[gmx-users] Re: Benching against different compilers - Help needed
Jones de Andrade
johannesrs at gmail.com
Wed May 3 15:17:10 CEST 2006
Hi again.
Well, here we go:
On 4/30/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Jones de Andrade wrote:
> > Up to now, I could finally compile it with Portland, in both single and
> > double precision version. But, on the other hand, while the single
> > precision works properly, the double precision fails in some tests, like
> > the "mixed" test on the "tutor" directory. It yelds me the following
> > error message:
> this is hard to debug, but what you could do is run the same tpr with
> different executables and do gmxcheck -e -e2 to compare energies. that
> might give a clue.
> > step 0
> > Step 1 Warning: pressure scaling more than 1%, mu: 1.01018 1.02193
> 1.08117
> > Step 2 Warning: pressure scaling more than 1%, mu: 1.01124 1.00787
> 1.08362
> > Step 143 Warning: pressure scaling more than 1%, mu: 1.00304 1.00017
> 1.01009
> > step 240, remaining runtime: 40 s
> > Program mdrun_d, VERSION 3.3
> > Source code file: stat.c, line: 283
> > Fatal error:
> > XTC error
Ok, I did gmxcheck for both double precision versions of gromacs I got: one
compiled with GCC, and the other with PGI. Here is what I got. Everything
looks to be ugly and different, btw; no idea where to look first:
*****************************************************************************************************************
comparing energy file ener.edr and ener2.edr
Opened ener.edr as double precision energy file
Opened ener2.edr as double precision energy file
There are 44 terms in the energy files
There are 44 terms to compare in the energy files
Reading frame 1 time 0.000 Pressure (bar) step 0:
2.26575e+06, step 0: -1212.92
pV step 0: 3.53269e+06, step 0: -1891.14
Vir-XX step 0: -475104, step 0: 2135.61
Vir-XY step 0: 491116, step 0: -544.385
Vir-XZ step 0: 763516, step 0: 180.112
Vir-YX step 0: 491225, step 0: -544.385
Vir-YY step 0: -1.02488e+06, step 0: 2008.1
Vir-YZ step 0: -1.53177e+06, step 0: 558.876
Vir-ZX step 0: 763218, step 0: 180.112
Vir-ZY step 0: -1.53059e+06, step 0: 558.876
Vir-ZZ step 0: -3.79554e+06, step 0: 2209.48
Pres-XX (bar) step 0: 610883, step 0: -1286.57
Pres-XY (bar) step 0: -630004, step 0: 664.233
Pres-XZ (bar) step 0: -979427, step 0: -271.252
Pres-YX (bar) step 0: -630144, step 0: 664.233
Pres-YY (bar) step 0: 1.3161e+06, step 0: -1124.86
Pres-YZ (bar) step 0: 1.96481e+06, step 0: -753.997
Pres-ZX (bar) step 0: -979044, step 0: -271.252
Pres-ZY (bar) step 0: 1.9633e+06, step 0: -753.997
Pres-ZZ (bar) step 0: 4.87027e+06, step 0: -1227.32
#Surf*SurfTen step 0: 9.18092e+06, step 0: -50.7689
Reading frame 3 time 0.100 Angle step
50: 1570.43, step 50: 306.588
LJ (SR) step 50: -449.51, step 50: -188.033
Disper. corr. step 50: -48.4547, step 50: -193.09
Coulomb (SR) step 50: -1821.5, step 50: -14751.3
Potential step 50: -749.035, step 50: -14825.8
Kinetic En. step 50: 4695.12, step 50: 3702.53
Total Energy step 50: 3946.09, step 50: -11123.3
Temperature step 50: 402.631, step 50: 317.511
Pressure (bar) step 50: 35297.3, step 50: -836.341
Box-X step 50: 6.85856, step 50: 4.68882
Box-Y step 50: 3.81751, step 50: 2.34589
Box-Z step 50: 3.93067, step 50: 2.34792
Volume step 50: 102.915, step 50: 25.8259
Density (SI) step 50: 174.458, step 50: 695.211
pV step 50: 218762, step 50: -1300.74
Vir-XX step 50: -34277.1, step 50: 1588.65
Vir-XY step 50: -19728.5, step 50: 108.132
Vir-XZ step 50: -14866.4, step 50: 14.285
Vir-YX step 50: -20282.2, step 50: 108.132
Vir-YY step 50: -185709, step 50: 2157.54
Vir-YZ step 50: -102950, step 50: -196.053
Vir-ZX step 50: -15598.4, step 50: 14.285
Vir-ZY step 50: -102762, step 50: -196.053
Vir-ZZ step 50: -103462, step 50: 1907.44
Pres-XX (bar) step 50: 11541.9, step 50: -445.503
Pres-XY (bar) step 50: 6367.62, step 50: -183.086
Pres-XZ (bar) step 50: 4787.13, step 50: -18.5143
Pres-YX (bar) step 50: 6546.3, step 50: -183.086
Pres-YY (bar) step 50: 60435.8, step 50: -1150.69
Pres-YZ (bar) step 50: 33194.4, step 50: 289.951
Pres-ZX (bar) step 50: 5023.35, step 50: -18.5143
Pres-ZY (bar) step 50: 33133.8, step 50: 289.951
Pres-ZZ (bar) step 50: 33914.2, step 50: -912.829
#Surf*SurfTen step 50: -8154.99, step 50: -269.382
Pcoupl-Mu-YY step 50: 1.00103, step 50: 0.999981
Mu-X step 50: 3.81572, step 50: 6.43379
Mu-Y step 50: -28.1838, step 50: -29.6693
Mu-Z step 50: -17.7016, step 50: -12.1778
T-MeOH step 50: 448.795, step 50: 306.87
T-SOL step 50: 348.773, step 50: 329.927
Lamb-MeOH step 50: 0.997024, step 50: 0.999745
.
.
.
Reading frame 10 time 0.500
End of file on ener.edr but not on ener2.edr
***************************************************************************************************************
I'm sorry for posting such a big output here, but I had no idea what to
select, and it is really starting to look like a not-yet documented issue,
at least for the gromacs+pgi combination.
Anyone with more experience on gmxcheck can help? Or did someone any time
found this or a problem like this?
Thanks a lot for all help already provided. :D
Jones
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