[AMBER-Developers] fftw questions

From: case <case.biomaps.rutgers.edu>
Date: Sat, 11 Feb 2012 22:40:47 -0500

Some questions about fftw:

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?

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.

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.


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Received on Sat Feb 11 2012 - 20:00:03 PST
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