Hi all!.<br>
<br>
First, sorry for the delay in getting in touch again. Bureaucracy. :P<br>
<br>
Second, thanks a lot for everybody for advising on this subject. It's helping me a lot to solve this! :)<br>
<br>
Anyway, here is where I'm now:<br>
<br>
Erik: I'm sure about the flags. Not using the ones for SSE3, despite my
processor having those. I'll just try to activate those as soon as I
get a compiling procedure. By now, I even using the
--disable-x86-64-sse flag for configure, just to be sure. ;) Also, I
tried the "CC_FOR_BUILD=gcc" environment, but despite it has gone throw
the invsqrt compilation, I looked in and it was compiling everything
with gcc, and nothing with icc. :(<br>
<br>
Yang: Yes, I'm using the intel compiler with emt64. I reinstalled the
software step by step specifically to be sure about this point. And I
understand that gromacs has an assembly core, and that this is
basically the "heart" of the program speed. But, even thow, 5-10% means
something, and every nano-second counts. Specially when you have a big
delay to deal with, and that this 10% mean 0.25ns. ;) Even then, after
I successfully compile it we will be able to say for sure how much if
extra performance (if it yelds any) does the intel compiler gives on
AMD64 machines. Moreover, as I said in a long time ago message: I want
to use QM/MM with gromacs+cpmd, and at this point I really dislike the
idea of compiling one thing with intel (cpmd) and the other with gcc
(gromacs). Since I can't make cpmd work on gcc, I'm trying to make
gromacs work on intel. ;)<br>
<br>
David (last but not the least): I removed the "-ipo" flag from the
compilations. Also, I've added "--without-motif-libraries
--without-motif-includes --without-x" flags to the configure script. On
the other hand, I've been "greping" a bit the directories for the
"invsqrt" calls.... My God, it's not the heart of the program, it's the
"sinapses" among its neurones. Am I wrong, or there is about some
thousands of those calls to be changed? Is it right?<br>
<br>
If it is, just let me know, cause I'm tracking those down (finding a
script way to back up original files before edition.) and at the same
time trying to find some sort of "magical flag" to convince icc to
*not* use the "invsqrt" function or the "math.h" file at all (second
choice seems to me a bit too strong). Seems that if it can be done on a
flag it will be really helpfull (and easier) for most of the users. The
good new is that there is no other error message in the ompilation, as
I can see (And just a few warnings to see later, since they look more
or less pointless).<br>
<br>
By the way, can I ask you what was the "mknb" program for, anyway? :)<br>
<br>
Again, thanks a lot to everybody in advance, for all the help an advices provided
up to now! If I manage to finish this one, I promisse to post those
extra benchmarks too, as well as a "tutorial" on "how to compile
gromacs on AMD64 machines with non-sense copilers". ;)<br>
<br>
Jones<br><br><div><span class="gmail_quote">On 6/1/06, <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;">
> make[3]: ** [grompp] Erro 1<br>> make[3]: Leaving directory<br>> `/home/johannes/src/gromacs/gromacs-3.3/src/kernel'<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>> Trying withou the "-ipo" flag now. It still yelds the same weird warning<br>> (warning #147: declaration is incompatible with "double invsqrt(double)"<br>> (declared at line 565 of "/usr/local/intel/include/math.h")
<br><br>rename all gromacs invsqrt calls to gmx_invsqrt<br><br>be assured that invsqrt didn't exist in the intel compiler in previous<br>releases, but now that it does we'll have to adapt it seems.<br><br>ipo is useless for gromacs.
<br><br>do also turn off X11 at the configure stage<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>
</blockquote></div>