# AMBER Archive (2004)Subject: RE: AMBER: question about parallel simulation

From: qlu_at_notes.cc.sunysb.edu
Date: Thu Dec 02 2004 - 14:30:28 CST

Hi Ross and other Amber users,

After the change of all bc_*** parameters. The code works fine for 2 nodes.
But the time scale between
2 and 4 nodes are almost the same. The list of the time difference bellow
shows that the problem is in
the force adjustment calculation. Is there a way to overcome this problem?

For 4 nodes

| Build the list 0.02 ( 2.09% of List )
| Other 1.00 (97.91% of List )
| List time 1.02 ( 0.41% of Nonbo)
| Short_ene time 99.91 (95.31% of Direc)
| Other 4.92 ( 4.69% of Direc)
| Direct Ewald time 104.83 (42.80% of Ewald)
| Force Adjust 113.30 (46.25% of Ewald)
| Virial junk 22.12 ( 9.03% of Ewald)
| Start sycnronization 1.52 ( 0.62% of Ewald)
| Other 3.18 ( 1.30% of Ewald)
| Ewald time 244.96 (99.01% of Nonbo)
| Other 1.42 ( 0.58% of Nonbo)
| Nonbond force 247.40 (74.52% of Force)
| Bond/Angle/Dihedral 25.82 ( 7.78% of Force)
| FRC Collect time 49.11 (14.79% of Force)
| Other 9.66 ( 2.91% of Force)
| Force time 331.99 (84.39% of Runmd)
| Verlet update time 24.57 ( 6.25% of Runmd)
| CRD distribute time 32.69 ( 8.31% of Runmd)
| Other 4.14 ( 1.05% of Runmd)
| Runmd Time 393.39 (100.0% of Total)
| Other 0.09 ( 0.02% of Total)
| Total time 393.48 (100.0% of ALL )

For 2 nodes

| Build the list 0.02 ( 2.15% of List )
| Other 1.07 (97.85% of List )
| List time 1.09 ( 0.43% of Nonbo)
| Short_ene time 198.41 (98.22% of Direc)
| Other 3.60 ( 1.78% of Direc)
| Direct Ewald time 202.00 (79.84% of Ewald)
| Force Adjust 36.96 (14.61% of Ewald)
| Virial junk 8.76 ( 3.46% of Ewald)
| Start sycnronization 1.50 ( 0.59% of Ewald)
| Other 3.80 ( 1.50% of Ewald)
| Ewald time 253.03 (98.93% of Nonbo)
| Other 1.65 ( 0.64% of Nonbo)
| Nonbond force 255.77 (79.07% of Force)
| Bond/Angle/Dihedral 47.91 (14.81% of Force)
| FRC Collect time 13.89 ( 4.30% of Force)
| Other 5.91 ( 1.83% of Force)
| Force time 323.49 (92.61% of Runmd)
| Verlet update time 12.60 ( 3.61% of Runmd)
| CRD distribute time 8.64 ( 2.47% of Runmd)
| Other 4.57 ( 1.31% of Runmd)
| Runmd Time 349.29 (100.0% of Total)
| Other 0.04 ( 0.01% of Total)
| Total time 349.34 (100.0% of ALL )

Best regards
Qiang

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