I've managed to install Amber11 and AmberTools 1.5 in parallel, by
directly adding -lmpi flag after each compiler on the configure files.
However, I got an incredible decrease on performance. E.g.: A system
that runs 10ns/day on 30 nodes, is running 0.3ns/day with 60 nodes
using pmemd.MPI and 0.1ns/day using sander.MPI.
Here is an example of my job:
#PBS -S /bin/sh
#
# Job's name
#PBS -N prod_t4p
#
#Error on the standard output
#PBS -j oe
#
# Calling the parallel environment and job numbers
#PBS -l select=72:ncpus=1
#
cd $PBS_O_WORKDIR
#!/bin/sh
#export sander=$AMBERHOME/exe/sander
#For optimal parallel performance use pmemd instead of sander
export sander=/home/u/bbr/bin/amber11/bin/sander.MPI
l=heat20
f=prod01
mpiexec -n 72 $sander -O -i $PWD/$f.in -o $PWD/$f.out -inf $PWD/$f.inf \
-c $PWD/1D20_wat_tip4pew.$l -ref $PWD/1D20_wat_tip4pew.$l -r
$PWD/1D20_wat_tip4pew.$f \
-p $PWD/1D20_wat_tip4pew.top -x $PWD/1D20_wat_tip4pew$f.x -e
$PWD/1D20_wat_tip4pew$f.ene
On 8/25/11, Bruno Rodrigues <bbrodrigues.gmail.com> wrote:
> Dear All,
>
> I'm trying to install Amber11 with AmberTools 1.5 on a SGI Altix with
> Novell
> SUSE Linux Enterprise Server 11-SP1. It came with MPT (Message Passing
> Toolkit) and intel version 12.0.0.
>
> The serial version installs correctly with gnu compilers. However, I get a
> lot of errors on the parallel version.
>
> Then I decided to install it with Intel, as there is an old post explaining
> how to make it in parallel (http://archive.ambermd.org/201103/0401.html).
> However, I'm getting an error at the very begin:
>
> ./configure -altix -noX11 intel
>
> Testing the icc compiler:
> icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> OK
>
> Testing the ifort compiler:
> ifort -O0 -o testp testp.f
> OK
>
> Testing mixed C/Fortran compilation:
> icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
> testp.c
> ifort -O0 -c -o testp.f.o testp.f
> icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o
> testp.f.o -L/opt/intel/composerxe-2011.0.084/lib/intel64/ -lifport -lifcore
> -lguide -lpthread -ldl
> ld: cannot find -lguide
> ./configure: line 1397: ./testp: No such file or directory
> Error: Unable to compile mixed C/Fortran code.
> Please check your compiler settings and configure flags.
>
>
> Looking at the configure file, I realized that there is a commentary
> stating
> that the flags might work for intel up to version 11, and I have version
> 12.
>
> So, coming back to the gnu, I have no idea about what changes should I make
> in order to correctly install AmberTools 1.5 and Amber11 on this cluster.
>
> The cpus are dodecacore AMD Opte- ron 6176 SE 2.3 GHz.
>
> Thank you in advance,
>
> --
> --
> Bruno Barbosa Rodrigues
> PhD Student - Physics Department
> Universidade Federal de Minas Gerais - UFMG
> Belo Horizonte - Brazil
>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Fri Aug 26 2011 - 05:00:03 PDT
