Dear Francesco,
I would advise you build the serial version first for two reasons.
1) Most of the auxiliary tools are not built in the parallel version (i.e.
leap, ptraj etc...)
2) Debugging in parallel is really dificult so you should make sure
everything works in serial before doing this.
If you have a copy of the Intel compilers then don't worry about g95 etc. Do
the following.
1) extract the tar file to a dir - e.g. /usr/local/amber9
2) set AMBERHOME=/usr/local/amber9
3) obtain the latest bugfix.all from the amber website and apply it to the
tree.
4) configure for serial (e.g. ./configure -static ifort_x86_64)
5) cd $AMBERHOME/src
6) make
7) cd ../test
8) make - check TEST_FAILURES.dat for any failures. If everything is good
move on to parallel compilation.
9) verify that MPI_HOME points to the correct place
10) verify that your MPI was built with the same version of the ifort
compiler
11) cd $AMBERHOME/src
12) ./configure -openmpi ifort_x86_64
13) make clean; make parallel
14) set up the mpi environment so you can mpirun...
15) export DO_PARALLEL='mpirun -np 2' - or whatever your mpi environment
needs.
16) cd ../test; make test.parallel (check TEST_FAILURES.dat)
If this all works then you can also build pmemd for parallel - see
$AMBERHOME/src/pmemd.
All the best
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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.
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Francesco Pietra
> Sent: Wednesday, June 27, 2007 07:59
> To: Amber
> Subject: Fwd: Re: AMBER: $AMBERHOME on PATH
>
> Setting of env variables is obviously correct as indicated
> below. I am here
> again to ask if step 2c of readme on amber9 CD should really
> be carried out as
> indicated, i.e., compiling serially with g95.
>
> That question because I'll move as soon as possible to
> parallel compilation
> with intel compilers (having already compiled and installed
> openmpi with them).
> In other words, will step 4 (compile with intels) compile
> everything with
> intels or some non-parallelized modules will remain compiled with g95?
>
> That just to know
>
> Thanks
>
> francesco pietra
>
>
>
> --- Francesco Pietra <chiendarret.yahoo.com> wrote:
>
> > Date: Wed, 27 Jun 2007 07:30:09 -0700 (PDT)
> > From: Francesco Pietra <chiendarret.yahoo.com>
> > Subject: Fwd: Re: AMBER: $AMBERHOME on PATH
> > To: Amber <amber.scripps.edu>
> >
> > Please, see note about "printenv" below
> >
> > --- Francesco Pietra <chiendarret.yahoo.com> wrote:
> >
> > > Date: Tue, 26 Jun 2007 13:15:11 -0700 (PDT)
> > > From: Francesco Pietra <chiendarret.yahoo.com>
> > > Subject: Re: AMBER: $AMBERHOME on PATH
> > > To: amber.scripps.edu
> > >
> > > David:
> > > Following your warning that setting AMBERHOME must
> precede that of PATH...,
> > I
> > > commented out "PATH .." in my .bashrc. That failed to
> bring back the env
> > var
> > > AMBERHOME, while ":exe" disappered from PATH ... , as
> obtained from
> > printenv.
> > >
> > > Then I set in my .bashrc the following two lines:
> > >
> > > AMBERHOME=/usr/local/amber9
> > >
> > > PATH=$PATH:$AMBERHOME/exe; export AMBERHOME PATH
> > >
> > > Now
> > >
> > >
> > > $ echo $AMBERHOME
> > > /usr/local/amber9
> > >
> > >
> > >
> > > $ echo $AMBERHOME/exe
> > > /usr/local/amber9/exe
> > >
> > >
> > >
> > > $ printenv
> > >
> > > reports /usr/local/amber9/exe
> >
> > NOTE: of course the outcome of "printenv" should be read,
> inter alia, as
> > follows:
> >
> >
> > PATH=/home ............:/usr/local/amber9/exe
> >
> > and
> >
> > AMBERHOME=/usr/local/amber9
> >
> > >
> > >
> > > Are these settings correct?
> > >
> > > Thanks
> > >
> > > francesco
> > >
> > >
> > > --- "David A. Case" <case.scripps.edu> wrote:
> > >
> > > > On Tue, Jun 26, 2007, Francesco Pietra wrote:
> > > >
> > > > > I must have done something very silly while at the
> first steps of
> > > > installing
> > > > > amber9. After untarring as described in the readme on
> the CD, getting
> > > > > /usr/local/amber9
> > > > >
> > > > > I set (bash shell)
> > > > >
> > > > > $ AMBERHOME=/usr/local/amber9; export AMBERHOME
> > > >
> > > > Did you also put this in your .bashrc? AMBERHOME needs
> to be set before
> > > > you refer to it here:
> > > >
> > > > > Then I set in my .bashrc
> > > > >
> > > > > PATH=$PATH:$AMBERHOME/exe; export AMBERHOME PATH
> > > > >
> > > >
> > > > I'm just guessing here; maybe someone else will see
> some other problem.
> > > >
> > > > ...dac
> > > >
> > > >
> --------------------------------------------------------------
> ---------
> > > > The AMBER Mail Reflector
> > > > To post, send mail to amber.scripps.edu
> > > > To unsubscribe, send "unsubscribe amber" to
> majordomo.scripps.edu
> > > >
> > >
> > >
> > >
> > >
> > >
> >
> ______________________________________________________________
> ______________________
> > > Now that's room service! Choose from over 150,000 hotels
> > > in 45,000 destinations on Yahoo! Travel to find your fit.
> > > http://farechase.yahoo.com/promo-generic-14795097
> > >
> >
> >
> >
> >
> >
> ______________________________________________________________
> ______________________
> > Yahoo! oneSearch: Finally, mobile search
> > that gives answers, not web links.
> > http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC
> >
>
>
>
>
> ______________________________________________________________
> ______________________
> Building a website is a piece of cake. Yahoo! Small Business
> gives you all the tools to get online.
> http://smallbusiness.yahoo.com/webhosting
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jul 01 2007 - 06:07:09 PDT
