[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
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
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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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