[gmx-users] PGI compilation error: --rpath problem?
David van der Spoel
spoel at xray.bmc.uu.se
Mon Apr 24 22:37:05 CEST 2006
Jones de Andrade wrote:
> Ok, thanks a lot. adding the wthout x and motif stuff in configure, plus
> the corrections for gmx_sgangle.c found at
> http://www.gromacs.org/pipermail/gmx-users/2005-December/018885.html
> made the compilation work.
>
> Now I'm having some strange problem: I am trying as test the "mixed"
> sample in the tutor directory. When trying it as is with the *double
> precision* version of gromacs I compiled, it yelds this error:
> .
> .
If you mention that change, didn't you download the 3.3.1 version for
this test?
> .
> 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: 0 s
> -------------------------------------------------------
> Program mdrun_d, VERSION 3.3
> Source code file: stat.c, line: 283
>
> Fatal error:
> XTC error
> -------------------------------------------------------
>
> "Fly to the Court of England and Unfold" (Macbeth, Act 3, Scene 6,
> William Shakespeare)
>
>
> And dies at this point.
>
> When using the single precision gromacs, it seems to runs smoothly. :)
> Same for both single and double precision compiled with gcc.
>
> Anyone got this kind of stuff before?
>
> Thanks a lot! :D
>
> On 4/24/06, *David van der Spoel* <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>> wrote:
>
> Jones de Andrade wrote:
> > Hi all!
> >
> > Ok, I did not acquired to compile gromacs with intel yet, but now I'm
> > also facing problems with PGI compilers (which also has the extra
> > problem of needin to be redownloaded soon).
> >
> > Just in case someone asks: I'm trying to benchmark gromacs in
> A64s with
> > different compilers. ;)
> >
> > Well, PGI is dieing here:
> > .
> > .
> > .
> > /usr/local/pgi/linux86-64/6.0
> > /bin/pgcc -tp=k8-64 -fastsse -Mipa=fast -Mipa=inline -o grompp
> topio.o
> > toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o
> splitter.o
> > vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o
> grompp.o
> > -L/usr/local/lib64/fftw/pgi/lib ../mdlib/.libs/libmd.a
> > -L/usr/X11R6/lib64 -L/usr/X11/lib ../gmxlib/.libs/libgmx.a -lnsl
> > /usr/local/lib64/fftw/pgi/lib/libfftw3f.a -lm
> /usr/X11R6/lib64/libXm.so
> > -lXmu -lSM -lICE -lXext -lXp -lXt -lX11 --rpath /usr/X11R6/lib64
> --rpath
> > /usr/X11R6/lib64
> > pgcc-Warning-Unknown switch: --rpath
> > pgcc-Warning-Unknown switch: --rpath
> > File with unknown suffix passed to linker: /usr/X11R6/lib64
> > File with unknown suffix passed to linker: /usr/X11R6/lib64
> > .
> try compiling without X windows in that case.
>
>
> > .
> > .
> >
> > I googled this kind of error, but it's only reported to LAM... in
> that
> > case, they basically recomend to pass the -Wl flag to the linker.
> >
> > Did anybody here faced this problem before? How it was solved? And
> > exactly how culd I pas that extra flag just to the linker (tried
> > straight the LDFLAGS, then the ./configure does not find that the
> > compiler can produce executables... :p )?
> >
> > Thanks you all for all the help. Promisse to send the results of the
> > benchs to here when they are finished. :)
> >
> > Thanks again,
> >
> > *Ops, sorry for the first message: wrong thread... :(
> >
> >
> >
> ------------------------------------------------------------------------
> >
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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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