/[MITgcm]/MITgcm_contrib/MPMice/beaufort/README_beaufort.txt
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revision 1.8 by dimitri, Fri Mar 9 00:00:42 2012 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/atmos/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 (this item needs to be updated)  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
# Line 31  face=6; ix=101:300; jx=290:449; kx=1:50; Line 27  face=6; ix=101:300; jx=290:449; kx=1:50;
27   ONCE ONLY: (only need to redo if geometry changes)   ONCE ONLY: (only need to redo if geometry changes)
28   cd MITgcm/ice   cd MITgcm/ice
29   mpirun -np 1 ICE_DIR/PM2-Pre   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 40  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   \cp ../../code/* .   ../tools/genmake2 -mo ../../code
  \mv CPP_EEOPTIONS.h_CPL_DEBUG CPP_EEOPTIONS.h  
  ../tools/genmake2  
55   make depend   make depend
56   make -j 16   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 lozenge.  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 ../../code/linux_amd64_gfortran_lozenge -mpi   ../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/* .   cp ../../input/* .
82   cp ../bin/mitgcmuv .   cp ../bin/mitgcmuv .
83   mpiexec -np 2 ./mitgcmuv >& output.txt   mpiexec -np 2 ./mitgcmuv &
84    
85  =============================================  =============================================
86  Running MITgcm and MPMice on lozenge.  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 99  Running MITgcm and MPMice on lozenge. Line 93  Running MITgcm and MPMice on lozenge.
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 ../../code/linux_amd64_gfortran_lozenge -mpi   ../tools/genmake2 -of ../../code/linux_gfortran_spiral -mpi
97   make depend   make depend
98   make -j   make -j
99    
# Line 108  Running MITgcm and MPMice on lozenge. Line 102  Running MITgcm and MPMice on lozenge.
102   cp ../../beaufort_020212/MITgcm/ice/* .   cp ../../beaufort_020212/MITgcm/ice/* .
103   cp /homes/hantran/MPM_Han/PM2/bin/PM2 .   cp /homes/hantran/MPM_Han/PM2/bin/PM2 .
104    
105  6. Model execution:  5. Model execution:
106   \rm out err a.out   \rm out err a.out
107   mkdir ocean   mkdir ocean
108   cd ocean   cd ocean
# Line 118  Running MITgcm and MPMice on lozenge. Line 112  Running MITgcm and MPMice on lozenge.
112   cd ..   cd ..
113   \cp bin/mitgcmuv .   \cp bin/mitgcmuv .
114   mpiexec -np 2 mitgcmuv : -np 1 PM2 > a.out &   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  
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