difference of job size

Clicked A Few Times

3:49:33 PM PDT - Fri, Oct 5th 2012
I have a question about the ccsd(t) job size. Right now, I am running a couple of CCSD(T) single point jobs. I have 3 jobs dealing with reactant, transition state and product. Simply those jobs have the same number of basis function, the same number of valence electrons, etc. I ran them with the same memory and the same number of nodes. however, the transition state may takes more than 2 times of wall time of that for the reactant and production. So why is there so much difference? What kind of factors contribute the job size? thanks a lot.

Forum Vet

3:50:50 PM PDT - Sat, Oct 6th 2012
Symmetry?
Does the transition state have the same symmetry as reactant and product? Cheers, Edo

Clicked A Few Times

8:59:31 AM PDT - Sun, Oct 7th 2012
yes, all of them have no symmetry. thanks

Forum Vet

9:07:47 AM PDT - Mon, Oct 8th 2012
Could you please post the output files or point to a website where they can accessed?

Clicked A Few Times

9:09:06 AM PDT - Tue, Oct 9th 2012

i post part of the outputs.

For the section of CCSD calculation, you can find the the difference of wall time for every iteration step.

For the triple calculation, I didn't see this much difference.

OUTPUT

For the reactant,

echo
start mo3o9.2pro.ccsdt.ad
permanent_dir /home/fang824/nwchem/1.prop.h2o
memory stack 1400 mb heap 200 mb global 5400 mb noverify
title "MO3O9.2pro CCSD(T)/aug-cc-pVDZ(-PP)//B3LYP/cc-pVDZ(-PP)"
charge 0

geometry

 MO     2.163481   -1.321205    0.334882

 MO    -1.102730   -2.258343   -0.139422

 MO    -0.292140    1.323388   -0.572350

 O      3.472707   -1.677453   -0.683835

 O      2.728020   -1.238043    1.935972

 O      0.749393   -2.584140    0.152893

 O      1.332473    0.273595   -0.143310

 O     -2.007443   -2.488804    1.280996

 O     -1.748919   -3.247449   -1.356718

 O     -0.280275    1.691732   -2.209625

 O     -1.119230   -0.463664   -0.635814

 O      0.633358    2.720026    0.207354

 C      1.653156    3.037099    1.154063

 H      1.153810    3.315688    2.093912

 H      2.235702    2.118073    1.326450

 C      2.534110    4.169604    0.639753

 H      1.907821    5.059077    0.478234

 H      3.233552    4.417888    1.453192

 C     -4.115431    2.013290    1.141856

 C     -3.315633    1.561999   -0.073171

 H     -3.976016    3.095051    1.278252

 H     -3.709713    1.517467    2.035048

 H     -3.386872    0.472845   -0.214283

 H     -3.665567    2.056249   -0.992375

 O     -1.931484    1.888193    0.093698

 C      3.305849    3.818373   -0.634689

 H      3.958074    2.947571   -0.477073

 H      2.622697    3.585765   -1.461947

 H      3.938211    4.658854   -0.948470

 C     -5.604263    1.685438    0.985322

 H     -5.766808    0.604070    0.872120

 H     -6.166451    2.016768    1.867856

 H     -6.035681    2.186561    0.106752

end

basis spherical
H library aug-cc-pVDZ

C library aug-cc-pVDZ

O library aug-cc-pVDZ

Mo library aug-cc-pVDZ-PP

end

ecp

ECP28MDF

Mo nelec 28
Mo S
2 10.097000 180.076853
2 4.375670 24.715920
Mo P
2 9.126564 41.227678
2 8.863223 82.452670
2 4.044948 6.345092
2 3.866657 12.458423
Mo D
2 7.535754 19.308744
2 7.278976 28.977674
2 2.763205 3.189516
2 2.772085 4.700169
Mo F
2 6.306633 -7.178888
2 6.356448 -9.745978
end

scf

  vectors output mo3o9.2pro.ccsdt.ad.movecs

vectors input project avdz mo3o9.2pro.ccsdt.ad.movecs output mo3o9.2pro.ccsdt.ad.movecs

  rhf

  singlet

  maxiter 100

thresh 1.0e-10
tol2e 1.0e-10

end

task scf

ccsd

  maxiter 60

  thresh 1e-6

  freeze 28

end
task ccsd(t)

.........

  ***** ccsd parameters *****

  iprt   =     0

  convi  = 0.100E-05

  maxit  =    60

  mxvec  =     5

memory                209250301

 IO offset     20.00000000000000

 IO error message >End of File

 file_read_ga: failing writing to 

/home/fang824/nwchem/1.prop.h2o/mo3o9.2pro.ccsdt.ad.t2

 Failed reading restart vector from

/home/fang824/nwchem/1.prop.h2o/mo3o9.2pro.ccsdt.ad.t2

 Using MP2 initial guess vector

iter     correlation     delta       rms       T2     Non-T2      Main

            energy      energy      error      ampl     ampl      Block

                                               time     time      time

  1     -3.3998305435 -3.400D+00  1.540D+00  1400.63     0.15  1215.18

  2     -3.8550746548 -4.552D-01  2.149D+00  1446.46     0.20  1259.83

  3     -3.6867553272  1.683D-01  2.060D-01  1442.33     0.25  1257.16

  4     -3.6945072521 -7.752D-03  4.042D-02  1762.81     0.30  1574.51

  5     -3.7125752865 -1.807D-02  1.243D-02  1517.22     0.35  1331.44

  6     -3.7164502994 -3.875D-03  1.829D-03  1509.63     0.35  1323.33

  7     -3.7154754886  9.748D-04  6.004D-03  1809.34     0.35  1620.66

  8     -3.7151492254  3.263D-04  4.905D-04  1505.20     0.34  1317.87

  9     -3.7154811674 -3.319D-04  6.775D-04  1462.38     0.35  1276.15

 10     -3.7150784690  4.027D-04  1.008D-03  1729.40     0.35  1541.65

 11     -3.7152067397 -1.283D-04  2.165D-04  1464.66     0.35  1279.04

 12     -3.7152051748  1.565D-06  1.251D-04  1461.88     0.35  1275.43

 13     -3.7151865414  1.863D-05  1.747D-04  1730.73     0.35  1543.63

 14     -3.7152004219 -1.388D-05  5.694D-05  1456.52     0.35  1270.34

 15     -3.7152089127 -8.491D-06  3.055D-05  1454.02     0.35  1266.94

 16     -3.7152051488  3.764D-06  1.480D-05  1677.36     0.35  1490.57

 17     -3.7152092010 -4.052D-06  4.501D-05  1470.24     0.35  1284.17

 18     -3.7152069978  2.203D-06  1.544D-05  1447.75     0.35  1262.78

 19     -3.7152062677  7.302D-07  3.562D-06  1614.81     0.35  1425.79

 20     -3.7152069258 -6.582D-07  1.330D-05  1445.85     0.35  1258.61

.......................................................

For the transition state molecule:

echo
start mo3o9.2pro.ts.ccsdt.ad.2
permanent_dir /home/fang824/nwchem/1.prop.h2o
memory stack 1400 mb heap 200 mb global 3000 mb noverify
title "MO3O9.2pro.ts CCSD(T)/aug-cc-pVDZ(-PP)//B3LYP/cc-pVDZ(-PP)"
charge 0

geometry

 MO     1.978340    1.578560   -0.079182

 MO     2.006568   -1.847359    0.089397

 MO    -1.326940   -0.181229   -0.138433

 O      2.526447    2.472055   -1.418029

 O      2.234156    2.495504    1.330666

 O      2.820049   -0.127368    0.031616

 O      0.189117    1.140510   -0.264255

 O      2.372519   -2.675427    1.529201

 O      2.480263   -2.813747   -1.226646

 O     -2.092067   -1.174109   -1.369206

 O      0.202987   -1.435031    0.005776

 O     -2.336515    1.367347   -0.363268

 C     -2.248261    2.771030   -0.570400

 H     -1.229865    3.006390   -0.912365

 H     -2.953431    3.018080   -1.378961

 C     -2.587942    3.539076    0.703619

 H     -3.590738    3.241633    1.042341

 H     -1.878823    3.245500    1.490835

 C     -3.658960   -2.856433   -0.075174

 C     -3.293740   -2.535147    1.240871

 H     -2.889313   -2.085549   -0.709566

 H     -3.210577   -3.787327   -0.447003

 H     -3.947624   -1.949694    1.884689

 H     -2.460126   -3.034493    1.729723

 O     -2.074305   -0.794890    1.301143

 C     -2.529975    5.053777    0.480372

 H     -2.776686    5.590639    1.405498

 H     -1.526426    5.374013    0.166321

 H     -3.244325    5.373312   -0.292348

 C     -5.057951   -2.534238   -0.591631

 H     -5.396030   -1.555442   -0.226631

 H     -5.070664   -2.509634   -1.687797

 H     -5.780250   -3.293418   -0.261549

end

basis spherical
H library aug-cc-pVDZ

C library aug-cc-pVDZ

O library aug-cc-pVDZ

Mo library aug-cc-pVDZ-PP

end

ecp

ECP28MDF

  vectors output mo3o9.2pro.ts.ccsdt.ad.2.movecs

vectors input project avdz mo3o9.2pro.ts.ccsdt.ad.2.movecs output mo3o9.2pro.ts.ccsdt.ad.2.movecs

  rhf

  singlet

  maxiter 100

thresh 1.0e-10
tol2e 1.0e-10

end

task scf

ccsd

  maxiter 60

  thresh 1e-6

  freeze 28

end
task ccsd(t)

..........................................................

  ***** ccsd parameters *****

  iprt   =     0

  convi  = 0.100E-05

  maxit  =    60

  mxvec  =     5

memory                209250301

 IO offset     20.00000000000000

 IO error message >End of File

 file_read_ga: failing writing to

/home/fang824/nwchem/1.prop.h2o/mo3o9.2pro.ts.ccsdt.ad.2.t2

 Failed reading restart vector from

/home/fang824/nwchem/1.prop.h2o/mo3o9.2pro.ts.ccsdt.ad.2.t2

 Using MP2 initial guess vector

iter     correlation     delta       rms       T2     Non-T2      Main

            energy      energy      error      ampl     ampl      Block

                                               time     time      time

  1     -3.4090672221 -3.409D+00  1.335D+00  5426.87     0.16  5268.69

  2     -3.8791939395 -4.701D-01  1.665D+00  5408.49     0.20  5250.03

  3     -3.7046403041  1.746D-01  8.828D-02  5378.57     0.24  5221.70

  4     -3.7127134683 -8.073D-03  7.606D-02  5395.71     0.29  5237.13

  5     -3.7315962984 -1.888D-02  3.099D-02  5404.65     0.33  5246.40

  6     -3.7358121629 -4.216D-03  1.956D-03  5431.07     0.33  5273.70

  7     -3.7347649909  1.047D-03  8.614D-03  5390.74     0.33  5230.55

  8     -3.7342975445  4.674D-04  2.647D-03  5453.68     0.33  5296.47

  9     -3.7347444657 -4.469D-04  2.603D-04  5404.64     0.33  5245.28

 10     -3.7343759950  3.685D-04  8.486D-04  5418.01     0.33  5261.09

 11     -3.7344748500 -9.885D-05  2.094D-04  5404.01     0.33  5246.82

 12     -3.7344655046  9.345D-06  8.106D-05  5404.49     0.33  5247.58

 13     -3.7344475874  1.792D-05  5.642D-05  5439.64     0.33  5282.74

 14     -3.7344560956 -8.508D-06  4.669D-05  5398.75     0.33  5240.14

 15     -3.7344624258 -6.330D-06  2.939D-05  5467.32     0.33  5307.92

 16     -3.7344571151  5.311D-06  8.741D-06  5443.40     0.33  5283.68

 17     -3.7344615408 -4.426D-06  3.032D-05  5440.20     0.33  5281.81

 18     -3.7344598070  1.734D-06  3.667D-06  5426.56     0.33  5267.08

........................................................

Quote:Edoapra Oct 8th 9:07 am

Could you please post the output files or point to a website where they can accessed?

Clicked A Few Times

9:11:21 AM PDT - Tue, Oct 9th 2012
by the way, I don't think it is the global memory issue.

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