Hi all.<br>
<br>
Well, if I do not use the clue provided in
<a href="http://www.gromacs.org/pipermail/gmx-users/2005-December/018885.html">http://www.gromacs.org/pipermail/gmx-users/2005-December/018885.html</a>, I
end up in the following error:<br>
<br>
.<br>
.<br>
.<br>
source='gmx_sgangle.c' object='gmx_sgangle.lo' libtool=yes \<br>
DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \<br>
/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<br>
/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<br>
PGC-S-0090-Scalar data type required for logical expression (gmx_sgangle.c: 313)<br>
PGC-S-0090-Scalar data type required for logical expression (gmx_sgangle.c: 320)<br>
PGC/x86-64 Linux/x86-64 6.0-5: compilation completed with severe errors<br>
make[3]: ** [gmx_sgangle.lo] Erro 1<br>
make[3]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src/tools'<br>
make[2]: ** [all-recursive] Erro 1<br>
make[2]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src'<br>
make[1]: ** [all] Erro 2<br>
make[1]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src'<br>
make: ** [all-recursive] Erro 1<br>
.<br>
<br>
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:<br>
<br>
.<br>
.<br>
.<br>
step 0<br>
Step 1 Warning: pressure scaling more than 1%, mu: 1.01018 1.02193 1.08117<br>
<br>
Step 2 Warning: pressure scaling more than 1%, mu: 1.01124 1.00787 1.08362<br>
<br>
Step 3 Warning: pressure scaling more than 1%, mu: 1.03039 1.0523 1.08046<br>
<br>
Step 4 Warning: pressure scaling more than 1%, mu: 1.04141 1.08638 1.09351<br>
<br>
Step 5 Warning: pressure scaling more than 1%, mu: 1.06415 1.0995 1.06772<br>
<br>
Step 6 Warning: pressure scaling more than 1%, mu: 1.04802 1.07721 1.04162<br>
<br>
Step 7 Warning: pressure scaling more than 1%, mu: 1.02981 1.03652 1.01836<br>
<br>
Step 8 Warning: pressure scaling more than 1%, mu: 1.01626 1.01848 1.00881<br>
<br>
Step 9 Warning: pressure scaling more than 1%, mu: 1.01081 1.01178 1.00552<br>
step 130, remaining runtime: 0 s<br>
Step 140 Warning: pressure scaling more than 1%, mu: 1.00411 1.00022 1.0102<br>
step 140, remaining runtime: 0 s<br>
Step 141 Warning: pressure scaling more than 1%, mu: 1.00439 1.00019 1.01173<br>
<br>
Step 142 Warning: pressure scaling more than 1%, mu: 1.00395 1.00019 1.01172<br>
<br>
Step 143 Warning: pressure scaling more than 1%, mu: 1.00304 1.00017 1.01009<br>
step 240, remaining runtime: 0 s<br>
-------------------------------------------------------<br>
Program mdrun_d, VERSION 3.3<br>
Source code file: stat.c, line: 283<br>
<br>
<div> Fatal error:<br>
XTC error<br>
-------------------------------------------------------<br>
<br>
"Fly to the Court of England and Unfold" (Macbeth, Act 3, Scene 6, William Shakespeare) </div>.<br>
<br>
<br>
Finally, it behaves like that while using the PGI compilers. It works properly with GCC.<br>
<br>
Any ideas of where to go now? :(<br>
<br>
Thanks for everything.<br>
<br>
Jones<br><br><div><span class="gmail_quote">On 4/24/06, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Jones de Andrade wrote:<br>> Ok, thanks a lot. adding the wthout x and motif stuff in configure, plus<br>> the corrections for gmx_sgangle.c found at<br>> <a href="http://www.gromacs.org/pipermail/gmx-users/2005-December/018885.html">
http://www.gromacs.org/pipermail/gmx-users/2005-December/018885.html</a><br>> made the compilation work.<br>><br>> Now I'm having some strange problem: I am trying as test the "mixed"<br>> sample in the tutor directory. When trying it as is with the *double
<br>> precision* version of gromacs I compiled, it yelds this error:<br>> .<br>> .<br>If you mention that change, didn't you download the 3.3.1 version for<br>this test?<br><br><br>> .<br>> step 0<br>> Step 1 Warning: pressure scaling more than 1%, mu:
1.01018 1.02193 1.08117<br>><br>> Step 2 Warning: pressure scaling more than 1%, mu: 1.01124 1.00787 1.08362<br>><br>> Step 3 Warning: pressure scaling more than 1%, mu: 1.03039 1.0523 1.08046<br>><br>> Step 4 Warning: pressure scaling more than 1%, mu:
1.04141 1.08638 1.09351<br>><br>> Step 5 Warning: pressure scaling more than 1%, mu: 1.06415 1.0995 1.06772<br>><br>> Step 6 Warning: pressure scaling more than 1%, mu: 1.04802 1.07721 1.04162<br>><br>> Step 7 Warning: pressure scaling more than 1%, mu:
1.02981 1.03652 1.01836<br>><br>> Step 8 Warning: pressure scaling more than 1%, mu: 1.01626 1.01848 1.00881<br>><br>> Step 9 Warning: pressure scaling more than 1%, mu: 1.01081 1.01178 1.00552<br>> step 130, remaining runtime: 0 s
<br>> Step 140 Warning: pressure scaling more than 1%, mu: 1.00411 1.00022 1.0102<br>> step 140, remaining runtime: 0 s<br>> Step 141 Warning: pressure scaling more than 1%, mu: 1.00439 1.00019<br>> 1.01173
<br>><br>> Step 142 Warning: pressure scaling more than 1%, mu: 1.00395 1.00019<br>> 1.01172<br>><br>> Step 143 Warning: pressure scaling more than 1%, mu: 1.00304 1.00017<br>> 1.01009<br>> step 240, remaining runtime: 0 s
<br>> -------------------------------------------------------<br>> Program mdrun_d, VERSION 3.3<br>> Source code file: stat.c, line: 283<br>><br>> Fatal error:<br>> XTC error<br>> -------------------------------------------------------
<br>><br>> "Fly to the Court of England and Unfold" (Macbeth, Act 3, Scene 6,<br>> William Shakespeare)<br>><br>><br>> And dies at this point.<br>><br>> When using the single precision gromacs, it seems to runs smoothly. :)
<br>> Same for both single and double precision compiled with gcc.<br>><br>> Anyone got this kind of stuff before?<br>><br>> Thanks a lot! :D<br>><br>> On 4/24/06, *David van der Spoel* <<a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>> wrote:<br>><br>> Jones de Andrade wrote:<br>> > Hi all!<br>> ><br>> > Ok, I did not acquired to compile gromacs with intel yet, but now I'm
<br>> > also facing problems with PGI compilers (which also has the extra<br>> > problem of needin to be redownloaded soon).<br>> ><br>> > Just in case someone asks: I'm trying to benchmark gromacs in
<br>> A64s with<br>> > different compilers. ;)<br>> ><br>> > Well, PGI is dieing here:<br>> > .<br>> > .<br>> > .<br>> > /usr/local/pgi/linux86-64/6.0
<br>> > /bin/pgcc -tp=k8-64 -fastsse -Mipa=fast -Mipa=inline -o grompp<br>> topio.o<br>> > toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o<br>> splitter.o<br>> > vsite_parm.o
readir.o add_par.o topexcl.o toputil.o topdirs.o<br>> grompp.o<br>> > -L/usr/local/lib64/fftw/pgi/lib ../mdlib/.libs/libmd.a<br>> > -L/usr/X11R6/lib64 -L/usr/X11/lib ../gmxlib/.libs/libgmx.a -lnsl
<br>> > /usr/local/lib64/fftw/pgi/lib/libfftw3f.a -lm<br>> /usr/X11R6/lib64/libXm.so<br>> > -lXmu -lSM -lICE -lXext -lXp -lXt -lX11 --rpath /usr/X11R6/lib64<br>> --rpath<br>> > /usr/X11R6/lib64
<br>> > pgcc-Warning-Unknown switch: --rpath<br>> > pgcc-Warning-Unknown switch: --rpath<br>> > File with unknown suffix passed to linker: /usr/X11R6/lib64<br>> > File with unknown suffix passed to linker: /usr/X11R6/lib64
<br>> > .<br>> try compiling without X windows in that case.<br>><br>><br>> > .<br>> > .<br>> ><br>> > I googled this kind of error, but it's only reported to LAM... in
<br>> that<br>> > case, they basically recomend to pass the -Wl flag to the linker.<br>> ><br>> > Did anybody here faced this problem before? How it was solved? And<br>> > exactly how culd I pas that extra flag just to the linker (tried
<br>> > straight the LDFLAGS, then the ./configure does not find that the<br>> > compiler can produce executables... :p )?<br>> ><br>> > Thanks you all for all the help. Promisse to send the results of the
<br>> > benchs to here when they are finished. :)<br>> ><br>> > Thanks again,<br>> ><br>> > *Ops, sorry for the first message: wrong thread... :(<br>> ><br>
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