FVCOM 2.6.1 on HA8000@hakozaki using Intel compilers

Table of Content

Change the shell

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

[cc] $ bash [/cc]

Compile METIS

Edit the makefile as follows:

[cc]

AR = xiar rv
CC = icc
OPTFLAGS = -O3

[/cc]
And then, compile as follows:
[cc] $ make [/cc]

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:

[cc]
CPP = /usr/bin/cpp
CPPFLAGS = $(DEF_FLAGS) -DINTEL
FC = mpiifort
DEBFLAGS =
OPT = -O3 -ipo -no-prec-div
CLIB =
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makedepf90 should be installed and then makedepends should be created. mpi.h should be deleted if existed.

[cc]
$ rm makedepends
$ rm mpi.h
$ touch makedepends
$ make depend
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Now you can compile:

[cc] $ make [/cc]

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

[cc] $ cp fvcom ../run/ [/cc]

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

[cc]
#!/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
[/cc]

Execution

Now you can execute on bat mode:

[cc] $ qsub run_mpi.sh [/cc]

You can check the job status using qstat:

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