/[MITgcm]/MITgcm_contrib/MPMice/beaufort/README_beaufort.txt
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revision 1.2 by dimitri, Mon Jun 1 05:43:47 2009 UTC revision 1.14 by dimitri, Thu Dec 3 01:58:40 2015 UTC
# Line 1  Line 1 
1  Instructions for running the "beaufort" 40x40x50 configuration  Instructions for running the "beaufort" 40x40x50 configuration
2  face=6; ix=101:300; jx=290:449; kx=1:50;  face=6; ix=101:300; jx=290:449; kx=1:50;
3    
4  1. Set up and log in to cvs server  1. Get code, input, and README files from CVS server
5    bash or sh shell: export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'    cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack \
6    tcsh or csh shell: setenv CVSROOT ':pserver:cvsanon@mitgcm.org:/u/gcmpack'        co -d beaufort MITgcm_contrib/MPMice/beaufort
   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  
7    cd beaufort    cd beaufort
8    cvs co MITgcm_code    cvs -d :pserver:cvsanon:cvsanon@mitgcm.org:/u/gcmpack co -P MITgcm_code
9    
10  3. Obtain copies of following directories and put them in beaufort  2. Obtain copies of following directories and put them in beaufort
11    ftp://ecco2.jpl.nasa.gov/data1/beaufort/run_template    wget -r -nH --cut-dirs=2 ftp://ecco2.jpl.nasa.gov/data1/beaufort/run_template
12    ftp://ecco2.jpl.nasa.gov/data1/data/blend_forcing/cube78_forcing    wget -r -nH --cut-dirs=4 ftp://ecco2.jpl.nasa.gov/data1/data/atmos/blend_forcing/cube78_forcing
13     (Note the forcing files in cube78_forcing span many years.     (Note the forcing files in cube78_forcing span many years.
14      To save time, you only need to download the years of interest,      To save time, you only need to download the years of interest,
15      *92 for example below, plus the runoff-360x180x12.bin file)      *92 for example below, plus the runoff-360x180x12.bin file)
16    
17  4. Get the ice code, PM2  3. Get the ice code, PM2 (this item needs to be updated)
18          Obtain directories PM2/F95 and PM2/config from ...??          Obtain directories PM2/F95 and PM2/config from ...??
19          call the directory containting PM2, ICE_DIR,          call the directory containting PM2, ICE_DIR,
20          in my case ICE_DIR=/dm5/bep/sulsky/seaice on pollux          in my case ICE_DIR=/dm5/bep/sulsky/seaice on pollux
21                     ICE_DIR=/workg/bep/sulsky/seacie on gemini                     ICE_DIR=/workg/bep/sulsky/seaice on gemini
22                      
23     cp -r /workg/bep/sulsky/seaice ICE_DIR
24     cd ICE_DIR/PM2
25     make
26    
27     ONCE ONLY: (only need to redo if geometry changes)
28     cd MITgcm/ice
29     mpirun -np 1 ICE_DIR/PM2-Pre
30    
31          The PM2/config/hosts files for gemini and pollux  assume petsc is installed in          The PM2/config/hosts files for gemini and pollux  assume petsc is installed in
32                  PETSCDIR = /dm5/bep/sulsky/Packages/petsc-2.3.3-p8  on pollux                  PETSCDIR = /dm5/bep/sulsky/Packages/petsc-2.3.3-p8  on pollux
33                  PETSCDIR = /workg/bep/sulsky/Packages/petsc-2.3.3-p8 on gemini                  PETSCDIR = /workg/bep/sulsky/Packages/petsc-2.3.3-p8 on gemini
# Line 32  face=6; ix=101:300; jx=290:449; kx=1:50; Line 36  face=6; ix=101:300; jx=290:449; kx=1:50;
36          ./config/configure.py --with-debug=1 --with-fc=/opt/intel/fc/9.1.051/bin/ifort          ./config/configure.py --with-debug=1 --with-fc=/opt/intel/fc/9.1.051/bin/ifort
37  --with-f90=/opt/intel/fc/9.1.051/bin/ifort --with-mpi-dir=/opt/mpich/ch-p4  --with-f90=/opt/intel/fc/9.1.051/bin/ifort --with-mpi-dir=/opt/mpich/ch-p4
38  --with-blas-lapack-dir=/opt/intel/mkl/9.1.023/lib/64  for debuggable code and  --with-blas-lapack-dir=/opt/intel/mkl/9.1.023/lib/64  for debuggable code and
39            
40          ./config/configure.py --with-debug=0 --with-fc=/opt/intel/fc/9.1.051/bin/ifort          ./config/configure.py --with-debug=0 --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  --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 optimized code.)  --with-blas-lapack-dir=/opt/intel/mkl/9.1.023/lib/64 for optimized code.)
43            
44          Input files go in MITgcm/ice (pm2input, pm2geometry) After compile step, run          Input files go in MITgcm/ice (pm2input, pm2geometry) After compile step, run
45          PM2-Pre once to generate pm2_grid.nc pm2_part.nc with initial geometry.          PM2-Pre once to generate pm2_grid.nc pm2_part.nc with initial geometry.
46            
47  =============================================  =============================================
48  Running on a linux workstation:  Running uncoupled, serial code
49    
50  5. Compile code:  4. Compile code:
51   cd MITgcm   cd MITgcm
52   mkdir bin exe   mkdir bin exe
53   cd bin   cd bin
54   ../tools/genmake2 -mods=../../code   ../tools/genmake2 -mo ../../code
55   make depend   make depend
56   make -j   make -j
57    
58  6. Model execution:  5. Model execution:
59   cd ../exe   cd ../exe
60   cp ../../run_template/* .   ln -sf ../../run_template/* .
61   cp ../../input/* .   cp ../../input/* .
62   cp ../bin/mitgcmuv .   cp ../bin/mitgcmuv .
63   ./mitgcmuv >& output.txt &   ./mitgcmuv >& output.txt &
64    
65  =============================================  =============================================
66  Running on gemini.  Running uncoupled MPI code
67    
68  5. Compile code:  4. Compile code:
69   cd MITgcm   cd MITgcm
70   mkdir bin exe   mkdir bin exe
71   cd bin   cd bin
72   \cp ../../code/* .   \cp ../../code/SIZE.h_2 SIZE.h
73   \mv SIZE.h_2 SIZE.h   \cp ../../code/CPP_EEOPTIONS.h_UNCOUPLED CPP_EEOPTIONS.h
74   ../tools/genmake2 -of ../tools/build_options/linux_ia64_ifort+mpi_altix_jpl   ../tools/genmake2 -mpi -mo ../../code
75   make depend   make depend
76   make -j   make -j
77    
78  6. Model execution:  5. Model execution:
79   cd ../exe   cd ../exe
80   cp ../../run_template/* .   ln -sf ../../run_template/* .
81     cp ../../input/* .
82   cp ../bin/mitgcmuv .   cp ../bin/mitgcmuv .
83   bsub < jobfile   mpiexec -np 2 ./mitgcmuv &
  bjobs  
84    
85  =============================================  =============================================
86  Running MITgcm and MPMice on gemini.  Running MITgcm and MPMice
87    
88  5. Compile code:  4. Compile code:
89   cd MITgcm   cd MITgcm
90   mkdir bin   mkdir bin
91   cd bin   cd bin
# Line 89  Running MITgcm and MPMice on gemini. Line 93  Running MITgcm and MPMice on gemini.
93   \cp ../../code/* .   \cp ../../code/* .
94   \mv SIZE.h_2 SIZE.h   \mv SIZE.h_2 SIZE.h
95   \mv CPP_EEOPTIONS.h_CPL CPP_EEOPTIONS.h   \mv CPP_EEOPTIONS.h_CPL CPP_EEOPTIONS.h
96   ../tools/genmake2 -of ../tools/build_options/linux_ia64_ifort+mpi_altix_jpl   ../tools/genmake2 -of ../../code/linux_gfortran_spiral -mpi
97   make depend   make depend
98   make -j   make -j
99    
  cd ICE_DIR  
  make  
   
  ONCE ONLY: (only need to redo if geometry changes)  
  cd MITgcm/ice  
  mpirun -np 1 ICE_DIR/PM2-Pre  
   
  cd MITgcm  
   
 6. Model execution:  
100   cd ..   cd ..
101   \rm out err   mkdir ice
102     cp ../../beaufort_020212/MITgcm/ice/* .
103     cp /homes/hantran/MPM_Han/PM2/bin/PM2 .
104    
105    5. Model execution:
106     \rm out err a.out
107   mkdir ocean   mkdir ocean
108   cd ocean   cd ocean
109   \rm *   \rm *
110   cp ../../run_template/* .   \cp ../../run_template/* .
111     \cp ../../input/* .
112   cd ..   cd ..
  cp -r ../ice .  
113   \cp bin/mitgcmuv .   \cp bin/mitgcmuv .
114   \cp ice/PM2 .   mpiexec -np 2 mitgcmuv : -np 1 PM2 > a.out &
  bsub < ocean/jobfile2  
  bjobs  
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