[AMBER-Developers] Clean target broken in Release candidate + other issues.

From: Ross Walker <ross.rosswalker.co.uk>
Date: Tue, 30 Mar 2010 19:35:11 -0700

Hi All,

There are issues with the clean target for AMBER in the release candidate:

clean:: netcdf_clean
        cd lib && $(MAKE) clean
        cd addles && $(MAKE) clean
        cd sander && $(MAKE) clean
        cd sqm && $(MAKE) clean
        cd nmr_aux && $(MAKE) clean
        cd nmode && $(MAKE) clean
        cd mm_pbsa && $(MAKE) clean
        cd pbsa && $(MAKE) clean
        cd mmpbsa_py && $(MAKE) clean
        (cd rism && $(MAKE) clean)
        (cd lapack && $(MAKE) clean)
        (cd blas && $(MAKE) clean)
        (cd arpack && $(MAKE) clean)
        -(cd pmemd && $(MAKE) clean)
        -(cd fftw-2.1.5 && $(MAKE) clean)

Note the cd sqm which returns:

cd sqm && make clean
/bin/sh: line 0: cd: sqm: No such file or directory
make: *** [clean] Error 1

The net result is that nothing beyond this gets cleaned. However, I also
think it is dangerous to not be cleaning sqm when one things they are inside
the amber11 directory, as opposed to AmberTools. Should this read something

cd ../AmberTools/src/sqm $$ $(MAKE) clean

or should the Amber11/src/ clean target somehow depend upon a full clean of

Similar problems exist with pbsa and rism and lapack and blas and arpack and

There is also some confusion with messages produced by the configure script.
For example:

The configuration file, config.h, was successfully created.
The next step is to type 'make cuda'
ln: `./sander': File exists

Firstly running configure more than once gives the error when linking in
sander. Secondly with cuda it says the next step is to make cuda. Should
this be updated to

The next step is to type 'cd ../../src; make cuda'?

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |

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Received on Tue Mar 30 2010 - 20:00:10 PDT
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