Here is a follow-up.
Just to be clear: I wasn't saying that I had forgotten to make clean. I'm saying that it is necessary to make clean immediately after the very first configure. Then, you have to configure again. So, something that is shipping out isn't "clean" in the first place.
You can't "make clean" at the very start because:
Makefile:7: config.h: No such file or directory
make: *** No rule to make target `config.h'. Stop.
And if you "make clean" without running "./configure intel" again, you get:
cd etc/Python-2.6.6 && make && make install
/bin/sh: line 0: cd: etc/Python-2.6.6: No such file or directory
make: *** [python] Error 1
I've tried to figure out what changes when you use "make clean; ./configure intel" before making anything. Turns out that it's a lot. Here's what I did:
In the tree amber.test1, I did:
(unpackage new)
cd AmberTools/src
./configure intel
In the tree amber.test2, I did:
(unpackage new)
cd AmberTools/src
./configure intel
make clean
./configure intel
Then, in the directory above both:
diff -r amber.test1/ amber.test2/ recursive_diff_amber_test1-test2
I would have expected those two procedures to produce very similar results, but they don't. The diffs are attached. Most at the top reflect the different directories. But, many lines of entries are all sorts of other stuff, including at least one automake change. I can't begin to make sense of all of the differences, but something in there is causing the install to fail.
Most of the non-directory differences that I see after a quick glance are in:
diff -r amber.test1/AmberTools/src/fftw-2.1.5/aclocal.m4 amber.test2/AmberTools/src/fftw-2.1.5/aclocal.m4
diff -r amber.test1/AmberTools/src/fftw-2.1.5/config.log amber.test2/AmberTools/src/fftw-2.1.5/config.log
diff -r amber.test1/AmberTools/src/fftw-2.1.5/config.status amber.test2/AmberTools/src/fftw-2.1.5/config.status
diff -r amber.test1/AmberTools/src/fftw-2.1.5/configure amber.test2/AmberTools/src/fftw-2.1.5/configure
diff -r amber.test1/AmberTools/src/fftw-2.1.5/libtool amber.test2/AmberTools/src/fftw-2.1.5/libtool
diff -r amber.test1/AmberTools/src/fftw-2.1.5/threads/Makefile amber.test2/AmberTools/src/fftw-2.1.5/threads/Makefile
diff -r amber.test1/AmberTools/src/fftw-2.1.5/threads/Makefile.in amber.test2/AmberTools/src/fftw-2.1.5/threads/Makefile.in
diff -r amber.test1/AmberTools/src/fftw2_config.log amber.test2/AmberTools/src/fftw2_config.log
:-) Lachele
Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
lfoley.uga.edu
http://glycam.ccrc.uga.edu
________________________________________
From: B. Lachele Foley [lfoley.uga.edu]
Sent: Wednesday, June 01, 2011 11:35 AM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] Intel AT/Automake issue
UNCLEAN!!! WE ARE UNCLEAN!!!
:-)
I think I found the problem by accident. Installation log files from 2 and 3 below are attached in case they might be useful. For some reason, "./configure intel ; make clean ; ./configure intel" fixes the problem.
Details that correspond to the attached logs:
Trying in: /programs/amber.git2
(this also happens with a patched official download of AT1.5)
1. copy over clean git repo (no bin dirs made, etc.)
2. set AMBERHOME and PATH
3. ./configure intel
4. wc fftw-2.1.5/Makefile
576 2304 18963 fftw-2.1.5/Makefile
5. cd fftw-2.1.5/ ; cp Makefile Makefile.save ; cd ..
6. make install | tee install2.log
[blah blah blah]
7. die with automake fftw complaint
8. diff fftw-2.1.5/Makefile.save fftw-2.1.5/Makefile (none)
Try in: /programs/amber.git3
1. copy over clean git repo (no bin dirs made, etc.)
2. set AMBERHOME and PATH
3. ./configure intel
4. make clean
5. ./configure intel
6. make install | tee install2.log
[blah blah blah]
7. "Installation of AmberTools, version 1.5 serial is complete at Wed Jun 1 16:02:32 IST 2011."
:-) Lachele
Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
lfoley.uga.edu
http://glycam.ccrc.uga.edu
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: Wednesday, June 01, 2011 8:31 AM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] Intel AT/Automake issue
On Tue, May 31, 2011, B. Lachele Foley wrote:
>
> > Lachele: can you post the *entire* log file involving fftw-2.1.5, i.e.
> > not just the immediate context?
>
> Done. Is there a log from the install somewhere? I can run it again
> and send more context. I was surprised to see "automake" in the middle
> of it.
What you sent was the fftw configure log, which looks fine. To get the real
configure log type something like this:
make install | tee install.log
Before doing this (but after running configure) you might check to see if the
file $AMBERHOME/AmberTools/src/fftw-2.1.5/thread/Makefile exists (and is
non-empty).
...thx...dac
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Received on Wed Jun 08 2011 - 10:00:03 PDT
