Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 from yasir.orionsolutions.co.in on 2016-12-10 (Amber Archive Dec 2016)

From: <yasir.orionsolutions.co.in>
Date: Sat, 10 Dec 2016 14:06:32 +0530

Hi Elvis
Below is the process which I'm doing & getting error log file attached.

First I check mpi using below command. (Output in Files Attached)
mpif90 -show
mpicc -show

Then set AMBERHOME properly.
cd $AMBERHOME
./configure -mpi gnu (As I'm using OpenMPI of Rocks 6.2)
make install

After this I've set DO_PARALLEL
export DO_PARALLEL='mpirun -np 8'
make test (Out of make test attached in mail)

#But I've not seen any amber.sh or amber.csh file on cd $AMBERHOME directory)

Please suggest your kind further action. Also help how to set amber use for all Rocks User's for Parallel use for same.

Thanks & Regards,
Yasir Israr

-----Original Message-----
From: Elvis Martis [mailto:elvis_bcp.elvismartis.in]
Sent: Friday, December 9, 2016 10:56 AM
To: Yasir Israr; AMBER Mailing List
Subject: Re: [AMBER] Installation of AMBER on Centos Rocks 6.2

Hi Yasir,
Can you elaborate on what exactly you are unable to do?

As far as setting the environment for AMBER is straightforward.
You can do two things here,
1) define the amber environment in your bashrc or cshrc file in the home directory. You can open and copy the contents of $AMBERHOME/amber.sh for bashrc or $AMBERHOME/amber.csh for cshrc. This will automatically set the environment in your profile.
2) Alternatively, you can source the amber.sh or amber.csh by typing "source </path_to_amber>/amber.sh" or "source </path_to_amber>/amber.csh"
to set the environment. Ignore the quotes.

However, amber.sh and amber.csh will only appear after you have successfully configured and compiled amber on your system.
All the best.

Regards

*Elvis Martis* Ph.D. Student, Bombay College of Pharmacy
[image: photo] Email: elvis_bcp.elvismartis.in <elvis_bcp.elvismartis.in>
Website: http://www.elvismartis.in <http://www.elvismartis.in/> group website: http://www.profeccoutinho.net.in/
Address:

Kalina, Santa Cruz [E]
, Mumbai, 400 098, INDIA

Alt. e-mail: emartis12.live.com
<https://in.linkedin.com/in/elvisadrianmartis>

On 9 December 2016 at 09:39, Yasir Israr <yasir.orionsolutions.co.in> wrote:

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>
> I follow same but couldn't able to complete installation. Can anybody
> let me know after installation how to set AMBER use to user & there
> environment & path setting ?
>
> Thanks & Regards
> Yasir Israr
>
> > On 09-Dec-2016, at 8:38 AM, Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
> >
> > HI Yasir,
> > Please follow Jason's page which gives step by step instructions for
> > installing AMBER on any OS.
> > http://jswails.wikidot.com/installing-amber14-and-ambertools14 <Also
> works
> > for Amber16>
> > All the best.
> >
> > Regards
> >
> > *Elvis Martis* Ph.D. Student, Bombay College of Pharmacy
> > [image: photo] Email: <elvis_bcp.elvismartis.in>
> > Website: http://www.elvismartis.in <http://www.elvismartis.in/>
> > group website: http://www.profeccoutinho.net.in/
> > Address:
> > 
> > Kalina, Santa Cruz [E]
> > , Mumbai, 400 098, INDIA
> >
> > Alt. e-mail: emartis12.live.com
> > <https://in.linkedin.com/in/elvisadrianmartis>
> >
> >
> >> On 9 December 2016 at 07:53, Yasir Israr
> >> <yasir.orionsolutions.co.in>
> wrote:
> >>
> >> [image: Boxbe] <https://www.boxbe.com/overview> This message is
> eligible
> >> for Automatic Cleanup! (yasir.orionsolutions.co.in) Add cleanup
> >> rule <https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.
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> >>
> >> Hi Admins
> >> Please help in sharing installation guide for Rocks Centos.
> >>
> >> Thanks & Regards
> >> Yasir Israr
> >>
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> >>
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Received on Sat Dec 10 2016 - 01:00:03 PST