hi Scott,
1. Per FEW error, please git clean your repo:
cd $AMBERHOME
git clean -fdx . # my favorite command to "veryclean"
# and redo the install again.
PS: Here is the reason why:
Originally, $AMBERHOME/bin/FEW.pl is just a symlink to
AmberTools/src/FEW/FEW.pl
I made change to make sure FEW.pl in bin folder is a actually a copy.
If your old "FEW.pl" (which is a symlink) still in bin/ folder, you'll get
the error "are the same file".
2. Per nab stuff (and antechamber, tleap...): If you use --skip-python,
"nab" will never be wrapped, it's still it.
And with that option, if you still got the "wrapped" script, that's
actually a bug and need to be fixed.
e.g: here the lines in nab's Makefile
$(BINDIR)/$(MPI)nab$(SFX)::
[......]
if [ "$(SKIP_PYTHON)" = "no" ]; then \
$(PYTHON) $(PATCH_AMBERHOME_SCRIPT) $(AMBER_PREFIX)/bin/nab
$(AMBER_PREFIX)/bin; fi
There is no special reason to why not using simple bash for wrapping nab
(setting PATH, LD_LIBRARY_PATH).
Originally I only make the wrapper for binary conda distribution
(Python-based). Dave preferred to have both source code and
binary distribution, so I went ahead update my change for conda build for
amber git too. I am not good at shell script, so I don't know potential
harm if using my "bash" script for different Linux distributions. So I just
used Python that I felt confidence to write code ( and the wrapper scripts
do work).
But if you and any one can write bash wrapper and willing to maintain it, I
am happy with that (I care more about final product rather than about a
specific language).
> It is not good practice to do everything
with one tool only because one does not know or does not want to learn
another.
Yes, I absolutely agree with you.
Hai
On Sun, Feb 12, 2017 at 12:51 AM, Scott Brozell <sbrozell.rci.rutgers.edu>
wrote:
> On Sat, Feb 11, 2017 at 06:57:50PM -0500, Jason Swails wrote:
> > On Sat, Feb 11, 2017 at 5:59 PM, Scott Brozell <sbrozell.rci.rutgers.edu
> >
> > > On Sat, Feb 11, 2017 at 10:50:54AM -0500, Hai Nguyen wrote:
> > > > On Sat, Feb 11, 2017 at 10:34 AM, David Case <david.case.rutgers.edu
> >
> > > > > On Fri, Feb 10, 2017, Hai Nguyen wrote:
> > > > >
> > > > > > PS2: "NEW" won't work with --skip-python option (there is no
> Python
> > > > > > code to wrap "nab" program to set LD_LIBRARY_PATH)
> > > > >
> > > > > Can't you use a shell script instead?....dac
> > > >
> > > > I do no want to support various shell types (like amber.sh,
> amber.csh).
> > >
> > > I don't know the details here, but i strongly prefer to have an
> > > installation process that does not need python; i might settle for
> > > a process that will work with any python.
> > >
> >
> > ???update_amber already requires Python, but works with every version in
> any
> > OS I've ever seen run Amber. I just tested Hai's new stuff with Python
> 2.4
> > (and --skip-python) and it works.
>
> 1. I'm concerned about this wrapping of nab. It's a principle of
> engineering
> to use simple tools. Again i didn't dig into the details, but why do we
> need
> the awesome power of python to do wrapping ? The Bourne shell is already
> required to install and use Amber. It is not good practice to do
> everything
> with one tool only because one does not know or does not want to learn
> another.
>
>
> 2. I'm getting mixed results: 3 repos updated at Sat Feb 11 18:57:28 EST
> 2017
> and then make veryclean:
> a. ./configure -mkl --skip-python intel
> Python 2.6.6
> Red Hat Enterprise Linux Server release 6.7 (Santiago)
> cp -f /tmp/amber/AmberTools/src/FEW/FEW.pl /tmp/amber/bin
> cp: `/tmp/amber/AmberTools/src/FEW/FEW.pl' and `/tmp/amber/bin/FEW.pl'
> are the same file
> make[2]: *** [install] Error 1
> make[2]: Leaving directory `/tmp/amber/AmberTools/src/FEW'
>
> b. ./configure --with-python /usr/local/anaconda2/bin/python gnu
> Python 2.7.12 :: Anaconda custom (64-bit)
> Red Hat Enterprise Linux Server release 6.7 (Santiago)
> cp -f /tmp/amber/AmberTools/src/FEW/FEW.pl /tmp/amber/bin
> cp: `/tmp/amber/AmberTools/src/FEW/FEW.pl' and `/tmp/amber/bin/FEW.pl'
> are the same file
> make[2]: *** [install] Error 1
>
> c. ./configure --skip-python pgi
> Python 2.7.5
> Red Hat Enterprise Linux Server release 7.2 (Maipo)
> Installation of Amber16 (serial) is complete at Sat Feb 11 19:36:49 EST
> 2017.
>
> This may be a cp exit status issue; I'll investigate tomw.
>
> scott
>
>
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Received on Sat Feb 11 2017 - 22:30:02 PST
