MPMice/beaufort/README_beaufort.txt

Instructions for running the "beaufort" 40x40x50 configuration
face=6; ix=101:300; jx=290:449; kx=1:50;

1. Set up and log in to cvs server
  bash or sh shell: export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
  tcsh or csh shell: setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
  cvs login ( enter the CVS password: "cvsanon" )

2. Get code, input, and README files from CVS server
  cvs co -d beaufort MITgcm_contrib/MPMice/beaufort
  cd beaufort
  cvs co MITgcm_code

3. Obtain copies of following directories and put them in beaufort
  ftp://ecco2.jpl.nasa.gov/data1/beaufort/run_template
  ftp://ecco2.jpl.nasa.gov/data1/data/atmos/blend_forcing/cube78_forcing
   (Note the forcing files in cube78_forcing span many years.
    To save time, you only need to download the years of interest,
    *92 for example below, plus the runoff-360x180x12.bin file)

4. Get the ice code, PM2 (this item needs to be updated)
        Obtain directories PM2/F95 and PM2/config from ...??
        call the directory containting PM2, ICE_DIR, 
        in my case ICE_DIR=/dm5/bep/sulsky/seaice on pollux
                   ICE_DIR=/workg/bep/sulsky/seaice on gemini

 cp -r /workg/bep/sulsky/seaice ICE_DIR
 cd ICE_DIR/PM2
 make
 
 ONCE ONLY: (only need to redo if geometry changes)
 cd MITgcm/ice
 mpirun -np 1 ICE_DIR/PM2-Pre
                   
        The PM2/config/hosts files for gemini and pollux  assume petsc is installed in
                PETSCDIR = /dm5/bep/sulsky/Packages/petsc-2.3.3-p8  on pollux
                PETSCDIR = /workg/bep/sulsky/Packages/petsc-2.3.3-p8 on gemini
        If petsc is installed elsewhere, then change the directory specification.
        (The configure command to build petsc on gemini or pollux is
        ./config/configure.py --with-debug=1 --with-fc=/opt/intel/fc/9.1.051/bin/ifort
--with-f90=/opt/intel/fc/9.1.051/bin/ifort --with-mpi-dir=/opt/mpich/ch-p4
--with-blas-lapack-dir=/opt/intel/mkl/9.1.023/lib/64  for debuggable code and
        
        ./config/configure.py --with-debug=0 --with-fc=/opt/intel/fc/9.1.051/bin/ifort
--with-f90=/opt/intel/fc/9.1.051/bin/ifort --with-mpi-dir=/opt/mpich/ch-p4
--with-blas-lapack-dir=/opt/intel/mkl/9.1.023/lib/64 for optimized code.)
        
        Input files go in MITgcm/ice (pm2input, pm2geometry) After compile step, run
        PM2-Pre once to generate pm2_grid.nc pm2_part.nc with initial geometry. 
        
=============================================
Running on a linux workstation:

5. Compile code:
 cd MITgcm
 mkdir bin exe
 cd bin
 \cp ../../code/* .
 \mv CPP_EEOPTIONS.h_CPL_DEBUG CPP_EEOPTIONS.h
 ../tools/genmake2
 make depend
 make -j 16

6. Model execution:
 cd ../exe
 cp ../../run_template/* .
 cp ../../input/* .
 cp ../bin/mitgcmuv .
 ./mitgcmuv >& output.txt &

=============================================
Running on lozenge.

5. Compile code:
 cd MITgcm
 mkdir bin exe
 cd bin
 \cp ../../code/* .
 \mv SIZE.h_2 SIZE.h
 ../tools/genmake2 -of ../../code/linux_amd64_gfortran_lozenge -mpi
 make depend
 make -j
 
6. Model execution:
 cd ../exe
 cp ../../run_template/* .
 cp ../../input/* .
 cp ../bin/mitgcmuv .
 mpiexec -np 2 ./mitgcmuv >& output.txt

=============================================
Running MITgcm and MPMice on lozenge.

5. Compile code:
 cd MITgcm
 mkdir bin
 cd bin
 \rm *
 \cp ../../code/* .
 \mv SIZE.h_2 SIZE.h
 \mv CPP_EEOPTIONS.h_CPL CPP_EEOPTIONS.h
 ../tools/genmake2 -of ../../code/linux_amd64_gfortran_lozenge -mpi
 make depend
 make -j

 cd ..
 mkdir ice
 cp ../../beaufort_020212/MITgcm/ice/* .
 cp /homes/hantran/MPM_Han/PM2/bin/PM2 .
 
6. Model execution:
 \rm out err a.out
 mkdir ocean
 cd ocean
 \rm *
 \cp ../../run_template/* .
 \cp ../../input/* .
 cd ..
 \cp bin/mitgcmuv .
 mpiexec -np 2 mitgcmuv : -np 1 PM2 > a.out &

=============================================
Running on gemini.

5. Compile code:
 cd MITgcm
 mkdir bin exe
 cd bin
 \cp ../../code/* .
 \mv SIZE.h_2 SIZE.h
 ../tools/genmake2 -of ../tools/build_options/linux_ia64_ifort+mpi_altix_jpl
 make depend
 make -j
 
6. Model execution:
 cd ../exe
 cp ../../run_template/* .
 cp ../../input/* .
 cp ../bin/mitgcmuv .
 qsub jobfile
 qstat

=============================================
Running MITgcm and MPMice on gemini.

5. Compile code:
 cd MITgcm
 mkdir bin
 cd bin
 \rm *
 \cp ../../code/* .
 \mv SIZE.h_2 SIZE.h
 \mv CPP_EEOPTIONS.h_CPL CPP_EEOPTIONS.h
 ../tools/genmake2 -of ../tools/build_options/linux_ia64_ifort+mpi_altix_jpl
 make depend
 make -j

 cd ..
 cp -r /workg/bep/dmenemen/MITgcm/ice .
 
6. Model execution:
 \rm out err
 mkdir ocean
 cd ocean
 \rm *
 \cp ../../run_template/* .
 \cp ../../input/* .
 cd ..
 \cp -r /workg/bep/dmenemen/MITgcm/ice .
 \cp bin/mitgcmuv .
 \cp ice/PM2 .
 bsub < ocean/jobfile2
 bjobs
1	dimitri	1.1	Instructions for running the "beaufort" 40x40x50 configuration
2			face=6; ix=101:300; jx=290:449; kx=1:50;
3
4	dimitri	1.2	1. Set up and log in to cvs server
5			bash or sh shell: export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
6			tcsh or csh shell: setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'
7			cvs login ( enter the CVS password: "cvsanon" )
8
9			2. Get code, input, and README files from CVS server
10			cvs co -d beaufort MITgcm_contrib/MPMice/beaufort
11			cd beaufort
12			cvs co MITgcm_code
13
14			3. Obtain copies of following directories and put them in beaufort
15			ftp://ecco2.jpl.nasa.gov/data1/beaufort/run_template
16	dimitri	1.4	ftp://ecco2.jpl.nasa.gov/data1/data/atmos/blend_forcing/cube78_forcing
17	dimitri	1.2	(Note the forcing files in cube78_forcing span many years.
18			To save time, you only need to download the years of interest,
19			*92 for example below, plus the runoff-360x180x12.bin file)
20	dimitri	1.1
21	dimitri	1.3	4. Get the ice code, PM2 (this item needs to be updated)
22	dimitri	1.1	Obtain directories PM2/F95 and PM2/config from ...??
23			call the directory containting PM2, ICE_DIR,
24			in my case ICE_DIR=/dm5/bep/sulsky/seaice on pollux
25	dimitri	1.3	ICE_DIR=/workg/bep/sulsky/seaice on gemini
26
27			cp -r /workg/bep/sulsky/seaice ICE_DIR
28			cd ICE_DIR/PM2
29			make
30
31			ONCE ONLY: (only need to redo if geometry changes)
32			cd MITgcm/ice
33			mpirun -np 1 ICE_DIR/PM2-Pre
34	dimitri	1.1
35			The PM2/config/hosts files for gemini and pollux assume petsc is installed in
36			PETSCDIR = /dm5/bep/sulsky/Packages/petsc-2.3.3-p8 on pollux
37			PETSCDIR = /workg/bep/sulsky/Packages/petsc-2.3.3-p8 on gemini
38			If petsc is installed elsewhere, then change the directory specification.
39			(The configure command to build petsc on gemini or pollux is
40			./config/configure.py --with-debug=1 --with-fc=/opt/intel/fc/9.1.051/bin/ifort
41			--with-f90=/opt/intel/fc/9.1.051/bin/ifort --with-mpi-dir=/opt/mpich/ch-p4
42			--with-blas-lapack-dir=/opt/intel/mkl/9.1.023/lib/64 for debuggable code and
43
44			./config/configure.py --with-debug=0 --with-fc=/opt/intel/fc/9.1.051/bin/ifort
45			--with-f90=/opt/intel/fc/9.1.051/bin/ifort --with-mpi-dir=/opt/mpich/ch-p4
46			--with-blas-lapack-dir=/opt/intel/mkl/9.1.023/lib/64 for optimized code.)
47
48			Input files go in MITgcm/ice (pm2input, pm2geometry) After compile step, run
49			PM2-Pre once to generate pm2_grid.nc pm2_part.nc with initial geometry.
50
51			=============================================
52			Running on a linux workstation:
53
54			5. Compile code:
55			cd MITgcm
56			mkdir bin exe
57			cd bin
58	dimitri	1.8	\cp ../../code/* .
59			\mv CPP_EEOPTIONS.h_CPL_DEBUG CPP_EEOPTIONS.h
60			../tools/genmake2
61	dimitri	1.1	make depend
62	dimitri	1.6	make -j 16
63	dimitri	1.1
64			6. Model execution:
65			cd ../exe
66			cp ../../run_template/* .
67	dimitri	1.2	cp ../../input/* .
68	dimitri	1.1	cp ../bin/mitgcmuv .
69			./mitgcmuv >& output.txt &
70
71			=============================================
72	dimitri	1.5	Running on lozenge.
73
74			5. Compile code:
75			cd MITgcm
76			mkdir bin exe
77			cd bin
78			\cp ../../code/* .
79			\mv SIZE.h_2 SIZE.h
80			../tools/genmake2 -of ../../code/linux_amd64_gfortran_lozenge -mpi
81			make depend
82			make -j
83
84			6. Model execution:
85			cd ../exe
86			cp ../../run_template/* .
87			cp ../../input/* .
88			cp ../bin/mitgcmuv .
89			mpiexec -np 2 ./mitgcmuv >& output.txt
90
91			=============================================
92	dimitri	1.7	Running MITgcm and MPMice on lozenge.
93
94			5. Compile code:
95			cd MITgcm
96			mkdir bin
97			cd bin
98			\rm *
99			\cp ../../code/* .
100			\mv SIZE.h_2 SIZE.h
101			\mv CPP_EEOPTIONS.h_CPL CPP_EEOPTIONS.h
102			../tools/genmake2 -of ../../code/linux_amd64_gfortran_lozenge -mpi
103			make depend
104			make -j
105
106			cd ..
107			mkdir ice
108			cp ../../beaufort_020212/MITgcm/ice/* .
109			cp /homes/hantran/MPM_Han/PM2/bin/PM2 .
110
111			6. Model execution:
112			\rm out err a.out
113			mkdir ocean
114			cd ocean
115			\rm *
116			\cp ../../run_template/* .
117			\cp ../../input/* .
118			cd ..
119			\cp bin/mitgcmuv .
120			mpiexec -np 2 mitgcmuv : -np 1 PM2 > a.out &
121
122			=============================================
123	dimitri	1.1	Running on gemini.
124
125			5. Compile code:
126			cd MITgcm
127			mkdir bin exe
128			cd bin
129			\cp ../../code/* .
130			\mv SIZE.h_2 SIZE.h
131			../tools/genmake2 -of ../tools/build_options/linux_ia64_ifort+mpi_altix_jpl
132			make depend
133			make -j
134
135			6. Model execution:
136			cd ../exe
137			cp ../../run_template/* .
138	dimitri	1.3	cp ../../input/* .
139	dimitri	1.1	cp ../bin/mitgcmuv .
140	dimitri	1.5	qsub jobfile
141			qstat
142	dimitri	1.1
143			=============================================
144			Running MITgcm and MPMice on gemini.
145
146			5. Compile code:
147			cd MITgcm
148			mkdir bin
149			cd bin
150			\rm *
151			\cp ../../code/* .
152			\mv SIZE.h_2 SIZE.h
153			\mv CPP_EEOPTIONS.h_CPL CPP_EEOPTIONS.h
154			../tools/genmake2 -of ../tools/build_options/linux_ia64_ifort+mpi_altix_jpl
155			make depend
156			make -j
157	dimitri	1.3
158			cd ..
159			cp -r /workg/bep/dmenemen/MITgcm/ice .
160	dimitri	1.1
161			6. Model execution:
162			\rm out err
163			mkdir ocean
164			cd ocean
165			\rm *
166	dimitri	1.3	\cp ../../run_template/* .
167			\cp ../../input/* .
168	dimitri	1.1	cd ..
169	dimitri	1.3	\cp -r /workg/bep/dmenemen/MITgcm/ice .
170	dimitri	1.1	\cp bin/mitgcmuv .
171			\cp ice/PM2 .
172			bsub < ocean/jobfile2
173			bjobs