Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler

From: Jiten <>
Date: Tue, 13 Jul 2004 18:52:06 +0900

Dear Dr. Scott,

I have recompiled the amber8 withe modifications as done by Mark
without -big option and after changing to k8-64 in config.h file. The number
of test FAILURE is same as reported by Mark. Here I notice that tleap is
PASSED. I still could not compile amber8 with 32 bit as the PGI-workstation
installed in our computer is 64-bit. We are not sure how to make it 32-bit

I such case can I use the sander atleast safely ?

Hello Mark - can you use xleap in your case,

With best wishes,


----- Original Message -----
From: "Scott Brozell" <>
To: <>
Sent: Tuesday, July 13, 2004 3:30 AM
Subject: RE: AMBER: Problem amber8 compilation in Opteron(Linux) with
PGI-workstation compiler

> dac> ./configure -opteron -verbose -big pgf90
> dac> Don't use the -big option, until you have tried everything without
> dac> option. I don't think it really works, or indeed in necessary.
> The idea of -big is to create executables that can access more than
> 2^32 bytes of memory. If you do not need that much address space then
> even on a 64 bit machine you do not need -big.
> Indeed -big may have a performance penalty.
> When we had an opteron at Scripps in Aug 2003 we had troubles building
> Charmm and Amber. But ultimately sander was built with
> configure -opteron -big pgf90 and configure -opteron pgf90.
> I do not have an opteron now, but I do not notice any glaring
> problems in the pgf90 section of configure.
> On Sun, 11 Jul 2004, Mark Williamson wrote:
> > ./configure -opteron -verbose pgf90
> >
> > [root.e01 root]# pgf90 -V
> > pgf90 5.1-6
> > pgf90 -c -tp k8-32 -O -v -V -Minfo=all -Minform=inform -Mneginfo -o
new2oldparm.o _new2oldparm.f
> > pgf90-Error--tp k8-32 not supported in this
> >
> > I'm assuming the error has occurred because I've only got the 64bit
> > compiler installed.
> pgf90 5.1-3 did not complain about -tp k8-32 when used on a pentium IV.
> > Now, why was configure using k8-32?
> because the default build size for amber is 32 bit regardless of the
> default word size of the architecture.
> > Surely this will only produce 32bit code?
> hopefully, since that is the intention.
> > In fact, there is no reference to k8-64 (AMD K8 Processor 64-bit mode)
> > in the configure script:
> again that is intentional because according to the pgf90 man page :
> The default in the absence of the -tp flag is
> to compile for type of CPU on which the compiler is
> So one only gets k8-64 when one builds on an opteron; this should be
> if one wants to do cross compilation, but my advice is 'builder beware'.
> > No idea why, but replacing every instance of k8-32 with k8-64 in the
> > config.h (from ./configure -opteron -verbose pgf90) produced a good
> This seems reasonable to me, but I have not been following every nuance
> of this thread to know if you are implying some contradiction.
> Jiten> Another problem I face after the compilation is that xleap seg
> xleap and tleap may not be 64 bit clean.
> Build leap for 32 bit, ie, without -big.
> Scott Brozell
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Received on Tue Jul 13 2004 - 10:53:01 PDT
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