| 1 |
For interactive session, Ivy Bridge nodes: |
| 2 |
qsub -I -q devel -l select=300:ncpus=20:model=ivy,walltime=02:00:00 -m abe |
| 3 |
qsub -I -q normal -l select=103:ncpus=20:model=ivy,walltime=8:00:00 -m abe |
| 4 |
qsub -I -q long -l select=300:ncpus=20:model=ivy,walltime=120:00:00 -m abe |
| 5 |
qsub -I -q long -l select=103:ncpus=20:model=ivy,min_walltime=30:00,max_walltime=120:00:00 -m abe |
| 6 |
|
| 7 |
########################## |
| 8 |
# 72x72_7666 configuration |
| 9 |
qsub -I -q long -l select=400:ncpus=20:model=ivy,walltime=120:00:00 -m abe |
| 10 |
module purge |
| 11 |
module load comp-intel/2016.2.181 mpi-hpe/mpt.2.17r13 hdf4/4.2.12 hdf5/1.8.18_mpt netcdf/4.4.1.1_mpt |
| 12 |
cd ~/llc_2160 |
| 13 |
git clone git@github.com:MITgcm/MITgcm.git |
| 14 |
cvs co MITgcm_contrib/llc_hires/llc_2160 |
| 15 |
cd ~/llc_2160/MITgcm |
| 16 |
mkdir build run |
| 17 |
cd ~/llc_2160/MITgcm/build |
| 18 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/code/SIZE.h_72x72_7666 SIZE.h |
| 19 |
../tools/genmake2 -of \ |
| 20 |
../../MITgcm_contrib/llc_hires/llc_2160/code-async/linux_amd64_ifort+mpi_ice_nas -mpi -mods \ |
| 21 |
'../../MITgcm_contrib/llc_hires/llc_2160/code ../../MITgcm_contrib/llc_hires/llc_2160/code-async' |
| 22 |
make depend |
| 23 |
make -j 16 |
| 24 |
|
| 25 |
cd ~/llc_2160/MITgcm/run |
| 26 |
cp ../build/mitgcmuv mitgcmuv_72x72_7666 |
| 27 |
ln -sf /nobackup/dmenemen/tarballs/llc_2160/run_template/* . |
| 28 |
ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 29 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/input/* . |
| 30 |
cp data.exch2_72x72x7666 data.exch2 |
| 31 |
emacs data |
| 32 |
|
| 33 |
mpiexec -n 8000 ./mitgcmuv_72x72_7666 |
| 34 |
|
| 35 |
tail -f STDOUT.00000 | grep advcfl_W |
| 36 |
|
| 37 |
################################################################### |
| 38 |
# 90x90_5004 configuration with newer code on electra special queue |
| 39 |
qsub -I -q electra -l select=200:ncpus=28:model=bro_ele:aoe=sles12 -l walltime=10:00:00 |
| 40 |
module purge |
| 41 |
module load comp-intel/2016.2.181 mpi-hpe/mpt.2.17r13 hdf4/4.2.12 hdf5/1.8.18_mpt netcdf/4.4.1.1_mpt |
| 42 |
cd ~/llc_2160 |
| 43 |
git clone git@github.com:MITgcm/MITgcm.git |
| 44 |
cvs co MITgcm_contrib/llc_hires/llc_2160 |
| 45 |
cd ~/llc_2160/MITgcm |
| 46 |
mkdir build run |
| 47 |
cd ~/llc_2160/MITgcm/build |
| 48 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/code/SIZE.h_90x90_5004 SIZE.h |
| 49 |
../tools/genmake2 -of \ |
| 50 |
../../MITgcm_contrib/llc_hires/llc_2160/code-async/linux_amd64_ifort+mpi_ice_nas -mpi -mods \ |
| 51 |
'../../MITgcm_contrib/llc_hires/llc_2160/code ../../MITgcm_contrib/llc_hires/llc_2160/code-async' |
| 52 |
make depend |
| 53 |
make -j 16 |
| 54 |
|
| 55 |
cd ~/llc_2160/MITgcm/run |
| 56 |
cp ../build/mitgcmuv mitgcmuv_90x90_5004 |
| 57 |
ln -sf /nobackup/dmenemen/tarballs/llc_2160/run_template/* . |
| 58 |
ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 59 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/input/* . |
| 60 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/input/data.exch2_90x90x5004 data.exch2 |
| 61 |
emacs data |
| 62 |
|
| 63 |
mpiexec -n 5500 ./mitgcmuv_90x90_5004 |
| 64 |
|
| 65 |
tail -f STDOUT.00000 | grep advcfl_W |
| 66 |
|
| 67 |
############################# |
| 68 |
# 60x60x10882 configuration |
| 69 |
|
| 70 |
qsub -I -q long -l select=600:ncpus=20:model=ivy,min_walltime=30:00,max_walltime=120:00:00 -m abe |
| 71 |
module purge |
| 72 |
module load comp-intel/2012.0.032 mpi-sgi/mpt.2.10r6 netcdf/4.0 |
| 73 |
cd ~/llc_2160 |
| 74 |
cvs co -r checkpoint64t MITgcm_code |
| 75 |
cvs co MITgcm_contrib/llc_hires/llc_2160 |
| 76 |
cd MITgcm |
| 77 |
mkdir build run |
| 78 |
cd build |
| 79 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/code/SIZE.h_60x60_10882 SIZE.h |
| 80 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/code-async/readtile_mpiio.c . |
| 81 |
emacs readtile_mpiio.c |
| 82 |
tileSizeX = 60; |
| 83 |
tileSizeY = 60; |
| 84 |
../tools/genmake2 -of \ |
| 85 |
../../MITgcm_contrib/llc_hires/llc_2160/code-async/linux_amd64_ifort+mpi_ice_nas -mpi -mods \ |
| 86 |
'../../MITgcm_contrib/llc_hires/llc_2160/code ../../MITgcm_contrib/llc_hires/llc_2160/code-async' |
| 87 |
make depend |
| 88 |
make -j 16 |
| 89 |
|
| 90 |
cd ~/llc_2160/MITgcm/run |
| 91 |
cp ../build/mitgcmuv mitgcmuv_60x60x10882 |
| 92 |
ln -sf /nobackup/dmenemen/tarballs/llc_2160/run_template/* . |
| 93 |
ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 94 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/input/* . |
| 95 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/input/data.exch2_60x60x10882 data.exch2 |
| 96 |
emacs data |
| 97 |
|
| 98 |
export MPI_BUFS_PER_PROC=1024 |
| 99 |
export MPI_REQUEST_MAX=65536 |
| 100 |
export MPI_GROUP_MAX=1024 |
| 101 |
export MPI_NUM_MEMORY_REGIONS=8 |
| 102 |
export MPI_UNBUFFERED_STDIO=1 |
| 103 |
export MPI_MEMMAP_OFF=1 |
| 104 |
export MPI_UD_TIMEOUT=100 |
| 105 |
mpiexec -n 12000 ./mitgcmuv_60x60x10882 |
| 106 |
|
| 107 |
tail -f STDOUT.00000 | grep advcfl_W |
| 108 |
|
| 109 |
################################################ |
| 110 |
# 144x144x2047 configuration for grid generation |
| 111 |
|
| 112 |
qsub -I -q devel -l select=103:ncpus=20:model=ivy,walltime=02:00:00 -m abe -M YOUR_EMAIL_HERE |
| 113 |
module purge |
| 114 |
module load comp-intel/2012.0.032 mpi-sgi/mpt.2.10r6 netcdf/4.0 |
| 115 |
cd ~/llc_2160 |
| 116 |
cvs co MITgcm_code |
| 117 |
cvs co MITgcm_contrib/llc_hires/llc_2160 |
| 118 |
cd MITgcm |
| 119 |
mkdir build run_grid |
| 120 |
lfs setstripe -c -1 run_grid |
| 121 |
cd build |
| 122 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/code/SIZE.h_144x144x2047 SIZE.h |
| 123 |
../tools/genmake2 -of \ |
| 124 |
../../MITgcm_contrib/llc_hires/llc_2160/code-async/linux_amd64_ifort+mpi_ice_nas \ |
| 125 |
-mpi -mods ../../MITgcm_contrib/llc_hires/llc_2160/code |
| 126 |
make depend |
| 127 |
make -j 16 |
| 128 |
|
| 129 |
cd ~/llc_2160/MITgcm/run_grid |
| 130 |
cp ../build/mitgcmuv mitgcmuv_144x144x2047 |
| 131 |
ln -sf /nobackup/dmenemen/tarballs/llc_2160/run_template/* . |
| 132 |
ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 133 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/input/* . |
| 134 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/input/data.exch2_144x144x2047 data.exch2 |
| 135 |
|
| 136 |
emacs data |
| 137 |
debuglevel=3, |
| 138 |
useSingleCPUio=.TRUE., |
| 139 |
endtime=0., |
| 140 |
deltaT = 1., |
| 141 |
|
| 142 |
mpiexec -n 2047 ./mitgcmuv_144x144x2047 |
| 143 |
|
| 144 |
============== |
| 145 |
|
| 146 |
cd ~/llc_2160 |
| 147 |
cvs co MITgcm_code |
| 148 |
cvs co MITgcm_contrib/llc_hires/llc_2160 |
| 149 |
cd MITgcm |
| 150 |
module purge |
| 151 |
module load comp-intel/2012.0.032 mpi-sgi/mpt.2.08r7 netcdf/4.0 |
| 152 |
mkdir build run |
| 153 |
lfs setstripe -c -1 run |
| 154 |
cd build |
| 155 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/code/SIZE.h_90x90_5004 SIZE.h |
| 156 |
../tools/genmake2 -of \ |
| 157 |
../../MITgcm_contrib/llc_hires/llc_2160/code-async/linux_amd64_ifort+mpi_ice_nas -mpi -mods \ |
| 158 |
'../../MITgcm_contrib/llc_hires/llc_2160/code ../../MITgcm_contrib/llc_hires/llc_2160/code-async' |
| 159 |
make depend |
| 160 |
make -j 16 |
| 161 |
cd ~/llc_2160/MITgcm/run |
| 162 |
ln -sf ../build/mitgcmuv . |
| 163 |
ln -sf /nobackup/dmenemen/tarballs/llc_2160/run_template/* . |
| 164 |
ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 165 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/input/* . |
| 166 |
mv data.exch2_90x90x5004 data.exch2 |
| 167 |
export MPI_NUM_MEMORY_REGIONS=256 |
| 168 |
mpiexec -n 6000 ./mitgcmuv |
| 169 |
|
| 170 |
============== |
| 171 |
|
| 172 |
look at output |
| 173 |
|
| 174 |
for ts=[0 120 600:10:980 1080:120:2280] |
| 175 |
fld=quikread_llc(['Eta.' myint2str(ts,10) '.data'],2160); |
| 176 |
clf,quikplot_llc(fld),caxis([-2.5 2]),thincolorbar |
| 177 |
title(ts) |
| 178 |
pause(.1) |
| 179 |
end |
| 180 |
|
| 181 |
============== |
| 182 |
|
| 183 |
to determine empty tiles: |
| 184 |
grep Empty STDOUT.* > empty.txt |
| 185 |
|
| 186 |
============== |
| 187 |
|
| 188 |
# generate 30x30 blank tiles |
| 189 |
qsub -I -q normal -l select=339:ncpus=28:model=bro,walltime=2:00:00 -m abe |
| 190 |
module purge |
| 191 |
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 |
| 192 |
cd ~/llc_2160/MITgcm |
| 193 |
mkdir run_30x30 |
| 194 |
lfs setstripe -c -1 run_30x30 |
| 195 |
cd build |
| 196 |
rm * |
| 197 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/code-async/readtile_mpiio.c . |
| 198 |
emacs readtile_mpiio.c |
| 199 |
tileSizeX = 30; |
| 200 |
tileSizeY = 30; |
| 201 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/code/SIZE.h_60x60_10882 SIZE.h |
| 202 |
emacs SIZE.h |
| 203 |
& sNx = 30, |
| 204 |
& sNy = 30, |
| 205 |
& nSx = 8, |
| 206 |
& nPx = 8424, |
| 207 |
& Nr = 2 ) |
| 208 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/code-async/eeboot_minimal.F . |
| 209 |
emacs eeboot_minimal.F |
| 210 |
C standardMessageUnit=errorMessageUnit |
| 211 |
WRITE(fNam,'(A,A)') 'STDOUT.', myProcessStr(1:5) |
| 212 |
OPEN(standardMessageUnit,FILE=fNam,STATUS='unknown') |
| 213 |
../tools/genmake2 -of \ |
| 214 |
../../MITgcm_contrib/llc_hires/llc_2160/code-async/linux_amd64_ifort+mpi_ice_nas -mpi -mods \ |
| 215 |
'../../MITgcm_contrib/llc_hires/llc_2160/code ../../MITgcm_contrib/llc_hires/llc_2160/code-async' |
| 216 |
make depend |
| 217 |
make -j 16 |
| 218 |
cd ~/llc_2160/MITgcm/run_30x30 |
| 219 |
cp ../build/mitgcmuv . |
| 220 |
ln -sf /nobackup/dmenemen/tarballs/llc_2160/run_template/* . |
| 221 |
ln -sf /nobackup/dmenemen/forcing/ECMWF_operational/* . |
| 222 |
cp ../../MITgcm_contrib/llc_hires/llc_2160/input/* . |
| 223 |
mv data.exch2_144x144x2047 data.exch2 |
| 224 |
emacs data.exch2 |
| 225 |
# remove the blank tile list |
| 226 |
emacs data |
| 227 |
tRef = 18.89, 18.89, |
| 228 |
sRef = 34.84, 34.84, |
| 229 |
endtime=45., |
| 230 |
delR = 1.00, 1.14, |
| 231 |
# hydrogThetaFile='THETA_llc1080_14jan2011_2160x28080x90_r4', |
| 232 |
# hydrogSaltFile ='SALT_llc1080_14jan2011_2160x28080x90_r4', |
| 233 |
# uVelInitFile ='UVEL_llc1080_14jan2011_2160x28080x90_r4', |
| 234 |
# vVelInitFile ='VVEL_llc1080_14jan2011_2160x28080x90_r4', |
| 235 |
# pSurfInitFile ='ETAN_llc1080_14jan2011_2160x28080_r4', |
| 236 |
mpiexec -n 9492 ./mitgcmuv |
| 237 |
|
| 238 |
============== |
| 239 |
|
| 240 |
memory requirements: |
| 241 |
nPx sNx sNy nSx cpu node0 total rank0 rankm |
| 242 |
936 180 180 2 san node ran out of memory and crashed with singlecpuio |
| 243 |
1053 240 240 1 san node ran out of memory and crashed with singlecpuio |
| 244 |
1300 216 216 1 san node ran out of memory and crashed with singlecpuio |
| 245 |
1872 180 180 1 wes node ran out of memory and crashed with singlecpuio |
| 246 |
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 |
| 247 |
1872 180 180 1 san node ran out of memory and crashed with singlecpuio |
| 248 |
1872 180 180 1 san 11,558,588kb 1,356,676,140kb singlecpuio=.FALSE. |
| 249 |
2925 144 144 1 san 8,374,668kb 1,538,454,112kb 886MB 892MB singlecpuio=.FALSE. |
| 250 |
2925 144 144 1 san 27,284,996kb 4,942,949,704kb node ran out of memory and crashed with singlecpuio |
| 251 |
3328 135 135 1 san rank 0 run out of memory |
| 252 |
3328 135 135 1 san some random node run out of memory (full node for rank 0) |
| 253 |
4212 120 120 1 san node ran out of memory |
| 254 |
5200 108 108 1 san node ran out of memory |
| 255 |
|
| 256 |
============= |
| 257 |
|
| 258 |
2 = 2 |
| 259 |
3 = 3 |
| 260 |
2*2 = 4 |
| 261 |
5 = 5 |
| 262 |
2*3 = 6 |
| 263 |
2*2*2 = 8 |
| 264 |
3*3 = 9 |
| 265 |
2*5 = 10 |
| 266 |
2*2*3 = 12 |
| 267 |
3*5 = 15 |
| 268 |
2*2*2*2 = 16 |
| 269 |
2*3*3 = 18 |
| 270 |
2*2*5 = 20 |
| 271 |
2*2*2*3 = 24 |
| 272 |
3*3*3 = 27 |
| 273 |
2*3*5 = 30 |
| 274 |
2*2*3*3 = 36 |
| 275 |
2*2*2*5 = 40 |
| 276 |
3*3*5 = 45 |
| 277 |
2*2*2*2*3 = 48 * 45 |
| 278 |
2*3*3*3 = 54 * 40 |
| 279 |
2*2*3*5 = 60 * 36 |
| 280 |
2*2*2*3*3 = 72 * 30 |
| 281 |
2*2*2*2*5 = 80 * 27 |
| 282 |
2*3*3*5 = 90 * 24 |
| 283 |
2*2*3*3*3 = 108 * 20 |
| 284 |
2*2*2*3*5 = 120 * 18 |
| 285 |
3*3*3*5 = 135 * 16 |
| 286 |
2*2*2*2*3*3 = 144 * 15 |
| 287 |
2*2*3*3*5 = 180 * 12 |
| 288 |
2*2*2*3*3*3 = 216 * 10 |
| 289 |
2*2*2*2*3*5 = 240 * 9 |
| 290 |
2*3*3*3*5 = 270 * 8 |
| 291 |
2*2*2*3*3*5 = 360 * 6 |
| 292 |
2*2*2*2*3*3*3 = 432 * 5 |
| 293 |
2*2*3*3*3*5 = 540 * 4 |
| 294 |
2*2*2*2*3*3*5 = 720 * 3 |
| 295 |
2*2*2*3*3*3*5 = 1080 * 2 |
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