On Thu, Feb 18, 2016 at 2:01 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Can we at least have a section in the document - and probably we'll
> ultimately need some detailed tutorials on the website on installing - that
> lists all of the dependencies needed for AMBER. For Redhat this would be a
> list of packages that should be installed with yum install.
>
> I would argue that if a package needed to compile AMBER (just serial AMBER
> I am talking about here) is not available as part of the standard OS
> packages (or at stretch also epel for Redhat) then that module, library etc
> should really not be used and instead one should code around the need for
> it.
>
I don't think 'code around' is a good idea. Most of AMBER developers are
not professional programmers, coding core library by our-self will
introduce enormous bugs and required enormous amount of time in testing.
One single AMBER developer can't beat the work-horse of 399 numpy
developers (high performance array in Python) with decades of development.(
https://github.com/numpy/numpy). Additionally, we don't want to end up that
a written program is unusable since the postdoc had moved on and there was
no funding to support it: http://archive.ambermd.org/201406/0502.html
By the way, Python packages in AMBER only require well-established
libraries like numpy or matplotlib (for plotting).
Hai
> All the best
> Ross
>
> > On Feb 18, 2016, at 10:55 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> > I think the check work properly but it needs clearer message.
> > Here is a suggested lists of Python packages: numpy, cython, matplotlib,
> > tkinter. If your python version does not has those, the a Python
> > distribution from Anaconda will be suggested.
> >
> > If you or user do not want to use Python, it's just to say 'N' to skip
> the
> > step.
> >
> > We (Case group) are exposing AMBER to external programs like Phenix or
> > Rosetta via Python so there are still audience for it.
> >
> > Hai
> >
> > On Thu, Feb 18, 2016 at 1:28 PM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
> >
> >> Enterprise system
> >>
> >> Redhat 7.0 - Default Developer Install - Fully up to date.
> >>
> >>> which Python
> >> /usr/bin/python
> >>
> >>> python -V
> >> Python 2.7.5
> >>
> >> And yet AMBER ./configure gnu gives:
> >>
> >> No compatible Python installation found. I can download one from
> Continuum
> >> via Miniconda with all prerequisites. This will only need to be done
> once.
> >> This may take several minutes and will require Internet access.
> >> Should I do that? [y/n]
> >>
> >> Is the check just not working properly?
> >>
> >> Can this be fixed please?
> >>
> >> In my opinion AMBER should build without issue on a Redhat default
> install
> >> given this represents >90% of commercial Linux installs so we should do
> our
> >> best to support this type of environment. We should only need to
> download a
> >> big third party python package on weird systems like OSX, ancient Linux
> >> OS's etc.
> >>
> >> All the best
> >> Ross
> >>
> >> /\
> >> \/
> >> |\oss Walker
> >>
> >> ---------------------------------------------------------
> >> | Associate Research Professor |
> >> | San Diego Supercomputer Center |
> >> | Adjunct Associate Professor |
> >> | Dept. of Chemistry and Biochemistry |
> >> | University of California San Diego |
> >> | NVIDIA Fellow |
> >> | http://www.rosswalker.co.uk | http://www.wmd-lab.org |
> >> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> >> ---------------------------------------------------------
> >>
> >> Note: Electronic Mail is not secure, has no guarantee of delivery, may
> not
> >> be read every day, and should not be used for urgent or sensitive
> issues.
> >>
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Received on Thu Feb 18 2016 - 12:30:03 PST
