Run LEEM Model

Run LEEM Model

1. make an input folder

[czhao4@compute-0-201 test_run]$ cd input/
[czhao4@compute-0-201 input]$ rsync -ave ssh /pexue5/chuyan/LEEM_Phase2/LEEM-Phase2_TechTransfer/Windows_files/WinModel/A2EM_UFV/LEEM_coarse/leem_wqc_097/P1_2013/input/* ./
[czhao4@compute-0-201 input]$ ls
atm.inp  ic.inp      kh_min.inp                 leem_wqc_097_2015_obc.dat  pc.inp  sed.inp
bc.inp   kh_max.inp  leem_wqc_097_2015_bfw.dat  leem_wqc_097_2015_riv.dat  ps.inp  sedtran.inp
[czhao4@compute-0-200 input]$ ln -s ../../P2_2014/output/out/RCAFIC.bin ./
[czhao4@compute-0-200 input]$ mv RCAFIC.bin RCAFIC.inp

2. copy “a2em_ufv”, biological model

[czhao4@compute-0-201 test_run]$ rsync -ave ssh /pexue6/chenfuh/LEEM_code/new_code/phase2/source_code/a2em_ufv ./
sending incremental file list
a2em_ufv -> /pexue6/chenfuh/LEEM_code/new_code/phase2/source_code/a2em_ufv

sent 140 bytes  received 19 bytes  318.00 bytes/sec
total size is 0  speedup is 0.00
[czhao4@compute-0-201 test_run]$ ls
a2em_ufv  input

3. copy “leem_c_2015_wy-02.nc” (output of FVCOM), which is corresponding to namelist “HYDFILNA”

[czhao4@compute-0-201 test_run]$ ln -s /pexue6/chenfuh/LEEM_code/run_phase2/run_fvcom/WY2015/output/leem_avg_0001.nc ./
[czhao4@compute-0-201 test_run]$ ls
a2em_ufv  input  leem_avg_0001.nc
[czhao4@compute-0-201 test_run]$ mv leem_avg_0001.nc leem_c_2015_wy-02.nc
[czhao4@compute-0-201 test_run]$ ls
a2em_ufv  input  leem_c_2015_wy-02.nc

4. copy “linkage”, output of SWAN

[czhao4@compute-0-201 test_run]$ mkdir linkage
[czhao4@compute-0-201 test_run]$ cd linkage/
[czhao4@compute-0-201 linkage]$ rsync -ave ssh /pexue6/chenfuh/LEEM_code/run_phase2/run_swan/leem_swc_wy2015/ori_output/SWAN_time.bin ./
sending incremental file list
SWAN_time.bin

sent 105,274 bytes  received 35 bytes  210,618.00 bytes/sec
total size is 105,132  speedup is 1.00
 
[czhao4@compute-0-201 linkage]$ rsync -ave ssh /pexue6/chenfuh/LEEM_code/run_phase2/run_swan/leem_swc_wy2015/WV*.bin ./
sending incremental file list
WVDIR.bin
WVHGT.bin
WVORB.bin
WVPER.bin

sent 159,120,716 bytes  received 92 bytes  35,360,179.56 bytes/sec
total size is 159,081,600  speedup is 1.00
[czhao4@compute-0-201 linkage]$ ls
SWAN_time.bin  WVDIR.bin  WVHGT.bin  WVORB.bin  WVPER.bin

5. copy “leem_wqc_097_2015_run.dat”, namelist

[czhao4@compute-0-201 test_run]$ rsync -ave ssh /pexue5/chuyan/LEEM_Phase2/LEEM-Phase2_TechTransfer/Windows_files/WinModel/A2EM_UFV/LEEM_coarse/leem_wqc_097/P1_2015/leem_wqc_097_2015_run.dat ./
sending incremental file list
leem_wqc_097_2015_run.dat

sent 3,906 bytes  received 35 bytes  7,882.00 bytes/sec
total size is 3,772  speedup is 0.96
[czhao4@compute-0-201 test_run]$ ls
a2em_ufv  input  leem_c_2015_wy-02.nc  leem_wqc_097_2015_run.dat  linkage

modify:
OUTDIR = ./output
CDF_OUT = T

6. copy qscript and run.sh

[czhao4@compute-0-201 test_run]$ rsync -ave ssh /pexue6/chenfuh/LEEM_code/run_phase2/run_leem/P1_2015/qsub_a2em_ufv.sh ./
sending incremental file list
qsub_a2em_ufv.sh

sent 1,490 bytes  received 35 bytes  3,050.00 bytes/sec
total size is 1,365  speedup is 0.90
[czhao4@compute-0-201 test_run]$ rsync -ave ssh /pexue6/chenfuh/LEEM_code/run_phase2/run_leem/P1_2015/run.sh ./
sending incremental file list
run.sh

sent 366 bytes  received 35 bytes  802.00 bytes/sec
total size is 252  speedup is 0.63
[czhao4@compute-0-201 test_run]$ ls
a2em_ufv  input  leem_c_2015_wy-02.nc  leem_wqc_097_2015_run.dat  linkage  qsub_a2em_ufv.sh  run.sh

7. Modify the parameters in the “pc.inp” in input folder