| 1 |
dimitri |
1.1 |
For interactive session, Ivy Bridge nodes: |
| 2 |
dimitri |
1.6 |
qsub -I -q devel -l select=300:ncpus=20:model=ivy,walltime=02:00:00 -m abe -M email |
| 3 |
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qsub -I -q normal -l select=300:ncpus=20:model=ivy,walltime=8:00:00 -m abe -M email |
| 4 |
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qsub -I -q long -l select=300:ncpus=20:model=ivy,walltime=120:00:00 -m abe -M email |
| 5 |
dimitri |
1.11 |
qsub -I -q long -l select=1020:ncpus=20:model=ivy,min_walltime=30:00,max_walltime=120:00:00 -m abe -M menemenlis@me.com |
| 6 |
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| 7 |
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############################# |
| 8 |
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# generate 60x60 blank tiles |
| 9 |
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| 10 |
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qsub -I -q long -l select=600:ncpus=20:model=ivy,min_walltime=30:00,max_walltime=120:00:00 -m abe -M menemenlis@me.com |
| 11 |
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module purge |
| 12 |
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module load comp-intel/2012.0.032 netcdf/4.0 |
| 13 |
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module use -a ~kjtaylor/modulefiles |
| 14 |
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module load sles11sp3/mpt-2.10-nasa201311271217 |
| 15 |
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cd ~/llc_4320/MITgcm |
| 16 |
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mkdir run_60x60 |
| 17 |
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lfs setstripe -c -1 run_60x60 |
| 18 |
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| 19 |
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cd build |
| 20 |
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rm * |
| 21 |
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cp ../../MITgcm_contrib/llc_hires/llc_4320/code-async/readtile_mpiio.c . |
| 22 |
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emacs readtile_mpiio.c |
| 23 |
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tileSizeX = 60; |
| 24 |
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tileSizeY = 60; |
| 25 |
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cp ../../MITgcm_contrib/llc_hires/llc_4320/code/SIZE.h_120x120x10901 SIZE.h |
| 26 |
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emacs SIZE.h |
| 27 |
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& sNx = 60, |
| 28 |
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& sNy = 60, |
| 29 |
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& nSx = 6, |
| 30 |
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& nPx = 11232, |
| 31 |
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& Nr = 2 ) |
| 32 |
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cp ../../MITgcm_contrib/llc_hires/llc_4320/code-async/eeboot_minimal.F . |
| 33 |
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emacs eeboot_minimal.F |
| 34 |
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C standardMessageUnit=errorMessageUnit |
| 35 |
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WRITE(fNam,'(A,A)') 'STDOUT.', myProcessStr(1:5) |
| 36 |
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OPEN(standardMessageUnit,FILE=fNam,STATUS='unknown') |
| 37 |
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| 38 |
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../tools/genmake2 -of \ |
| 39 |
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../../MITgcm_contrib/llc_hires/llc_4320/code-async/linux_amd64_ifort+mpi_ice_nas -mpi -mods \ |
| 40 |
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'../../MITgcm_contrib/llc_hires/llc_4320/code ../../MITgcm_contrib/llc_hires/llc_4320/code-async' |
| 41 |
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make depend |
| 42 |
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make -j 16 |
| 43 |
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| 44 |
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cd ~/llc_4320/MITgcm/run_60x60 |
| 45 |
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cp ../build/mitgcmuv . |
| 46 |
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ln -sf /nobackup/dmenemen/tarballs/llc_4320/run_template/* . |
| 47 |
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ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 48 |
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cp ../../MITgcm_contrib/llc_hires/llc_4320/input/* . |
| 49 |
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mv data.exch2_120x120x10901 data.exch2 |
| 50 |
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| 51 |
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emacs data |
| 52 |
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tRef = 18.89, 18.89, |
| 53 |
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sRef = 34.84, 34.84, |
| 54 |
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endtime=20., |
| 55 |
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delR = 1.00, 1.14, |
| 56 |
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# hydrogThetaFile='THETA_llc2160_10sep2011_4320x56160x90_r4', |
| 57 |
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# hydrogSaltFile ='SALT_llc2160_10sep2011_4320x56160x90_r4', |
| 58 |
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# uVelInitFile ='UVEL_llc2160_10sep2011_4320x56160x90_r4', |
| 59 |
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# vVelInitFile ='VVEL_llc2160_10sep2011_4320x56160x90_r4', |
| 60 |
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# pSurfInitFile ='ETAN_llc2160_10sep2011_4320x56160_r4', |
| 61 |
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| 62 |
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emacs data.exch2 |
| 63 |
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# remove the blank tile list |
| 64 |
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| 65 |
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export MPI_BUFS_PER_PROC=1024 |
| 66 |
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export MPI_REQUEST_MAX=65536 |
| 67 |
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export MPI_GROUP_MAX=1024 |
| 68 |
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export MPI_NUM_MEMORY_REGIONS=8 |
| 69 |
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export MPI_UNBUFFERED_STDIO=1 |
| 70 |
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export MPI_MEMMAP_OFF=1 |
| 71 |
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mpiexec -n 12000 ./mitgcmuv |
| 72 |
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| 73 |
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############################# |
| 74 |
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# generate 45x45 blank tiles |
| 75 |
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| 76 |
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qsub -I -q long -l select=600:ncpus=20:model=ivy,min_walltime=30:00,max_walltime=120:00:00 -m abe -M menemenlis@me.com |
| 77 |
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module purge |
| 78 |
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module load comp-intel/2012.0.032 netcdf/4.0 |
| 79 |
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module use -a ~kjtaylor/modulefiles |
| 80 |
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module load sles11sp3/mpt-2.10-nasa201311271217 |
| 81 |
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cd ~/llc_4320/MITgcm |
| 82 |
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mkdir run_45x45 |
| 83 |
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lfs setstripe -c -1 run_45x45 |
| 84 |
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| 85 |
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cd build |
| 86 |
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rm * |
| 87 |
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cp ../../MITgcm_contrib/llc_hires/llc_4320/code-async/readtile_mpiio.c . |
| 88 |
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emacs readtile_mpiio.c |
| 89 |
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tileSizeX = 45; |
| 90 |
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tileSizeY = 45; |
| 91 |
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cp ../../MITgcm_contrib/llc_hires/llc_4320/code/SIZE.h_120x120x10901 SIZE.h |
| 92 |
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emacs SIZE.h |
| 93 |
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& sNx = 45, |
| 94 |
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& sNy = 45, |
| 95 |
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& nSx = 12, |
| 96 |
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& nPx = 9984, |
| 97 |
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& Nr = 2 ) |
| 98 |
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cp ../../MITgcm_contrib/llc_hires/llc_4320/code-async/eeboot_minimal.F . |
| 99 |
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emacs eeboot_minimal.F |
| 100 |
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C standardMessageUnit=errorMessageUnit |
| 101 |
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WRITE(fNam,'(A,A)') 'STDOUT.', myProcessStr(1:5) |
| 102 |
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OPEN(standardMessageUnit,FILE=fNam,STATUS='unknown') |
| 103 |
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| 104 |
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../tools/genmake2 -of \ |
| 105 |
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../../MITgcm_contrib/llc_hires/llc_4320/code-async/linux_amd64_ifort+mpi_ice_nas -mpi -mods \ |
| 106 |
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'../../MITgcm_contrib/llc_hires/llc_4320/code ../../MITgcm_contrib/llc_hires/llc_4320/code-async' |
| 107 |
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make depend |
| 108 |
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make -j 16 |
| 109 |
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| 110 |
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cd ~/llc_4320/MITgcm/run_45x45 |
| 111 |
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cp ../build/mitgcmuv . |
| 112 |
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ln -sf /nobackup/dmenemen/tarballs/llc_4320/run_template/* . |
| 113 |
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ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 114 |
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cp ../../MITgcm_contrib/llc_hires/llc_4320/input/* . |
| 115 |
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mv data.exch2_120x120x10901 data.exch2 |
| 116 |
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| 117 |
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emacs data |
| 118 |
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tRef = 18.89, 18.89, |
| 119 |
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sRef = 34.84, 34.84, |
| 120 |
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endtime=20., |
| 121 |
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delR = 1.00, 1.14, |
| 122 |
|
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# hydrogThetaFile='THETA_llc2160_10sep2011_4320x56160x90_r4', |
| 123 |
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# hydrogSaltFile ='SALT_llc2160_10sep2011_4320x56160x90_r4', |
| 124 |
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# uVelInitFile ='UVEL_llc2160_10sep2011_4320x56160x90_r4', |
| 125 |
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# vVelInitFile ='VVEL_llc2160_10sep2011_4320x56160x90_r4', |
| 126 |
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# pSurfInitFile ='ETAN_llc2160_10sep2011_4320x56160_r4', |
| 127 |
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| 128 |
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emacs data.exch2 |
| 129 |
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# remove the blank tile list |
| 130 |
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| 131 |
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export MPI_BUFS_PER_PROC=1024 |
| 132 |
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export MPI_REQUEST_MAX=65536 |
| 133 |
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export MPI_GROUP_MAX=1024 |
| 134 |
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export MPI_NUM_MEMORY_REGIONS=8 |
| 135 |
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export MPI_UNBUFFERED_STDIO=1 |
| 136 |
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export MPI_MEMMAP_OFF=1 |
| 137 |
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mpiexec -n 12000 ./mitgcmuv |
| 138 |
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| 139 |
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| 140 |
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############################# |
| 141 |
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# 120x120x10901 configuration |
| 142 |
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| 143 |
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qsub -I -q long -l select=600:ncpus=20:model=ivy,min_walltime=30:00,max_walltime=120:00:00 -m abe -M menemenlis@me.com |
| 144 |
|
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module purge |
| 145 |
|
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module load comp-intel/2012.0.032 netcdf/4.0 |
| 146 |
|
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module use -a ~kjtaylor/modulefiles |
| 147 |
|
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module load sles11sp3/mpt-2.10-nasa201311271217 |
| 148 |
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cd ~/llc_4320 |
| 149 |
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cvs co MITgcm_code |
| 150 |
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cvs co MITgcm_contrib/llc_hires/llc_4320 |
| 151 |
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cd MITgcm |
| 152 |
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mkdir build run |
| 153 |
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lfs setstripe -c -1 run |
| 154 |
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cd build |
| 155 |
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cp ../../MITgcm_contrib/llc_hires/llc_4320/code/SIZE.h_120x120x10901 SIZE.h |
| 156 |
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cp ../../MITgcm_contrib/llc_hires/llc_4320/code-async/readtile_mpiio.c . |
| 157 |
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emacs readtile_mpiio.c |
| 158 |
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tileSizeX = 120; |
| 159 |
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tileSizeY = 120; |
| 160 |
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../tools/genmake2 -of \ |
| 161 |
|
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../../MITgcm_contrib/llc_hires/llc_4320/code-async/linux_amd64_ifort+mpi_ice_nas -mpi -mods \ |
| 162 |
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'../../MITgcm_contrib/llc_hires/llc_4320/code ../../MITgcm_contrib/llc_hires/llc_4320/code-async' |
| 163 |
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make depend |
| 164 |
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make -j 16 |
| 165 |
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| 166 |
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cd ~/llc_4320/MITgcm/run |
| 167 |
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cp ../build/mitgcmuv mitgcmuv_120x120x10901 |
| 168 |
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ln -sf /nobackup/dmenemen/tarballs/llc_4320/run_template/* . |
| 169 |
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ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 170 |
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cp ../../MITgcm_contrib/llc_hires/llc_4320/input/* . |
| 171 |
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mv data.exch2_120x120x10901 data.exch2 |
| 172 |
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emacs data |
| 173 |
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| 174 |
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export MPI_BUFS_PER_PROC=1024 |
| 175 |
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export MPI_REQUEST_MAX=65536 |
| 176 |
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export MPI_GROUP_MAX=1024 |
| 177 |
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export MPI_NUM_MEMORY_REGIONS=8 |
| 178 |
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export MPI_UNBUFFERED_STDIO=1 |
| 179 |
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export MPI_MEMMAP_OFF=1 |
| 180 |
|
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mpiexec -n 12000 ./mitgcmuv_120x120x10901 |
| 181 |
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| 182 |
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tail -f STDOUT.00000 | grep advcfl_W |
| 183 |
dimitri |
1.5 |
|
| 184 |
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============== |
| 185 |
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| 186 |
dimitri |
1.10 |
qsub -I -q R3089666 -l select=1750:model=ivy:aoe=sles11,walltime=04:00:00 |
| 187 |
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tcsh |
| 188 |
|
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cd ~/llc_4320/MITgcm |
| 189 |
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mkdir run |
| 190 |
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lfs setstripe -c -1 run |
| 191 |
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cd run |
| 192 |
|
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cat $PBS_NODEFILE | awk '{for (i=0;i<20;++i) print $0}' > mynodes |
| 193 |
|
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setenv PBS_NODEFILE mynodes |
| 194 |
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cp /nobackupp8/chenze/run/mitgcmuv_72x72x29297 . |
| 195 |
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ln -sf /nobackupp8/chenze/run/pickup_seaice_0000000360.meta pickup_seaice.0000000180.meta |
| 196 |
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ln -sf /nobackupp8/chenze/run/pickup_seaice_0000000360.data pickup_seaice.0000000180.data |
| 197 |
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ln -sf /nobackupp8/chenze/run/pickup_0000000360.meta pickup.0000000180.meta |
| 198 |
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ln -sf /nobackupp8/chenze/run/pickup_0000000360.data pickup.0000000180.data |
| 199 |
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ln -sf /nobackup/dmenemen/tarballs/llc_4320/run_template/* . |
| 200 |
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ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 201 |
|
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cp ../../MITgcm_contrib/llc_hires/llc_4320/input/* . |
| 202 |
|
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mv data.exch2_72x72x29297 data.exch2 |
| 203 |
|
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module purge |
| 204 |
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module load comp-intel/2012.0.032 netcdf/4.0 |
| 205 |
|
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module use -a ~kjtaylor/modulefiles |
| 206 |
|
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module load sles11sp3/mpt-2.10-nasa201311271217 |
| 207 |
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setenv MPI_BUFS_PER_PROC 512 |
| 208 |
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setenv MPI_REQUEST_MAX 65536 |
| 209 |
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setenv MPI_GROUP_MAX 1024 |
| 210 |
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setenv MPI_NUM_MEMORY_REGIONS 8 |
| 211 |
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setenv MPI_UNBUFFERED_STDIO 1 |
| 212 |
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setenv MPI_MEMMAP_OFF 1 |
| 213 |
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| 214 |
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mpiexec -n 35000 ./mitgcmuv_72x72x29297 |
| 215 |
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| 216 |
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tail -f STDOUT.00000 | grep advcfl_w |
| 217 |
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| 218 |
|
|
============== |
| 219 |
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| 220 |
dimitri |
1.5 |
cd ~/llc_4320 |
| 221 |
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cvs co MITgcm_code |
| 222 |
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cvs co MITgcm_contrib/llc_hires/llc_4320 |
| 223 |
dimitri |
1.9 |
# set correct tileSizeX and tileSizeY in MITgcm_contrib/llc_hires/llc_4320/cpde-asyn/readtile_mpiio.c |
| 224 |
dimitri |
1.5 |
cd MITgcm |
| 225 |
|
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module purge |
| 226 |
|
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module load comp-intel/2012.0.032 mpi-sgi/mpt.2.08r7 netcdf/4.0 |
| 227 |
|
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mkdir build run |
| 228 |
|
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lfs setstripe -c -1 run |
| 229 |
|
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cd build |
| 230 |
dimitri |
1.3 |
cp ../../MITgcm_contrib/llc_hires/llc_4320/code/SIZE.h_72x72x29297 SIZE.h |
| 231 |
|
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../tools/genmake2 -of \ |
| 232 |
|
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../../MITgcm_contrib/llc_hires/llc_4320/code-async/linux_amd64_ifort+mpi_ice_nas -mpi -mods \ |
| 233 |
|
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'../../MITgcm_contrib/llc_hires/llc_4320/code ../../MITgcm_contrib/llc_hires/llc_4320/code-async' |
| 234 |
|
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make depend |
| 235 |
dimitri |
1.8 |
make -j 16 |
| 236 |
dimitri |
1.3 |
cd ../run |
| 237 |
dimitri |
1.9 |
cp ../build/mitgcmuv mitgcmuv_72x72x29297 |
| 238 |
dimitri |
1.3 |
ln -sf /nobackup/dmenemen/tarballs/llc_4320/run_template/* . |
| 239 |
|
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ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 240 |
|
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cp ../../MITgcm_contrib/llc_hires/llc_4320/input/* . |
| 241 |
|
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mv data.exch2_72x72x29297 data.exch2 |
| 242 |
dimitri |
1.7 |
export MPI_NUM_MEMORY_REGIONS=256 |
| 243 |
dimitri |
1.9 |
mpiexec -n 35000 ./mitgcmuv_72x72x29297 |
| 244 |
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| 245 |
dimitri |
1.10 |
tail -f STDOUT.00000 | grep advcfl_w |
| 246 |
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| 247 |
dimitri |
1.9 |
============== |
| 248 |
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| 249 |
|
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cd ~/llc_4320 |
| 250 |
|
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cvs co MITgcm_code |
| 251 |
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cvs co MITgcm_contrib/llc_hires/llc_4320 |
| 252 |
|
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# set correct tileSizeX and tileSizeY in MITgcm_contrib/llc_hires/llc_4320/cpde-asyn/readtile_mpiio.c |
| 253 |
|
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cd MITgcm |
| 254 |
|
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module purge |
| 255 |
|
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module load comp-intel/2012.0.032 mpi-sgi/mpt.2.08r7 netcdf/4.0 |
| 256 |
|
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mkdir build run_180x180x5015 |
| 257 |
|
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lfs setstripe -c -1 run_180x180x5015 |
| 258 |
|
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cd build |
| 259 |
|
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cp ../../MITgcm_contrib/llc_hires/llc_4320/code/SIZE.h_180x180x5015 SIZE.h |
| 260 |
|
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../tools/genmake2 -of \ |
| 261 |
|
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../../MITgcm_contrib/llc_hires/llc_4320/code-async/linux_amd64_ifort+mpi_ice_nas -mpi -mods \ |
| 262 |
|
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'../../MITgcm_contrib/llc_hires/llc_4320/code ../../MITgcm_contrib/llc_hires/llc_4320/code-async' |
| 263 |
|
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make depend |
| 264 |
|
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make -j 16 |
| 265 |
|
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cd ../run_180x180x5015 |
| 266 |
|
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cp ../build/mitgcmuv mitgcmuv_180x180x5015 |
| 267 |
|
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ln -sf /nobackup/dmenemen/tarballs/llc_4320/run_template/* . |
| 268 |
|
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ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 269 |
|
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cp ../../MITgcm_contrib/llc_hires/llc_4320/input/* . |
| 270 |
|
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mv data.exch2_72x72x29297 data.exch2 |
| 271 |
|
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export MPI_NUM_MEMORY_REGIONS=256 |
| 272 |
|
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mpiexec -n 6000 ./mitgcmuv_180x180x5015 |
| 273 |
dimitri |
1.3 |
|
| 274 |
|
|
============== |
| 275 |
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|
| 276 |
dimitri |
1.1 |
look at output |
| 277 |
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| 278 |
|
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for ts=[0 120 600:10:980 1080:120:2280] |
| 279 |
|
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fld=quikread_llc(['Eta.' myint2str(ts,10) '.data'],4320); |
| 280 |
|
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clf,quikplot_llc(fld),caxis([-2.5 2]),thincolorbar |
| 281 |
|
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title(ts) |
| 282 |
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pause(.1) |
| 283 |
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end |
| 284 |
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| 285 |
|
|
============== |
| 286 |
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| 287 |
|
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to determine empty tiles: |
| 288 |
|
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grep Empty STDOUT.* |
| 289 |
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| 290 |
|
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============= |
| 291 |
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| 292 |
|
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memory requirements: |
| 293 |
|
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nPx sNx sNy nSx cpu node0 total |
| 294 |
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3744 180 180 2 san 22,106,128kb 5,195,641,224kb - node ran out of memory and crashed |
| 295 |
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5616 120 120 3 san - node ran out of memory and crashed |
| 296 |
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7488 180 180 1 san |
| 297 |
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| 298 |
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============= |
| 299 |
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| 300 |
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2 = 2 |
| 301 |
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3 = 3 |
| 302 |
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2*2 = 4 |
| 303 |
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5 = 5 |
| 304 |
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2*3 = 6 |
| 305 |
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2*2*2 = 8 |
| 306 |
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3*3 = 9 |
| 307 |
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2*5 = 10 |
| 308 |
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2*2*3 = 12 |
| 309 |
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3*5 = 15 |
| 310 |
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2*2*2*2 = 16 |
| 311 |
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2*3*3 = 18 |
| 312 |
|
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2*2*5 = 20 |
| 313 |
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2*2*2*3 = 24 |
| 314 |
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3*3*3 = 27 |
| 315 |
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2*3*5 = 30 |
| 316 |
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2*2*2*2*2 = 32 |
| 317 |
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2*2*3*3 = 36 |
| 318 |
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2*2*2*5 = 40 |
| 319 |
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3*3*5 = 45 |
| 320 |
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2*2*2*2*3 = 48 |
| 321 |
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2*3*3*3 = 54 |
| 322 |
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2*2*3*5 = 60 |
| 323 |
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2*2*2*3*3 = 72 * 60 |
| 324 |
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2*2*2*2*5 = 80 * 54 |
| 325 |
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2*3*3*5 = 90 * 48 |
| 326 |
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2*2*2*2*2*3 = 96 * 45 |
| 327 |
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2*2*3*3*3 = 108 * 40 |
| 328 |
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2*2*2*3*5 = 120 * 36 |
| 329 |
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3*3*3*5 = 135 * 32 |
| 330 |
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2*2*2*2*3*3 = 144 * 30 |
| 331 |
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2*2*2*2*2*5 = 160 * 27 |
| 332 |
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2*2*3*3*5 = 180 * 24 |
| 333 |
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2*2*2*3*3*3 = 216 * 20 |
| 334 |
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2*2*2*2*3*5 = 240 * 18 |
| 335 |
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2*3*3*3*5 = 270 * 16 |
| 336 |
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2*2*2*2*2*3*3 = 288 * 15 |
| 337 |
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2*2*2*3*3*5 = 360 * 12 |
| 338 |
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2*2*2*2*3*3*3 = 432 * 10 |
| 339 |
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2*2*2*2*2*3*5 = 480 * 9 |
| 340 |
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2*2*3*3*3*5 = 540 * 8 |
| 341 |
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2*2*2*2*3*3*5 = 720 * 6 |
| 342 |
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2*2*2*2*2*3*3*3 = 864 * 5 |
| 343 |
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2*2*2*3*3*3*5 = 1080 * 4 |
| 344 |
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2*2*2*2*2*3*3*5 = 1440 * 3 |
| 345 |
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2*2*2*2*3*3*3*5 = 2160 * 2 |
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