Re: [AMBER-Developers] fftw questions

From: Scott Brozell <>
Date: Sun, 12 Feb 2012 00:33:21 -0500


On Sat, Feb 11, 2012 at 10:40:47PM -0500, case wrote:
> 1. Do we still need fftw2? The configure2 script configures it if both
> rims and mdgx are set to "no", but I don't understand why. What codes are
> using fftw2?

The preprocessor name FFTW2 is still used in 4 files in
If this usage is eliminated then it looks like fftw2 can be to.

> Note that there is buglet in the Makefile: the clean and uninstall targets
> try to run "make" inside fftw-2.1.5, but if those are not configured, then
> there is no Makefile to be run inside those directories.
> 2. I'm still having problems with fftw3, on an i386 Intel mac (OS 10.5.8).
> I find that I have to add -nosse to the configure2 script: this wasn't caught
> before because of a bug (now fixed) in configure2 that never passed sse flags
> to fftw3 even if sse was turned on. I'd be interested to hear if anyone else
> can confirm this; and if sse problems occur on other Macs, or other platforms.
> (I'm using gcc 4.5.2).
> 3. In general, all this stuff about SSE seems fragile and possibly
> un-necessary. Can't compilers optimize code with minimal help
> from the user? That is, do we know that just using -mtune=native (or -fast
> for Intel) doesn't do a good job. Should I be expected to know the
> differences between SSE2, SSE3 and SSE4.1 or 4.2??? It would sure be nice
> to simplify this.

I investigated this a little more since my Feb 7 email.
>From the ifort Version Build 20110811 man page
it looks like -fast will do the right thing if amber is
built on the machine that it will be run on.
There have been a lot of am-dev emails related to this.

I hope to test this on at least 1 machine soon.

> 4. Do we really need the -nomdgx or -nocpptraj flags? I'd be inclined to
> have fewer flags, and ask users to just comment out the relevant lines in the
> Makefile if they happen on a machine where these programs fail to compile.
> Probably the same answer for -nomtkpp. I'm inclined to keep
> -noX11, since that is a relatively common option.

Probably we do not need those flags except noX11.
It'd be nice to know if people have used them ?


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Received on Sat Feb 11 2012 - 22:00:02 PST
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