AMBER Archive (2008)

Subject: AMBER: AMBER10 Compilation (SGI Altix)

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Hi Users:
Today I try to compile AMBER10 on a SGI Altix (uname -a : Linux gelato
2.6.5-7.283-sn2 #1 SMP Wed Nov 29 16:55:53 UTC 2006 ia64 ia64 ia64 GNU/Linux)
To configure I use sgi_altix option (icc v 9.0 , ifort v9.0 , MKL v9.0). It
seems to compile without error but all the test fail. Also some of the test
from amber tools fail. I check the netcdf (make check) and pass all test.
Here is the output for the test.serial (TEST_FAILURES.diff):

possible FAILURE: check mdout.dmp.dif
/tmp/amber/amber10/test/dmp
67,68c67,68
< 1 -4.2572E+1 1.2493E+1 5.6294E+1 P8 6
< BOND = 0.7921 ANGLE = 2.0379 DIHED =
0.7121

---
>       1      -4.2573E+1     1.2492E+1     5.6291E+1     P8          6
>  BOND    =        0.7921  ANGLE   =        2.0379  DIHED      =        
0.7120
74,75c74,75
<       2      -4.2582E+1     1.2460E+1     5.6128E+1     P8          6
<  BOND    =        0.7874  ANGLE   =        2.0325  DIHED      =        
0.7121
---
>       2      -4.2582E+1     1.2459E+1     5.6125E+1     P8          6
>  BOND    =        0.7874  ANGLE   =        2.0325  DIHED      =        
0.7120
81,82c81,82
<       3      -4.2593E+1     1.2420E+1     5.5930E+1     P8          6
<  BOND    =        0.7817  ANGLE   =        2.0260  DIHED      =        
0.7120
---
>       3      -4.2593E+1     1.2420E+1     5.5927E+1     P8          6
>  BOND    =        0.7817  ANGLE   =        2.0260  DIHED      =        
0.7119
88,89c88,89
<       4      -4.2606E+1     1.2373E+1     5.5692E+1     P8          6
<  BOND    =        0.7750  ANGLE   =        2.0182  DIHED      =        
0.7119
---
>       4      -4.2606E+1     1.2373E+1     5.5689E+1     P8          6
>  BOND    =        0.7750  ANGLE   =        2.0182  DIHED      =        
0.7118
95,96c95,96
<       5      -4.2622E+1     1.2317E+1     5.5407E+1     P8          6
<  BOND    =        0.7669  ANGLE   =        2.0089  DIHED      =        
0.7117
---
>       5      -4.2622E+1     1.2316E+1     5.5404E+1     P8          6
>  BOND    =        0.7669  ANGLE   =        2.0089  DIHED      =        
0.7116
104,105c104,105
<       5      -4.2622E+1     1.2317E+1     5.5407E+1     P8          6
<  BOND    =        0.7669  ANGLE   =        2.0089  DIHED      =        
0.7117
---
>       5      -4.2622E+1     1.2316E+1     5.5404E+1     P8          6
>  BOND    =        0.7669  ANGLE   =        2.0089  DIHED      =        
0.7116
---------------------------------------
possible FAILURE:  check mdout.adenine.dif
/tmp/amber/amber10/test/adenine
69,70c69,70
<       1       1.4956     4.7935     2.7454E+1     N3         25
<  BOND    =        0.4545  ANGLE   =        5.3215  DIHED      =       
17.5374
---
>       1       1.5174     4.7855     2.7453E+1     N3         25
>  BOND    =        0.4545  ANGLE   =        5.3215  DIHED      =       
17.5592
76,77c76,77
<       2       1.2908     3.4147     1.7746E+1     N3         25
<  BOND    =        0.4346  ANGLE   =        5.1757  DIHED      =       
17.5358
---
>       2     NaN            NaN              0.     H5T         1
>  BOND    =        0.4346  ANGLE   =        5.1751  DIHED      =  NaN
79c79
<  1-4 VDW =        7.1923  1-4 EEL =        6.1795  RESTRAINT  =        0.
---
>  1-4 VDW =        7.1922  1-4 EEL =        6.1795  RESTRAINT  =        0.
83,137c83,137
<       3       1.1266     2.1977     9.9540     N3         25
<  BOND    =        0.4585  ANGLE   =        5.0362  DIHED      =       
17.5348
<  VDWAALS =       -3.6387  EEL     =      -24.8259  HBOND      =        0.
<  1-4 VDW =        7.1691  1-4 EEL =        6.1467  RESTRAINT  =        0.
<  EPOLAR  =       -6.7540
<  Dipole convergence: rms =  0.258E-6 iters =   3.00
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       4       1.0010     1.6429     7.4065     EP23       26
<  BOND    =        0.4942  ANGLE   =        4.9350  DIHED      =       
17.5342
<  VDWAALS =       -3.6421  EEL     =      -24.7961  HBOND      =        0.
<  1-4 VDW =        7.1421  1-4 EEL =        6.0892  RESTRAINT  =        0.
<  EPOLAR  =       -6.7554
<  Dipole convergence: rms =  0.659E-6 iters =   3.00
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       5       9.2259E-1     3.1051     1.3689E+1     EP23       26
<  BOND    =        0.4804  ANGLE   =        4.9120  DIHED      =       
17.5322
<  VDWAALS =       -3.6456  EEL     =      -24.7132  HBOND      =        0.
<  1-4 VDW =        7.1263  1-4 EEL =        5.9910  RESTRAINT  =        0.
<  EPOLAR  =       -6.7605
<  Dipole convergence: rms =  0.766E-6 iters =   3.00
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       6       1.1652     8.9082     4.6701E+1     N3         25
<  BOND    =        0.4929  ANGLE   =        5.1589  DIHED      =       
17.5309
<  VDWAALS =       -3.6507  EEL     =      -24.7333  HBOND      =        0.
<  1-4 VDW =        7.1146  1-4 EEL =        6.0155  RESTRAINT  =        0.
<  EPOLAR  =       -6.7637
<  Dipole convergence: rms =  0.269E-6 iters =   4.00
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       7       8.6292E-1     2.7405     1.4587E+1     N3         25
<  BOND    =        0.4660  ANGLE   =        4.8797  DIHED      =       
17.5307
<  VDWAALS =       -3.6498  EEL     =      -24.7002  HBOND      =        0.
<  1-4 VDW =        7.1191  1-4 EEL =        5.9808  RESTRAINT  =        0.
<  EPOLAR  =       -6.7633
<  Dipole convergence: rms =  0.365E-6 iters =   4.00
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       8       8.9665E-1     4.6266     2.1383E+1     N3         25
<  BOND    =        0.4635  ANGLE   =        4.9140  DIHED      =       
17.5299
<  VDWAALS =       -3.6499  EEL     =      -24.6488  HBOND      =        0.
<  1-4 VDW =        7.1229  1-4 EEL =        5.9289  RESTRAINT  =        0.
<  EPOLAR  =       -6.7640
<  Dipole convergence: rms =  0.348E-6 iters =   3.00
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<       9       8.0872E-1     1.2342     5.5340     EP23       26
<  BOND    =        0.4542  ANGLE   =        4.8390  DIHED      =       
17.5297
<  VDWAALS =       -3.6511  EEL     =      -24.6601  HBOND      =        0.
<  1-4 VDW =        7.1201  1-4 EEL =        5.9415  RESTRAINT  =        0.
<  EPOLAR  =       -6.7647
<  Dipole convergence: rms =  0.180E-6 iters =   4.00
<    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
<      10       7.9896E-1     2.3141     1.2573E+1     N3         25
<  BOND    =        0.4486  ANGLE   =        4.8418  DIHED      =       
17.5287
<  VDWAALS =       -3.6535  EEL     =      -24.6493  HBOND      =        0.
<  1-4 VDW =        7.1163  1-4 EEL =        5.9331  RESTRAINT  =        0.
<  EPOLAR  =       -6.7666
<  Dipole convergence: rms =  0.436E-6 iters =   3.00
---
>       3     NaN            NaN              0.     H5T         1
>  BOND    =  NaN           ANGLE   =  NaN           DIHED      =  NaN
>  VDWAALS =        0.  EEL     =        0.  HBOND      =        0.
>  1-4 VDW =  NaN           1-4 EEL =  NaN           RESTRAINT  =        0.
>  EPOLAR  =  NaN
>  Dipole convergence: rms =  NaN       iters =  21.00
>    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
>       4     NaN            NaN              0.     H5T         1
>  BOND    =  NaN           ANGLE   =  NaN           DIHED      =  NaN
>  VDWAALS =        0.  EEL     =        0.  HBOND      =        0.
>  1-4 VDW =  NaN           1-4 EEL =  NaN           RESTRAINT  =        0.
>  EPOLAR  =  NaN
>  Dipole convergence: rms =  NaN       iters =  21.00
>    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
>       5     NaN            NaN              0.     H5T         1
>  BOND    =  NaN           ANGLE   =  NaN           DIHED      =  NaN
>  VDWAALS =        0.  EEL     =        0.  HBOND      =        0.
>  1-4 VDW =  NaN           1-4 EEL =  NaN           RESTRAINT  =        0.
>  EPOLAR  =  NaN
>  Dipole convergence: rms =  NaN       iters =  21.00
>    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
>       6     NaN            NaN              0.     H5T         1
>  BOND    =  NaN           ANGLE   =  NaN           DIHED      =  NaN
>  VDWAALS =        0.  EEL     =        0.  HBOND      =        0.
>  1-4 VDW =  NaN           1-4 EEL =  NaN           RESTRAINT  =        0.
>  EPOLAR  =  NaN
>  Dipole convergence: rms =  NaN       iters =  21.00
>    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
>       7     NaN            NaN              0.     H5T         1
>  BOND    =  NaN           ANGLE   =  NaN           DIHED      =  NaN
>  VDWAALS =        0.  EEL     =        0.  HBOND      =        0.
>  1-4 VDW =  NaN           1-4 EEL =  NaN           RESTRAINT  =        0.
>  EPOLAR  =  NaN
>  Dipole convergence: rms =  NaN       iters =  21.00
>    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
>       8     NaN            NaN              0.     H5T         1
>  BOND    =  NaN           ANGLE   =  NaN           DIHED      =  NaN
>  VDWAALS =        0.  EEL     =        0.  HBOND      =        0.
>  1-4 VDW =  NaN           1-4 EEL =  NaN           RESTRAINT  =        0.
>  EPOLAR  =  NaN
>  Dipole convergence: rms =  NaN       iters =  21.00
>    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
>       9     NaN            NaN              0.     H5T         1
>  BOND    =  NaN           ANGLE   =  NaN           DIHED      =  NaN
>  VDWAALS =        0.  EEL     =        0.  HBOND      =        0.
>  1-4 VDW =  NaN           1-4 EEL =  NaN           RESTRAINT  =        0.
>  EPOLAR  =  NaN
>  Dipole convergence: rms =  NaN       iters =  21.00
>    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
>      10     NaN            NaN              0.     H5T         1
>  BOND    =  NaN           ANGLE   =  NaN           DIHED      =  NaN
>  VDWAALS =        0.  EEL     =        0.  HBOND      =        0.
>  1-4 VDW =  NaN           1-4 EEL =  NaN           RESTRAINT  =        0.
>  EPOLAR  =  NaN
>  Dipole convergence: rms =  NaN       iters =  21.00
141,146c141,146
<      10       7.9896E-1     2.3141     1.2573E+1     N3         25
<  BOND    =        0.4486  ANGLE   =        4.8418  DIHED      =       
17.5287
<  VDWAALS =       -3.6535  EEL     =      -24.6493  HBOND      =        0.
<  1-4 VDW =        7.1163  1-4 EEL =        5.9331  RESTRAINT  =        0.
<  EPOLAR  =       -6.7666
<  Dipole convergence: rms =  0.436E-6 iters =   3.00
---
>      10     NaN            NaN              0.     H5T         1
>  BOND    =  NaN           ANGLE   =  NaN           DIHED      =  NaN
>  VDWAALS =        0.  EEL     =        0.  HBOND      =        0.
>  1-4 VDW =  NaN           1-4 EEL =  NaN           RESTRAINT  =        0.
>  EPOLAR  =  NaN
>  Dipole convergence: rms =  NaN       iters =  21.00
---------------------------------------
What could be the problem?
Cheers,
Anthony
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• Next message: Bill Ross: "Re: AMBER: 3fe-4s cluster parameter file generation"
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