[gmx-users] Re: Benching against different compilers - Help needed

Jones de Andrade johannesrs at gmail.com
Thu May 4 05:18:39 CEST 2006


Hi.

Bad news. :( I was compiling it in portland with the -tp=k8-64 -fastsse
-Mipa=fast -Mipa=inline.

Oficially, as in some AMD documentation, the first two are mandatory. So, I
first tried without the -Mipa ones, and it yelded me the same results as
with them.

Then, I tried to remove the -fastsse flag also. Gromacs did not even
compiled. :(

I'm really starting to get fed up with the portland compilation, depict it
to my supervisors as "non-recomended", and try again to find out what is the
mistake in the intel compiler compilation (which one worries about the
inverse square root).

Anyway, thanks a lot in advance for all the help already provided, and
really sorry for spending so much space of the list on this subject already.

Anyway: Does anybody have any last/final shoot/chance idea/clue at this
point?

Jones

On 5/3/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Jones de Andrade wrote:
> > 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
>
>
> you have different pressure and virial, that means different forces.
> maybe you can try to compile with portland but without optimization.
>
>
>
> > 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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>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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