Maciej -
Thanks for the feedback about the lam-required libraries and the fact that
ifort 8.1.017 seems to work. By any chance could you tell us which version
of lam you are using, and on what version on linux? I am hoping to get
around to releasing some updated config_data files to support new platforms
and changing conditions, and will benefit from your experience.
Regards - Bob
----- Original Message -----
From: "Maciej" <makay22.wp.pl>
To: <amber.scripps.edu>
Sent: Thursday, February 24, 2005 2:43 AM
Subject: AMBER: RE:Amber 8 with lam compilation problem
> 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
>> >
>
>
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Received on Thu Feb 24 2005 - 14:53:01 PST
