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From: cailliez <Fabien.Cailliez.ibpc.fr>

Date: Fri, 09 Jul 2004 11:50:25 +0200

Dear all,

I have questions about execution times that are printed at the end of

the mdout file.

I am running MD on a protein with AMBER7 on 16 processors SGI Origin 3800.

I had a problem with a trajectory file that was corrupted during one of

my run, in spite

of the fact that the job finished apparently normally. So I ran the same

job once again

on the same machines.

The results I obtained were totally similar : the restrt and mdene files

are totally identical.

For mdtrj, only a small part in the middle was different (I suppose my

problem of corrupted

file was a problem of writing because of som computer problems) and the

only differences in

the mdout files concern the timing.

There is a great difference in the time of calculation needed (35000 s

for one and 41000s for the

second), despite this is the same calculation (the identical results

show it has been the same).

Is it normal ?

And what is even stranger for me is that some times do not appear in

both reports : there are

one time Other after RunMDTime (left column) and one time Other after

FRC Collect Time (right

column).

Her is the sdiff report of the two mdout files :

|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> |>>>>>>>>PROFILE of Average TIMES>>>>>>>>>

| Check list validity 1581.11 (25.14% of L | | Check list validity 2237.69 (29.29% of L

| reorder water 1499.74 (23.85% of L | | reorder water 2094.80 (27.42% of L

| Map frac coords 106.59 ( 1.69% of L | | Map frac coords 174.62 ( 2.29% of L

| Grid unit cell 33.64 ( 0.53% of L | | Grid unit cell 38.75 ( 0.51% of L

| Grid image cell 16.24 ( 0.26% of L | | Grid image cell 23.73 ( 0.31% of L

| Build the list 3051.18 (48.52% of L | | Build the list 3069.43 (40.18% of L

| List time 6288.63 (23.91% of Nonb | | List time 7639.19 (25.67% of Nonb

| Direct Ewald time 10659.67 (53.26% of E | | Direct Ewald time 11480.51 (51.90% of E

| Adjust Ewald time 110.61 ( 0.55% of E | | Adjust Ewald time 123.95 ( 0.56% of E

| Finish NB virial 726.75 ( 3.63% of E | | Finish NB virial 1218.90 ( 5.51% of E

| Fill Bspline coeffs 793.03 (11.29% o | | Fill Bspline coeffs 1235.30 (15.86% o

| Fill charge grid 1015.93 (14.47% o | | Fill charge grid 1087.23 (13.96% o

| Scalar sum 948.71 (13.51% o | | Scalar sum 948.92 (12.18% o

| Grad sum 1393.40 (19.84% o | | Grad sum 1414.55 (18.16% o

| FFT communication ti 1105.21 (39.90 | | FFT communication ti 1447.38 (47.97

| Other 1665.03 (60.10 | | Other 1570.06 (52.03

| FFT time 2770.24 (39.45% o | | FFT time 3017.44 (38.73% o

| Other 100.83 ( 1.44% o | | Other 87.22 ( 1.12% o

| Recip Ewald time 7022.15 (35.08% of E | | Recip Ewald time 7790.65 (35.22% of E

| Ewald MPI wait 200.97 ( 1.00% of E | | Ewald MPI wait 165.46 ( 0.75% of E

| Other 1294.31 ( 6.47% of E | | Other 1338.69 ( 6.05% of E

| Ewald time 20015.20 (76.09% of Nonb | | Ewald time 22118.94 (74.33% of Nonb

| Nonbond force 26303.83 (91.43% of Force) | | Nonbond force 29758.13 (91.93% of Force)

| Bond energy 4.42 ( 0.02% of Force) | | Bond energy 5.52 ( 0.02% of Force)

| Angle energy 16.93 ( 0.06% of Force) | | Angle energy 17.57 ( 0.05% of Force)

| Dihedral energy 55.16 ( 0.19% of Force) | | Dihedral energy 59.42 ( 0.18% of Force)

| FRC Collect time 2389.98 ( 8.31% of Force) | | FRC Collect time 2502.32 ( 7.73% of Force)

| Force time 28770.51 (80.04% of Runmd) | | Other 27.23 ( 0.08% of Force)

| Shake time 246.06 ( 0.68% of Runmd) | | Force time 32370.39 (77.87% of Runmd)

| Verlet update time 871.95 ( 2.43% of Runmd) | | Shake time 288.91 ( 0.70% of Runmd)

| Ekcmr time 1671.96 ( 4.65% of Runmd) | | Verlet update time 1181.29 ( 2.84% of Runmd)

| CRD distribute time 4042.44 (11.25% of Runmd) | | Ekcmr time 1830.59 ( 4.40% of Runmd)

| Other 341.53 ( 0.95% of Runmd) | | CRD distribute time 5831.61 (14.03% of Runmd)

| Runmd Time 35944.45 (100.0% of Total) | | Other 64.47 ( 0.16% of Runmd)

| Other 2.23 ( 0.01% of Total) | | Runmd Time 41567.25 (100.0% of Total)

| Total time 35946.74 (100.0% of ALL ) | | Total time 41407.32 (100.0% of ALL )

| Highest rstack allocated: 1104324 | Highest rstack allocated: 1104324

| Highest istack allocated: 3197790 | Highest istack allocated: 3197790

| Setup wallclock 7 seconds | Setup wallclock 7 seconds

| Nonsetup wallclock 35942 seconds | | Nonsetup wallclock 41402 seconds

Thanks in advance for all the answers,

Fabien

__________________________________________________________________

Fabien Cailliez Tel : 01 58 41 51 63

Laboratoire de Biochimie Théorique e-mail : cailliez.ibpc.fr

IBPC 13, rue Pierre et Marie Curie

75005 Paris

__________________________________________________________________

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The AMBER Mail Reflector

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Received on Fri Jul 09 2004 - 11:53:00 PDT

Date: Fri, 09 Jul 2004 11:50:25 +0200

Dear all,

I have questions about execution times that are printed at the end of

the mdout file.

I am running MD on a protein with AMBER7 on 16 processors SGI Origin 3800.

I had a problem with a trajectory file that was corrupted during one of

my run, in spite

of the fact that the job finished apparently normally. So I ran the same

job once again

on the same machines.

The results I obtained were totally similar : the restrt and mdene files

are totally identical.

For mdtrj, only a small part in the middle was different (I suppose my

problem of corrupted

file was a problem of writing because of som computer problems) and the

only differences in

the mdout files concern the timing.

There is a great difference in the time of calculation needed (35000 s

for one and 41000s for the

second), despite this is the same calculation (the identical results

show it has been the same).

Is it normal ?

And what is even stranger for me is that some times do not appear in

both reports : there are

one time Other after RunMDTime (left column) and one time Other after

FRC Collect Time (right

column).

Her is the sdiff report of the two mdout files :

|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> |>>>>>>>>PROFILE of Average TIMES>>>>>>>>>

| Check list validity 1581.11 (25.14% of L | | Check list validity 2237.69 (29.29% of L

| reorder water 1499.74 (23.85% of L | | reorder water 2094.80 (27.42% of L

| Map frac coords 106.59 ( 1.69% of L | | Map frac coords 174.62 ( 2.29% of L

| Grid unit cell 33.64 ( 0.53% of L | | Grid unit cell 38.75 ( 0.51% of L

| Grid image cell 16.24 ( 0.26% of L | | Grid image cell 23.73 ( 0.31% of L

| Build the list 3051.18 (48.52% of L | | Build the list 3069.43 (40.18% of L

| List time 6288.63 (23.91% of Nonb | | List time 7639.19 (25.67% of Nonb

| Direct Ewald time 10659.67 (53.26% of E | | Direct Ewald time 11480.51 (51.90% of E

| Adjust Ewald time 110.61 ( 0.55% of E | | Adjust Ewald time 123.95 ( 0.56% of E

| Finish NB virial 726.75 ( 3.63% of E | | Finish NB virial 1218.90 ( 5.51% of E

| Fill Bspline coeffs 793.03 (11.29% o | | Fill Bspline coeffs 1235.30 (15.86% o

| Fill charge grid 1015.93 (14.47% o | | Fill charge grid 1087.23 (13.96% o

| Scalar sum 948.71 (13.51% o | | Scalar sum 948.92 (12.18% o

| Grad sum 1393.40 (19.84% o | | Grad sum 1414.55 (18.16% o

| FFT communication ti 1105.21 (39.90 | | FFT communication ti 1447.38 (47.97

| Other 1665.03 (60.10 | | Other 1570.06 (52.03

| FFT time 2770.24 (39.45% o | | FFT time 3017.44 (38.73% o

| Other 100.83 ( 1.44% o | | Other 87.22 ( 1.12% o

| Recip Ewald time 7022.15 (35.08% of E | | Recip Ewald time 7790.65 (35.22% of E

| Ewald MPI wait 200.97 ( 1.00% of E | | Ewald MPI wait 165.46 ( 0.75% of E

| Other 1294.31 ( 6.47% of E | | Other 1338.69 ( 6.05% of E

| Ewald time 20015.20 (76.09% of Nonb | | Ewald time 22118.94 (74.33% of Nonb

| Nonbond force 26303.83 (91.43% of Force) | | Nonbond force 29758.13 (91.93% of Force)

| Bond energy 4.42 ( 0.02% of Force) | | Bond energy 5.52 ( 0.02% of Force)

| Angle energy 16.93 ( 0.06% of Force) | | Angle energy 17.57 ( 0.05% of Force)

| Dihedral energy 55.16 ( 0.19% of Force) | | Dihedral energy 59.42 ( 0.18% of Force)

| FRC Collect time 2389.98 ( 8.31% of Force) | | FRC Collect time 2502.32 ( 7.73% of Force)

| Force time 28770.51 (80.04% of Runmd) | | Other 27.23 ( 0.08% of Force)

| Shake time 246.06 ( 0.68% of Runmd) | | Force time 32370.39 (77.87% of Runmd)

| Verlet update time 871.95 ( 2.43% of Runmd) | | Shake time 288.91 ( 0.70% of Runmd)

| Ekcmr time 1671.96 ( 4.65% of Runmd) | | Verlet update time 1181.29 ( 2.84% of Runmd)

| CRD distribute time 4042.44 (11.25% of Runmd) | | Ekcmr time 1830.59 ( 4.40% of Runmd)

| Other 341.53 ( 0.95% of Runmd) | | CRD distribute time 5831.61 (14.03% of Runmd)

| Runmd Time 35944.45 (100.0% of Total) | | Other 64.47 ( 0.16% of Runmd)

| Other 2.23 ( 0.01% of Total) | | Runmd Time 41567.25 (100.0% of Total)

| Total time 35946.74 (100.0% of ALL ) | | Total time 41407.32 (100.0% of ALL )

| Highest rstack allocated: 1104324 | Highest rstack allocated: 1104324

| Highest istack allocated: 3197790 | Highest istack allocated: 3197790

| Setup wallclock 7 seconds | Setup wallclock 7 seconds

| Nonsetup wallclock 35942 seconds | | Nonsetup wallclock 41402 seconds

Thanks in advance for all the answers,

Fabien

__________________________________________________________________

Fabien Cailliez Tel : 01 58 41 51 63

Laboratoire de Biochimie Théorique e-mail : cailliez.ibpc.fr

IBPC 13, rue Pierre et Marie Curie

75005 Paris

__________________________________________________________________

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Fri Jul 09 2004 - 11:53:00 PDT

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