Thx Bob for script it works :)
Ihave to change in my config.h line
setenv MPILIB "-L$LAM_LIBDIR -llamf77mpi -lmpi -llam"
to
setenv MPILIB "-L$LAM_LIBDIR -llamf77mpi -lmpi -llam - ldl - lpthread"
I used Intel fortran compiler 8.1-017 and it compiled without errors .
----- Original Message -----
From: "Amber admin" <amber-admin.scripps.edu>
To: <amber.scripps.edu>
Sent: Wednesday, February 23, 2005 9:39 PM
Subject: Re: AMBER: RE:Amber 8 with lam compilation problem
> (From Bob Duke:)
>
> Marciej -
> Sorry, I have not been following this thread.
>
> There are instructions for config files for pmemd when using ifort 8 and
> mpich out on the amber web site, amber.scripps.edu, under the major
heading
> "Amber-related links" and the minor heading "Running Amber on Linux using
> ifc8 and mpich (Provided by Bob Duke)". If you just reference lam stuff
> rather than mpich stuff, it should basically work. In the interest of
> hopefully making this problem go away longer term, I have constructed a
> linux_p4.ifort.lam which you can stick under amber8/src/pmemd/config_data;
> then under the pmemd dir do a "./configure linux_p4 ifort lam" and answer
> the question about where the lam home is. This should work. I will send
> you this file as gzipped text separately for your convenience, but the
text
> is:
>
> +++
> setenv LAM_INCLUDE $LAM_HOME/include
> setenv LAM_LIBDIR $LAM_HOME/lib
> setenv MPILIB "-L$LAM_LIBDIR -llamf77mpi -lmpi -llam"
> setenv PREPROCFLAGS "-DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_VECT_OPT"
> setenv CPP "/lib/cpp -traditional -I$LAM_INCLUDE"
> setenv OPT_LO "ifort -c -auto -tpp7 -mp1 -O0"
> setenv OPT_MED "ifort -c -auto -tpp7 -mp1 -O2"
> setenv OPT_HI "ifort -c -auto -tpp7 -xW -mp1 -ip -O3"
> setenv LOAD "ifort"
> setenv LOADLIB " -limf -lsvml $MPILIB"
> ----
> Regards - Bob Duke
>
> ----- Original Message -----
> From: "Ross Walker" <ross.rosswalker.co.uk>
> To: <amber.scripps.edu>
> Sent: Wednesday, February 23, 2005 1:02 PM
> Subject: RE: AMBER: RE:Amber 8 with lam compilation problem
>
>
> >> Thx very much it is working :) . I understand that i must have 2
> >> ambers on
> >> my computers when i want run seriall jobs and somtimes run
> >> parallel , but i
> >> must have two different AMBERHOME variables. How to solve this
> >> not setting
> >> it always when i want to run seriall ? . Can i add somehow AMBERHOME2
> >> variable ?
> >
> > You don't actually need $AMBERHOME set to run sander. It is only
actually
> > required for Leap. I just use it in my examples as a kind of generic
amber
> > path. If you use the full path in your scripts (always a good idea in my
> > opinion) then you won't have any problems. Alternatively you could just
> > copy
> > the parallel sander and sander.LES executables out of the parallel
> > compilation directory and put them in the serial directory called
> > sander.mpi
> > and sander.LES.mpi or something similar. Then just remember to use these
> > names instead of just sander when running in parallel.
> >
> >> Is it possible to compile pmemd with intel fortran 8.1 compiler
> >> ?? becouse i
> >> cant configure it .
> >
> > Yes, although you need a special configure script. There is a note
posted
> > on
> > the archive somewhere about it. Check http://amber.ch.ic.ac.uk/archive.
> > There may also be something on the amber website about it but I forget
> > where. If you can't find it in the archive or on the website post a
> > message
> > to the mailing list again and Bob Duke will probably help you out.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Feb 24 2005 - 07:53:01 PST
