Re: [AMBER-Developers] Intel AT/Automake issue

From: B. Lachele Foley <lfoley.uga.edu>
Date: Wed, 8 Jun 2011 16:30:15 +0000

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 _______________________________________________ AMBER-Developers mailing list AMBER-Developers@ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developers

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Received on Wed Jun 08 2011 - 10:00:03 PDT
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