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

Jones de Andrade johannesrs at gmail.com
Tue Apr 25 04:47:25 CEST 2006


Hi all.

Well, if I do not use the clue provided in
http://www.gromacs.org/pipermail/gmx-users/2005-December/018885.html, I end
up in the following error:

.
.
.
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
make[3]: ** [gmx_sgangle.lo] Erro 1
make[3]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3
/src/tools'
make[2]: ** [all-recursive] Erro 1
make[2]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src'
make[1]: ** [all] Erro 2
make[1]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src'
make: ** [all-recursive] Erro 1
.

On the other hand, using that modified version of the gmx_sgangle.c ended up
in errors when using the double precision version of gromacs (I'm using the
3.1.1 version) to run the mixed test simulation from tutor directory:

.
.
.
 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)
.


Finally, it behaves like that while using the PGI compilers. It works
properly with GCC.

Any ideas of where to go now? :(

Thanks for everything.

Jones

On 4/24/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> 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... :(
> >      >
> >      >
> >      >
> >
> ------------------------------------------------------------------------
> >      >
> >      > _______________________________________________
> >      > gmx-users mailing list    gmx-users at gromacs.org
> >     <mailto:gmx-users at gromacs.org>
> >      > http://www.gromacs.org/mailman/listinfo/gmx-users
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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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