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)
.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 <[EMAIL PROTECTED]> 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* < [EMAIL PROTECTED]
> <mailto:[EMAIL PROTECTED]>> 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
> [EMAIL PROTECTED]
> <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]
> <mailto:[EMAIL PROTECTED]> 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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