Hi All.<br>
<br>
Well, first of all, I would like to thank a lot David for all the help
he gave me up to now. I don't know how to thank for so much help
neither how to apologize for bothering you this much.<br>
<br>
Up to now, I could finally compile it with Portland, in both single and
double precision version. But, on the other hand, while the single
precision works properly, the double precision fails in some tests,
like the "mixed" test on the "tutor" directory. It yelds me the
following error message:<br>
<br>
_________________________________________________________________________<br>
starting mdrun 'Pure Methanol - Yummie! (and some water)'<br>
10000 steps, 20.0 ps.<br>
<br>
<br>
Back Off! I just backed up traj.trr to ./#traj.trr.10#<br>
<br>
Back Off! I just backed up traj.xtc to ./#traj.xtc.10#<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: 40
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>
"May the Force Be With You" (Star Wars)<br>
___________________________________________________________________________<br>
<br>
<br>
By the way: this test runs properly and without any error in both
(single and double precision) compilations with GCC, and in the single
precision compilation with Portland. :(<br>
<br>
Does anybody have any idea of this kind of error? Is it a known issue, someone has came across this kind of behavior before?<br>
<br>
Thanks a lot everybody for all and any help in advance! ;)<br>
<br>
Jones<br>
<br>
<div><span class="gmail_quote">On 4/27/06, <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.<br>><br>> Sorry if it looks like a stupidy question (and it is), but I'm quite bad<br>> on C (fortran addicted).<br>><br>> I found 4 entries in the file like the one you told me to change. May I
<br>> change all them, or which ones?<br>><br>only the one in the function that the compiler complains about. goto<br>line 313 and then upwards from there until you find the offensive<br>declaration.<br><br>> Thanks a lot,
<br>><br>> Jones<br>><br>> On 4/26/06, *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>> > Well, some time ago I decided to bench gromacs on AMD64 machines<br>> > compiled with different compilers (both single and double precision,
<br>> > both internal and external blas and lapack, just FFTw 3 for fourier)<br>> > in order to see which one performs better.<br>> ><br>> > To time, I have available GCC, PGI and Intel compilers. Pathscale
<br>> is a<br>> > future option.<br>> ><br>> > Unfortunatelly, I was able to properly compile it just with GCC<br>> (all 4<br>> > flavours, despite the fact that the external libraries of ACML didn't
<br>> > seem to improve so much the performance as I expected), but failed on<br>> > both PGI and Intel compilers at different points. So, I'm asking for<br>> > help on those compilation issues.
<br>> ><br>> > For Intel, the compilation ends up with a segmentation fault at the<br>> > following point:<br>> ><br>> ><br>> ***********************************************************************************
<br>><br>> > ./mknb -software_invsqrt<br>> > >>> Gromacs nonbonded kernel generator (-h for help)<br>> > >>> Generating single precision functions in C.<br>> > >>> Using Gromacs software version of 1/sqrt(x).
<br>> > make[5]: *** [kernel-stamp] Falha de segmentação<br>> > make[5]: Leaving directory<br>> ><br>> `/home/johannes/src/gromacs/gromacs-3.3/src/gmxlib/nonbonded/nb_kernel'<br>> > make[4]: ** [all-recursive] Erro 1
<br>> ><br>> ***********************************************************************************<br>> ><br>> > And, for PGI, it dies at the following point (after using the<br>> > --without-x --without-motif-libraries -- without-motif-includes
<br>> flags<br>> > for configure):<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<br>> > /usr/local/pgi/linux86-64/6.0/bin/pgcc -DHAVE_CONFIG_H -I. -I.
<br>> > -I../../src -I../../include<br>> > -DGMXLIBDIR=\"/usr/local/bin/chemistry/gromacs/PSI//share/top\"<br>> > -I/usr/local/lib64/fftw/pgi/include -tp=k8-64 -fastsse -Mipa=fast
<br>> > -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.<br>> > -I../../src -I../../include<br>> > -DGMXLIBDIR=\"/usr/local/bin/chemistry/gromacs/PSI//share/top\"
<br>> > -I/usr/local/lib64/fftw/pgi/include -tp=k8-64 -fastsse -Mipa=fast<br>> > -Mipa=inline -c gmx_sgangle.c -o gmx_sgangle.o<br>> > PGC-S-0090-Scalar data type required for logical expression
<br>> > (gmx_sgangle.c: 313)<br>> > PGC-S-0090-Scalar data type required for logical expression<br>> > (gmx_sgangle.c: 320)<br>> > PGC/x86-64 Linux/x86-64 6.0-5: compilation completed with severe
<br>> errors<br>> ><br>> **************************************************************************************<br>><br>> ><br>> Shitty compiler...<br>><br>> replace in the header of the function
<br>> matrix box,<br>> by<br>> rvec *box<br>><br>><br>> > Did anyone run into those problems before when trying to compile<br>> > gromacs with those compilers?<br>> >
<br>> > Any help will be very welcome. :)<br>> ><br>> > Thanks a lot in advance,<br>> ><br>> > Jones<br>> ><br>> > P.S.: I'm using the "mixed" run simulation of the "tutor"
<br>> directory as<br>> > a compilation test.<br>> > _______________________________________________<br>> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
</a><br>> <mailto:<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>> <mailto:
<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>><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><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
</a><br>> <mailto:<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>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <mailto:<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>> <<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>> <mailto:<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>> ------------------------------------------------------------------------<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>_______________________________________________<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></blockquote></div><br>