[gmx-users] CFLAGS

[Joanne Hanna]

Joanne Hanna
Department of Chemistry
University of Warwick
Coventry
CV4 7AL

J.F.Hanna at warwick.ac.uk
>>> Florian.Haberl at chemie.uni-erlangen.de 11/16/05 17:05 PM >>>
hi,

On Wednesday 16 November 2005 17:47, Joanne Hanna wrote:
> Hi
>
> So if my machine is Intel Itanium2 should i really use version 3.3? and if
> i use 3.2.1 should i use the -O3 cflags option? Sorry I am quite new to
> compiling!

Normally you don^t use optimazition flags for compiling gromacs, only if you 
want to test further improvement of the speed, as Erik Lindal mentioned, 
there is not much speed improvement (i guess below 2% not more).

I would use gromacs 3.3 cause this is the version with buildin assembly loops, 
this means much better performance as version 3.2.1 on Itanium2 cpus (factor 
2 or so overall).

Okay so this should pick up the cflags automatically, as v3.2.1 does not and thats why i had to define them.
Also does this apply to my machine?
Add "--enable-sse" if you computers are i686 or x86-64.

Sorry for very obvious questions.
Jo

>
> Thanks
> Jo
>
> Joanne Hanna
> Department of Chemistry
> University of Warwick
> Coventry
> CV4 7AL
>
> J.F.Hanna at warwick.ac.uk
>
> >>> lindahl at sbc.su.se 11/16/05 15:05 PM >>>
>
> Hi,
>
> The intel compilers should support both -O3 (our default when icc is
> detected) and -O2. The difference isn't very large, though, since our
> assembly loops bypass the compiler on both ia32, X86-64, and ia64 -
> but then you need to use gromacs 3.3 or later!!! (3.2 only includes
> ia32 assembly loops).
>
> If you're only having problems when compiling with MPI support the
> culprit is likely the mpi wrapper script for the compiler.
>
> Cheers,
>
> Erik
>
> On Nov 16, 2005, at 2:53 PM, Joanne Hanna wrote:
> > Hi
> >
> > I have recently compiled an mpi version of gromacs 3.2.1 with the
> > icc compiler. I ran into troubles with this error, at the ./
> > configure stage:
> > * Sorry, these optimization settings don't seem to work for       *
> > * your C compiler. Use make CFLAGS=..., or edit the top Makefile. *
> > I decided to use the cflags option -O2.
> > Can anyone tell me whether this is a good option to use. I
> > understand that -O3 enables more aggressive optimisations such as
> > loop and  memory  access transformation. and is recommended for
> > applications that have loops with heavy use of float-ing point
> > calculations and process large data sets (as from the manual). But
> > i don't know which i should use.
> > I have been told that optimising too aggressively can produce the
> > wrong numbers.
> >
> > Anu advice would be much appreciated.
> >
> > Thanks
> > Jo
> >
> >
> > Joanne Hanna
> > Department of Chemistry
> > University of Warwick
> > Coventry
> > CV4 7AL
> >
> > J.F.Hanna at warwick.ac.uk
> > _______________________________________________
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>
> -----------------------------------------------------------
> Erik Lindahl  <lindahl at sbc.su.se>
> Assistant Professor, Stockholm Bioinformatics Center
> Stockholm University, SE 106 91 Stockholm
> Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
>

Greetings,
Florian

-- 
---------------------------------------------------------------------------------------------------
 Florian Haberl                             Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen
 
 Mailto: florian.haberl AT chemie.uni-erlangen.de
 
---------------------------------------------------------------------------------------------------

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