First, sorry for the delay in getting in touch again. Bureaucracy. :P
Second, thanks a lot for everybody for advising on this subject. It's helping me a lot to solve this! :)
Anyway, here is where I'm now:
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. :(
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. ;)
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?
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).
By the way, can I ask you what was the "mknb" program for, anyway? :)
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". ;)
Jones
On 6/1/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
> make[3]: ** [grompp] Erro 1
> make[3]: Leaving directory
> `/home/johannes/src/gromacs/gromacs-3.3/src/kernel'
> 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
> **********************************************************************************************
>
> Trying withou the "-ipo" flag now. It still yelds the same weird warning
> (warning #147: declaration is incompatible with "double invsqrt(double)"
> (declared at line 565 of "/usr/local/intel/include/math.h")
rename all gromacs invsqrt calls to gmx_invsqrt
be assured that invsqrt didn't exist in the intel compiler in previous
releases, but now that it does we'll have to adapt it seems.
ipo is useless for gromacs.
do also turn off X11 at the configure stage
--
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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