Hi Ross,
I do not worry, just like to know if everything is OK with running amber
programs after root installation. eg Jason said that MMPBSA.py want run.
Anyway, we installed Amber on our cluster as well and I already ran there
mmpbsa and it's OK so far.
Best wishes
Zoran
-----Original Message-----
From: Ross Walker
Sent: Sunday, February 7, 2016 6:36 PM
To: zoran matovic ; AMBER Mailing List
Subject: Re: [AMBER] MMPBSA ImportError
Hi Zoran,
You don't need to worry here. It will not affect how your copy of AMBER
works etc. If it installed okay you'll be fine. Installing as root really
just comes down to your personal comfort level with risk. E.g. if a typo in
the script causes your root directory to get erased and you are like "oh
well, guess I'll reimage from my backup" then it doesn't really matter.
If it installed okay as root and now you are running as a regular user you
have nothing to worry about, all will be good.
All the best
Ross
> On Feb 6, 2016, at 10:10, zoran matovic <zmatovic.kg.ac.rs> wrote:
>
> Just recently I installed Amber (including pmemd.cuda(MPI)) as a root
> (using
> su - a; mode that Ross suggests). Everything went fine I mean all the
> tests
> passed running them as a root. I am running now all the Amber programs as
> a
> user. So far there were no problems. However if there are something we
> (users) should now here is the place for u people to let us know.
> Zoran
>
>
> -----Original Message-----
> From: Ross Walker
> Sent: Saturday, February 6, 2016 6:29 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] MMPBSA ImportError
>
>>
>> On Fri, Feb 5, 2016 at 7:46 PM, Ross Walker <ross.rosswalker.co.uk>
>> wrote:
>>
>>> I cannot see the problem here.
>>>
>>
>> Except that the OP ran this script and MMPBSA.py didn't work.
>>
>>
>
> I mean I cannot see the problem with the script. Clearly there is a
> problem
> somewhere else.
>
>>> su -
>>> cd /usr/local/amber14
>>>
>>> ./update_amber --update
>>>
>>> ./configure gnu
>>> make -j8 install
>>> make clean
>>> ./configure -mpi gnu
>>> make -j8 install
>>> make clean
>>> ./configure -cuda gnu
>>> make -j8 install
>>> make clean
>>> ./configure -cuda -mpi gnu
>>> make -j8 install
>>> make clean
>>>
>>> Is PERFECTLY valid. If it does not work then someone broke the AMBER
>>> install process and it should be fixed.
>>>
>>
>> There are always machines and configurations that AMBER doesn't work on,
>> and it's possible to break the Amber build by breaking a component of
>> your
>> system that AMBER depends on. And environment setups are so customizable
>> that it's impossible to test every possible setup a user might have.
>>
>
> Sigh it didn't use to be this way. AMBER used to be very resilient and
> self
> contained and as long the compilers and MPI were working everything would
> keep working. It is somewhat tragic that we are now in a situation where
> we
> rely on OS components that these days seem to be held together by a
> combination of duck tape, superglue, and second hand chewing gum. :-(
>
> 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 Sun Feb 07 2016 - 11:00:03 PST
