I: Libraries linked in sander and pmemd: [TempID@nkstar2 exe]$ ldd sander libgm.so.0 => /opt/xcat/gm/lib/libgm.so.0 (0x2aae0000) libsvml.so => /nfs/s08r1p3/TempID/intel/fc/9.0/lib/libsvml.so (0x2aaf7000) libvml.so => /opt/intel/mkl70/lib/32/libvml.so (0x2ab4a000) libmkl_lapack64.so => /opt/intel/mkl70/lib/32/libmkl_lapack64.so (0x2ab7b000) libmkl.so => /opt/intel/mkl70/lib/32/libmkl.so (0x2add4000) libguide.so => /nfs/s08r1p3/TempID/intel/fc/9.0/lib/libguide.so (0x2ae09000) libpthread.so.0 => /lib/i686/libpthread.so.0 (0x2ae3a000) libimf.so => /nfs/s08r1p3/TempID/intel/fc/9.0/lib/libimf.so (0x2ae8b000) libm.so.6 => /lib/i686/libm.so.6 (0x2b06c000) libc.so.6 => /lib/i686/libc.so.6 (0x2b08e000) libdl.so.2 => /lib/libdl.so.2 (0x2b1c7000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x2aaab000) [TempID@nkstar2 exe]$ ldd pmemd libgm.so.0 => /opt/xcat/gm/lib/libgm.so.0 (0x2aac2000) libpthread.so.0 => /lib/i686/libpthread.so.0 (0x2aaf7000) libimf.so => /nfs/s08r1p3/TempID/intel/fc/9.0/lib/libimf.so (0x2ab47000) libsvml.so => /nfs/s08r1p3/TempID/intel/fc/9.0/lib/libsvml.so (0x2ad28000) libm.so.6 => /lib/i686/libm.so.6 (0x2ad7b000) libc.so.6 => /lib/i686/libc.so.6 (0x2ad9d000) libdl.so.2 => /lib/libdl.so.2 (0x2aed7000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x2aaab000) II: We use Platform LSF system to submit jobs, the following is the output file after I have did my 16-cpu benchmark for pmemd. Sender: LSF System Subject: Job 101642: Done Job was submitted from host by user . Job was executed on host(s) <2*node018>, in queue , as user . <2*node123> <2*node102> <2*node014> <2*node092> <2*node048> <2*node020> <2*node120> was used as the home directory. was used as the working directory. Started at Sun May 14 22:45:49 2006 Results reported at Sun May 14 22:47:42 2006 Your job looked like: ------------------------------------------------------------ # LSBATCH: User input #!/bin/bash #BSUB -q normal #BSUB -J pme16 #BSUB -a mpich_gm #BSUB -o %J.output #BSUB -n 16 #BSUB -R span[ptile=2] mpirun.lsf $AMBERHOME/exe/pmemd -O -i mdin -c inpcrd.equil -o bench.jac.out.16cpu ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 1529.31 sec. Max Memory : 899 MB Max Swap : 977 MB Max Processes : 16 Max Threads : 16 The output (if any) follows: TID HOST_NAME COMMAND_LINE STATUS TERMINATION_TIME ==== ========== ================ ======================= =================== 0001 node018 -O -i mdin -c i Done 05/14/2006 22:47:38 0002 node018 -O -i mdin -c i Done 05/14/2006 22:47:38 0003 node014 -O -i mdin -c i Done 05/14/2006 22:47:38 0004 node048 -O -i mdin -c i Done 05/14/2006 22:47:38 0005 node102 -O -i mdin -c i Done 05/14/2006 22:47:38 0006 node102 -O -i mdin -c i Done 05/14/2006 22:47:38 0007 node014 -O -i mdin -c i Done 05/14/2006 22:47:38 0008 node092 -O -i mdin -c i Done 05/14/2006 22:47:38 0009 node092 -O -i mdin -c i Done 05/14/2006 22:47:38 0010 node048 -O -i mdin -c i Done 05/14/2006 22:47:38 0011 node123 -O -i mdin -c i Done 05/14/2006 22:47:38 0012 node123 -O -i mdin -c i Done 05/14/2006 22:47:38 0013 node020 -O -i mdin -c i Done 05/14/2006 22:47:38 0014 node020 -O -i mdin -c i Done 05/14/2006 22:47:38 0015 node120 -O -i mdin -c i Done 05/14/2006 22:47:38 0016 node120 -O -i mdin -c i Done 05/14/2006 22:47:38 III: Here is the "logfile" resulted from paralleled pmemd Parallel Profiling Results A N n F o g X n B S R O T d b n h u t o i o d a n h t P s n D k m e a E t d i e d r l --------------------------------------------------------------------- 0 27.3 45.5 0.7 0.1 5.8 0.2 79.6 1 28.5 59.2 1.4 0.3 5.1 0.1 94.6 2 30.0 61.5 0.4 0.2 5.1 0.0 97.3 3 28.5 60.1 0.1 0.3 4.8 0.0 93.9 4 28.3 59.3 0.2 0.1 5.6 0.0 93.5 5 30.1 61.8 0.0 0.3 5.5 0.0 97.8 6 29.5 58.3 0.0 0.2 5.2 0.0 93.3 7 30.1 62.1 0.0 0.2 5.2 0.0 97.7 8 28.7 60.0 0.0 0.2 5.6 0.1 94.6 9 29.3 61.6 0.0 0.2 5.4 0.0 96.5 10 28.7 60.0 0.0 0.2 5.0 0.0 93.9 11 29.6 62.4 0.1 0.2 5.3 0.0 97.7 12 28.6 59.3 0.0 0.2 5.1 0.0 93.3 13 30.1 61.5 0.6 0.2 5.3 0.0 97.6 14 23.6 59.7 0.8 0.2 3.0 0.0 87.3 15 28.2 54.3 0.4 0.2 3.5 0.0 86.6 av 28.7 59.2 0.3 0.2 5.0 std 1.5 4.0 0.4 0.0 0.7 min 23.6 45.5 0.0 0.1 3.0 max 30.1 62.4 1.5 0.3 5.8 --------------------------------------------------------------------- IV: Here is the profile_mpi resulted from paralleled sander |>>>>>>>>PROFILE of TIMES for process 0 | Read coords time 0.11 ( 0.09% of Total) | Build the list 4.06 (78.45% of List ) | Other 1.11 (21.55% of List ) | List time 5.17 ( 5.99% of Nonbo) | Short_ene time 38.95 (90.79% of Direc) | Other 3.95 ( 9.21% of Direc) | Direct Ewald time 42.91 (52.85% of Ewald) | Adjust Ewald time 0.34 ( 0.42% of Ewald) | Self Ewald time 0.01 ( 0.01% of Ewald) | Fill Bspline coeffs 2.16 (11.63% of Recip) | Fill charge grid 0.99 ( 5.32% of Recip) | Scalar sum 1.02 ( 5.50% of Recip) | Grad sum 1.76 ( 9.47% of Recip) | FFT communication ti 5.67 (47.66% of FFT t) | Other 6.22 (52.34% of FFT t) | FFT time 11.89 (64.02% of Recip) | Other 0.75 ( 4.07% of Recip) | Recip Ewald time 18.57 (22.87% of Ewald) | Force Adjust 15.74 (19.38% of Ewald) | Virial junk 3.24 ( 3.99% of Ewald) | Start sycnronization 0.36 ( 0.44% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 81.18 (94.00% of Nonbo) | Nonbond force 86.36 (90.48% of Force) | Bond/Angle/Dihedral 0.37 ( 0.39% of Force) | FRC Collect time 6.25 ( 6.55% of Force) | Other 2.47 ( 2.59% of Force) | Force time 95.44 (80.80% of Runmd) | Shake time 0.51 ( 0.43% of Runmd) | Verlet update time 15.60 (13.21% of Runmd) | CRD distribute time 6.56 ( 5.55% of Runmd) | Other 0.01 ( 0.01% of Runmd) | Runmd Time 118.13 (98.06% of Total) | Other 2.23 ( 1.85% of Total) | Total time 120.47 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 1 | Build the list 3.80 (76.82% of List ) | Other 1.15 (23.18% of List ) | List time 4.95 ( 4.97% of Nonbo) | Short_ene time 37.46 (90.56% of Direc) | Other 3.90 ( 9.44% of Direc) | Direct Ewald time 41.36 (43.69% of Ewald) | Adjust Ewald time 0.39 ( 0.41% of Ewald) | Self Ewald time 0.01 ( 0.01% of Ewald) | Fill Bspline coeffs 2.44 ( 7.62% of Recip) | Fill charge grid 0.97 ( 3.03% of Recip) | Scalar sum 1.11 ( 3.48% of Recip) | Grad sum 1.79 ( 5.60% of Recip) | FFT communication ti 5.92 (23.65% of FFT t) | Other 19.13 (76.35% of FFT t) | FFT time 25.05 (78.39% of Recip) | Other 0.60 ( 1.88% of Recip) | Recip Ewald time 31.95 (33.76% of Ewald) | Force Adjust 17.29 (18.26% of Ewald) | Virial junk 3.28 ( 3.47% of Ewald) | Start sycnronization 0.37 ( 0.39% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 94.66 (95.03% of Nonbo) | Nonbond force 99.61 (91.66% of Force) | Bond/Angle/Dihedral 0.37 ( 0.34% of Force) | FRC Collect time 6.23 ( 5.74% of Force) | Other 2.46 ( 2.26% of Force) | Force time 108.67 (92.22% of Runmd) | Shake time 0.73 ( 0.62% of Runmd) | Verlet update time 1.77 ( 1.50% of Runmd) | CRD distribute time 6.66 ( 5.65% of Runmd) | Other 0.01 ( 0.01% of Runmd) | Runmd Time 117.84 (98.05% of Total) | Other 2.34 ( 1.95% of Total) | Total time 120.18 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 2 | Build the list 3.91 (75.40% of List ) | Other 1.28 (24.60% of List ) | List time 5.19 ( 5.21% of Nonbo) | Short_ene time 36.53 (90.50% of Direc) | Other 3.84 ( 9.50% of Direc) | Direct Ewald time 40.37 (42.69% of Ewald) | Adjust Ewald time 0.34 ( 0.36% of Ewald) | Fill Bspline coeffs 2.02 ( 6.33% of Recip) | Fill charge grid 0.96 ( 3.02% of Recip) | Scalar sum 0.97 ( 3.06% of Recip) | Grad sum 1.75 ( 5.49% of Recip) | FFT communication ti 5.56 (21.96% of FFT t) | Other 19.75 (78.04% of FFT t) | FFT time 25.30 (79.40% of Recip) | Other 0.86 ( 2.70% of Recip) | Recip Ewald time 31.87 (33.70% of Ewald) | Force Adjust 18.32 (19.38% of Ewald) | Virial junk 3.29 ( 3.48% of Ewald) | Start sycnronization 0.36 ( 0.38% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 94.56 (94.79% of Nonbo) | Nonbond force 99.76 (91.65% of Force) | Bond/Angle/Dihedral 0.36 ( 0.33% of Force) | FRC Collect time 6.27 ( 5.76% of Force) | Other 2.46 ( 2.26% of Force) | Force time 108.84 (92.37% of Runmd) | Shake time 0.41 ( 0.34% of Runmd) | Verlet update time 2.07 ( 1.76% of Runmd) | CRD distribute time 6.49 ( 5.51% of Runmd) | Other 0.02 ( 0.02% of Runmd) | Runmd Time 117.83 (98.04% of Total) | Other 2.35 ( 1.96% of Total) | Total time 120.18 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 3 | Build the list 3.86 (75.37% of List ) | Other 1.26 (24.63% of List ) | List time 5.12 ( 5.12% of Nonbo) | Short_ene time 38.15 (90.51% of Direc) | Other 4.00 ( 9.49% of Direc) | Direct Ewald time 42.15 (44.38% of Ewald) | Adjust Ewald time 0.33 ( 0.35% of Ewald) | Fill Bspline coeffs 2.03 ( 6.38% of Recip) | Fill charge grid 0.96 ( 3.00% of Recip) | Scalar sum 0.99 ( 3.12% of Recip) | Grad sum 1.75 ( 5.49% of Recip) | FFT communication ti 5.73 (22.63% of FFT t) | Other 19.61 (77.37% of FFT t) | FFT time 25.34 (79.57% of Recip) | Other 0.78 ( 2.44% of Recip) | Recip Ewald time 31.85 (33.53% of Ewald) | Force Adjust 16.51 (17.38% of Ewald) | Virial junk 3.76 ( 3.96% of Ewald) | Start sycnronization 0.37 ( 0.38% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 94.99 (94.88% of Nonbo) | Nonbond force 100.11 (92.04% of Force) | Bond/Angle/Dihedral 0.41 ( 0.37% of Force) | FRC Collect time 6.25 ( 5.75% of Force) | Other 2.01 ( 1.84% of Force) | Force time 108.77 (92.31% of Runmd) | Shake time 0.41 ( 0.35% of Runmd) | Verlet update time 2.08 ( 1.76% of Runmd) | CRD distribute time 6.55 ( 5.56% of Runmd) | Other 0.02 ( 0.02% of Runmd) | Runmd Time 117.83 (98.04% of Total) | Other 2.35 ( 1.96% of Total) | Total time 120.18 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 4 | Build the list 3.79 (72.32% of List ) | Other 1.45 (27.68% of List ) | List time 5.24 ( 5.21% of Nonbo) | Short_ene time 36.43 (90.07% of Direc) | Other 4.01 ( 9.93% of Direc) | Direct Ewald time 40.44 (42.41% of Ewald) | Adjust Ewald time 0.34 ( 0.36% of Ewald) | Fill Bspline coeffs 1.99 ( 6.26% of Recip) | Fill charge grid 1.13 ( 3.57% of Recip) | Scalar sum 0.99 ( 3.12% of Recip) | Grad sum 1.81 ( 5.69% of Recip) | FFT communication ti 5.41 (21.66% of FFT t) | Other 19.56 (78.34% of FFT t) | FFT time 24.96 (78.54% of Recip) | Other 0.90 ( 2.82% of Recip) | Recip Ewald time 31.78 (33.33% of Ewald) | Force Adjust 18.27 (19.16% of Ewald) | Virial junk 4.12 ( 4.32% of Ewald) | Start sycnronization 0.38 ( 0.39% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 95.35 (94.79% of Nonbo) | Nonbond force 100.59 (92.54% of Force) | Bond/Angle/Dihedral 0.53 ( 0.49% of Force) | FRC Collect time 6.02 ( 5.54% of Force) | Other 1.55 ( 1.43% of Force) | Force time 108.70 (92.25% of Runmd) | Shake time 0.41 ( 0.35% of Runmd) | Verlet update time 2.13 ( 1.81% of Runmd) | CRD distribute time 6.57 ( 5.58% of Runmd) | Other 0.02 ( 0.02% of Runmd) | Runmd Time 117.83 (98.04% of Total) | Other 2.35 ( 1.96% of Total) | Total time 120.18 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 5 | Build the list 3.75 (73.15% of List ) | Other 1.37 (26.85% of List ) | List time 5.12 ( 5.13% of Nonbo) | Short_ene time 35.88 (90.06% of Direc) | Other 3.96 ( 9.94% of Direc) | Direct Ewald time 39.85 (42.06% of Ewald) | Adjust Ewald time 0.33 ( 0.35% of Ewald) | Fill Bspline coeffs 1.97 ( 6.17% of Recip) | Fill charge grid 0.95 ( 2.98% of Recip) | Scalar sum 0.97 ( 3.05% of Recip) | Grad sum 1.71 ( 5.37% of Recip) | FFT communication ti 6.05 (23.82% of FFT t) | Other 19.34 (76.18% of FFT t) | FFT time 25.39 (79.67% of Recip) | Other 0.88 ( 2.75% of Recip) | Recip Ewald time 31.87 (33.64% of Ewald) | Force Adjust 19.01 (20.06% of Ewald) | Virial junk 3.29 ( 3.47% of Ewald) | Start sycnronization 0.37 ( 0.39% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 94.73 (94.87% of Nonbo) | Nonbond force 99.86 (91.86% of Force) | Bond/Angle/Dihedral 0.36 ( 0.33% of Force) | FRC Collect time 6.18 ( 5.69% of Force) | Other 2.30 ( 2.12% of Force) | Force time 108.71 (92.26% of Runmd) | Shake time 0.41 ( 0.35% of Runmd) | Verlet update time 2.14 ( 1.82% of Runmd) | CRD distribute time 6.55 ( 5.56% of Runmd) | Other 0.02 ( 0.02% of Runmd) | Runmd Time 117.83 (98.04% of Total) | Other 2.35 ( 1.96% of Total) | Total time 120.18 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 6 | Build the list 3.79 (72.44% of List ) | Other 1.44 (27.56% of List ) | List time 5.23 ( 5.25% of Nonbo) | Short_ene time 39.67 (90.81% of Direc) | Other 4.01 ( 9.19% of Direc) | Direct Ewald time 43.69 (46.28% of Ewald) | Adjust Ewald time 0.28 ( 0.30% of Ewald) | Fill Bspline coeffs 2.00 ( 6.31% of Recip) | Fill charge grid 0.99 ( 3.11% of Recip) | Scalar sum 1.00 ( 3.14% of Recip) | Grad sum 1.75 ( 5.53% of Recip) | FFT communication ti 5.78 (23.01% of FFT t) | Other 19.34 (76.99% of FFT t) | FFT time 25.12 (79.31% of Recip) | Other 0.82 ( 2.60% of Recip) | Recip Ewald time 31.67 (33.55% of Ewald) | Force Adjust 15.12 (16.02% of Ewald) | Virial junk 3.24 ( 3.43% of Ewald) | Start sycnronization 0.38 ( 0.40% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 94.40 (94.75% of Nonbo) | Nonbond force 99.63 (91.67% of Force) | Bond/Angle/Dihedral 0.36 ( 0.34% of Force) | FRC Collect time 6.20 ( 5.71% of Force) | Other 2.48 ( 2.29% of Force) | Force time 108.69 (92.24% of Runmd) | Shake time 0.41 ( 0.35% of Runmd) | Verlet update time 2.14 ( 1.81% of Runmd) | CRD distribute time 6.55 ( 5.55% of Runmd) | Other 0.06 ( 0.05% of Runmd) | Runmd Time 117.83 (98.04% of Total) | Other 2.35 ( 1.96% of Total) | Total time 120.18 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 7 | Build the list 3.75 (72.66% of List ) | Other 1.41 (27.34% of List ) | List time 5.16 ( 5.17% of Nonbo) | Short_ene time 36.34 (90.29% of Direc) | Other 3.91 ( 9.71% of Direc) | Direct Ewald time 40.25 (42.59% of Ewald) | Adjust Ewald time 0.23 ( 0.24% of Ewald) | Fill Bspline coeffs 1.94 ( 6.10% of Recip) | Fill charge grid 0.96 ( 3.01% of Recip) | Scalar sum 0.98 ( 3.07% of Recip) | Grad sum 1.73 ( 5.45% of Recip) | FFT communication ti 5.99 (23.67% of FFT t) | Other 19.32 (76.33% of FFT t) | FFT time 25.32 (79.68% of Recip) | Other 0.85 ( 2.68% of Recip) | Recip Ewald time 31.77 (33.62% of Ewald) | Force Adjust 18.56 (19.63% of Ewald) | Virial junk 3.31 ( 3.50% of Ewald) | Start sycnronization 0.38 ( 0.40% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 94.51 (94.82% of Nonbo) | Nonbond force 99.67 (91.71% of Force) | Bond/Angle/Dihedral 0.36 ( 0.33% of Force) | FRC Collect time 6.19 ( 5.69% of Force) | Other 2.46 ( 2.27% of Force) | Force time 108.68 (92.23% of Runmd) | Shake time 0.41 ( 0.34% of Runmd) | Verlet update time 2.15 ( 1.83% of Runmd) | CRD distribute time 6.54 ( 5.55% of Runmd) | Other 0.06 ( 0.05% of Runmd) | Runmd Time 117.83 (98.04% of Total) | Other 2.35 ( 1.96% of Total) | Total time 120.19 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 8 | Build the list 3.82 (73.75% of List ) | Other 1.36 (26.25% of List ) | List time 5.18 ( 5.20% of Nonbo) | Short_ene time 37.50 (90.25% of Direc) | Other 4.05 ( 9.75% of Direc) | Direct Ewald time 41.55 (43.98% of Ewald) | Adjust Ewald time 0.23 ( 0.25% of Ewald) | Fill Bspline coeffs 1.93 ( 6.07% of Recip) | Fill charge grid 0.97 ( 3.05% of Recip) | Scalar sum 1.01 ( 3.18% of Recip) | Grad sum 1.77 ( 5.57% of Recip) | FFT communication ti 5.76 (22.84% of FFT t) | Other 19.46 (77.16% of FFT t) | FFT time 25.23 (79.25% of Recip) | Other 0.91 ( 2.87% of Recip) | Recip Ewald time 31.83 (33.69% of Ewald) | Force Adjust 17.43 (18.45% of Ewald) | Virial junk 3.02 ( 3.20% of Ewald) | Start sycnronization 0.38 ( 0.41% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 94.46 (94.78% of Nonbo) | Other 0.02 ( 0.02% of Nonbo) | Nonbond force 99.67 (91.34% of Force) | Bond/Angle/Dihedral 0.37 ( 0.34% of Force) | FRC Collect time 6.61 ( 6.06% of Force) | Other 2.47 ( 2.26% of Force) | Force time 109.12 (92.61% of Runmd) | Shake time 0.45 ( 0.38% of Runmd) | Verlet update time 1.69 ( 1.43% of Runmd) | CRD distribute time 6.56 ( 5.56% of Runmd) | Other 0.02 ( 0.02% of Runmd) | Runmd Time 117.83 (98.04% of Total) | Other 2.35 ( 1.96% of Total) | Total time 120.18 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 9 | Build the list 3.75 (73.27% of List ) | Other 1.37 (26.73% of List ) | List time 5.12 ( 5.13% of Nonbo) | Short_ene time 35.97 (90.21% of Direc) | Other 3.90 ( 9.79% of Direc) | Direct Ewald time 39.88 (42.15% of Ewald) | Adjust Ewald time 0.23 ( 0.24% of Ewald) | Fill Bspline coeffs 1.84 ( 5.76% of Recip) | Fill charge grid 0.97 ( 3.04% of Recip) | Scalar sum 1.00 ( 3.12% of Recip) | Grad sum 1.73 ( 5.43% of Recip) | FFT communication ti 6.01 (23.55% of FFT t) | Other 19.51 (76.45% of FFT t) | FFT time 25.52 (79.96% of Recip) | Other 0.86 ( 2.69% of Recip) | Recip Ewald time 31.91 (33.73% of Ewald) | Force Adjust 18.95 (20.03% of Ewald) | Virial junk 3.27 ( 3.45% of Ewald) | Start sycnronization 0.36 ( 0.38% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 94.61 (94.87% of Nonbo) | Nonbond force 99.73 (91.36% of Force) | Bond/Angle/Dihedral 0.36 ( 0.33% of Force) | FRC Collect time 6.59 ( 6.04% of Force) | Other 2.48 ( 2.27% of Force) | Force time 109.16 (92.64% of Runmd) | Shake time 0.40 ( 0.34% of Runmd) | Verlet update time 1.75 ( 1.48% of Runmd) | CRD distribute time 6.50 ( 5.52% of Runmd) | Other 0.02 ( 0.02% of Runmd) | Runmd Time 117.83 (98.04% of Total) | Other 2.35 ( 1.96% of Total) | Total time 120.18 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 10 | Build the list 3.81 (73.47% of List ) | Other 1.37 (26.53% of List ) | List time 5.18 ( 5.20% of Nonbo) | Short_ene time 36.58 (90.07% of Direc) | Other 4.03 ( 9.93% of Direc) | Direct Ewald time 40.61 (42.96% of Ewald) | Adjust Ewald time 0.23 ( 0.24% of Ewald) | Fill Bspline coeffs 1.86 ( 5.84% of Recip) | Fill charge grid 0.96 ( 3.02% of Recip) | Scalar sum 0.98 ( 3.08% of Recip) | Grad sum 1.76 ( 5.54% of Recip) | FFT communication ti 5.64 (22.17% of FFT t) | Other 19.78 (77.83% of FFT t) | FFT time 25.42 (79.86% of Recip) | Other 0.85 ( 2.67% of Recip) | Recip Ewald time 31.83 (33.67% of Ewald) | Force Adjust 18.20 (19.25% of Ewald) | Virial junk 3.28 ( 3.47% of Ewald) | Start sycnronization 0.37 ( 0.39% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 94.54 (94.80% of Nonbo) | Nonbond force 99.73 (91.34% of Force) | Bond/Angle/Dihedral 0.37 ( 0.34% of Force) | FRC Collect time 6.62 ( 6.06% of Force) | Other 2.47 ( 2.27% of Force) | Force time 109.19 (92.66% of Runmd) | Shake time 0.41 ( 0.35% of Runmd) | Verlet update time 1.72 ( 1.46% of Runmd) | CRD distribute time 6.49 ( 5.51% of Runmd) | Other 0.02 ( 0.02% of Runmd) | Runmd Time 117.84 (98.05% of Total) | Other 2.35 ( 1.95% of Total) | Total time 120.18 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 11 | Build the list 3.76 (72.39% of List ) | Other 1.43 (27.61% of List ) | List time 5.19 ( 5.21% of Nonbo) | Short_ene time 38.10 (90.32% of Direc) | Other 4.08 ( 9.68% of Direc) | Direct Ewald time 42.19 (44.69% of Ewald) | Adjust Ewald time 0.24 ( 0.25% of Ewald) | Fill Bspline coeffs 1.87 ( 5.93% of Recip) | Fill charge grid 0.97 ( 3.08% of Recip) | Scalar sum 1.19 ( 3.78% of Recip) | Grad sum 1.70 ( 5.40% of Recip) | FFT communication ti 6.07 (24.23% of FFT t) | Other 18.99 (75.77% of FFT t) | FFT time 25.06 (79.57% of Recip) | Other 0.71 ( 2.24% of Recip) | Recip Ewald time 31.50 (33.37% of Ewald) | Force Adjust 16.62 (17.61% of Ewald) | Virial junk 3.45 ( 3.66% of Ewald) | Start sycnronization 0.38 ( 0.40% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 94.40 (94.78% of Nonbo) | Nonbond force 99.59 (91.44% of Force) | Bond/Angle/Dihedral 0.39 ( 0.35% of Force) | FRC Collect time 6.61 ( 6.07% of Force) | Other 2.32 ( 2.13% of Force) | Force time 108.91 (92.43% of Runmd) | Shake time 0.42 ( 0.36% of Runmd) | Verlet update time 1.71 ( 1.45% of Runmd) | CRD distribute time 6.77 ( 5.75% of Runmd) | Other 0.02 ( 0.02% of Runmd) | Runmd Time 117.83 (98.05% of Total) | Other 2.35 ( 1.95% of Total) | Total time 120.18 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 12 | Build the list 3.90 (75.08% of List ) | Other 1.29 (24.92% of List ) | List time 5.19 ( 5.21% of Nonbo) | Short_ene time 35.80 (90.19% of Direc) | Other 3.89 ( 9.81% of Direc) | Direct Ewald time 39.69 (42.03% of Ewald) | Adjust Ewald time 0.23 ( 0.24% of Ewald) | Fill Bspline coeffs 1.83 ( 5.76% of Recip) | Fill charge grid 0.95 ( 2.99% of Recip) | Scalar sum 0.98 ( 3.06% of Recip) | Grad sum 1.72 ( 5.42% of Recip) | FFT communication ti 5.91 (23.15% of FFT t) | Other 19.61 (76.85% of FFT t) | FFT time 25.52 (80.17% of Recip) | Other 0.83 ( 2.60% of Recip) | Recip Ewald time 31.83 (33.70% of Ewald) | Force Adjust 19.04 (20.16% of Ewald) | Virial junk 3.26 ( 3.46% of Ewald) | Start sycnronization 0.37 ( 0.39% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 94.45 (94.79% of Nonbo) | Nonbond force 99.64 (91.39% of Force) | Bond/Angle/Dihedral 0.36 ( 0.33% of Force) | FRC Collect time 6.54 ( 6.00% of Force) | Other 2.48 ( 2.27% of Force) | Force time 109.03 (92.53% of Runmd) | Shake time 0.40 ( 0.34% of Runmd) | Verlet update time 1.81 ( 1.53% of Runmd) | CRD distribute time 6.58 ( 5.58% of Runmd) | Other 0.02 ( 0.02% of Runmd) | Runmd Time 117.83 (98.04% of Total) | Other 2.35 ( 1.96% of Total) | Total time 120.18 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 13 | Build the list 3.85 (74.51% of List ) | Other 1.32 (25.49% of List ) | List time 5.17 ( 5.18% of Nonbo) | Short_ene time 38.09 (90.35% of Direc) | Other 4.07 ( 9.65% of Direc) | Direct Ewald time 42.16 (44.55% of Ewald) | Adjust Ewald time 0.23 ( 0.25% of Ewald) | Fill Bspline coeffs 1.84 ( 5.81% of Recip) | Fill charge grid 1.02 ( 3.22% of Recip) | Scalar sum 1.00 ( 3.14% of Recip) | Grad sum 1.77 ( 5.58% of Recip) | FFT communication ti 6.01 (23.60% of FFT t) | Other 19.47 (76.40% of FFT t) | FFT time 25.49 (80.28% of Recip) | Other 0.63 ( 1.97% of Recip) | Recip Ewald time 31.75 (33.55% of Ewald) | Force Adjust 16.88 (17.84% of Ewald) | Virial junk 3.20 ( 3.38% of Ewald) | Start sycnronization 0.40 ( 0.42% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 94.64 (94.81% of Nonbo) | Nonbond force 99.81 (91.55% of Force) | Bond/Angle/Dihedral 0.45 ( 0.42% of Force) | FRC Collect time 6.53 ( 5.99% of Force) | Other 2.23 ( 2.05% of Force) | Force time 109.03 (92.53% of Runmd) | Shake time 0.44 ( 0.37% of Runmd) | Verlet update time 1.78 ( 1.51% of Runmd) | CRD distribute time 6.57 ( 5.57% of Runmd) | Other 0.02 ( 0.02% of Runmd) | Runmd Time 117.83 (98.04% of Total) | Other 2.35 ( 1.96% of Total) | Total time 120.19 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 14 | Build the list 3.80 (74.75% of List ) | Other 1.28 (25.25% of List ) | List time 5.08 ( 5.10% of Nonbo) | Short_ene time 36.00 (90.34% of Direc) | Other 3.85 ( 9.66% of Direc) | Direct Ewald time 39.85 (42.18% of Ewald) | Adjust Ewald time 0.23 ( 0.24% of Ewald) | Fill Bspline coeffs 1.78 ( 5.61% of Recip) | Fill charge grid 0.96 ( 3.03% of Recip) | Scalar sum 0.90 ( 2.83% of Recip) | Grad sum 1.63 ( 5.15% of Recip) | FFT communication ti 5.90 (22.99% of FFT t) | Other 19.78 (77.01% of FFT t) | FFT time 25.68 (80.84% of Recip) | Other 0.81 ( 2.54% of Recip) | Recip Ewald time 31.77 (33.62% of Ewald) | Force Adjust 18.94 (20.04% of Ewald) | Virial junk 3.31 ( 3.50% of Ewald) | Start sycnronization 0.37 ( 0.40% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 94.49 (94.89% of Nonbo) | Nonbond force 99.57 (91.53% of Force) | Bond/Angle/Dihedral 0.38 ( 0.35% of Force) | FRC Collect time 6.37 ( 5.86% of Force) | Other 2.46 ( 2.26% of Force) | Force time 108.79 (92.32% of Runmd) | Shake time 0.40 ( 0.34% of Runmd) | Verlet update time 1.98 ( 1.68% of Runmd) | CRD distribute time 6.53 ( 5.54% of Runmd) | Other 0.14 ( 0.12% of Runmd) | Runmd Time 117.83 (98.04% of Total) | Other 2.35 ( 1.96% of Total) | Total time 120.18 (100.0% of ALL ) |>>>>>>>>PROFILE of TIMES for process 15 | Build the list 3.76 (73.70% of List ) | Other 1.34 (26.30% of List ) | List time 5.11 ( 5.13% of Nonbo) | Short_ene time 37.25 (90.42% of Direc) | Other 3.95 ( 9.58% of Direc) | Direct Ewald time 41.20 (43.61% of Ewald) | Adjust Ewald time 0.23 ( 0.25% of Ewald) | Fill Bspline coeffs 1.83 ( 5.79% of Recip) | Fill charge grid 0.98 ( 3.10% of Recip) | Scalar sum 0.91 ( 2.88% of Recip) | Grad sum 1.76 ( 5.54% of Recip) | FFT communication ti 6.15 (24.04% of FFT t) | Other 19.43 (75.96% of FFT t) | FFT time 25.58 (80.66% of Recip) | Other 0.65 ( 2.04% of Recip) | Recip Ewald time 31.72 (33.58% of Ewald) | Force Adjust 17.60 (18.63% of Ewald) | Virial junk 3.32 ( 3.51% of Ewald) | Start sycnronization 0.38 ( 0.40% of Ewald) | Other 0.02 ( 0.02% of Ewald) | Ewald time 94.47 (94.87% of Nonbo) | Nonbond force 99.58 (91.57% of Force) | Bond/Angle/Dihedral 0.44 ( 0.40% of Force) | FRC Collect time 6.37 ( 5.86% of Force) | Other 2.36 ( 2.17% of Force) | Force time 108.75 (92.29% of Runmd) | Shake time 0.41 ( 0.34% of Runmd) | Verlet update time 1.98 ( 1.68% of Runmd) | CRD distribute time 6.56 ( 5.57% of Runmd) | Other 0.14 ( 0.12% of Runmd) | Runmd Time 117.83 (98.04% of Total) | Other 2.35 ( 1.96% of Total) | Total time 120.19 (100.0% of ALL ) |>>>>>>>>Statistics of TIMES>>>>>>>>> |>>>>>>>>Printed as average time (min,max,sd) >>>>>>>>> | Read coords time 0.01 ( 0.00 0.11 0.03) | Build the list 3.82 ( 3.75 4.06 0.08) | Other 1.33 ( 1.11 1.45 0.09) | List time 5.15 ( 4.95 5.24 0.07) | Short_ene time 37.17 ( 35.80 39.67 1.14) | Other 3.96 ( 3.84 4.08 0.08) | Direct Ewald time 41.13 ( 39.69 43.69 1.18) | Adjust Ewald time 0.28 ( 0.23 0.39 0.06) | Fill Bspline coeffs 1.96 ( 1.78 2.44 0.16) | Fill charge grid 0.98 ( 0.95 1.13 0.04) | Scalar sum 1.00 ( 0.90 1.19 0.07) | Grad sum 1.74 ( 1.63 1.81 0.04) | FFT communication ti 5.85 ( 5.41 6.15 0.20) | Other 18.64 ( 6.22 19.78 3.21) | FFT time 24.49 ( 11.89 25.68 3.26) | Other 0.79 ( 0.60 0.91 0.10) | Recip Ewald time 30.97 ( 18.57 31.95 3.20) | Force Adjust 17.65 ( 15.12 19.04 1.18) | Virial junk 3.35 ( 3.02 4.12 0.25) | Start sycnronization 0.37 ( 0.36 0.40 0.01) | Other 0.02 ( 0.02 0.02 0.00) | Ewald time 93.78 ( 81.18 95.35 3.26) | Other 0.01 ( 0.00 0.02 0.00) | Nonbond force 98.93 ( 86.36 100.59 3.26) | Bond/Angle/Dihedral 0.39 ( 0.36 0.53 0.05) | FRC Collect time 6.37 ( 6.02 6.62 0.19) | Other 2.34 ( 1.55 2.48 0.24) | Force time 108.03 ( 95.44 109.19 3.25) | Shake time 0.44 ( 0.40 0.73 0.08) | Verlet update time 2.78 ( 1.69 15.60 3.32) | CRD distribute time 6.56 ( 6.49 6.77 0.07) | Other 0.04 ( 0.01 0.14 0.04) | Runmd Time 117.85 ( 117.83 118.13 0.07) | Other 2.34 ( 2.23 2.35 0.03) | Total time 120.20 ( 120.18 120.47 0.07)