[gmx-users] Benching against different compilers - Help needed
David van der Spoel
spoel at xray.bmc.uu.se
Sun Apr 30 22:35:51 CEST 2006
Jones de Andrade wrote:
> Hi All.
>
> Well, first of all, I would like to thank a lot David for all the help
> he gave me up to now. I don't know how to thank for so much help neither
> how to apologize for bothering you this much.
>
> 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.
> _________________________________________________________________________
> starting mdrun 'Pure Methanol - Yummie! (and some water)'
> 10000 steps, 20.0 ps.
>
>
> Back Off! I just backed up traj.trr to ./#traj.trr.10#
>
> Back Off! I just backed up traj.xtc to ./#traj.xtc.10#
> 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 3 Warning: pressure scaling more than 1%, mu: 1.03039 1.0523 1.08046
>
> Step 4 Warning: pressure scaling more than 1%, mu: 1.04141 1.08638 1.09351
>
> Step 5 Warning: pressure scaling more than 1%, mu: 1.06415 1.0995 1.06772
>
> Step 6 Warning: pressure scaling more than 1%, mu: 1.04802 1.07721 1.04162
>
> Step 7 Warning: pressure scaling more than 1%, mu: 1.02981 1.03652 1.01836
>
> Step 8 Warning: pressure scaling more than 1%, mu: 1.01626 1.01848 1.00881
>
> Step 9 Warning: pressure scaling more than 1%, mu: 1.01081 1.01178 1.00552
> step 130, remaining runtime: 0 s
> Step 140 Warning: pressure scaling more than 1%, mu: 1.00411 1.00022 1.0102
> step 140, remaining runtime: 0 s
> Step 141 Warning: pressure scaling more than 1%, mu: 1.00439 1.00019
> 1.01173
>
> Step 142 Warning: pressure scaling more than 1%, mu: 1.00395 1.00019
> 1.01172
>
> 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
> -------------------------------------------------------
>
> "May the Force Be With You" (Star Wars)
> ___________________________________________________________________________
>
>
> By the way: this test runs properly and without any error in both
> (single and double precision) compilations with GCC, and in the single
> precision compilation with Portland. :(
>
> Does anybody have any idea of this kind of error? Is it a known issue,
> someone has came across this kind of behavior before?
>
> Thanks a lot everybody for all and any help in advance! ;)
>
> Jones
>
> On 4/27/06, *David van der Spoel* <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>> wrote:
>
> Jones de Andrade wrote:
> > Hi.
> >
> > Sorry if it looks like a stupidy question (and it is), but I'm
> quite bad
> > on C (fortran addicted).
> >
> > I found 4 entries in the file like the one you told me to change.
> May I
> > change all them, or which ones?
> >
> only the one in the function that the compiler complains about. goto
> line 313 and then upwards from there until you find the offensive
> declaration.
>
> > Thanks a lot,
> >
> > Jones
> >
> > On 4/26/06, *David van der Spoel* <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>
> > <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se> >> wrote:
> >
> > Jones de Andrade wrote:
> > > Hi all.
> > >
> > > Well, some time ago I decided to bench gromacs on AMD64
> machines
> > > compiled with different compilers (both single and double
> precision,
> > > both internal and external blas and lapack, just FFTw 3
> for fourier)
> > > in order to see which one performs better.
> > >
> > > To time, I have available GCC, PGI and Intel compilers.
> Pathscale
> > is a
> > > future option.
> > >
> > > Unfortunatelly, I was able to properly compile it just
> with GCC
> > (all 4
> > > flavours, despite the fact that the external libraries of
> ACML didn't
> > > seem to improve so much the performance as I expected),
> but failed on
> > > both PGI and Intel compilers at different points. So, I'm
> asking for
> > > help on those compilation issues.
> > >
> > > For Intel, the compilation ends up with a segmentation
> fault at the
> > > following point:
> > >
> > >
> >
> ***********************************************************************************
>
> >
> > > ./mknb -software_invsqrt
> > > >>> Gromacs nonbonded kernel generator (-h for help)
> > > >>> Generating single precision functions in C.
> > > >>> Using Gromacs software version of 1/sqrt(x).
> > > make[5]: *** [kernel-stamp] Falha de segmentação
> > > make[5]: Leaving directory
> > >
> >
> `/home/johannes/src/gromacs/gromacs-3.3/src/gmxlib/nonbonded/nb_kernel'
> > > make[4]: ** [all-recursive] Erro 1
> > >
> >
> ***********************************************************************************
> > >
> > > And, for PGI, it dies at the following point (after using the
> > > --without-x --without-motif-libraries --
> without-motif-includes
> > flags
> > > for configure):
> > >
> > >
> >
> ****************************************************************************************
> > > source='gmx_sgangle.c' object='gmx_sgangle.lo' libtool=yes \
> > > DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
> > > /bin/sh ../../libtool --mode=compile --tag=CC
> > > /usr/local/pgi/linux86-64/6.0/bin/pgcc -DHAVE_CONFIG_H -I.
> -I.
> > > -I../../src -I../../include
> > >
> -DGMXLIBDIR=\"/usr/local/bin/chemistry/gromacs/PSI//share/top\"
> > > -I/usr/local/lib64/fftw/pgi/include -tp=k8-64 -fastsse
> -Mipa=fast
> > > -Mipa=inline -c -o gmx_sgangle.lo gmx_sgangle.c
> > > /usr/local/pgi/linux86-64/6.0/bin/pgcc -DHAVE_CONFIG_H
> -I. -I.
> > > -I../../src -I../../include
> > >
> -DGMXLIBDIR=\"/usr/local/bin/chemistry/gromacs/PSI//share/top\"
> > > -I/usr/local/lib64/fftw/pgi/include -tp=k8-64 -fastsse
> -Mipa=fast
> > > -Mipa=inline -c gmx_sgangle.c -o gmx_sgangle.o
> > > PGC-S-0090-Scalar data type required for logical expression
> > > (gmx_sgangle.c: 313)
> > > PGC-S-0090-Scalar data type required for logical expression
> > > (gmx_sgangle.c: 320)
> > > PGC/x86-64 Linux/x86-64 6.0-5: compilation completed with
> severe
> > errors
> > >
> >
> **************************************************************************************
> >
> > >
> > Shitty compiler...
> >
> > replace in the header of the function
> > matrix box,
> > by
> > rvec *box
> >
> >
> > > Did anyone run into those problems before when trying to
> compile
> > > gromacs with those compilers?
> > >
> > > Any help will be very welcome. :)
> > >
> > > Thanks a lot in advance,
> > >
> > > Jones
> > >
> > > P.S.: I'm using the "mixed" run simulation of the "tutor"
> > directory as
> > > a compilation test.
> > > _______________________________________________
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> > <mailto:gmx-users at gromacs.org <mailto: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 <mailto:spoel at xray.bmc.uu.se>
> > <mailto:spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>> spoel at gromacs.org
> <mailto:spoel at gromacs.org>
> > <mailto:spoel at gromacs.org <mailto:spoel at gromacs.org>>
> http://folding.bmc.uu.se
> >
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> >
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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
> <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org
> <mailto:spoel at gromacs.org> http://folding.bmc.uu.se
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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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