| 1 |
dimitri |
1.1 |
For interactive session, Ivy Bridge nodes: |
| 2 |
dimitri |
1.10 |
qsub -I -q devel -l select=300:ncpus=20:model=ivy,walltime=02:00:00 -m abe -M YOUR_EMAIL_HERE |
| 3 |
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qsub -I -q normal -l select=103:ncpus=20:model=ivy,walltime=8:00:00 -m abe -M YOUR_EMAIL_HERE |
| 4 |
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qsub -I -q long -l select=300:ncpus=20:model=ivy,walltime=120:00:00 -m abe -M YOUR_EMAIL_HERE |
| 5 |
|
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qsub -I -q long -l select=103:ncpus=20:model=ivy,min_walltime=30:00,max_walltime=120:00:00 -m abe -M YOUR_EMAIL_HERE |
| 6 |
dimitri |
1.1 |
|
| 7 |
dimitri |
1.7 |
############################# |
| 8 |
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# 60x60x10882 configuration |
| 9 |
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| 10 |
dimitri |
1.10 |
qsub -I -q long -l select=600:ncpus=20:model=ivy,min_walltime=30:00,max_walltime=120:00:00 -m abe -M YOUR_EMAIL_HERE |
| 11 |
dimitri |
1.7 |
module purge |
| 12 |
dimitri |
1.10 |
module load comp-intel/2012.0.032 mpi-sgi/mpt.2.10r6 netcdf/4.0 |
| 13 |
dimitri |
1.7 |
cd ~/llc_2160 |
| 14 |
dimitri |
1.12 |
cvs co -r checkpoint64t MITgcm_code |
| 15 |
dimitri |
1.8 |
cvs co MITgcm_contrib/llc_hires/llc_2160 |
| 16 |
dimitri |
1.7 |
cd MITgcm |
| 17 |
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mkdir build run |
| 18 |
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cd build |
| 19 |
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cp ../../MITgcm_contrib/llc_hires/llc_2160/code/SIZE.h_60x60_10882 SIZE.h |
| 20 |
|
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cp ../../MITgcm_contrib/llc_hires/llc_2160/code-async/readtile_mpiio.c . |
| 21 |
|
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emacs readtile_mpiio.c |
| 22 |
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tileSizeX = 60; |
| 23 |
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tileSizeY = 60; |
| 24 |
|
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../tools/genmake2 -of \ |
| 25 |
|
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../../MITgcm_contrib/llc_hires/llc_2160/code-async/linux_amd64_ifort+mpi_ice_nas -mpi -mods \ |
| 26 |
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'../../MITgcm_contrib/llc_hires/llc_2160/code ../../MITgcm_contrib/llc_hires/llc_2160/code-async' |
| 27 |
|
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make depend |
| 28 |
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make -j 16 |
| 29 |
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| 30 |
dimitri |
1.9 |
cd ~/llc_2160/MITgcm/run |
| 31 |
dimitri |
1.7 |
cp ../build/mitgcmuv mitgcmuv_60x60x10882 |
| 32 |
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ln -sf /nobackup/dmenemen/tarballs/llc_2160/run_template/* . |
| 33 |
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ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 34 |
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cp ../../MITgcm_contrib/llc_hires/llc_2160/input/* . |
| 35 |
dimitri |
1.10 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/input/data.exch2_60x60x10882 data.exch2 |
| 36 |
dimitri |
1.7 |
emacs data |
| 37 |
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| 38 |
|
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export MPI_BUFS_PER_PROC=1024 |
| 39 |
|
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export MPI_REQUEST_MAX=65536 |
| 40 |
|
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export MPI_GROUP_MAX=1024 |
| 41 |
|
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export MPI_NUM_MEMORY_REGIONS=8 |
| 42 |
|
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export MPI_UNBUFFERED_STDIO=1 |
| 43 |
|
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export MPI_MEMMAP_OFF=1 |
| 44 |
dimitri |
1.8 |
export MPI_UD_TIMEOUT=100 |
| 45 |
dimitri |
1.7 |
mpiexec -n 12000 ./mitgcmuv_60x60x10882 |
| 46 |
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| 47 |
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tail -f STDOUT.00000 | grep advcfl_W |
| 48 |
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| 49 |
dimitri |
1.10 |
################################################ |
| 50 |
|
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# 144x144x2047 configuration for grid generation |
| 51 |
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| 52 |
|
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qsub -I -q devel -l select=103:ncpus=20:model=ivy,walltime=02:00:00 -m abe -M YOUR_EMAIL_HERE |
| 53 |
|
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module purge |
| 54 |
|
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module load comp-intel/2012.0.032 mpi-sgi/mpt.2.10r6 netcdf/4.0 |
| 55 |
|
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cd ~/llc_2160 |
| 56 |
|
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cvs co MITgcm_code |
| 57 |
|
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cvs co MITgcm_contrib/llc_hires/llc_2160 |
| 58 |
|
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cd MITgcm |
| 59 |
|
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mkdir build run_grid |
| 60 |
|
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lfs setstripe -c -1 run_grid |
| 61 |
|
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cd build |
| 62 |
|
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cp ../../MITgcm_contrib/llc_hires/llc_2160/code/SIZE.h_144x144x2047 SIZE.h |
| 63 |
|
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../tools/genmake2 -of \ |
| 64 |
|
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../../MITgcm_contrib/llc_hires/llc_2160/code-async/linux_amd64_ifort+mpi_ice_nas \ |
| 65 |
|
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-mpi -mods ../../MITgcm_contrib/llc_hires/llc_2160/code |
| 66 |
|
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make depend |
| 67 |
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make -j 16 |
| 68 |
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| 69 |
|
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cd ~/llc_2160/MITgcm/run_grid |
| 70 |
|
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cp ../build/mitgcmuv mitgcmuv_144x144x2047 |
| 71 |
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ln -sf /nobackup/dmenemen/tarballs/llc_2160/run_template/* . |
| 72 |
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ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 73 |
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cp ../../MITgcm_contrib/llc_hires/llc_2160/input/* . |
| 74 |
|
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cp ../../MITgcm_contrib/llc_hires/llc_2160/input/data.exch2_144x144x2047 data.exch2 |
| 75 |
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| 76 |
|
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emacs data |
| 77 |
|
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debuglevel=3, |
| 78 |
|
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useSingleCPUio=.TRUE., |
| 79 |
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endtime=0., |
| 80 |
|
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deltaT = 1., |
| 81 |
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| 82 |
|
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mpiexec -n 2047 ./mitgcmuv_144x144x2047 |
| 83 |
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| 84 |
dimitri |
1.1 |
============== |
| 85 |
|
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|
| 86 |
dimitri |
1.2 |
cd ~/llc_2160 |
| 87 |
dimitri |
1.1 |
cvs co MITgcm_code |
| 88 |
dimitri |
1.2 |
cvs co MITgcm_contrib/llc_hires/llc_2160 |
| 89 |
dimitri |
1.1 |
cd MITgcm |
| 90 |
|
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module purge |
| 91 |
dimitri |
1.4 |
module load comp-intel/2012.0.032 mpi-sgi/mpt.2.08r7 netcdf/4.0 |
| 92 |
dimitri |
1.1 |
mkdir build run |
| 93 |
dimitri |
1.2 |
lfs setstripe -c -1 run |
| 94 |
dimitri |
1.1 |
cd build |
| 95 |
dimitri |
1.3 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/code/SIZE.h_90x90_5004 SIZE.h |
| 96 |
dimitri |
1.2 |
../tools/genmake2 -of \ |
| 97 |
|
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../../MITgcm_contrib/llc_hires/llc_2160/code-async/linux_amd64_ifort+mpi_ice_nas -mpi -mods \ |
| 98 |
|
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'../../MITgcm_contrib/llc_hires/llc_2160/code ../../MITgcm_contrib/llc_hires/llc_2160/code-async' |
| 99 |
dimitri |
1.1 |
make depend |
| 100 |
|
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make -j 16 |
| 101 |
dimitri |
1.4 |
cd ~/llc_2160/MITgcm/run |
| 102 |
dimitri |
1.1 |
ln -sf ../build/mitgcmuv . |
| 103 |
|
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ln -sf /nobackup/dmenemen/tarballs/llc_2160/run_template/* . |
| 104 |
dimitri |
1.2 |
ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 105 |
|
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cp ../../MITgcm_contrib/llc_hires/llc_2160/input/* . |
| 106 |
dimitri |
1.3 |
mv data.exch2_90x90x5004 data.exch2 |
| 107 |
dimitri |
1.5 |
export MPI_NUM_MEMORY_REGIONS=256 |
| 108 |
dimitri |
1.6 |
mpiexec -n 6000 ./mitgcmuv |
| 109 |
dimitri |
1.1 |
|
| 110 |
|
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============== |
| 111 |
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| 112 |
|
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look at output |
| 113 |
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| 114 |
|
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for ts=[0 120 600:10:980 1080:120:2280] |
| 115 |
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fld=quikread_llc(['Eta.' myint2str(ts,10) '.data'],2160); |
| 116 |
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clf,quikplot_llc(fld),caxis([-2.5 2]),thincolorbar |
| 117 |
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title(ts) |
| 118 |
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pause(.1) |
| 119 |
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end |
| 120 |
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| 121 |
|
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============== |
| 122 |
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| 123 |
|
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to determine empty tiles: |
| 124 |
dimitri |
1.13 |
grep Empty STDOUT.* > empty.txt |
| 125 |
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| 126 |
|
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============== |
| 127 |
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| 128 |
|
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# generate 30x30 blank tiles |
| 129 |
|
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qsub -I -q normal -l select=339:ncpus=28:model=bro,walltime=2:00:00 -m abe |
| 130 |
|
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module purge |
| 131 |
|
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module load comp-intel/2016.2.181 mpi-sgi/mpt.2.14r19 hdf4/4.2.12 hdf5/1.8.18_mpt netcdf/4.4.1.1_mpt |
| 132 |
|
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cd ~/llc_2160/MITgcm |
| 133 |
|
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mkdir run_30x30 |
| 134 |
|
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lfs setstripe -c -1 run_30x30 |
| 135 |
|
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cd build |
| 136 |
|
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rm * |
| 137 |
|
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cp ../../MITgcm_contrib/llc_hires/llc_2160/code-async/readtile_mpiio.c . |
| 138 |
|
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emacs readtile_mpiio.c |
| 139 |
|
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tileSizeX = 30; |
| 140 |
|
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tileSizeY = 30; |
| 141 |
|
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cp ../../MITgcm_contrib/llc_hires/llc_2160/code/SIZE.h_60x60_10882 SIZE.h |
| 142 |
|
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emacs SIZE.h |
| 143 |
|
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& sNx = 30, |
| 144 |
|
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& sNy = 30, |
| 145 |
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& nSx = 8, |
| 146 |
|
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& nPx = 8424, |
| 147 |
|
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& Nr = 2 ) |
| 148 |
|
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cp ../../MITgcm_contrib/llc_hires/llc_2160/code-async/eeboot_minimal.F . |
| 149 |
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emacs eeboot_minimal.F |
| 150 |
|
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C standardMessageUnit=errorMessageUnit |
| 151 |
|
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WRITE(fNam,'(A,A)') 'STDOUT.', myProcessStr(1:5) |
| 152 |
|
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OPEN(standardMessageUnit,FILE=fNam,STATUS='unknown') |
| 153 |
|
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../tools/genmake2 -of \ |
| 154 |
|
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../../MITgcm_contrib/llc_hires/llc_2160/code-async/linux_amd64_ifort+mpi_ice_nas -mpi -mods \ |
| 155 |
|
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'../../MITgcm_contrib/llc_hires/llc_2160/code ../../MITgcm_contrib/llc_hires/llc_2160/code-async' |
| 156 |
|
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make depend |
| 157 |
|
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make -j 16 |
| 158 |
|
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cd ~/llc_2160/MITgcm/run_30x30 |
| 159 |
|
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cp ../build/mitgcmuv . |
| 160 |
|
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ln -sf /nobackup/dmenemen/tarballs/llc_2160/run_template/* . |
| 161 |
|
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ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 162 |
|
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cp ../../MITgcm_contrib/llc_hires/llc_2160/input/* . |
| 163 |
|
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mv data.exch2_144x144x2047 data.exch2 |
| 164 |
|
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emacs data.exch2 |
| 165 |
|
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# remove the blank tile list |
| 166 |
|
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emacs data |
| 167 |
|
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tRef = 18.89, 18.89, |
| 168 |
|
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sRef = 34.84, 34.84, |
| 169 |
|
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endtime=45., |
| 170 |
|
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delR = 1.00, 1.14, |
| 171 |
|
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# hydrogThetaFile='THETA_llc1080_14jan2011_2160x28080x90_r4', |
| 172 |
|
|
# hydrogSaltFile ='SALT_llc1080_14jan2011_2160x28080x90_r4', |
| 173 |
|
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# uVelInitFile ='UVEL_llc1080_14jan2011_2160x28080x90_r4', |
| 174 |
|
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# vVelInitFile ='VVEL_llc1080_14jan2011_2160x28080x90_r4', |
| 175 |
|
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# pSurfInitFile ='ETAN_llc1080_14jan2011_2160x28080_r4', |
| 176 |
|
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mpiexec -n 9492 ./mitgcmuv |
| 177 |
dimitri |
1.1 |
|
| 178 |
|
|
============== |
| 179 |
|
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|
| 180 |
|
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memory requirements: |
| 181 |
|
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nPx sNx sNy nSx cpu node0 total rank0 rankm |
| 182 |
|
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936 180 180 2 san node ran out of memory and crashed with singlecpuio |
| 183 |
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1053 240 240 1 san node ran out of memory and crashed with singlecpuio |
| 184 |
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1300 216 216 1 san node ran out of memory and crashed with singlecpuio |
| 185 |
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1872 180 180 1 wes node ran out of memory and crashed with singlecpuio |
| 186 |
|
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1872 180 180 1 wes 21,377,644kb 3,294,676,080kb node ran out of memory with singlecpuio and bigmem=true:mem=90GB for node 0 |
| 187 |
|
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1872 180 180 1 san node ran out of memory and crashed with singlecpuio |
| 188 |
|
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1872 180 180 1 san 11,558,588kb 1,356,676,140kb singlecpuio=.FALSE. |
| 189 |
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2925 144 144 1 san 8,374,668kb 1,538,454,112kb 886MB 892MB singlecpuio=.FALSE. |
| 190 |
|
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2925 144 144 1 san 27,284,996kb 4,942,949,704kb node ran out of memory and crashed with singlecpuio |
| 191 |
|
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3328 135 135 1 san rank 0 run out of memory |
| 192 |
|
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3328 135 135 1 san some random node run out of memory (full node for rank 0) |
| 193 |
|
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4212 120 120 1 san node ran out of memory |
| 194 |
|
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5200 108 108 1 san node ran out of memory |
| 195 |
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| 196 |
|
|
============= |
| 197 |
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| 198 |
|
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2 = 2 |
| 199 |
|
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3 = 3 |
| 200 |
|
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2*2 = 4 |
| 201 |
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5 = 5 |
| 202 |
|
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2*3 = 6 |
| 203 |
|
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2*2*2 = 8 |
| 204 |
|
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3*3 = 9 |
| 205 |
|
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2*5 = 10 |
| 206 |
|
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2*2*3 = 12 |
| 207 |
|
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3*5 = 15 |
| 208 |
|
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2*2*2*2 = 16 |
| 209 |
|
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2*3*3 = 18 |
| 210 |
|
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2*2*5 = 20 |
| 211 |
|
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2*2*2*3 = 24 |
| 212 |
|
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3*3*3 = 27 |
| 213 |
|
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2*3*5 = 30 |
| 214 |
|
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2*2*3*3 = 36 |
| 215 |
|
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2*2*2*5 = 40 |
| 216 |
|
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3*3*5 = 45 |
| 217 |
|
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2*2*2*2*3 = 48 * 45 |
| 218 |
|
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2*3*3*3 = 54 * 40 |
| 219 |
|
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2*2*3*5 = 60 * 36 |
| 220 |
|
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2*2*2*3*3 = 72 * 30 |
| 221 |
|
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2*2*2*2*5 = 80 * 27 |
| 222 |
|
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2*3*3*5 = 90 * 24 |
| 223 |
|
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2*2*3*3*3 = 108 * 20 |
| 224 |
|
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2*2*2*3*5 = 120 * 18 |
| 225 |
|
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3*3*3*5 = 135 * 16 |
| 226 |
|
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2*2*2*2*3*3 = 144 * 15 |
| 227 |
|
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2*2*3*3*5 = 180 * 12 |
| 228 |
|
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2*2*2*3*3*3 = 216 * 10 |
| 229 |
|
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2*2*2*2*3*5 = 240 * 9 |
| 230 |
|
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2*3*3*3*5 = 270 * 8 |
| 231 |
|
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2*2*2*3*3*5 = 360 * 6 |
| 232 |
|
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2*2*2*2*3*3*3 = 432 * 5 |
| 233 |
|
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2*2*3*3*3*5 = 540 * 4 |
| 234 |
|
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2*2*2*2*3*3*5 = 720 * 3 |
| 235 |
|
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2*2*2*3*3*3*5 = 1080 * 2 |
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