HfS multiprocessor procedures

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HfS multiprocessor procedures are versions that use Open MPI (www.open-mpi.org) and run in parallel using a number of processors available in the machines, or in more than one host. The multiprocessor procedures hfs_cube_mp and hfs_nh3_cube_mp are naked versions of the single-processor versions, hfs_cube_sp and hfs_nh3_cube_sp, without any graphic output.

Compilation

$ mpifort -fno-range-check -mcmodel=medium -ohfs_cube_mp hfs_cube_mp.f90

$ mpifort -fno-range-check -mcmodel=medium -ohfs_nh3_cube_mp hfs_cube_mp.f90

No need of linking with PGplot and X11 libraries. The compilation is performed by the shell script hfs_compile (see Installation in the HfS main page).

Running locally

$ mpirun -np <N> hfs_cube_mp <parfile>.par

$ mpirun -np <N> hfs_nh3_cube_mp <parfile>.par

where <N> is the number of processors to use. To know the number (and characteristics) of processors in a Linux system, use

$ cat /proc/cpuinfo

Running in more than one host

For example, running in localhost and another host <otherhost>:

$ mpirun -np <N> -host localhost,<otherhost> hfs_cube_mp <parfile>.par

$ mpirun -np <N> -host localhost,<otherhost> hfs_nh3_cube_mp <parfile>.par

Here <N> is the total number of processors to use, distributed among the hosts listed after -host. If you want to know which are the processes run in each host, use the option -display-map.

Requisites for running in a remote host <otherhost>

• ssh access to <otherhost>, without having to enter the passwd. To achieve this, in localhost, make:

$ cd $HOME/.ssh

$ ssh-keygen

> enter passphrase: <RET>

A file id_rsa_pub is created, and has to be copied to <otherhost>:.ssh/ in a file called authorized_keys2:

$ scp ~/.ssh/id_rsa.pub <user>@<otherhost>:.ssh/authorized_keys2

or, if the file .ssh/authorized_keys2 already exists in <otherhost>:

$ scp ~/.ssh/id_rsa.pub <user>@<otherhost>:.ssh/id.tmp

$ ssh <otherhost> 'cat .ssh/id.tmp >> .ssh/authorized_keys2; rm .ssh/id.tmp'

Sometimes it is necessary to run in <otherhost>:

• Open MPI installed in <otherhost>. Your PATH and LD_LIBRARY_PATH in <otherhost> have to point to the openmpi bin and lib folders in the installation directory. For example, if openmpi is installed in /usr/local/openmpi, you can include in the file <otherhost>:.bashrc the lines:

export PATH=$PATH:/usr/local/openmpi/bin

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/openmpi/lib

• The same data file structure in <otherhost> and in localhost, i.e. the same directory from where you run hfs_cube_mp, with the same paramater file <parfile> and data files. The log files of the different processors, log/<parfile>_##.log, will be written in the host where each processor runs.