AMBER Archive (2009)

Subject: [AMBER] REM_hybrid test fails on AIX

From: Shan-ho Tsai (tsai_at_hal.physast.uga.edu)
Date: Thu Jan 22 2009 - 14:28:04 CST

Dear all,

I am trying to build Amber10 using XLF 9.1 on an IBM
power4+ node, running AIX 5.2. The serial version
compiled fine and all tests passed. I am building the
parallel version with

./configure_amber -mpi -nobintraj xlf90_aix

(The -nobintraj option was necessary to avoid an
error in the netcdf support. I got the hint from
a posting in the Amber mailing-list archive.)

gmake parallel

There were no fatal errors, although there were
some compilation warnings. I will send this in,
if they are helpful in troubleshooting.

I ran the tests with 2 and with 4 processors and the
rem_hybrid test failed drastically. All other tests
passed (for rem_gb_2rep, rem_wat, and rem_gb_4rep
I had to replace the final "&end" by "/" in rem.in.000,
etc, then the tests ran and passed).

For rem_hybrid the differences in the results are
shown below (sorry for the long attachment). The
results that I get with 2 and with 4 processors
are basically the same.

Any ideas where the problem is coming from? Does this
indicate a problem in my build of sander.MPI, or could
it be in some other components of the package?

I will appreciate any help, thank you very much!

Sincerely,
Shan-Ho Tsai

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

cd test/rem_hybrid
more rem.log.dif
11,12c11,12
< 1 1.05 0. -615.76 300.00 330.00 0. -1
< 2 0.95 0. -615.76 330.00 300.00 2.00 -1 

---
>  1      1.05      0.  -1449.96    300.00    330.00      0.      -1
>  2      0.95      0.  -1449.96    330.00    300.00      2.00      -1
14,15c14,15
<  1     -1.00    306.08   -631.47    330.00    330.00      1.00      -1
<  2     -1.00    287.73   -633.87    300.00    300.00      0.      -1
---
>  1     -1.00    306.08  -1476.92    330.00    330.00      1.00      -1
>  2     -1.00    287.73  -1483.62    300.00    300.00      0.      -1
17,18c17,18
<  1      0.95    315.08   -637.77    330.00    300.00      1.33      -1
<  2      1.05    293.57   -646.02    300.00    330.00      0.      -1
---
>  1      0.95    315.08  -1460.95    330.00    300.00      1.33      -1
>  2      1.05    293.57  -1469.42    300.00    330.00      0.      -1
20,21c20,21
<  1     -1.00    304.94   -644.16    300.00    300.00      0.      -1
<  2     -1.00    314.73   -618.46    330.00    330.00      1.00      -1
---
>  1      1.05    304.94  -1446.49    300.00    330.00      0.50      -1
>  2      0.95    314.73  -1443.87    330.00    300.00      1.00      -1
23,24c23,24
<  1      1.05    305.31   -632.00    300.00    330.00      0.      -1
<  2      0.95    331.82   -634.68    330.00    300.00      1.20      -1
---
>  1     -1.00    328.73  -1423.95    330.00    330.00      0.80      -1
>  2     -1.00    302.93  -1464.90    300.00    300.00      0.40      -1

  more rem.out.000.dif
103c103
<  Etot   =         0.  EKtot   =         0.  EPtot      =      -615.7571
>  Etot   =         0.  EKtot   =         0.  EPtot      =     -1449.9604
105c105
<  1-4 NB =         7.4866  1-4 EEL =       188.0174  VDWAALS    = 
40.1059
>  1-4 NB =         7.4866  1-4 EEL =       188.0174  VDWAALS    = 
-33.3155
106c106
<  EELEC  =      -554.0010  EGB     =      -351.4090  RESTRAINT  = 
0.
>  EELEC  =     -1666.1920  EHBOND  =         0.  RESTRAINT  =         0.
109c109
< HYBRID REMD: myEptot=  -615.757076 myTargetTemp= 300.00
> HYBRID REMD: myEptot= -1449.960432 myTargetTemp= 300.00
112c112
< REMD: myEptot=       -615.7571 myTargetTemp= 300.00 mytemp=   0.
> REMD: myEptot=      -1449.9604 myTargetTemp= 300.00 mytemp=   0.
115c115
< Replica          Temp= 300.00 Indx=  1 Rep#=  1 EPot=    -615.76
> Replica          Temp= 300.00 Indx=  1 Rep#=  1 EPot=   -1449.96
116c116
< Partner          Temp= 330.00 Indx=  2 Rep#=  2 EPot=    -615.76
> Partner          Temp= 330.00 Indx=  2 Rep#=  2 EPot=   -1449.96
134c134
<  Etot   =     -4423.4456  EKtot   =      1116.4185  EPtot      = 
-631.4715
>  Etot   =     -4423.4456  EKtot   =      1116.4185  EPtot      = 
-1476.9172
136c136
<  1-4 NB =         7.5326  1-4 EEL =       189.5146  VDWAALS    = 
48.5476
>  1-4 NB =         7.5326  1-4 EEL =       189.5146  VDWAALS    = 
-24.9332
137c137
<  EELEC  =      -588.8497  EGB     =      -340.5247  RESTRAINT  = 
0.
>  EELEC  =     -1701.3395  EHBOND  =         0.  RESTRAINT  =         0.
140c140
< HYBRID REMD: myEptot=  -631.471470 myTargetTemp= 330.00
> HYBRID REMD: myEptot= -1476.917212 myTargetTemp= 330.00
143c143
< REMD: myEptot=       -631.4715 myTargetTemp= 330.00 mytemp= 306.08
> REMD: myEptot=      -1476.9172 myTargetTemp= 330.00 mytemp= 306.08
146c146
< Replica          Temp= 330.00 Indx=  2 Rep#=  1 EPot=    -631.47
> Replica          Temp= 330.00 Indx=  2 Rep#=  1 EPot=   -1476.92
147c147
< Partner          Temp= 300.00 Indx=  1 Rep#=  2 EPot=    -633.87
> Partner          Temp= 300.00 Indx=  1 Rep#=  2 EPot=   -1483.62
148c148
< Metrop=     0.693339 delta=     0.366236 o_scaling=      -1.00
> Metrop=     0.360092 delta=     0.102140E+1 o_scaling=      -1.00
164c164
<  Etot   =     -4361.1223  EKtot   =      1149.2439  EPtot      = 
-637.7723
>  Etot   =     -4361.1223  EKtot   =      1149.2439  EPtot      = 
-1460.9523
166c166
<  1-4 NB =         7.5561  1-4 EEL =       193.2855  VDWAALS    = 
23.7733
>  1-4 NB =         7.5561  1-4 EEL =       193.2855  VDWAALS    = 
-49.5774
167c167
<  EELEC  =      -547.2488  EGB     =      -362.8246  RESTRAINT  = 
0.
>  EELEC  =     -1659.9027  EHBOND  =         0.  RESTRAINT  =         0.
170c170
< HYBRID REMD: myEptot=  -637.772305 myTargetTemp= 330.00
> HYBRID REMD: myEptot= -1460.952281 myTargetTemp= 330.00
173c173
< REMD: myEptot=       -637.7723 myTargetTemp= 330.00 mytemp= 315.08
> REMD: myEptot=      -1460.9523 myTargetTemp= 330.00 mytemp= 315.08
176c176
< Replica          Temp= 330.00 Indx=  2 Rep#=  1 EPot=    -637.77
> Replica          Temp= 330.00 Indx=  2 Rep#=  1 EPot=   -1460.95
177c177
< Partner          Temp= 300.00 Indx=  1 Rep#=  2 EPot=    -646.02
> Partner          Temp= 300.00 Indx=  1 Rep#=  2 EPot=   -1469.42
178c178
< Metrop=     0.284459 delta=     0.125717E+1 o_scaling=       1.05
> Metrop=     0.275217 delta=     0.129019E+1 o_scaling=       1.05
195c195
<  Etot   =     -4505.9643  EKtot   =      1112.2506  EPtot      = 
-644.1607
>  Etot   =     -4505.9643  EKtot   =      1112.2506  EPtot      = 
-1446.4932
197c197
<  1-4 NB =         4.7484  1-4 EEL =       187.9445  VDWAALS    = 
31.3683
>  1-4 NB =         4.7484  1-4 EEL =       187.9445  VDWAALS    = 
-42.1405
198c198
<  EELEC  =      -539.5024  EGB     =      -383.9046  RESTRAINT  = 
0.
>  EELEC  =     -1652.2307  EHBOND  =         0.  RESTRAINT  =         0.
201c201
< HYBRID REMD: myEptot=  -644.160702 myTargetTemp= 300.00
> HYBRID REMD: myEptot= -1446.493151 myTargetTemp= 300.00
204c204
< REMD: myEptot=       -644.1607 myTargetTemp= 300.00 mytemp= 304.94
> REMD: myEptot=      -1446.4932 myTargetTemp= 300.00 mytemp= 304.94
207c207
< Replica          Temp= 300.00 Indx=  1 Rep#=  1 EPot=    -644.16
> Replica          Temp= 300.00 Indx=  1 Rep#=  1 EPot=   -1446.49
208c208
< Partner          Temp= 330.00 Indx=  2 Rep#=  2 EPot=    -618.46
> Partner          Temp= 330.00 Indx=  2 Rep#=  2 EPot=   -1443.87
210c210
< Rand=       0.386803 MyScaling=      -1.00 Success= F
> Rand=       0.386803 MyScaling=       1.05 Success= T
212c212
< REMD: checking to see if bath T has changed: 300.00->300.00
> REMD: checking to see if bath T has changed: 300.00->330.00
213c213
<  NSTEP =      100   TIME(PS) =      15.800  TEMP(K) =   305.31  PRESS = 
0.> REMD: scaling velocities by    1.049 to match new bath T  330.000
214c214
<  Etot   =     -4556.3305  EKtot   =      1113.6288  EPtot      = 
-5669.9593
>  NSTEP =      100   TIME(PS) =      15.800  TEMP(K) =   328.73  PRESS = 
0.215c215
<  BOND   =         4.2564  ANGLE   =        17.6520  DIHED      = 
31.5411
>  Etot   =     -4373.0998  EKtot   =      1199.0250  EPtot      = 
-5572.1248
216c216
<  1-4 NB =         7.6838  1-4 EEL =       194.7946  VDWAALS    = 
791.0854
>  BOND   =         4.7470  ANGLE   =        19.1743  DIHED      = 
32.7969
217c217
<  EELEC  =     -6716.9724  EHBOND  =         0.  RESTRAINT  =         0.
>  1-4 NB =         8.0789  1-4 EEL =       195.0715  VDWAALS    = 
784.4455
218c218
<  TEMP0  =       300.0000  REPNUM  =              1  EXCHANGE#  =
4
>  EELEC  =     -6616.4389  EHBOND  =         0.  RESTRAINT  =         0.
219c219
< 
------------------------------------------------------------------------------
>  TEMP0  =       330.0000  REPNUM  =              1  EXCHANGE#  =
4
220c220
< =================HYBRID REMD: energy calc for exch 
5=================> 
------------------------------------------------------------------------------
221c221
< HYBRID REMD: Stripping waters
> =================HYBRID REMD: energy calc for exch 
5=================222c222
< HYBRID REMD: New natom=      192
> HYBRID REMD: Stripping waters
223c223
< HYBRID REMD: Calling force.
> HYBRID REMD: New natom=      192
224c224
<  NSTEP =      100   TIME(PS) =      15.800  TEMP(K) =   305.31  PRESS = 
0.> HYBRID REMD: Calling force.
225c225
<  Etot   =     -4556.3305  EKtot   =      1113.6288  EPtot      = 
-632.0033
>  NSTEP =      100   TIME(PS) =      15.800  TEMP(K) =   328.73  PRESS = 
0.226c226
<  BOND   =         4.8229  ANGLE   =        18.4858  DIHED      = 
30.1789
>  Etot   =     -4373.0998  EKtot   =      1199.0250  EPtot      = 
-1423.9451
227c227
<  1-4 NB =         7.3038  1-4 EEL =       194.7493  VDWAALS    = 
22.4060
>  BOND   =         5.3650  ANGLE   =        20.2923  DIHED      = 
31.2661
228c228
<  EELEC  =      -532.2645  EGB     =      -377.6855  RESTRAINT  = 
0.
>  1-4 NB =         7.6322  1-4 EEL =       195.0276  VDWAALS    = 
-54.3902
229c229
<  TEMP0  =       300.0000  REPNUM  =              1  EXCHANGE#  =
4
>  EELEC  =     -1629.1382  EHBOND  =         0.  RESTRAINT  =         0.
230c230
< 
------------------------------------------------------------------------------
>  TEMP0  =       330.0000  REPNUM  =              1  EXCHANGE#  =
4
231c231
< HYBRID REMD: myEptot=  -632.003252 myTargetTemp= 300.00
> 
------------------------------------------------------------------------------
232c232
< HYBRID REMD: Restoring...
> HYBRID REMD: myEptot= -1423.945135 myTargetTemp= 330.00
233c233
< =========================END HYBRID REMD energy 
calc.=========================> HYBRID REMD: Restoring...
234c234
< REMD: myEptot=       -632.0033 myTargetTemp= 300.00 mytemp= 305.31
> =========================END HYBRID REMD energy 
calc.=========================235c235
< ==========================REMD EXCHANGE 
CALCULATION==========================
> REMD: myEptot=      -1423.9451 myTargetTemp= 330.00 mytemp= 328.73
236c236
< Exch=          5 RREMD= 0
> ==========================REMD EXCHANGE 
CALCULATION==========================
237c237
< Replica          Temp= 300.00 Indx=  1 Rep#=  1 EPot=    -632.00
> Exch=          5 RREMD= 0
238c238
< Partner          Temp= 330.00 Indx=  2 Rep#=  2 EPot=    -634.68
> Replica          Temp= 330.00 Indx=  2 Rep#=  1 EPot=   -1423.95
239c239
< Not controlling exchange.
> Partner          Temp= 300.00 Indx=  1 Rep#=  2 EPot=   -1464.90
240c240
< Rand=       0.470507E-2 MyScaling=       1.05 Success= T
> Metrop=     0.194365E-2 delta=     0.624319E+1 o_scaling=      -1.00
241c241
< ========================END REMD EXCHANGE 
CALCULATION========================
> Rand=       0.470507E-2 MyScaling=      -1.00 Success= F
242c242
< REMD: checking to see if bath T has changed: 300.00->330.00
> ========================END REMD EXCHANGE 
CALCULATION========================
243c243
< REMD: scaling velocities by    1.049 to match new bath T  330.000
> REMD: checking to see if bath T has changed: 330.00->330.00
247c247
<  NSTEP =      100   TIME(PS) =      16.000  TEMP(K) =   326.47  PRESS = 
0.>  NSTEP =      100   TIME(PS) =      16.000  TEMP(K) =   336.21  PRESS 
=     0.248c248
<  Etot   =     -4385.2341  EKtot   =      1190.8114  EPtot      = 
-5576.0455
>  Etot   =     -4353.4141  EKtot   =      1226.3075  EPtot      = 
-5579.7216
249c249
<  BOND   =         6.9897  ANGLE   =        22.5884  DIHED      = 
27.7377
>  BOND   =         7.9891  ANGLE   =        23.2259  DIHED      = 
27.8315
250c250
<  1-4 NB =         6.9502  1-4 EEL =       186.3490  VDWAALS    = 
794.2917
>  1-4 NB =         7.2725  1-4 EEL =       186.5165  VDWAALS    = 
838.7776
251c251
<  EELEC  =     -6620.9521  EHBOND  =         0.  RESTRAINT  =         0.
>  EELEC  =     -6671.3347  EHBOND  =         0.  RESTRAINT  =         0.
258c258
<  NSTEP =      100   TIME(PS) =      16.000  TEMP(K) =   326.47  PRESS = 
0.>  NSTEP =      100   TIME(PS) =      16.000  TEMP(K) =   336.21  PRESS 
=     0.259c259
<  Etot   =     -4385.2341  EKtot   =      1190.8114  EPtot      = 
-631.1708
>  Etot   =     -4353.4141  EKtot   =      1226.3075  EPtot      = 
-1434.4536
260c260
<  BOND   =         9.6817  ANGLE   =        18.3629  DIHED      = 
26.7447
>  BOND   =        10.8267  ANGLE   =        19.8228  DIHED      = 
26.8090
261c261
<  1-4 NB =         6.9195  1-4 EEL =       185.4399  VDWAALS    = 
26.6514
>  1-4 NB =         7.3387  1-4 EEL =       185.8639  VDWAALS    = 
-56.6052
262c262
<  EELEC  =      -510.5562  EGB     =      -394.4147  RESTRAINT  = 
0.
>  EELEC  =     -1628.5094  EHBOND  =         0.  RESTRAINT  =         0.
265c265
< HYBRID REMD: myEptot=  -631.170812 myTargetTemp= 330.00
> HYBRID REMD: myEptot= -1434.453579 myTargetTemp= 330.00
268c268
< REMD: myEptot=       -631.1708 myTargetTemp= 330.00 mytemp= 326.47
> REMD: myEptot=      -1434.4536 myTargetTemp= 330.00 mytemp= 336.21
### Maximum absolute error in matching lines = 1.12e+03 at line 262 field 
3
### Maximum relative error in matching lines = 3.09e+00 at line 166 field 
11

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