<font size="2">Ok, thanks a lot. adding the wthout x and motif stuff in configure, plus the corrections for </font><font style="font-weight: normal;" size="2">gmx_sgangle.c found at <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> made the compilation work.</font><br>
<br>
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:<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>
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, William Shakespeare)<br>
<br>
<br>
And dies at this point.<br>
<br>
When using the single precision gromacs, it seems to runs smoothly. :)
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>
<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>> 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 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 topio.o<br>> toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o<br>> vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o
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 /usr/X11R6/lib64/libXm.so
<br>> -lXmu -lSM -lICE -lXext -lXp -lXt -lX11 --rpath /usr/X11R6/lib64 --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 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>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________
<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">
http://www.gromacs.org/mailing_lists/users.php</a><br><br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>_______________________________________________
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</a><br></blockquote></div><br>