AMBER Archive (2003)

Subject: Re: Amber7 & mpich

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Feb 05 2003 - 08:58:25 CST

Dear All,

Thanks to all, I just got better results for "sander":

1- I used the following MACHINE file:
http://www.amber.ucsf.edu/amber/cluster_info/Machine.pgf77_mpich
 
2- Setted "setenv SYSDIR Machines/standard" in this file

3- I put the file "farg.f" in ~src/lib, ~src/lapack and ~src/sander
directories (needed for compiling sander) and compiled 'manually' it using
"pgf77 -c farg.f"

As said Michael F. Crowley, Florian Barth & David Case, I had to remove the
"-Msecond_underscore" flag. (I use pgi 4.x, using "nm")

4- I used the farg.f file provided by Viktor Hornak:
------------------
integer function mpir_iargc()
mpir_iargc = iargc()
return
end

subroutine mpir_getarg( i, s )
integer i
character*(*) s
call getarg(i,s)
return
end
------------------

5- I also removed in the "COMPILER ALIASES" section the "-Msecond_underscore"
flag.

6- I also added "-lgm" as I use the gm device of mpich (to take into account of
our myrinet 2GB network) i.e. I used the following line:

setenv LOADLIB "-lm -L$MPICH_LIBDIR farg.o -l$MPICH_LIB -L/usr/non-deb/lib -lgm"

7- My env. variables for MPICH are indeed the following:
setenv MPICH_HOME /usr/pgi/linux86
setenv MPICH_INCLUDE $MPICH_HOME/include
setenv MPICH_LIBDIR $MPICH_HOME/lib
setenv MPICH_LIB mpich

Then, I ran "make install" in the ~src/sander directory and got the sander
binary. On the contray, if I run "make install" in the global ~src directory I
still get errors for other AMBER binaries (i.e. for mm_pbsa, antechamber,
carnal, nmr_aux and leap)... However, I wonder it is useful to compile ALL the
AMBER binaries using the file Machine.pgf77_mpich.

Is it OK to compile only "sander" with mpich (i.e. with the file
Machine.pgf77_mpich) and all the other binaries without mpich (i.e. with the
file Machine.pgf77) ? Indeed, only sander can be ran with mpi ? right ?
Is there some plans to run nmode, mm_pbsa or roar in parallel ?

Thanks for your patience, regards, Francois