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)