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. Relying on lots of third party stuff by default is just going to make things massively fragile going forward.
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
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>>
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Received on Thu Feb 18 2016 - 11:30:03 PST
