking for SHAKE constraints on bonds crossing into the SC region Sum of charges from parm topology file = 0.00000000 @@ -278,39 +281,39 @@ 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.04% of Total) -| Build the list 0.07 (36.76% of List ) -| Other 0.12 (63.24% of List ) -| List time 0.19 ( 2.30% of Nonbo) -| Short_ene time 6.88 (99.19% of Direc) -| Other 0.06 ( 0.81% of Direc) -| Direct Ewald time 6.94 (88.03% of Ewald) -| Adjust Ewald time 0.03 ( 0.40% of Ewald) +| Read coords time 0.00 ( 0.05% of Total) +| Build the list 0.04 (69.99% of List ) +| Other 0.02 (30.01% of List ) +| List time 0.06 ( 1.62% of Nonbo) +| Short_ene time 2.66 (98.83% of Direc) +| Other 0.03 ( 1.17% of Direc) +| Direct Ewald time 2.69 (78.88% of Ewald) +| Adjust Ewald time 0.02 ( 0.54% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.06 ( 6.54% of Recip) -| Fill charge grid 0.15 (16.67% of Recip) -| Scalar sum 0.17 (18.99% of Recip) -| Grad sum 0.20 (21.95% of Recip) -| FFT back comm time 0.00 ( 0.03% of FFT t) -| Other 0.32 (100.0% of FFT t) -| FFT time 0.32 (35.67% of Recip) -| Other 0.00 ( 0.17% of Recip) -| Recip Ewald time 0.90 (11.47% of Ewald) -| Force Adjust 0.00 ( 0.02% of Ewald) -| Virial junk 0.01 ( 0.07% of Ewald) -| Other 0.00 ( 0.01% of Ewald) -| Ewald time 7.88 (97.69% of Nonbo) -| Nonbond force 8.06 (99.78% of Force) -| Bond/Angle/Dihedral 0.02 ( 0.20% of Force) -| Other 0.00 ( 0.02% of Force) -| Force time 8.08 (100.0% of Runmd) -| Runmd Time 8.08 (58.43% of Total) -| Other 5.75 (41.53% of Total) -| Total time 13.83 (100.0% of ALL ) +| Fill Bspline coeffs 0.09 (12.90% of Recip) +| Fill charge grid 0.10 (14.45% of Recip) +| Scalar sum 0.21 (29.84% of Recip) +| Grad sum 0.12 (17.50% of Recip) +| FFT back comm time 0.00 ( 0.04% of FFT t) +| Other 0.18 (100.0% of FFT t) +| FFT time 0.18 (25.22% of Recip) +| Other 0.00 ( 0.09% of Recip) +| Recip Ewald time 0.70 (20.46% of Ewald) +| Force Adjust 0.00 ( 0.03% of Ewald) +| Virial junk 0.00 ( 0.06% of Ewald) +| Other 0.00 ( 0.02% of Ewald) +| Ewald time 3.41 (98.38% of Nonbo) +| Nonbond force 3.46 (99.69% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.26% of Force) +| Other 0.00 ( 0.05% of Force) +| Force time 3.47 (100.0% of Runmd) +| Runmd Time 3.47 (81.10% of Total) +| Other 0.81 (18.84% of Total) +| Total time 4.28 (100.0% of ALL ) | Highest rstack allocated: 136308 | Highest istack allocated: 2700 -| Job began at 15:10:09.679 on 10/20/2007 -| Setup done at 15:10:09.790 on 10/20/2007 -| Run done at 15:10:23.513 on 10/20/2007 +| Job began at 15:32:22.409 on 11/10/2008 +| Setup done at 15:32:22.438 on 11/10/2008 +| Run done at 15:32:26.690 on 11/10/2008 | wallclock() was called 4410 times --- test/softcore/short_md/out.0.save 2008-11-10 15:39:59.000000000 -0800 +++ test/softcore/short_md/out.0.save 2008-11-10 15:40:58.000000000 -0800 @@ -3,7 +3,7 @@ Amber 10 SANDER 2008 ------------------------------------------------------- -| Run on 12/21/2007 at 17:36:15 +| Run on 11/10/2008 at 15:33:03 [-O]verwriting output File Assignments: @@ -35,13 +35,13 @@ icfe=1, clambda = 0.50000, ifsc=1, scmask=':1', logdvdl=0, - / + / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: MPI +| Flags: MPI USE_MPI_IN_PLACE getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read @@ -145,7 +145,8 @@ Softcore Mask :1; matches 15 atoms this run corresponds to V0, its softcore atoms interact fully for lambda=0 this process: 2715 atoms, partner process: 2700 atoms - Checking for mismatched coordinates + Checking for mismatched coordinates. + Molecule 1 is completely softcore and skipped for C.O.M.. Checking for SHAKE constraints on bonds crossing into the SC region Sum of charges from parm topology file = 0.00000000 @@ -431,45 +432,44 @@ 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.11% of Total) -| Build the list 0.49 (95.41% of List ) -| Other 0.02 ( 4.59% of List ) -| List time 0.51 ( 8.65% of Nonbo) -| Short_ene time 4.61 (99.21% of Direc) -| Other 0.04 ( 0.79% of Direc) -| Direct Ewald time 4.65 (86.26% of Ewald) -| Adjust Ewald time 0.03 ( 0.51% of Ewald) +| Read coords time 0.00 ( 0.09% of Total) +| Build the list 0.35 (95.55% of List ) +| Other 0.02 ( 4.45% of List ) +| List time 0.36 ( 9.70% of Nonbo) +| Short_ene time 2.62 (98.77% of Direc) +| Other 0.03 ( 1.23% of Direc) +| Direct Ewald time 2.65 (78.64% of Ewald) +| Adjust Ewald time 0.02 ( 0.56% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.05 ( 7.17% of Recip) -| Fill charge grid 0.11 (15.94% of Recip) -| Scalar sum 0.13 (18.71% of Recip) -| Grad sum 0.17 (23.85% of Recip) -| FFT back comm time 0.00 ( 0.09% of FFT t) -| Other 0.24 (100.0% of FFT t) -| FFT time 0.24 (34.23% of Recip) -| Other 0.00 ( 0.10% of Recip) -| Recip Ewald time 0.71 (13.10% of Ewald) -| Force Adjust 0.00 ( 0.04% of Ewald) -| Virial junk 0.00 ( 0.06% of Ewald) +| Fill Bspline coeffs 0.09 (12.39% of Recip) +| Fill charge grid 0.08 (11.50% of Recip) +| Scalar sum 0.23 (32.71% of Recip) +| Grad sum 0.12 (17.54% of Recip) +| FFT back comm time 0.00 ( 0.04% of FFT t) +| Other 0.18 (100.0% of FFT t) +| FFT time 0.18 (25.77% of Recip) +| Other 0.00 ( 0.08% of Recip) +| Recip Ewald time 0.69 (20.59% of Ewald) +| Force Adjust 0.00 ( 0.05% of Ewald) +| Virial junk 0.00 ( 0.13% of Ewald) | Other 0.00 ( 0.02% of Ewald) -| Ewald time 5.39 (91.34% of Nonbo) -| Other 0.00 ( 0.01% of Nonbo) -| Nonbond force 5.90 (99.71% of Force) -| Bond/Angle/Dihedral 0.02 ( 0.26% of Force) -| Other 0.00 ( 0.03% of Force) -| Force time 5.92 (96.21% of Runmd) -| Shake time 0.03 ( 0.51% of Runmd) -| Verlet update time 0.17 ( 2.77% of Runmd) +| Ewald time 3.37 (90.29% of Nonbo) +| Nonbond force 3.74 (99.63% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.33% of Force) +| Other 0.00 ( 0.04% of Force) +| Force time 3.75 (83.09% of Runmd) +| Shake time 0.02 ( 0.46% of Runmd) +| Verlet update time 0.11 ( 2.43% of Runmd) | Ekcmr time 0.00 ( 0.07% of Runmd) -| CRD distribute time 0.00 ( 0.01% of Runmd) -| Other 0.03 ( 0.43% of Runmd) -| Runmd Time 6.15 (99.18% of Total) -| Other 0.04 ( 0.71% of Total) -| Total time 6.20 (100.0% of ALL ) +| CRD distribute time 0.00 ( 0.02% of Runmd) +| Other 0.63 (13.93% of Runmd) +| Runmd Time 4.51 (99.44% of Total) +| Other 0.02 ( 0.47% of Total) +| Total time 4.54 (100.0% of ALL ) | Highest rstack allocated: 136713 | Highest istack allocated: 2715 -| Job began at 17:36:15.884 on 12/21/2007 -| Setup done at 17:36:15.934 on 12/21/2007 -| Run done at 17:36:22.084 on 12/21/2007 +| Job began at 15:33:03.302 on 11/10/2008 +| Setup done at 15:33:03.328 on 11/10/2008 +| Run done at 15:33:07.840 on 11/10/2008 | wallclock() was called 5530 times --- test/softcore/short_md/out.1.save 2008-11-10 15:40:10.000000000 -0800 +++ test/softcore/short_md/out.1.save 2008-11-10 15:41:03.000000000 -0800 @@ -3,7 +3,7 @@ Amber 10 SANDER 2008 ------------------------------------------------------- -| Run on 12/21/2007 at 17:36:15 +| Run on 11/10/2008 at 15:33:03 [-O]verwriting output File Assignments: @@ -35,13 +35,13 @@ icfe=1, clambda = 0.50000, ifsc=1, scmask='', logdvdl=0, - / + / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: MPI +| Flags: MPI USE_MPI_IN_PLACE getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read @@ -145,7 +145,7 @@ Softcore Mask matches 0 atoms this run corresponds to V1, its softcore atoms interact fully for lambda=1 this process: 2700 atoms, partner process: 2715 atoms - Checking for mismatched coordinates + Checking for mismatched coordinates. Checking for SHAKE constraints on bonds crossing into the SC region Sum of charges from parm topology file = 0.00000000 @@ -343,45 +343,44 @@ 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.01 ( 0.11% of Total) -| Build the list 0.48 (95.38% of List ) -| Other 0.02 ( 4.62% of List ) -| List time 0.50 ( 8.67% of Nonbo) -| Short_ene time 4.54 (99.21% of Direc) -| Other 0.04 ( 0.79% of Direc) -| Direct Ewald time 4.57 (86.08% of Ewald) -| Adjust Ewald time 0.03 ( 0.50% of Ewald) +| Read coords time 0.00 ( 0.09% of Total) +| Build the list 0.34 (95.40% of List ) +| Other 0.02 ( 4.60% of List ) +| List time 0.36 ( 9.54% of Nonbo) +| Short_ene time 2.66 (98.81% of Direc) +| Other 0.03 ( 1.19% of Direc) +| Direct Ewald time 2.69 (79.39% of Ewald) +| Adjust Ewald time 0.02 ( 0.54% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.05 ( 6.83% of Recip) -| Fill charge grid 0.12 (16.43% of Recip) -| Scalar sum 0.13 (18.71% of Recip) -| Grad sum 0.17 (23.77% of Recip) -| FFT back comm time 0.00 ( 0.09% of FFT t) -| Other 0.24 (100.0% of FFT t) -| FFT time 0.24 (34.16% of Recip) -| Other 0.00 ( 0.11% of Recip) -| Recip Ewald time 0.71 (13.30% of Ewald) -| Force Adjust 0.00 ( 0.04% of Ewald) -| Virial junk 0.00 ( 0.06% of Ewald) +| Fill Bspline coeffs 0.08 (11.86% of Recip) +| Fill charge grid 0.08 (12.01% of Recip) +| Scalar sum 0.21 (31.84% of Recip) +| Grad sum 0.12 (17.92% of Recip) +| FFT back comm time 0.00 ( 0.04% of FFT t) +| Other 0.18 (100.0% of FFT t) +| FFT time 0.18 (26.28% of Recip) +| Other 0.00 ( 0.09% of Recip) +| Recip Ewald time 0.67 (19.86% of Ewald) +| Force Adjust 0.00 ( 0.05% of Ewald) +| Virial junk 0.00 ( 0.13% of Ewald) | Other 0.00 ( 0.02% of Ewald) -| Ewald time 5.31 (91.32% of Nonbo) -| Other 0.00 ( 0.01% of Nonbo) -| Nonbond force 5.82 (99.76% of Force) -| Bond/Angle/Dihedral 0.01 ( 0.21% of Force) -| Other 0.00 ( 0.03% of Force) -| Force time 5.83 (94.88% of Runmd) -| Shake time 0.03 ( 0.45% of Runmd) -| Verlet update time 0.17 ( 2.75% of Runmd) +| Ewald time 3.39 (90.45% of Nonbo) +| Nonbond force 3.75 (99.72% of Force) +| Bond/Angle/Dihedral 0.01 ( 0.24% of Force) +| Other 0.00 ( 0.04% of Force) +| Force time 3.76 (83.31% of Runmd) +| Shake time 0.02 ( 0.40% of Runmd) +| Verlet update time 0.17 ( 3.78% of Runmd) | Ekcmr time 0.00 ( 0.07% of Runmd) -| CRD distribute time 0.00 ( 0.02% of Runmd) -| Other 0.11 ( 1.82% of Runmd) -| Runmd Time 6.15 (99.18% of Total) -| Other 0.04 ( 0.71% of Total) -| Total time 6.20 (100.0% of ALL ) +| CRD distribute time 0.00 ( 0.04% of Runmd) +| Other 0.56 (12.39% of Runmd) +| Runmd Time 4.51 (99.37% of Total) +| Other 0.02 ( 0.54% of Total) +| Total time 4.54 (100.0% of ALL ) | Highest rstack allocated: 136308 | Highest istack allocated: 2700 -| Job began at 17:36:15.883 on 12/21/2007 -| Setup done at 17:36:15.934 on 12/21/2007 -| Run done at 17:36:22.083 on 12/21/2007 +| Job began at 15:33:03.299 on 11/10/2008 +| Setup done at 15:33:03.328 on 11/10/2008 +| Run done at 15:33:07.840 on 11/10/2008 | wallclock() was called 5530 times --- test/softcore/short_md/out2.0.save 2008-11-10 15:40:41.000000000 -0800 +++ test/softcore/short_md/out2.0.save 2008-11-10 15:41:12.000000000 -0800 @@ -3,7 +3,7 @@ Amber 10 SANDER 2008 ------------------------------------------------------- -| Run on 12/21/2007 at 17:36:23 +| Run on 11/10/2008 at 15:33:09 [-O]verwriting output File Assignments: @@ -36,13 +36,13 @@ icfe=1, clambda = 0.50000, ifsc=1, scmask=':1', logdvdl=0, - / + / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: MPI +| Flags: MPI USE_MPI_IN_PLACE getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read @@ -146,7 +146,8 @@ Softcore Mask :1; matches 15 atoms this run corresponds to V0, its softcore atoms interact fully for lambda=0 this process: 2715 atoms, partner process: 2700 atoms - Checking for mismatched coordinates + Checking for mismatched coordinates. + Molecule 1 is completely softcore and skipped for C.O.M.. Checking for SHAKE constraints on bonds crossing into the SC region Sum of charges from parm topology file = 0.00000000 @@ -452,45 +453,44 @@ 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.00 ( 0.63% of Total) -| Fast Water setup 0.00 ( 0.02% of Total) -| Build the list 0.05 (71.50% of List ) -| Other 0.02 (28.50% of List ) -| List time 0.07 (10.93% of Nonbo) -| Short_ene time 0.51 (99.18% of Direc) -| Other 0.00 ( 0.82% of Direc) -| Direct Ewald time 0.51 (85.75% of Ewald) -| Adjust Ewald time 0.00 ( 0.51% of Ewald) +| Read coords time 0.00 ( 0.29% of Total) +| Fast Water setup 0.00 ( 0.01% of Total) +| Build the list 0.03 (72.52% of List ) +| Other 0.01 (27.48% of List ) +| List time 0.05 ( 8.28% of Nonbo) +| Short_ene time 0.28 (98.89% of Direc) +| Other 0.00 ( 1.11% of Direc) +| Direct Ewald time 0.29 (55.51% of Ewald) +| Adjust Ewald time 0.00 ( 0.39% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.01 ( 7.61% of Recip) -| Fill charge grid 0.01 (14.98% of Recip) -| Scalar sum 0.01 (17.91% of Recip) -| Grad sum 0.02 (22.81% of Recip) -| FFT back comm time 0.00 ( 0.09% of FFT t) -| Other 0.03 (100.0% of FFT t) -| FFT time 0.03 (36.56% of Recip) -| Other 0.00 ( 0.13% of Recip) -| Recip Ewald time 0.08 (13.60% of Ewald) +| Fill Bspline coeffs 0.01 ( 3.28% of Recip) +| Fill charge grid 0.01 ( 3.78% of Recip) +| Scalar sum 0.17 (76.75% of Recip) +| Grad sum 0.01 ( 5.69% of Recip) +| FFT back comm time 0.00 ( 0.03% of FFT t) +| Other 0.02 (100.0% of FFT t) +| FFT time 0.02 (10.47% of Recip) +| Other 0.00 ( 0.02% of Recip) +| Recip Ewald time 0.23 (43.95% of Ewald) | Force Adjust 0.00 ( 0.04% of Ewald) -| Virial junk 0.00 ( 0.06% of Ewald) +| Virial junk 0.00 ( 0.08% of Ewald) | Other 0.00 ( 0.02% of Ewald) -| Ewald time 0.60 (89.05% of Nonbo) -| Other 0.00 ( 0.01% of Nonbo) -| Nonbond force 0.67 (99.70% of Force) -| Bond/Angle/Dihedral 0.00 ( 0.26% of Force) +| Ewald time 0.52 (91.72% of Nonbo) +| Nonbond force 0.56 (99.72% of Force) +| Bond/Angle/Dihedral 0.00 ( 0.24% of Force) | Other 0.00 ( 0.04% of Force) -| Force time 0.67 (94.79% of Runmd) -| Shake time 0.00 ( 0.45% of Runmd) -| Verlet update time 0.03 ( 3.65% of Runmd) -| Ekcmr time 0.00 ( 0.06% of Runmd) -| Other 0.01 ( 1.05% of Runmd) -| Runmd Time 0.71 (94.07% of Total) -| Other 0.04 ( 5.28% of Total) -| Total time 0.76 (100.0% of ALL ) +| Force time 0.57 (61.28% of Runmd) +| Shake time 0.00 ( 0.22% of Runmd) +| Verlet update time 0.01 ( 1.58% of Runmd) +| Ekcmr time 0.00 ( 0.03% of Runmd) +| Other 0.34 (36.87% of Runmd) +| Runmd Time 0.92 (89.47% of Total) +| Other 0.11 (10.24% of Total) +| Total time 1.03 (100.0% of ALL ) | Highest rstack allocated: 136713 | Highest istack allocated: 2715 -| Job began at 17:36:23.060 on 12/21/2007 -| Setup done at 17:36:23.105 on 12/21/2007 -| Run done at 17:36:23.815 on 12/21/2007 +| Job began at 15:33:09.462 on 11/10/2008 +| Setup done at 15:33:09.571 on 11/10/2008 +| Run done at 15:33:10.495 on 11/10/2008 | wallclock() was called 606 times --- test/softcore/short_md/out2.1.save 2008-11-10 15:40:47.000000000 -0800 +++ test/softcore/short_md/out2.1.save 2008-11-10 15:41:18.000000000 -0800 @@ -3,7 +3,7 @@ Amber 10 SANDER 2008 ------------------------------------------------------- -| Run on 12/21/2007 at 17:36:23 +| Run on 11/10/2008 at 15:33:09 [-O]verwriting output File Assignments: @@ -36,13 +36,13 @@ icfe=1, clambda = 0.50000, ifsc=1, scmask='', logdvdl=0, - / + / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: MPI +| Flags: MPI USE_MPI_IN_PLACE getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read @@ -146,7 +146,7 @@ Softcore Mask matches 0 atoms this run corresponds to V1, its softcore atoms interact fully for lambda=1 this process: 2700 atoms, partner process: 2715 atoms - Checking for mismatched coordinates + Checking for mismatched coordinates. Checking for SHAKE constraints on bonds crossing into the SC region Sum of charges from parm topology file = 0.00000000 @@ -358,45 +358,44 @@ 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.00 ( 0.62% of Total) -| Fast Water setup 0.00 ( 0.02% of Total) -| Build the list 0.05 (71.22% of List ) -| Other 0.02 (28.78% of List ) -| List time 0.07 (10.99% of Nonbo) -| Short_ene time 0.50 (99.21% of Direc) -| Other 0.00 ( 0.79% of Direc) -| Direct Ewald time 0.50 (85.56% of Ewald) -| Adjust Ewald time 0.00 ( 0.50% of Ewald) +| Read coords time 0.00 ( 0.28% of Total) +| Fast Water setup 0.00 ( 0.01% of Total) +| Build the list 0.03 (72.04% of List ) +| Other 0.01 (27.96% of List ) +| List time 0.05 ( 7.59% of Nonbo) +| Short_ene time 0.28 (98.84% of Direc) +| Other 0.00 ( 1.16% of Direc) +| Direct Ewald time 0.29 (50.43% of Ewald) +| Adjust Ewald time 0.00 ( 0.35% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) -| Fill Bspline coeffs 0.01 ( 7.27% of Recip) -| Fill charge grid 0.01 (15.76% of Recip) -| Scalar sum 0.01 (17.88% of Recip) -| Grad sum 0.02 (22.60% of Recip) -| FFT back comm time 0.00 ( 0.08% of FFT t) -| Other 0.03 (100.0% of FFT t) -| FFT time 0.03 (36.38% of Recip) -| Other 0.00 ( 0.11% of Recip) -| Recip Ewald time 0.08 (13.82% of Ewald) -| Force Adjust 0.00 ( 0.04% of Ewald) -| Virial junk 0.00 ( 0.06% of Ewald) -| Other 0.00 ( 0.02% of Ewald) -| Ewald time 0.59 (89.00% of Nonbo) -| Other 0.00 ( 0.01% of Nonbo) -| Nonbond force 0.66 (99.76% of Force) -| Bond/Angle/Dihedral 0.00 ( 0.20% of Force) +| Fill Bspline coeffs 0.00 ( 1.67% of Recip) +| Fill charge grid 0.04 (13.50% of Recip) +| Scalar sum 0.20 (72.79% of Recip) +| Grad sum 0.01 ( 4.77% of Recip) +| FFT back comm time 0.00 ( 0.03% of FFT t) +| Other 0.02 (100.0% of FFT t) +| FFT time 0.02 ( 7.26% of Recip) +| Other 0.00 ( 0.02% of Recip) +| Recip Ewald time 0.28 (49.09% of Ewald) +| Force Adjust 0.00 ( 0.03% of Ewald) +| Virial junk 0.00 ( 0.08% of Ewald) +| Other 0.00 ( 0.01% of Ewald) +| Ewald time 0.57 (92.41% of Nonbo) +| Nonbond force 0.62 (99.82% of Force) +| Bond/Angle/Dihedral 0.00 ( 0.15% of Force) | Other 0.00 ( 0.04% of Force) -| Force time 0.66 (93.33% of Runmd) -| Shake time 0.00 ( 0.39% of Runmd) -| Verlet update time 0.02 ( 3.48% of Runmd) -| Ekcmr time 0.00 ( 0.07% of Runmd) -| Other 0.02 ( 2.73% of Runmd) -| Runmd Time 0.71 (94.07% of Total) -| Other 0.04 ( 5.29% of Total) -| Total time 0.75 (100.0% of ALL ) +| Force time 0.62 (66.12% of Runmd) +| Shake time 0.00 ( 0.19% of Runmd) +| Verlet update time 0.01 ( 1.49% of Runmd) +| Ekcmr time 0.00 ( 0.03% of Runmd) +| Other 0.30 (32.16% of Runmd) +| Runmd Time 0.94 (89.59% of Total) +| Other 0.11 (10.12% of Total) +| Total time 1.04 (100.0% of ALL ) | Highest rstack allocated: 136308 | Highest istack allocated: 2700 -| Job began at 17:36:23.060 on 12/21/2007 -| Setup done at 17:36:23.105 on 12/21/2007 -| Run done at 17:36:23.815 on 12/21/2007 +| Job began at 15:33:09.462 on 11/10/2008 +| Setup done at 15:33:09.571 on 11/10/2008 +| Run done at 15:33:10.507 on 11/10/2008 | wallclock() was called 606 times --- test/softcore/complex/out.1.save 2008-11-10 15:36:40.000000000 -0800 +++ test/softcore/complex/out.1.save 2008-11-10 15:45:25.000000000 -0800 @@ -3,7 +3,7 @@ Amber 10 SANDER 2008 ------------------------------------------------------- -| Run on 12/21/2007 at 17:35:26 +| Run on 11/10/2008 at 15:32:27 [-O]verwriting output File Assignments: @@ -35,13 +35,13 @@ icfe=1, clambda = 0.6, ifsc=1, scmask=':PHN@H6,O1', crgmask=':PHN@H6,O1', - / + / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- -| Flags: MPI +| Flags: MPI USE_MPI_IN_PLACE getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read @@ -149,7 +149,8 @@ Softcore Mask :PHN@H6,O1; matches 2 atoms this run corresponds to V1, its softcore atoms interact fully for lambda=1 this process: 29882 atoms, partner process: 29881 atoms - Checking for mismatched coordinates + Checking for mismatched coordinates. + Molecule 2 is partially softcore on this side or the corresponding partner molecule is. Checking for SHAKE constraints on bonds crossing into the SC region Sum of charges from parm topology file = 0.17486081 @@ -422,42 +423,43 @@ 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.07 ( 0.18% of Total) -| Build the list 3.70 (97.65% of List ) -| Other 0.09 ( 2.35% of List ) -| List time 3.79 ( 9.94% of Nonbo) -| Short_ene time 26.70 (99.04% of Direc) -| Other 0.26 ( 0.96% of Direc) -| Direct Ewald time 26.96 (78.50% of Ewald) -| Adjust Ewald time 0.20 ( 0.59% of Ewald) -| Fill Bspline coeffs 0.46 ( 6.40% of Recip) -| Fill charge grid 1.46 (20.53% of Recip) -| Scalar sum 0.88 (12.34% of Recip) -| Grad sum 1.63 (22.86% of Recip) -| FFT back comm time 0.00 ( 0.02% of FFT t) -| Other 2.70 (100.0% of FFT t) -| FFT time 2.70 (37.85% of Recip) +| Read coords time 0.04 ( 0.17% of Total) +| Build the list 2.54 (98.45% of List ) +| Other 0.04 ( 1.55% of List ) +| List time 2.58 (11.55% of Nonbo) +| Short_ene time 15.39 (98.74% of Direc) +| Other 0.20 ( 1.26% of Direc) +| Direct Ewald time 15.58 (78.79% of Ewald) +| Adjust Ewald time 0.14 ( 0.73% of Ewald) +| Fill Bspline coeffs 0.26 ( 6.50% of Recip) +| Fill charge grid 0.63 (15.66% of Recip) +| Scalar sum 0.73 (18.25% of Recip) +| Grad sum 0.88 (21.90% of Recip) +| FFT back comm time 0.00 ( 0.01% of FFT t) +| Other 1.51 (100.0% of FFT t) +| FFT time 1.51 (37.67% of Recip) | Other 0.00 ( 0.01% of Recip) -| Recip Ewald time 7.12 (20.74% of Ewald) -| Force Adjust 0.04 ( 0.11% of Ewald) -| Virial junk 0.02 ( 0.05% of Ewald) -| Ewald time 34.35 (90.06% of Nonbo) -| Nonbond force 38.14 (99.22% of Force) -| Bond/Angle/Dihedral 0.26 ( 0.68% of Force) -| Other 0.04 ( 0.10% of Force) -| Force time 38.44 (95.32% of Runmd) -| Shake time 0.21 ( 0.52% of Runmd) -| Verlet update time 1.13 ( 2.79% of Runmd) -| Ekcmr time 0.06 ( 0.15% of Runmd) -| CRD distribute time 0.01 ( 0.02% of Runmd) -| Other 0.48 ( 1.20% of Runmd) -| Runmd Time 40.32 (98.54% of Total) -| Other 0.53 ( 1.28% of Total) -| Total time 40.92 (100.0% of ALL ) +| Recip Ewald time 4.00 (20.23% of Ewald) +| Force Adjust 0.01 ( 0.03% of Ewald) +| Virial junk 0.02 ( 0.11% of Ewald) +| Other 0.02 ( 0.10% of Ewald) +| Ewald time 19.78 (88.44% of Nonbo) +| Nonbond force 22.37 (99.24% of Force) +| Bond/Angle/Dihedral 0.15 ( 0.68% of Force) +| Other 0.02 ( 0.08% of Force) +| Force time 22.54 (89.06% of Runmd) +| Shake time 0.24 ( 0.96% of Runmd) +| Verlet update time 1.11 ( 4.41% of Runmd) +| Ekcmr time 0.02 ( 0.09% of Runmd) +| CRD distribute time 0.01 ( 0.03% of Runmd) +| Other 1.38 ( 5.45% of Runmd) +| Runmd Time 25.30 (97.70% of Total) +| Other 0.55 ( 2.12% of Total) +| Total time 25.90 (100.0% of ALL ) | Highest rstack allocated: 1551768 | Highest istack allocated: 29882 -| Job began at 17:35:26.756 on 12/21/2007 -| Setup done at 17:35:27.355 on 12/21/2007 -| Run done at 17:36:07.680 on 12/21/2007 +| Job began at 15:32:27.938 on 11/10/2008 +| Setup done at 15:32:28.533 on 11/10/2008 +| Run done at 15:32:53.837 on 11/10/2008 | wallclock() was called 2772 times ------------------------------------------------------------------------------ Temporary Workarounds: None