[gmx-users] PGI compilation error: --rpath problem?

[Jones de Andrade]

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:
.
.
.
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> 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    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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