[gmx-users] CFLAGS

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 17 16:00:58 CET 2005 

On Thu, 2005-11-17 at 13:57 +0000, Joanne Hanna wrote:
> Hello
> 
> Thanks very much. I think I am beginning to understand what i am doing now. my system is running RedHat Enterprise Linux AS 3.0 / SGI ProPack but when i try to configure i produce a ia64-unknown-linux-gnu executable, is this okay?
yes. 
> 
> Thanks
> Jo 
> 
> >>> lindahl at sbc.su.se 11/17/05 13:05 PM >>>
> Hi,
> 
> The configure script does a pretty good job of detecting things  
> automatically. The appropriate assembly loops are enabled by default  
> - use the switches if you want to disable them for some reason.
> 
> The same thing goes for the compiler options - just set them manually  
> if the automatic detection doesn't work.
> 
> ia64 is a bit special in that the nonbonded loops are very optimized  
> relative to the neighborsearching (compared to ia32 or x86_64). Since  
> the neighborsearching is compiled code you probably want to use the  
> intel compiler and "-O3" (should be set automatically if you define  
> CC=icc) for better performance.
> 
> Cheers,
> 
> Erik
> 
> 
> 
> On Nov 16, 2005, at 6:18 PM, Joanne Hanna wrote:
> 
> > 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
> >>> _______________________________________________
> >>> gmx-users mailing list
> >>> gmx-users at gromacs.org
> >>> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>> Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or send it to gmx-users-request at gromacs.org.
> >>
> >> -----------------------------------------------------------
> >> 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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> 
> -----------------------------------------------------------
> 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
> 
> 
> 
> 
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-- 
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
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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