Hi,
The -xP for pmemd is clearly wrong as your build demonstrates.
Assuming some compilers for pmemd still cannot handle -ipo then
the only difference between pmemd and sander should be -ip vs -ipo.
However, assuming -ipo doesn't enhance sander then we arrive at
-ip -O3 -no-prec-div -xHost
for versions 11 and 12.
For older versions:
-ip -O3 -no-prec-div -axSTPW
(So the difference between mine and Ross's is -no-prec-div
which is supported at least back to 9.1.)
Ideally we should be using -fast for all versions and programs
(and be ignoring heterogenous platforms).
I built amber11 pmemd with 12.1.0 and
-ipo -O3 -no-prec-div -xSSE4.2 -static-intel
which is almost equivalent to -fast (-static-intel vs -static a local issue)
So has anyone tried to build amber12 pmemd with fast on new compilers ?
Perhaps we should just use -fast for new compilers ?
Perhaps we should break equilvalence between sander and pmemd
and use -fast for sander ?
On Sun, Mar 18, 2012 at 10:00:18AM -0700, Ross Walker wrote:
> I think this is mostly historical divergence.
>
> Ideally we should have:
>
> old compilers = -fast
>
> new compilers = -ipo -xhost
Why ? -fast for version 12 equals
-ipo -O3 -no-prec-div -xHost -static
scott
> The issue is that -fast enables -ipo by default and this caused compiler
> crashes when trying to link pmemd. Thus pmemd was switched back to -ip -O3
> -xP
>
> I am not sure when it got changed to -xP though. For new compilers (11 and
> newer?) you just specify -xhost and it will use the optimum vector
> parameters for the host you are compiling on. This means it won't run on
> different chip versions so causes problems with people with heterogeneous
> clusters but maybe we shouldn't worry about that and let them figure it for
> themselves?
>
> Otherwise we have to specify all of the SSE vectorization options and the
> problem is that Intel keeps changing the options as well as the syntax with
> every compiler.
>
> For the pre 11 compilers I think one uses the -xAAA options. Here -x means
> create vector code only. -ax also means generate generic x86 code. Thus -axP
> will make an executable that always works but it will only run fast on chip
> versions that support the 'P' vectorization options. Once can try to add
> them all which is what is in sander and is probably what SHOULD be in pmemd.
> So for intel <11 it should probably be:
>
> -ip -O3 -axSTPW
>
> I 'think' this will work with all ifort versions from 9 to 10 and should be
> optimum performance (although a massive executable) on most Intel and AMD
> chips exluding the latest Sandybridge chips but I think one should probably
> use ifort v12 for those anyway which would then use -xhost since from 11
> onwards it changed to /QhostBLAH in which case we should just use -xhost and
> let the compiler figure it automatically.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: case [mailto:case.biomaps.rutgers.edu]
> > Sent: Sunday, March 18, 2012 5:51 AM
> > To: amber-developers.ambermd.org
> > Subject: [AMBER-Developers] SSE-based compile flags for intel
> >
> > Does anyone understand why we use the flags we do for Intel compilers?
> >
> > For sander, we have -ip -O3 -axSTPW; for pmemd, it is -ipo -O3 -no-
> > prec-div
> > -xP. Is there a good reason for the difference?
> >
> > For me, with intel compiler 10.1, pmemd with the default install
> > creates
> > an unusable executable ("Fatal Error: This program was not built to run
> > on the processor in your system. The allowed processors are: Intel(R)
> > Pentium(R) 4 and compatible Intel processors with Streaming SIMD
> > Extensions 3 (SSE3) instruction support.)
> >
> > Rather oddly(?), pmemd.amoeba, which seems to be compiled with the same
> > options, is OK. (Code for pmemd.amoeba has changed very little from
> > Amber
> > 11).
> >
> > If I change -xP to -axP, pmemd is fine for ifort 10.1.
> >
> > So: why are sander optimizations different than pmemd? Are we
> > somewhere near
> > optimal? Do users really need to learn the ins and outs of SSE_TYPES?
> > What
> > is the best thing to do for pmemd on ifort 10? (e.g. would changing -
> > xP to
> > -axP do harm on ifort 11 or 12?)
> >
> > ...thx...dac
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Received on Sun Mar 18 2012 - 15:00:03 PDT
