Re: [AMBER] Amber 12 Installation errors relevant to fftw3

From: M. L. Dodson <>
Date: Thu, 26 Apr 2012 10:32:44 -0500

See below.

On Apr 26, 2012, at 9:29 AM, Jason Swails wrote:

> On Wed, Apr 25, 2012 at 10:30 PM, case <> wrote:
>> On Thu, Apr 26, 2012, Shulin Zhuang wrote:
>>> Following your suggestions ,I got the same information using gcc -v and
>>> gfortran --v :
>>> gcc version 4.1.2 20080704 (Red Hat 4.1.2-46)
>> OK...this compiler version cannot be used to compile fftw3. As Jason said,
>> the configure script should have told you that. Very near the top of
>> configure's output there are lines like this:
>> Obtaining the gnu suite version:
>> gcc -v
>> The version is 4.6.2
>> What are the corresponding lines on your machine? That will help us figure
>> out why the error message is not being triggered. Thanks.
>>> I re-configured it using the -nofftw3 and can successfully installed the
>>> serial and parallel version of amber 12.
>> This is the best you can do without upgrading to the 4.3 or greater
>> versions
>> of the gnu compilers.
>> (Aside to Jason: are those bash-isms at line 711 of configure2?)
> They don't appear to be bash-isms -- dash handles them fine.

Hmmm. Line 711 appears to be bog standard Bourne sh. Here's what my line 711 is if
one of you is using a development version:
 echo "ERROR: RISM and PBSA FFT solver require version 4.3 or higher of the GNU compiler."

But 713 uses a syntax I've never seen before, and I have written a lot of a lot of /bin/sh
scripts (although a long time ago). My sh book is boxed up, so I can't look it up. The
backtic command within an echo argument is what I am talking about:
 echo " `mod_command_args '-rism' '-nofftw3'`"

I believe the canonical Bourne sh way of doing things would be to use the echo flag that
prevents a final newline after the argument, echo -c , IIRC:
 echo -c " "; `mod_command_args '-rism' '-nofftw3'`

I suspect the reason this works is because mod_command_args is a routine internal to the
script. If it were an external program, I think the script would gag on it. But you may
have a hard time finding an authentic Bourne sh to try it out. (Solaris?). I suggest
/bin/sh on a FreeBSD box if you have access to one. There /bin/sh is ash and seems to
adhere to Bourne sh syntax much closer than the Linux shells ("closer" in the "picky"
sense). (Although ash is really supposed to be a ksh clone, IIRC.)

Bud Dodson

PS, I just remembered I have a BSD box in my garage if you really think this is important
enough to dig it out.

> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list

M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Thu Apr 26 2012 - 09:00:02 PDT
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