Hello,
These are round-off errors and not something to really worry about. If you
want to get rid of them completely, you can edit the test files to add a "-t
3" to the dacdif calls to truncate the last 3 decimal places in each number
(or maybe more if it differs by more than 3 decimal places), but it's really
not necessary. Also keep in mind that such simulations are chaotic, so a
tiny difference in the first step will compound in later steps.
Hope this helps,
Jason
On Thu, Sep 2, 2010 at 7:08 AM, Rasale, Anupama <Anupama.Rasale.amd.com>wrote:
> Hi,
> Below are the verification failures I am observing while
> running amber10 tests and amber10 benchmarks with Open64 compiler. Similar
> verification failures are to be seen with Intel and gnu compilers as well.
> Please let us know how do we go about this verification failures fix?
>
> Amber10 Benchmarks:
>
> Open64 - Compiler:
>
> 1. Benchmark: factor_ix
> File: bench.factor_ix
> 108c108
> < Etot = -234217.9535 EKtot = 54902.7462 EPtot =
> -289120.6997
> ---
> > Etot = -234217.9535 EKtot = 54902.7461 EPtot =
> -289120.6996
> 111c111
> < EELEC = -348445.8550 EHBOND = 0. RESTRAINT = 0.
> ---
> > EELEC = -348445.8549 EHBOND = 0. RESTRAINT = 0.
>
>
> 2. Benchmark: hb
>
> File: bench.hb.out.dif
>
>
> 78,81c78,81
> < Etot = -97461.3670 EKtot = 27563.9306 EPtot =
> -125025.2975
> < BOND = 1636.7016 ANGLE = 4931.4781 DIHED =
> 5418.6881
> < 1-4 NB = 2093.3861 1-4 EEL = 29303.0867 VDWAALS =
> 10389.3302
> < EELEC = -178797.9683 EHBOND = 0. RESTRAINT = 0.
> ---
> > Etot = -97461.3673 EKtot = 27563.9307 EPtot =
> -125025.2980
> > BOND = 1636.7016 ANGLE = 4931.4782 DIHED =
> 5418.6881
> > 1-4 NB = 2093.3861 1-4 EEL = 29303.0867 VDWAALS =
> 10389.3303
> > EELEC = -178797.9690 EHBOND = 0. RESTRAINT = 0.
> 84,87c84,87
> < Etot = -97462.0628 EKtot = 27588.1463 EPtot =
> -125050.2091
> < BOND = 1653.1482 ANGLE = 4810.9659 DIHED =
> 5412.5285
> < 1-4 NB = 2122.7479 1-4 EEL = 29314.8959 VDWAALS =
> 10728.3723
> < EELEC = -179092.8678 EHBOND = 0. RESTRAINT = 0.
> ---
> > Etot = -97462.0633 EKtot = 27588.1481 EPtot =
> -125050.2114
> > BOND = 1653.1483 ANGLE = 4810.9660 DIHED =
> 5412.5286
> > 1-4 NB = 2122.7480 1-4 EEL = 29314.8960 VDWAALS =
> 10728.3710
> > EELEC = -179092.8692 EHBOND = 0. RESTRAINT = 0.
> 90,93c90,93
> < Etot = -97460.6194 EKtot = 27763.8663 EPtot =
> -125224.4856
> < BOND = 1655.1222 ANGLE = 4833.4214 DIHED =
> 5369.3648
> < 1-4 NB = 2121.5899 1-4 EEL = 29303.1234 VDWAALS =
> 10723.7589
> < EELEC = -179230.8662 EHBOND = 0. RESTRAINT = 0.
> ---
> > Etot = -97460.6124 EKtot = 27763.8586 EPtot =
> -125224.4710
> > BOND = 1655.1219 ANGLE = 4833.4212 DIHED =
> 5369.3651
> > 1-4 NB = 2121.5899 1-4 EEL = 29303.1233 VDWAALS =
> 10723.7619
> > EELEC = -179230.8544 EHBOND = 0. RESTRAINT = 0.
> 96,99c96,99
> < Etot = -97458.4271 EKtot = 27568.7383 EPtot =
> -125027.1654
> < BOND = 1624.9539 ANGLE = 4879.7318 DIHED =
> 5381.1618
> < 1-4 NB = 2107.9490 1-4 EEL = 29313.2300 VDWAALS =
> 10784.0282
> < EELEC = -179118.2201 EHBOND = 0. RESTRAINT = 0.
> ---
> > Etot = -97458.4334 EKtot = 27568.7213 EPtot =
> -125027.1547
> > BOND = 1624.9528 ANGLE = 4879.7304 DIHED =
> 5381.1623
> > 1-4 NB = 2107.9494 1-4 EEL = 29313.2315 VDWAALS =
> 10784.0294
> > EELEC = -179118.2104 EHBOND = 0. RESTRAINT = 0.
> 102,105c102,105
> < Etot = -97456.2847 EKtot = 27565.4602 EPtot =
> -125021.7449
> < BOND = 1608.6611 ANGLE = 4874.3358 DIHED =
> 5423.5868
> < 1-4 NB = 2133.5063 1-4 EEL = 29293.4952 VDWAALS =
> 10537.7739
> < EELEC = -178893.1041 EHBOND = 0. RESTRAINT = 0.
> ---
> > Etot = -97456.2845 EKtot = 27565.2028 EPtot =
> -125021.4873
> > BOND = 1608.6617 ANGLE = 4874.3434 DIHED =
> 5423.5979
> > 1-4 NB = 2133.5056 1-4 EEL = 29293.4975 VDWAALS =
> 10537.7035
> > EELEC = -178892.7970 EHBOND = 0. RESTRAINT = 0.
> 109,112c109,112
> < Etot = -97460.7330 EKtot = 27680.7405 EPtot =
> -125141.4735
> < BOND = 1626.3583 ANGLE = 4859.0349 DIHED =
> 5387.9010
> < 1-4 NB = 2115.9788 1-4 EEL = 29289.3020 VDWAALS =
> 10613.7831
> < EELEC = -179033.8317 EHBOND = 0. RESTRAINT = 0.
> ---
> > Etot = -97460.7336 EKtot = 27680.7401 EPtot =
> -125141.4737
> > BOND = 1626.3586 ANGLE = 4859.0352 DIHED =
> 5387.9012
> > 1-4 NB = 2115.9786 1-4 EEL = 29289.3018 VDWAALS =
> 10613.7726
> > EELEC = -179033.8216 EHBOND = 0. RESTRAINT = 0.
> 116,119c116,119
> < Etot = 1.5412 EKtot = 106.1874 EPtot =
> 106.3567
> < BOND = 29.5935 ANGLE = 37.3044 DIHED =
> 25.6279
> < 1-4 NB = 15.4221 1-4 EEL = 35.4767 VDWAALS =
> 129.6679
> < EELEC = 161.1560 EHBOND = 0. RESTRAINT = 0.
> ---
> > Etot = 1.5410 EKtot = 106.1863 EPtot =
> 106.3557
> > BOND = 29.5938 ANGLE = 37.3044 DIHED =
> 25.6280
> > 1-4 NB = 15.4218 1-4 EEL = 35.4771 VDWAALS =
> 129.6646
> > EELEC = 161.1628 EHBOND = 0. RESTRAINT = 0.
>
>
> 3. Benchmark: jac
>
> Filename: bench.jac.out.dif
> 18d17
> < a=62.2, b=62.2, c=62.2,
> 125c124
> < Etot = -58173.566 EKtot = 14196.823 EPtot =
> -72370.389
> ---
> > Etot = -58173.566 EKtot = 14196.824 EPtot =
> -72370.390
> 127,128c126,127
> < 1-4 NB = 542.726 1-4 EEL = 6603.211 VDWAALS =
> 8342.386
> < EELEC = -90449.058 EHBOND = 0. RESTRAINT = 0.
> ---
> > 1-4 NB = 542.726 1-4 EEL = 6603.211 VDWAALS =
> 8342.387
> > EELEC = -90449.059 EHBOND = 0. RESTRAINT = 0.
> 131c130
> < Etot = -58174.039 EKtot = 14277.263 EPtot =
> -72451.303
> ---
> > Etot = -58174.037 EKtot = 14277.269 EPtot =
> -72451.306
> 133,134c132,133
> < 1-4 NB = 539.871 1-4 EEL = 6587.210 VDWAALS =
> 8419.440
> < EELEC = -90625.797 EHBOND = 0. RESTRAINT = 0.
> ---
> > 1-4 NB = 539.871 1-4 EEL = 6587.210 VDWAALS =
> 8419.439
> > EELEC = -90625.799 EHBOND = 0. RESTRAINT = 0.
> 138,141c137,140
> < Etot = -58174.071 EKtot = 14165.178 EPtot =
> -72339.249
> < BOND = 442.771 ANGLE = 1147.687 DIHED =
> 995.589
> < 1-4 NB = 562.376 1-4 EEL = 6614.858 VDWAALS =
> 8290.663
> < EELEC = -90393.195 EHBOND = 0. RESTRAINT = 0.
> ---
> > Etot = -58174.078 EKtot = 14165.206 EPtot =
> -72339.284
> > BOND = 442.771 ANGLE = 1147.686 DIHED =
> 995.589
> > 1-4 NB = 562.376 1-4 EEL = 6614.858 VDWAALS =
> 8290.676
> > EELEC = -90393.243 EHBOND = 0. RESTRAINT = 0.
> 145,146c144,145
> < Etot = -58173.320 EKtot = 14222.198 EPtot =
> -72395.518
> < BOND = 422.572 ANGLE = 1166.021 DIHED =
> 976.669
> ---
> > Etot = -58173.320 EKtot = 14222.197 EPtot =
> -72395.518
> > BOND = 422.571 ANGLE = 1166.021 DIHED =
> 976.669
>
>
> 4. Benchmark: trx
>
> Filename: bench.trx.out.dif
>
> 91c91
> < Etot = -34117.6276 EKtot = 8391.6105 EPtot =
> -42509.2382
> ---
> > Etot = -34117.6276 EKtot = 8391.6106 EPtot =
> -42509.2382
> 99c99
> < Etot = -34117.9742 EKtot = 8423.5594 EPtot =
> -42541.5336
> ---
> > Etot = -34117.9741 EKtot = 8423.5595 EPtot =
> -42541.5336
> 101c101
> < 1-4 NB = 384.9161 1-4 EEL = 6692.7528 VDWAALS =
> 4992.8175
> ---
> > 1-4 NB = 384.9161 1-4 EEL = 6692.7527 VDWAALS =
> 4992.8175
> 107,108c107,108
> < Etot = -34117.7029 EKtot = 8437.8008 EPtot =
> -42555.5038
> < BOND = 306.1822 ANGLE = 787.0116 DIHED =
> 1003.6434
> ---
> > Etot = -34117.7029 EKtot = 8437.8008 EPtot =
> -42555.5037
> > BOND = 306.1823 ANGLE = 787.0118 DIHED =
> 1003.6433
> 115,118c115,118
> < Etot = -34117.1926 EKtot = 8300.6574 EPtot =
> -42417.8500
> < BOND = 296.3611 ANGLE = 790.2164 DIHED =
> 1010.9573
> < 1-4 NB = 379.5156 1-4 EEL = 6737.9479 VDWAALS =
> 4889.1665
> < EELEC = -55968.7200 EHBOND = 0. RESTRAINT = 0.
> ---
> > Etot = -34117.1925 EKtot = 8300.6575 EPtot =
> -42417.8500
> > BOND = 296.3611 ANGLE = 790.2164 DIHED =
> 1010.9572
> > 1-4 NB = 379.5156 1-4 EEL = 6737.9479 VDWAALS =
> 4889.1667
> > EELEC = -55968.7202 EHBOND = 0. RESTRAINT = 0.
> 124,125c124,125
> < Etot = -34117.6969 EKtot = 8389.2443 EPtot =
> -42506.9412
> < BOND = 286.3579 ANGLE = 791.1263 DIHED =
> 1008.9145
> ---
> > Etot = -34117.6968 EKtot = 8389.2443 EPtot =
> -42506.9411
> > BOND = 286.3579 ANGLE = 791.1264 DIHED =
> 1008.9144
> 133c133
> < Etot = 0.2764 EKtot = 47.4544 EPtot =
> 47.6337
> ---
> > Etot = 0.2765 EKtot = 47.4544 EPtot =
> 47.6337
> 136c136
> < EELEC = 52.6299 EHBOND = 0. RESTRAINT = 0.
> ---
> > EELEC = 52.6298 EHBOND = 0. RESTRAINT = 0.
>
> Verification failures were observed with GNU and Intel compilers also.
>
> Amber10 serial tests:
>
> Open64 Compiler:
>
> 1. Test name: ambpdb_first_protein
>
> Filename: /first.pdb.di
> 2147c2147
> < HETATM 2145 X BMH G 62 29.312 38.819 37.740 0. 0. 62 N
> ---
> > HETATM 2145 X BMH G 62 29.313 38.819 37.740 0. 0. 62 N
>
>
> 2. Test name: ambpdb_first_rna
>
> File name: first.pdb.dif
> 2493c2493
> < HETATM 2491 X BMH G 8 23.812 6.343 -13.815 0. 0. 8 N
> ---
> > HETATM 2491 X BMH G 8 23.813 6.343 -13.815 0. 0. 8 N
> 2588c2588
> < HETATM 2586 X BMH G 39 15.716 26.812 -17.572 0. 0. 39 N
> ---
> > HETATM 2586 X BMH G 39 15.716 26.813 -17.572 0. 0. 39 N
> 2734c2734
> < HETATM 2732 X BMH G 88 -20.948 -1.812 -9.912 0. 0. 88 N
> ---
> > HETATM 2732 X BMH G 88 -20.948 -1.813 -9.912 0. 0. 88 N
>
>
> 3. Test Name: rdc
>
> File name: gcg.dip.o.dif
> 352c352
> < 196 H5'1 DA 7 0.14 0.62 0.96
> ---
> > 196 H5'1 DA 7 0.14 0.63 0.96
> 377c377
> < 512 H5'1 DA 17 0.13 0.62 0.98
> ---
> > 512 H5'1 DA 17 0.13 0.63 0.98
>
>
> 4. Test Name: tip5p
>
> File Name: mdout.tip5p.dif
> 180c180
> < EKCMT = 0.2952 VIRIAL = 9.6699 VOLUME =
> 0.0001
> ---
> > EKCMT = 0.2952 VIRIAL = 9.6699 VOLUME =
> 0.0002
>
> Similar verification errors are seen for GNU, pathscale compilers also.
>
> Thanks
> Anupama
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Sep 02 2010 - 06:00:07 PDT
