Change the shell

The login shell on HA8000@hakozaki is tcsh. First change it to bash:

 $ bash

Compile METIS

Edit the makefile as follows:

AR = xiar rv
CC = icc
OPTFLAGS = -O3

And then, compile as follows:

 $ make

Compile FVCOM

Edit the setting for netcdf and compilation in makefile. netcdf should be installed before FVCOM compilation. The setting for MPI Intel compiler should be as follows:

CPP = /usr/bin/cpp
CPPFLAGS = $(DEF_FLAGS) -DINTEL
FC = mpiifort
DEBFLAGS =
OPT = -O3 -ipo -no-prec-div
CLIB =

makedepf90 should be installed and then makedepends should be created. mpi.h should be deleted if existed.

$ rm makedepends
$ rm mpi.h
$ touch makedepends
$ make depend

Now you can compile:

 $ make

After creating an executable file of fvcom, copy it onto ./run/:

 $ cp fvcom ../run/

Edit the bat script run_mpi.sh for execution. Following is an example for debugging:

#!/bin/bash
#@$-q ha-dbg
#@$-N 32
#@$-J T24
#@$-lE 1:00:00
cd ~/FVCOM2.6.1/run
mpirun -machinefile $PBS_NODEFILE -n $PBS_NP ./fvcom tst_run
date

Execution

Now you can execute on bat mode:

 $ qsub run_mpi.sh

You can check the job status using qstat:

$ qstat ### check the status of your jobs
$ qstat -b ### check the status of all of the jobs