Re: [AMBER] Installation of AMBER on Centos Rocks 6.2

From: <yasir.orionsolutions.co.in>
Date: Sat, 10 Dec 2016 14:27:55 +0530

Refer point 7. (Its telling to run MPI)

If you are new to Amber, you should look at the tutorials and this manual and become
familiar with how things work. If and when you wish to compile parallel (MPI) versions
of Amber, do this:
cd $AMBERHOME
./configure -mpi <....other options....> <compiler-choice>
make install
# Note the value below may depend on your MPI implementation
export DO_PARALLEL=”mpirun -np 2”
make test
# Note, some tests, like the replica exchange tests, require more
# than 2 threads, so we suggest that you test with either 4 or 8
# threads as well
export DO_PARALLEL=”mpirun -np 8”
make test




Thanks & Regards,
Yasir Israr

-----Original Message-----
From: Hai Nguyen [mailto:nhai.qn.gmail.com]
Sent: Saturday, December 10, 2016 2:18 PM
To: AMBER Mailing List
Cc: elvis_bcp.elvismartis.in
Subject: Re: [AMBER] Installation of AMBER on Centos Rocks 6.2

so do it (serial) first then.

page 23 of amber16 manual says:
"Do not choose any parallel options at this step! You will need to install the serial version first; options for parallel builds are described below at Step 8. "

I think we should make that clearer (@Dave: bring it to the top of instalation guide? Or adding checking script to make sure user already build serially?)

Hai

On Sat, Dec 10, 2016 at 3:43 AM, <yasir.orionsolutions.co.in> wrote:

> No. Because I don't want to build serial. I want parallel only.
>
> Thanks & Regards,
> Yasir Israr
>
> -----Original Message-----
> From: Hai Nguyen [mailto:nhai.qn.gmail.com]
> Sent: Saturday, December 10, 2016 2:10 PM
> To: AMBER Mailing List
> Cc: elvis_bcp.elvismartis.in
> Subject: Re: [AMBER] Installation of AMBER on Centos Rocks 6.2
>
> have you performed serial build yet?
>
> Hai
>
> On Sat, Dec 10, 2016 at 3:36 AM, <yasir.orionsolutions.co.in> wrote:
>
> > 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:
> >
> > > [image: Boxbe] <https://www.boxbe.com/overview> Yasir Israr (
> > > yasir.orionsolutions.co.in) is not on your Guest List
> > > <https://www.boxbe.com/approved-list?tc_serial=27923477727&tc_rand
> > > =2
> > > 01
> > > 7345861&utm_source=stf&utm_medium=email&utm_campaign=ANNO_MWTP&utm
> > > _c
> > > on
> > > tent=001&key=hzan1%2BtMEch0ZWSgvq68eGLvNDNg9hqAr2ZbrNx464Y%3D&toke
> > > n=
> > > Fb
> > > VQK36r6c8ysBYazDtJ1uzaByiecGUWgNVh05yu3M%2FJ2i%2Bhlp2l7y2c3SLXOvj6
> > > >
> > > | Approve sender
> > > <https://www.boxbe.com/anno?tc_serial=27923477727&tc_rand=20173458
> > > 61
> > > &u
> > > tm_source=stf&utm_medium=email&utm_campaign=ANNO_MWTP&utm_content=
> > > 00
> > > 1&
> > > key=hzan1%2BtMEch0ZWSgvq68eGLvNDNg9hqAr2ZbrNx464Y%3D&token=FbVQK36
> > > r6
> > > c8 ysBYazDtJ1uzaByiecGUWgNVh05yu3M%2FJ2i%2Bhlp2l7y2c3SLXOvj6>
> > > | Approve domain
> > > <https://www.boxbe.com/anno?tc_serial=27923477727&tc_rand=20173458
> > > 61
> > > &u
> > > tm_source=stf&utm_medium=email&utm_campaign=ANNO_MWTP&utm_content=
> > > 00
> > > 1&
> > > dom&key=hzan1%2BtMEch0ZWSgvq68eGLvNDNg9hqAr2ZbrNx464Y%3D&token=FbV
> > > QK
> > > 36 r6c8ysBYazDtJ1uzaByiecGUWgNVh05yu3M%2FJ2i%2Bhlp2l7y2c3SLXOvj6>
> > >
> > > 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.
> > > com%2Fcleanup%3Fkey%3DUbFQXKO9y1kHqH0wUC8X%252FPb64xtTtA82S1K7bnUq
> > > UR
> > > g%
> > > 253D%26token%3DyKqT71Am245cLlsYECZ1FSBfV9vAxI74MJjQZw9U%252F0rkaRH
> > > xS jH hD% 252F89lsDlZaVK7MtRSq2dZKEHq9ltTuuimKRlvRJxjkg1KQwF%
> > > 252Fbcl6Zlkw6REKU8XrBIg%252BsgMuCvAtpS7rQJb84VQ15debTN
> > > 6zg%253D%253D&tc_serial=27922260677&tc_rand=1078535676&utm_source=
> > > st f& utm_
> > > medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001>
> > > >> | More info
> > > >> <http://blog.boxbe.com/general/boxbe-automatic-
> > > cleanup?tc_serial=27922260677&tc_rand=1078535676&utm_source=
> > > stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
> > > >
> > > >>
> > > >> Hi Admins
> > > >> Please help in sharing installation guide for Rocks Centos.
> > > >>
> > > >> Thanks & Regards
> > > >> Yasir Israr
> > > >>
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > >>
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Dec 10 2016 - 01:00:06 PST
Custom Search