Hi,
In a fresh repo of the master:
./configure -mkl --skip-python intel
make
...
make[2]: Leaving directory `/tmp/amber/AmberTools/src/nfe-umbrella-slice'
(if [ "yes" = "no" ]; then \
make python_serial ;\
fi;\
)
(python conda-recipe/scripts/patch_amberhome/copy_and_post_process_bin.py /tmp/amber/bin /tmp/amber/bi
n)
Traceback (most recent call last):
File "conda-recipe/scripts/patch_amberhome/copy_and_post_process_bin.py", line 228, in <module>
main()
File "conda-recipe/scripts/patch_amberhome/copy_and_post_process_bin.py", line 224, in main
script_template=script_template)
File "conda-recipe/scripts/patch_amberhome/copy_and_post_process_bin.py", line 158, in copy_to_targe
t_folder
print('patching {}'.format(final_exe_path))
ValueError: zero length field name in format
make[1]: *** [serial] Error 1
make[1]: Leaving directory `/tmp/amber/AmberTools/src'
make: *** [install] Error 2
On Sat, Feb 04, 2017 at 08:24:01PM -0500, Hai Nguyen wrote:
> after some testings, I go head merging my change for --prefix option to
> master branch.
>
> Those commits should not affect your regular workflow (hopefully) but if
> any, please let me know (or even better if make a new commit to fix :D).
>
> Usage example: You can try different compilers by
>
> mkdir $HOME/try_amber_prefix
> cd amber17
> ./configure --prefix $HOME/try_amber_prefix gnu
> source amber.sh
> make install
>
> After the regular install, all installed files will be in
> $HOME/try_amber_prefix.
>
> Of course, to run programs in try_amber_prefix folder, you still need to
> source $HOME/try_amber_prefix/amber.sh
>
> Expected failures if running the tests for "--prefix" option:
> FEW.pl: I don't know Perl well to make change, so just let it be.
> pymsmt: It's using some library in its source folder at run time. I think
> Pengfei is working on this.
>
> Hai
>
> On Thu, Feb 2, 2017 at 1:05 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > thanks. I will look at the Python stuff.
> >
> > Should expect not able to run some (most?) tests (even if copying
> > $AMBERHOME/test and AmberTools/test to $PREFIX)
> > since some of the tests point to the source folder.
> >
> > cheers.
> > Hai
> >
> >
> > On Thu, Feb 2, 2017 at 1:02 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> >> PS - The 'prefix' install was 328MB, compared to 2.5 GB for a full
> >> Amber 16 install. Very nice.
> >>
> >> On Thu, Feb 2, 2017 at 1:00 PM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >> > Got a chance to try this today. I haven't tested thoroughly but it
> >> > seems to work well. Nice work Hai!
> >> >
> >> > I hit a brief hiccup during my initial attempt with python stuff:
> >> > ```
> >> > Checking .pth file support in
> >> > /u/droe/Amber/TEMP/prefix/lib/python2.7/site-packages/
> >> > /mnt/local/droe/anaconda2/bin/python -E -c pass
> >> > TEST FAILED: /u/droe/Amber/TEMP/prefix/lib/python2.7/site-packages/
> >> > does NOT support .pth files
> >> > error: bad install directory or PYTHONPATH
> >> > ```
> >> > It went on to describe the problem and potential solutions which was
> >> > really nice, but the real issue was I had forgotten to source amber.sh
> >> > - that fixed the problem. So maybe that could be the first thing you
> >> > suggest for potential solutions?
> >> >
> >> > -Dan
> >> >
> >> >
> >> > On Wed, Jan 25, 2017 at 3:48 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >> >> Oops, no "="
> >> >>
> >> >> ./configure --prefix $HOME/try_another_folder gnu
> >> >>
> >> >> On Wed, Jan 25, 2017 at 3:31 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
> >> >>
> >> >>> > If I happen to get free time before
> >> >>> now and the code freeze maybe I'll take another crack at making this
> >> >>> happen.
> >> >>>
> >> >>> .Dan: I have working code in amber_prefix_Hai branch. Feel free to
> >> try and
> >> >>> update that.
> >> >>>
> >> >>> ./configure --prefix=$HOME/try_another_folder gnu
> >> >>>
> >> >>> Hai
> >> >>>
> >> >>> On Thu, Dec 22, 2016 at 9:44 AM, Daniel Roe <daniel.r.roe.gmail.com>
> >> >>> wrote:
> >> >>>
> >> >>> On Wed, Dec 21, 2016 at 10:04 PM, David Case
> >> >>> <dacase.scarletmail.rutgers.edu> wrote:
> >> >>> >
> >> >>> > On Wed, Dec 21, 2016, Dan Roe wrote:
> >> >>> >
> >> >>> >>
> >> >>> >> But I think it is important that these tests happen at 'configure'
> >> >>> >> time, and it doesn't seem to me to be that difficult....
> >> >>> >
> >> >>> > It may indeed be do-able, but it is not just a matter of seeing if
> >> >>> "import
> >> >>> > numpy" throws an error. The configure script would have to compile
> >> >>> python
> >> >>> > extensions in the same way the real code will (which is actually
> >> several
> >> >>> > ways), and make sure they all work. And since only developers will
> >> >>> decline
> >> >>> > the miniconda download, and since they can find out by trial and
> >> error if
> >> >>> > their system python works, writing and maintaining this
> >> functionality
> >> >>> seems
> >> >>> > like a lot of work for only a small payback.
> >> >>>
> >> >>> I think that some users (maybe installs at HPC sites etc) may also
> >> >>> want to decline the miniconda download, but it does seem like python
> >> >>> detection is problematic. As long as the '--with-python' flag works I
> >> >>> think it's fine anyway. It would be nice to have configure be able to
> >> >>> test the python ecosystem but if it's too much work then I'll just put
> >> >>> it on my wishlist.
> >> >>>
> >> >>> > For those who want to play with this, configure2 alreay *has* a
> >> >>> > check_compatible_python() function. We commented out the call to
> >> this
> >> >>> > function (about line 935) since it was not reliable enough: having
> >> >>> > configure say a python is OK when it is not is quite annoying and
> >> >>> confusing.
> >> >>>
> >> >>> Agreed - that's worse from a user standpoint for certain.
> >> >>>
> >> >>> > Knowing I'm repeating myself: we *really* don't want users
> >> installing
> >> >>> > packages into their existing python just to install Amber. There
> >> is too
> >> >>> > much danger of creating incompatibilities with other things that
> >> require
> >> >>> > python: that is, we increase the danger that installing Amber breaks
> >> >>> > something else on the user's computer. [numpy, in particular,
> >> exists in
> >> >>> > several incompatible releases; it is quite easy for program A to
> >> require
> >> >>> > version 1.9 and program B to require version 1.10. We can't solve
> >> that
> >> >>> > problem, but should not make it worse, either.]
> >> >>>
> >> >>> This is one of the gotchas of living in the python universe. Advanced
> >> >>> users can just use the '--with-python' flag. "Normal" users can have a
> >> >>> built-in miniconda. We just have to make it clear during configure
> >> >>> time exactly why miniconda is a good idea instead of the vague "well,
> >> >>> maybe stuff won't work" message of the past.
> >> >>>
> >> >>> >> I'll have to test '--with-python', but if it works there is not
> >> much
> >> >>> >> of a downside that I can see other than that Amber installation is
> >> now
> >> >>> >> the "python keystone", so I'd better not ever move it or I will
> >> break
> >> >>> >> every Amber install based on it (and it's another configure flag
> >> that
> >> >>> >> has to be specified each time).
> >> >>>
> >> >>> I was being a bit facetious about having to specify an extra flag :-)
> >> >>> - that stuff doesn't come through in email sometimes. I think the
> >> >>> '--with-python' flag is the correct solution.
> >> >>>
> >> >>> >> > [Next thing we know, people are going to want to be able to
> >> specify a
> >> >>> build
> >> >>> >> > directory, separate from the sources.....]
> >> >>> >>
> >> >>> >> I still want this :-). For separate installs the size can really
> >> add
> >> >>> >> up, more because the Amber 16 source tree weighs in at 2.3 GB - the
> >> >>> >> miniconda install adds 635 MB to that (sizable but not egregious).
> >> >>> >
> >> >>> > Has anyone tried to just make a shadow directory (using "cp -as" or
> >> >>> lndir),
> >> >>> > with links to a clean amber tree, then build in the shadow
> >> directory?
> >> >>>
> >> >>> Unfortunately, this can't work for multiple parallel library/CUDA
> >> >>> version builds (maybe I'm not understanding what you mean).
> >> >>>
> >> >>> > Realistically, I'd recommend bigger disks. You can get 500 Gb
> >> external
> >> >>> > SSD drives with USB-3 or USB-C interconnects that are quite fast
> >> and will
> >> >>> > allow you create all the Amber images you are ever likely to
> >> need....
> >> >>>
> >> >>> Just because disk space is cheap doesn't mean we should be wasteful. I
> >> >>> would like to do with Amber what I can do with every other linux
> >> >>> source code package: have one giant source directory that I can point
> >> >>> to an install directory with '--prefix', and then that install
> >> >>> directory contains only what I need to run that version of Amber.
> >> >>> AMBERHOME can point to the common source, but PATH and LD_LIBRARY_PATH
> >> >>> point to the install directory. If I happen to get free time before
> >> >>> now and the code freeze maybe I'll take another crack at making this
> >> >>> happen.
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Received on Sun Feb 05 2017 - 22:30:03 PST
