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runens.noaa.R
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#--- ENSEMBLE SCRIPT FOR GEOS-CHEM
set.seed(27)
#--Queing software, nasa, torque or sge
que_soft = "nasa"
#-- Propagation Choices are 'none', 'pure' or 'ct'
prop_model = "ct"
#-- Required libs
if(que_soft=="sge"){require(Rsge)}
#-- If NASA, initialize cluster for duration of script run
#if(que_soft=="nasa")
#{
# library(Rmpi)
# np <- mpi.universe.size()
# library(snow)
# cluster <- makeMPIcluster(np)
#}
require(ncdf4)
require(plyr)
require(lubridate)
#-- Use options
ensembles = 200
cycle_length = 14
lag_cycle_length=5
cycles = 1:(26*5+1)
startcycle = cycles[1]
endcycle = cycles[length(cycles)]
inflation.factor = 1.1
startdate = as.POSIXlt(strptime('2008-01-01 00:00:00', '%Y-%m-%d %H:%M:%S'),tz="GMT")
startdate$isdst = 0
estimate_land_ocean_bias = FALSE
args = commandArgs(TRUE)
print(args)
if(length(args)==0){
print("No arguments supplied.")
}else{
for(i in 1:length(args)){
eval(parse(text=args[[i]]))
}
print(paste("startcycle now:",startcycle))
print(paste("endcycle now:",endcycle))
}
#-- User directories
run_dir_4x5 = "/discover/nobackup/aschuh/run.v9-02_test_4x5/"
run_dir_2x2.5 = "/discover/nobackup/aschuh/run.v9-02_test_2x25/"
outdir_4x5 = "/discover/nobackup/aschuh/GEOS-CHEM_output/v9.2_test_4x5"
outdir_2x2.5 = "/discover/nobackup/aschuh/GEOS-CHEM_output/v9.2_test_2x25"
input_geos_file_4x5 = paste(run_dir_4x5,"/input.geos",sep="")
input_geos_file_2x2.5 = paste(run_dir_2x2.5,"/input.geos",sep="")
orig_betas_file_2x2.5 = "/discover/nobackup/aschuh/data/betas/betas.041514_2x2.5.nc"
orig_betas_file_4x5 = "/discover/nobackup/aschuh/data/betas/betas.041514_4x5.nc"
#-- Set working directory and sun grid eng. options
setwd(paste(run_dir_4x5,"../run/ENSCODE",sep=""))
#-- Necessary code
source("merge_ens_data.R")
source("optimize_betas_new.R")
source("output2ncdf_lag.R")
source("utils.R")
source("create_noaa_data.R")
source("create_prior.R")
#source("jobscript.NASA.pbs.R")
#-- Checking outdir against a few lines in input.geos which MUST match
geos_inputfile_check(input_geos_file_4x5,outdir_4x5,prop_model)
geos_inputfile_check(input_geos_file_2x2.5,outdir_2x2.5,prop_model)
if(que_soft=="sge"){sge.options(sge.use.cluster=TRUE,sge.save.global=TRUE,sge.remove.files=FALSE)}
#orig_betas_file = paste(run_dir,"ENSCODE/betas.071212.nc",sep="")
#-- for bamboo
#system(paste("/usr/local/nco4-gcc/bin/ncks -F -d ensemble,0,",ensembles-1,
# " ",orig_betas_file," -o ",outdir,"/betas/betas_cycle_prior_000.nc",sep=""))
#-- For sequoia
#system(paste("ncks -F -d ensemble,1,",ensembles,
# " ",orig_betas_file," -o ",outdir,"/betas/betas_cycle_prior_000.nc",sep=""))
#system(paste("cp ",outdir,"/betas/betas_cycle_prior_000.nc ",outdir,"/betas/betas_cycle_post_000.nc",sep=""))
#-- THIS PART MAKES NEW PBS_NODEFILE W/O HEAD NODE so that GEOS doesn't run on "this" node running R
#system(paste("grep -v ",Sys.getenv('SLURM_STEP_NODELIST')," ",Sys.getenv('PBS_NODEFILE')," > temp && mv temp ",Sys.getenv('PBS_NODEFILE'),'.mod',sep=""))
#Sys.setenv(PBS_NODEFILE_MOD = paste(Sys.getenv('PBS_NODEFILE'),'.mod',sep="") )
Sys.getenv('HOST')
system(paste("sed -i '/",Sys.getenv('HOST'),"/d' ",Sys.getenv('PBS_NODEFILE'),sep=""))
print(paste("Head node process running on ... ",Sys.getenv('HOST')))
print(paste("running pods.sh on :"))
system(paste("cat ",Sys.getenv('PBS_NODEFILE')))
#-- *Need to check that output directories are there
#-- We should check for existence of output files now*
for(i in startcycle:endcycle)
{
print(paste("Garbage collection:"))
gc()
objects()
#-- Adjust ensemble start date to cycle start date
#rundate = as.POSIXlt(startdate + 3600*24*(cycles[i]-1)*cycle_length)
rundate = as.POSIXlt(startdate + 3600*24*((cycles[i]-1)*cycle_length))
rdate_arg = paste( rundate$year + 1900, pad(rundate$mon+1,width=2,fill="0"),
pad(rundate$mday, width=2, fill="0"),sep="")
rundate_lag = as.POSIXlt(startdate + -3600*24*lag_cycle_length*cycle_length + 3600*24*((cycles[i]-1)*cycle_length))
rdate_arg_lag = paste( rundate_lag$year + 1900, pad(rundate_lag$mon+1,width=2,fill="0"),
pad(rundate_lag$mday, width=2, fill="0"),sep="")
prior_betas_tminus1_file = list()
post_betas_tminus1_file = list()
post_betas_t_file = list()
for(r in 1:(lag_cycle_length+1))
{
if(r==6){od = outdir_2x2.5}else{od=outdir_4x5}
prior_betas_tminus1_file[[r]] = paste(od,"/betas/betas_cycle_prior_",pad(r,width=3,fill="0"),
"_",pad(cycles[i]-1,width=3,fill="0"),".nc",sep="")
post_betas_tminus1_file[[r]] = paste(od,"/betas/betas_cycle_post_",pad(r,width=3,fill="0"),
"_",pad(cycles[i]-1,width=3,fill="0"),".nc",sep="")
post_betas_t_file[[r]] = paste(od,"/betas/betas_cycle_post_",pad(r,width=3,fill="0"),
"_",pad(cycles[i],width=3,fill="0"),".nc",sep="")
}
post_betas_t_file_regrid = paste(outdir_4x5,"/betas/betas_cycle_post_regrid_",pad(6,width=3,fill="0"),
"_",pad(cycles[i],width=3,fill="0"),".nc",sep="")
#-- HERE IS WHERE WE NEED CDO CALL TO CREATE betas_cycle_prior_00X.nc file (X=cycles[i]-1)
#-- as function of (X-1) and (X-2) files, (betas_000 + betas_(X-1) + betas+(X-2) ) / 3
#-- Try to create in same ../betas folder if possible. Final output betas should still
#-- write to 'regularly' named betas file, w/o 'prior'
#-- call will look something like (haven't tested yet):
if(prop_model == "ct")
{
#vv = sapply(c(0,max(0,cycles[i]-2):(cycles[i]-1)),pad,width=3,fill="0")
#ifiles = paste(outdir,"/betas/betas_cycle_post_",vv,".nc",sep="",collapse=" ")
#system(paste("ncea ",ifiles," ",prior_betas_tminus1_file,sep=""))
#vv = sapply(c(0,max(0,cycles[i]-1):(cycles[i]-1)),pad,width=3,fill="0")
vv_lag = sapply(c(max(0,cycles[i]-1)),pad,width=3,fill="0")
vv_first = sapply(c(0,max(0,cycles[i]-1):(cycles[i]-1)),pad,width=3,fill="0")
ifiles=list()
pr_ind = list()
for(r in 1:(lag_cycle_length+1))
{
if(r==(lag_cycle_length+1))
{
bfile=orig_betas_file_2x2.5
outdir_tmp = outdir_2x2.5
ifiles[[r]] = paste(outdir_tmp,"/betas/betas_cycle_post_",pad(r,width=3,fill="0"),"_",vv_first,".nc",sep="")
pr_ind[[r]] = vv_first == "000"
ifiles[[r]][pr_ind[[r]]] = bfile
}
if(r==lag_cycle_length)
{
bfile=orig_betas_file_4x5
outdir_tmp = outdir_4x5
ifiles[[r]] = paste(outdir_tmp,"/betas/betas_cycle_post_regrid_",pad(r+1,width=3,fill="0"),"_",vv_lag,".nc",sep="")
pr_ind[[r]] = vv_lag == "000"
ifiles[[r]][pr_ind[[r]]] = bfile
}
if(r!=lag_cycle_length & r!=(lag_cycle_length+1))
{
bfile=orig_betas_file_4x5
outdir_tmp = outdir_4x5
ifiles[[r]] = paste(outdir_tmp,"/betas/betas_cycle_post_",pad(r+1,width=3,fill="0"),"_",vv_lag,".nc",sep="")
pr_ind[[r]] = vv_lag == "000"
ifiles[[r]][pr_ind[[r]]] = bfile
}
}
#for(k in 1:length(ifiles))
# {
# if(k==1)
# {
# if(pr_ind[k]){
# #-- currently orig_betas_file has 1000 ensembles in it
# samp = c(1,sample(1:1000,ensembles-1))
# for(j in 1:ensembles){
# ifiles.fil = nc_open(ifiles[k],readunlim=FALSE)
# if(j==1){
# test = ncvar_get(ifiles.fil,"BETAGPP",start=c(1,1,1,1),count=c(-1,-1,1,1))
# BETAGPP = array(dim=c(dim(test)[1],dim(test)[2],ensembles))
# BETARESP = array(dim=c(dim(test)[1],dim(test)[2],ensembles))
# BETAOCEAN = array(dim=c(dim(test)[1],dim(test)[2],ensembles))
# }
# BETAGPP[,,j] = ncvar_get(ifiles.fil,"BETAGPP",start=c(1,1,samp[j],1),count=c(-1,-1,1,1))#/length(ifiles)
# BETARESP[,,j] = ncvar_get(ifiles.fil,"BETARESP",start=c(1,1,samp[j],1),count=c(-1,-1,1,1))#/length(ifiles)
# BETAOCEAN[,,j] = ncvar_get(ifiles.fil,"BETAOCEAN",start=c(1,1,samp[j],1),count=c(-1,-1,1,1))#/length(ifiles)
# }
# #-- Important, we need to convert deviations to variations before we weight, and add
# BETAGPP[,,2:ensembles] = aperm(aaply(BETAGPP[,,2:ensembles],c(3),.fun=function(x){x-BETAGPP[,,1]}),c(2,3,1))
# BETARESP[,,2:ensembles] = aperm(aaply(BETARESP[,,2:ensembles],c(3),.fun=function(x){x-BETARESP[,,1]}),c(2,3,1))
# BETAOCEAN[,,2:ensembles] = aperm(aaply(BETAOCEAN[,,2:ensembles],c(3),.fun=function(x){x-BETAOCEAN[,,1]}),c(2,3,1))
#
# BETAGPP[,,2:ensembles][BETAGPP[,,2:ensembles] <= 0] = ( -(BETAGPP[,,2:ensembles][BETAGPP[,,2:ensembles] <= 0] ) ^2 ) / length(ifiles)
# BETAGPP[,,2:ensembles][BETAGPP[,,2:ensembles] > 0] = ( (BETAGPP[,,2:ensembles][BETAGPP[,,2:ensembles] > 0] ) ^2 ) / length(ifiles)
#
# BETARESP[,,2:ensembles][BETARESP[,,2:ensembles] <= 0] = ( -(BETARESP[,,2:ensembles][BETARESP[,,2:ensembles] <= 0] ) ^2 ) / length(ifiles)
# BETARESP[,,2:ensembles][BETARESP[,,2:ensembles] > 0] = ( (BETARESP[,,2:ensembles][BETARESP[,,2:ensembles] > 0] ) ^2 ) / length(ifiles)
#
# BETAOCEAN[,,2:ensembles][BETAOCEAN[,,2:ensembles] <= 0] = ( -(BETAOCEAN[,,2:ensembles][BETAOCEAN[,,2:ensembles] <= 0] ) ^2 ) / length(ifiles)
# BETAOCEAN[,,2:ensembles][BETAOCEAN[,,2:ensembles] > 0] = ( (BETAOCEAN[,,2:ensembles][BETAOCEAN[,,2:ensembles] > 0] ) ^2 ) / length(ifiles)
#
# }else{
# ifiles.fil = nc_open(ifiles[k])
# BETAGPP = ncvar_get(ifiles.fil,"BETAGPP")
# BETARESP = ncvar_get(ifiles.fil,"BETARESP")
# BETAOCEAN = ncvar_get(ifiles.fil,"BETAOCEAN")
# nc_close(ifiles.fil)
#
# #-- Important, we need to convert deviations to variations before we weight, and add
# BETAGPP[,,2:ensembles] = aperm(aaply(BETAGPP[,,2:ensembles],c(3),.fun=function(x){x-BETAGPP[,,1]}),c(2,3,1))
# BETARESP[,,2:ensembles] = aperm(aaply(BETARESP[,,2:ensembles],c(3),.fun=function(x){x-BETARESP[,,1]}),c(2,3,1))
# BETAOCEAN[,,2:ensembles] = aperm(aaply(BETAOCEAN[,,2:ensembles],c(3),.fun=function(x){x-BETAOCEAN[,,1]}),c(2,3,1))
#
# BETAGPP[,,2:ensembles][BETAGPP[,,2:ensembles] <= 0] = ( -(BETAGPP[,,2:ensembles][BETAGPP[,,2:ensembles] <= 0] ) ^2 ) / length(ifiles)
# BETAGPP[,,2:ensembles][BETAGPP[,,2:ensembles] > 0] = ( (BETAGPP[,,2:ensembles][BETAGPP[,,2:ensembles] > 0] ) ^2 ) / length(ifiles)
#
# BETARESP[,,2:ensembles][BETARESP[,,2:ensembles] <= 0] = ( -(BETARESP[,,2:ensembles][BETARESP[,,2:ensembles] <= 0] ) ^2 ) / length(ifiles)
# BETARESP[,,2:ensembles][BETARESP[,,2:ensembles] > 0] = ( (BETARESP[,,2:ensembles][BETARESP[,,2:ensembles] > 0] ) ^2 ) / length(ifiles)
#
# BETAOCEAN[,,2:ensembles][BETAOCEAN[,,2:ensembles] <= 0] = ( -(BETAOCEAN[,,2:ensembles][BETAOCEAN[,,2:ensembles] <= 0] ) ^2 ) / length(ifiles)
# BETAOCEAN[,,2:ensembles][BETAOCEAN[,,2:ensembles] > 0] = ( (BETAOCEAN[,,2:ensembles][BETAOCEAN[,,2:ensembles] > 0] ) ^2 ) / length(ifiles)
# }
# }else
# {
# if(pr_ind[k]){
# #-- For now, just use first 'prior' pull for both prior files, usually just first/second cycles
# BETAGPP = BETAGPP *2
# BETARESP = BETARESP *2
# BETAOCEAN = BETAOCEAN *2
# }else{
# ifiles.fil = nc_open(ifiles[k])
# BETAGPP_NEW = ncvar_get(ifiles.fil,"BETAGPP")#/length(ifiles)
# BETARESP_NEW = ncvar_get(ifiles.fil,"BETARESP")#/length(ifiles)
# BETAOCEAN_NEW = ncvar_get(ifiles.fil,"BETAOCEAN")#/length(ifiles)
# nc_close(ifiles.fil)
# #-- Important, we need to convert deviations to variations before we weight, and add
# BETAGPP_NEW[,,2:ensembles] = aperm(aaply(BETAGPP_NEW[,,2:ensembles],c(3),.fun=function(x){x-BETAGPP_NEW[,,1]}),c(2,3,1))
# BETARESP_NEW[,,2:ensembles] = aperm(aaply(BETARESP_NEW[,,2:ensembles],c(3),.fun=function(x){x-BETARESP_NEW[,,1]}),c(2,3,1))
# BETAOCEAN_NEW[,,2:ensembles] = aperm(aaply(BETAOCEAN_NEW[,,2:ensembles],c(3),.fun=function(x){x-BETAOCEAN_NEW[,,1]}),c(2,3,1))
# BETAGPP_NEW[,,2:ensembles][BETAGPP_NEW[,,2:ensembles] <= 0] = ( -(BETAGPP_NEW[,,2:ensembles][BETAGPP_NEW[,,2:ensembles] <= 0] ) ^2 ) / length(ifiles)
# BETAGPP_NEW[,,2:ensembles][BETAGPP_NEW[,,2:ensembles] > 0] = ( (BETAGPP_NEW[,,2:ensembles][BETAGPP_NEW[,,2:ensembles] > 0] ) ^2 ) / length(ifiles)
# BETARESP_NEW[,,2:ensembles][BETARESP_NEW[,,2:ensembles] <= 0] = ( -(BETARESP_NEW[,,2:ensembles][BETARESP_NEW[,,2:ensembles] <= 0] ) ^2 ) / length(ifiles)
# BETARESP_NEW[,,2:ensembles][BETARESP_NEW[,,2:ensembles] > 0] = ( (BETARESP_NEW[,,2:ensembles][BETARESP_NEW[,,2:ensembles] > 0] ) ^2 ) / length(ifiles)
# BETAOCEAN_NEW[,,2:ensembles][BETAOCEAN_NEW[,,2:ensembles] <= 0] = ( -(BETAOCEAN_NEW[,,2:ensembles][BETAOCEAN_NEW[,,2:ensembles] <= 0] ) ^2 ) / length(ifiles)
# BETAOCEAN_NEW[,,2:ensembles][BETAOCEAN_NEW[,,2:ensembles] > 0] = ( (BETAOCEAN_NEW[,,2:ensembles][BETAOCEAN_NEW[,,2:ensembles] > 0] ) ^2 ) / length(ifiles)
# BETAGPP = BETAGPP + BETAGPP_NEW
# BETARESP = BETARESP + BETARESP_NEW
# BETAOCEAN = BETAOCEAN + BETAOCEAN_NEW
# }
# }
#}
#-- Convert back into deviations from variations
#BETAGPP[,,2:ensembles][BETAGPP[,,2:ensembles] <= 0] = ( -(-BETAGPP[,,2:ensembles][BETAGPP[,,2:ensembles] <= 0] ) ^0.5 )
#BETAGPP[,,2:ensembles][BETAGPP[,,2:ensembles] > 0] = ( (BETAGPP[,,2:ensembles][BETAGPP[,,2:ensembles] > 0] ) ^0.5 )
#BETARESP[,,2:ensembles][BETARESP[,,2:ensembles] <= 0] = ( -(-BETARESP[,,2:ensembles][BETARESP[,,2:ensembles] <= 0] ) ^0.5 )
#BETARESP[,,2:ensembles][BETARESP[,,2:ensembles] > 0] = ( (BETARESP[,,2:ensembles][BETARESP[,,2:ensembles] > 0] ) ^0.5 )
#BETAOCEAN[,,2:ensembles][BETAOCEAN[,,2:ensembles] <= 0] = ( -(-BETAOCEAN[,,2:ensembles][BETAOCEAN[,,2:ensembles] <= 0] ) ^0.5 )
#BETAOCEAN[,,2:ensembles][BETAOCEAN[,,2:ensembles] > 0] = ( (BETAOCEAN[,,2:ensembles][BETAOCEAN[,,2:ensembles] > 0] ) ^0.5 )
##-- Adjust mean (which is currently just added together) by weighting
#BETAGPP[,,1] = BETAGPP[,,1]/length(ifiles)
#BETARESP[,,1] = BETARESP[,,1]/length(ifiles)
#BETAOCEAN[,,1] = BETAOCEAN[,,1]/length(ifiles)
#-- add back mean into deviations
#BETAGPP[,,2:ensembles] = aperm(aaply(BETAGPP[,,2:ensembles],c(3),.fun=function(x){x + BETAGPP[,,1]}),c(2,3,1))
#BETARESP[,,2:ensembles] = aperm(aaply(BETARESP[,,2:ensembles],c(3),.fun=function(x){x + BETARESP[,,1]}),c(2,3,1))
#BETAOCEAN[,,2:ensembles] = aperm(aaply(BETAOCEAN[,,2:ensembles],c(3),.fun=function(x){x + BETAOCEAN[,,1]}),c(2,3,1))
#write_new_priors_nc(BETAOCEAN=BETAOCEAN,BETAGPP=BETAGPP,BETARESP=BETARESP,fileout=prior_betas_tminus1_file,grid.x=2.5,grid.y=2)
if(estimate_land_ocean_bias)
{
ret2 = create_prior_landoceanbias(ifiles=ifiles,pr_ind=pr_ind,ensembles=ensembles)
ret = create_prior(ifiles=ifiles,pr_ind=pr_ind,ensembles=ensembles)
write_new_priors_nc(BETAOCEAN=ret$BETAOCEAN,BETAGPP=ret$BETAGPP,
BETARESP=ret$BETARESP,
OBSLANDBIAS=ret2$OBSLANDBIAS,
OBSOCEANBIAS=ret2$OBSOCEANBIAS,
fileout=prior_betas_tminus1_file,grid.x=2.5,grid.y=2)
}else{
for(r in 1:(lag_cycle_length+1))
{
if(r==(lag_cycle_length+1)){grid.x=2.5;grid.y=2}else{grid.x=5;grid.y=4}
print(paste("creating prior for lag step",r,"..."))
ret = create_prior(ifiles=ifiles[[r]],pr_ind=pr_ind[[r]],ensembles=ensembles)
write_new_priors_nc(BETAOCEAN=ret$BETAOCEAN,BETAGPP=ret$BETAGPP,
BETARESP=ret$BETARESP,
fileout=prior_betas_tminus1_file[[r]],grid.x=grid.x,grid.y=grid.y)
}
}
}else
{
system(paste("cp ",post_betas_tminus1_file," ",prior_betas_tminus1_file,sep=""))
}
print(paste("Working on cycle",i))
print(paste("running stuff like: ./geos ",1," ",cycles[i]," ",
rdate_arg_lag," ",cycle_length*lag_cycle_length," 0",sep=""))
print(paste("running stuff like: ./geos ",1," ",cycles[i]," ",
rdate_arg," ",cycle_length," 0",sep=""))
#-- Ensemble run
if(prop_model %in% c('pure','ct') )
{
print("Using mean propagation...")
###########################################
#-- SGE (Sun Grid Engine)
###########################################
if(que_soft=="sge"){
sge.parSapply(X=1:ensembles,
FUN=function(x) {system(paste("./geos ",x," ",cycles[i]," ",
rdate_arg," ",cycle_length," 0",sep=""))},
njobs=100) }
###########################################
#-- end SGE
###########################################
###########################################
#-- NASA (PBS), experimental
###########################################
if(que_soft=="nasa2"){
#working_dir = "/discover/nobackup/aschuh/run"
reg.folder = "/discover/nobackup/aschuh/reg_folders/my_job_dir38"
if(file.exists(reg.folder)){
system(paste("rm -rf ",reg.folder,sep=""))
}
system(paste("mkdir ",reg.folder,sep=""))
system(paste("ln -s ",run_dir,"/geos ",reg.folder,"/geos",sep=""))
system(paste("cp ",run_dir,"/input.geos ",reg.folder,"/input.geos",sep=""))
clusterExport(cluster,list=c("i","reg.folder","cycles","rdate_arg",
"cycle_length"))
parSapply(cluster,X=1:ensembles,FUN=function(x) {system(paste("cd ",reg.folder,";./geos ",x," ",cycles[i]," ",
rdate_arg," ",cycle_length," 0 > output",x,sep=""))})
}
###########################################
#-- end NASA (PBS)
###########################################
###########################################
#-- NASA (pods.sh), default NASA
###########################################
if(que_soft=="nasa"){
#working_dir = "/discover/nobackup/aschuh/run"
reg.folder = "/discover/nobackup/aschuh/reg_folders/my_job_dir_noaa"
#-- Begin working on 4x5 part of the transport
if(file.exists(reg.folder)){
system(paste("rm -rf ",reg.folder,sep=""))
}
system(paste("mkdir ",reg.folder,sep=""))
system(paste("ln -s ",run_dir_4x5,"/geos ",reg.folder,"/geos",sep=""))
system(paste("cp ",run_dir_4x5,"/input.geos ",reg.folder,"/input.geos",sep=""))
con = file(description=paste(reg.folder,"/exec.script",sep=""),open="w")
for(k in 1:ensembles)
{
writeLines(paste("./geos ",k," ",cycles[i]," 1 ",
rdate_arg_lag," ",cycle_length*lag_cycle_length," 0 > ",reg.folder,"/outfile.",k,sep=""),con=con)
}
close(con)
system("/discover/nobackup/aschuh/pods.sh /discover/nobackup/aschuh/reg_folders/my_job_dir_noaa/exec.script 6")
#stop("forced stop")
#-- This part interpolates the 3D CO2 field to 2x2.5
con = file(description=paste(reg.folder,"/exec.script",sep=""),open="w")
for(k in 1:ensembles)
{
ens_lab = pad(k,width=4,fill="0")
writeLines(paste("/discover/nobackup/aschuh/R-3.0.1/bin/Rscript ",run_dir_4x5,"../run/ENSCODE/interp_restart_wargs.R ",
run_dir_4x5,"../run/ENSCODE ",
outdir_4x5,"/CO2/ts_1h_avg.",rdate_arg,"00.",ens_lab,".h5.nc ",
outdir_2x2.5,"/CO2/ts_1h_avg.",rdate_arg,"00.",ens_lab,".h5.nc ",
" >& ",reg.folder,"/outfile.",k,sep=""),con=con)
}
close(con)
#stop("forced stop")
system("/discover/nobackup/aschuh/pods.sh /discover/nobackup/aschuh/reg_folders/my_job_dir_noaa/exec.script 6")
#stop("forced stop")
#-- This part runs the model for another cycle at 2x2.5
if(file.exists(reg.folder)){
system(paste("rm -rf ",reg.folder,sep=""))
}
system(paste("mkdir ",reg.folder,sep=""))
system(paste("ln -s ",run_dir_2x2.5,"/geos ",reg.folder,"/geos",sep=""))
system(paste("cp ",run_dir_2x2.5,"/input.geos ",reg.folder,"/input.geos",sep=""))
con = file(description=paste(reg.folder,"/exec.script",sep=""),open="w")
for(k in 1:ensembles)
{
writeLines(paste("./geos ",k," ",cycles[i]," 6 ",
rdate_arg," ",cycle_length," 0 > ",reg.folder,"/outfile.",k,sep=""),con=con)
}
close(con)
system("/discover/nobackup/aschuh/pods.sh /discover/nobackup/aschuh/reg_folders/my_job_dir_noaa/exec.script 6")
#stop("forced stop")
}
###########################################
#-- end NASA (pods.sh)
###########################################
##############################################
#-- use BatchJobs package and "torque" (CIRA)
##############################################
if(que_soft=="torque"){
#default.resources = list(queue="batch1", walltime="96:00:00")
library(BatchJobs)
working_dir = "/discover/nobackup/aschuh/run"
reg.folder = "/discover/nobackup/aschuh/reg_folders/my_job_dir38"
if(file.exists(reg.folder)){
system(paste("rm -rf ",reg.folder,sep=""))
}
reg <- makeRegistry(id="my_reg", seed=123, work.dir=working_dir,file.dir=reg.folder)
run.geos = function(x,cycles,cycle_length,i,rdate_arg,rerun,run_dir)
{
system(paste("cd ",run_dir,sep=""))
system(paste(run_dir,"geos ","ENS_NUMBER"," ",cycles[i]," ",
rdate_arg," ",cycle_length," ",rerun,sep=""))
}
xs <- 1:ensembles
batchMap(reg, run.geos,xs,more.args=list(run_dir=run_dir,rdate_arg=rdate_arg,
i=i,cycle_length=cycle_length,cycles=cycles,rerun=0))
ids <- getJobIds(reg)
chunk = 4
ids_list = lapply(1:(ceiling(max(xs/chunk))),
FUN=function(x){return(seq((x-1)*chunk+1,x*chunk,1))})
llen = length(ids_list)
ids_list[llen] = list(as.vector(unlist(ids_list[llen]))[as.vector(unlist(ids_list[llen])) <= max(xs) ] )
submitJobs(reg,ids_list,job.delay=TRUE)
success = waitForJobs(reg,sleep=60)
if(success){
#log_files = list.files(working_dir,full.names=TRUE,pattern="master.log")
#file.remove(log_files)
}
}
}
###############################################
## End BatchJobs/torque (CIRA)
###############################################
if(prop_model == 'none')
{
print("Not using mean propagation...")
#-- This option fixes cycles[i] = 1 so that we don't propagate correction factors
#-- but start at same prior every time
sge.parSapply(cl,1:ensembles,
function(x) {system(paste("./geos ",x," ",1," ",
rdate_arg," ",cycle_length," 0",sep=""))},
njobs=ensembles)
}
################################################
#--
################################################
#-- Pull ensemble data from run
#noaa_dir = "/home/aschuh/carbontracker.obs"
#noaa_dir = "/discover/nobackup/aschuh/carbontracker.obs"
noaa_dir = "/discover/nobackup/aschuh/obspack_co2_1_PROTOTYPE_v1.0.4b_2014-02-13/data/nc"
print("merging data...")
#-- Check for leap day
noaa_start_date = as.numeric(julian((i-1)*14*3600*24 + startdate,origin="2000-01-01 00:00:00 UTC"))
noaa_end_date = as.numeric(julian(i*14*3600*24 + startdate,origin="2000-01-01 00:00:00 UTC"))
observation.matrix = create_noaa_data(noaa_data_dir=noaa_dir,
min.time=noaa_start_date,
max.time=noaa_end_date)
fulldat = merge_ens_data(observation.matrix,ensemble.dir=paste(outdir_2x2.5,"/stations/",sep=""),date=rdate_arg)
fulldat$obs = fulldat$obs * 10^6 # converts to ppm
#-- sort of screwed up, optimize_betas multiplies by 10^6 which leaves the resultant
#-- at co2PPM*10^-6, which is compared to fulldat$obs (same units), need to streamline IN FUTURE
#fulldat$fullensdat = fulldat$fullensdat * 10^-12
#-- Optimize the betas
print("optimizing ....")
#-- All the optimization is done here
#-- Loop over all, chunk by chunk
if(dim(fulldat$fullensdat)[1]>5000)
{
#-- Watch out for this if it is exactly length 5001
brks = c(seq(1,dim(fulldat$fullensdat)[1],by=5000),dim(fulldat$fullensdat)[1])
for(k in 1:(length(brks)-1))
{
print(paste("working on obs: ",brks[k]," to ",brks[k+1],sep=""))
betas_arg = prior_betas_tminus1_file
ret = optimize_betas(betas_file=betas_arg,
Rdiag_vector=fulldat$err[brks[k]:brks[k+1]]^2,
ens_matrix=fulldat$fullensdat[brks[k]:brks[k+1],],
obs_vector=fulldat$obs[brks[k]:brks[k+1]],method=2,
localize=TRUE,diags=TRUE)
betas_arg = ret$X_post
}
}else
{
ret = optimize_betas(betas_file=prior_betas_tminus1_file,Rdiag_vector=fulldat$err^2,
ens_matrix=fulldat$fullensdat,obs_vector=fulldat$obs,method=2,
localize=FALSE,diags=TRUE)
}
X_post = ret$X_post
rm(ret)
#-- Inflate variance of ensemble for "mean propagation" case
if(prop_model %in% c('pure','ct') )
{
X_post = (X_post - X_post[,1])*inflation.factor + X_post[,1]
}
#-- Output the betas to netcdf for next cycle
print("outputting new betas ...")
#output2ncdf(betas=X_post,fileout=paste(outdir,"/betas/betas_cycle_post_",
# pad(cycles[i],width=3,fill="0"),".nc",sep=""),output_biases=FALSE)
output2ncdf(betas=X_post,fileout=post_betas_t_file,output_biases=FALSE)
#-- Regrid 2x25 betas to 4x5
regrid_2x25_betas(post_betas_t_file[[6]],
post_betas_t_file_regrid,x_res_out=5,y_res_out=4)
#-- Create diagnostics
#diags(X_post)
#-- Remove objects
rm(fulldat)
rm(X_post)
#-- Single rerun of mean to get restart CO2 for next cycle
print("launching mean beta rerun to generate new CO2 field ....")
###########################################
#-- NASA (pods.sh), default NASA
###########################################
if(que_soft == "nasa")
{
#working_dir = "/discover/nobackup/aschuh/run"
#reg.folder = "/discover/nobackup/aschuh/reg_folders/my_job_dir_noaa"
#if(file.exists(reg.folder)){
# system(paste("rm -rf ",reg.folder,sep=""))
#}
#system(paste("mkdir ",reg.folder,sep=""))
#system(paste("ln -s ",run_dir,"/geos ",reg.folder,"/geos",sep=""))
#system(paste("cp ",run_dir,"/input.geos ",reg.folder,"/input.geos",sep=""))
#con = file(description=paste(reg.folder,"/exec.script",sep=""),open="w")
# for(k in ((j-1)*block.size+1):(min(j*block.size,ensembles) ) )
#for(k in 1:1)
# {
# writeLines(paste("./geos ",k," ",cycles[i]," ",
# rdate_arg," ",cycle_length," 1 > ",reg.folder,"/outfile.",k,sep=""),con=con)
# }
#close(con)
#system("/discover/nobackup/aschuh/pods.sh /discover/nobackup/aschuh/reg_folders/my_job_dir_noaa/exec.script 1")
#working_dir = "/discover/nobackup/aschuh/run"
reg.folder = "/discover/nobackup/aschuh/reg_folders/my_job_dir_noaa"
#-- Begin working on 4x5 part of the transport
#-- Run the first two weeks and save CO2 field
if(file.exists(reg.folder)){
system(paste("rm -rf ",reg.folder,sep=""))
}
system(paste("mkdir ",reg.folder,sep=""))
system(paste("ln -s ",run_dir_4x5,"/geos ",reg.folder,"/geos",sep=""))
system(paste("cp ",run_dir_4x5,"/input.geos ",reg.folder,"/input.geos",sep=""))
con = file(description=paste(reg.folder,"/exec.script",sep=""),open="w")
for(k in 1:1)
{
#writeLines(paste("./geos ",k," ",cycles[i]," 1 ",
# rdate_arg_lag," ",cycle_length*lag_cycle_length," 1 > ",reg.folder,"/outfile.",k,sep=""),con=con)
writeLines(paste("./geos ",k," ",cycles[i]," 1 ",
rdate_arg_lag," ",cycle_length," 1 > ",reg.folder,"/outfile.",k,sep=""),con=con)
}
close(con)
system("/discover/nobackup/aschuh/pods.sh /discover/nobackup/aschuh/reg_folders/my_job_dir_noaa/exec.script 1")
#stop("forced stop")
########################################
#- FOR NOW I'M NOT SURE I NEED BELOW
########################################
#-- This part interpolates the 3D CO2 field to 2x2.5
#con = file(description=paste(reg.folder,"/exec.script",sep=""),open="w")
#for(k in 1:1)
# {
# ens_lab = pad(k,width=4,fill="0")
# writeLines(paste("/discover/nobackup/aschuh/R-3.0.1/bin/Rscript ",run_dir_4x5,"../run/ENSCODE/interp_restart_wargs.R ",
# run_dir_4x5,"../run/ENSCODE ",
# outdir_4x5,"/CO2/ts_1h_avg.",rdate_arg,"00.",ens_lab,".h5.nc ",
# outdir_2x2.5,"/CO2/ts_1h_avg.",rdate_arg,"00.",ens_lab,".h5.nc ",
# " >& ",reg.folder,"/outfile.",k,sep=""),con=con)
# }
#close(con)
#stop("forced stop")
#system("/discover/nobackup/aschuh/pods.sh /discover/nobackup/aschuh/reg_folders/my_job_dir_noaa/exec.script 1")
#stop("forced stop")
#-- This part runs the model for another cycle at 2x2.5
#if(file.exists(reg.folder)){
# system(paste("rm -rf ",reg.folder,sep=""))
#}
#system(paste("mkdir ",reg.folder,sep=""))
#system(paste("ln -s ",run_dir_2x2.5,"/geos ",reg.folder,"/geos",sep=""))
#system(paste("cp ",run_dir_2x2.5,"/input.geos ",reg.folder,"/input.geos",sep=""))
#con = file(description=paste(reg.folder,"/exec.script",sep=""),open="w")
#for(k in 1:1)
# {
# writeLines(paste("./geos ",k," ",cycles[i]," 6 ",
# rdate_arg," ",cycle_length," 1 > ",reg.folder,"/outfile.",k,sep=""),con=con)
# }
#close(con)
#system("/discover/nobackup/aschuh/pods.sh /discover/nobackup/aschuh/reg_folders/my_job_dir_noaa/exec.script 1")
#stop("forced stop")
}
###########################################
#-- End NASA (pods.sh), default NASA
###########################################
##############################################
#-- use BatchJobs package and "torque" (CIRA)
##############################################
if(que_soft == "torque")
{
#default.resources = list(queue="batch1", walltime="96:00:00")
library(BatchJobs)
working_dir = "/home/aschuh/run.noaa"
reg.folder = "/home/aschuh/reg_folders/my_job_dir38"
if(file.exists(reg.folder)){
system(paste("rm -rf ",reg.folder,sep=""))
}
reg <- makeRegistry(id="my_reg", seed=123, work.dir=working_dir,file.dir="/home/aschuh/reg_folders/my_job_dir38")
xs <- 1
#batchMap(reg, run.geos.reload, xs)
batchMap(reg, run.geos, xs,more.args=list(rdate_arg=rdate_arg,
i=i,cycle_length=cycle_length,cycles=cycles,rerun=1))
ids <- getJobIds(reg)
submitJobs(reg, resources=default.resources,ids)
success = waitForJobs(reg,sleep=300)
if(success){
log_files = list.files(working_dir,full.names=TRUE,pattern="master.log")
file.remove(log_files)
}
}
##############################################
#-- End BatchJobs package and "torque" (CIRA)
##############################################
##############################################
#-- Start SGE (sun grid engine)
##############################################
if(que_soft == "sge" )
{
sge.parSapply(1,
function(x) {system(paste("./geos 1 ",cycles[i]," ",rdate_arg," ",cycle_length," 1",sep=""))},
njobs=1)
}
##############################################
#-- End SGE (sun grid engine)
##############################################
#-- Remove gosat files, but leave FINALRUN files, this is important
#-- because the model assumes that current cycle's
#-- data is in this directory, regardless of name. It simply lists and sorts files.
#modelfiles = list.files(paste(outdir,"/gosat/",sep=""),full.names=TRUE)
#-- We want to keep "FINALRUN" files as well as prior CO2 guesses for each cyle
#first_files = list.files(paste(outdir,"/gosat/",sep=""),full.names=TRUE,pattern="ens.0001")
#noremove_files = list.files(paste(outdir,"/gosat/",sep=""),full.names=TRUE,pattern="ens.0001.FINALRUN")
#prior_files = list.files(paste(outdir,"/gosat/",sep=""),full.names=TRUE,pattern="ens.0001.PRIOR.nc")
#move_files = first_files[ (!first_files %in% noremove_files) & (!first_files %in% prior_files)]
#if(length(move_files) > 0)
#{
# for(k in 1:length(move_files))
# {
# newfilenm = paste(move_files[k],".PRIOR",sep="")
# file.copy(move_files[k],newfilenm)
# file.remove(move_files[k])
# }
#}
#remove_files = modelfiles[!modelfiles %in% first_files]
#file.remove(remove_files)
#############################################
#-- Same for surface "STATIONS" files
#############################################
#modelfiles = list.files(paste(outdir_2x2.5,"/stations/",sep=""),full.names=TRUE)
#-- We want to keep "FINALRUN" files as well as prior CO2 guesses for each cyle
#first_files = list.files(paste(outdir_2x2.5,"/stations/",sep=""),full.names=TRUE,pattern="ens.0001")
#noremove_files = list.files(paste(outdir_2x2.5,"/stations/",sep=""),full.names=TRUE,pattern="FINALRUN.ens.0001")
#prior_files = list.files(paste(outdir_2x2.5,"/stations/",sep=""),full.names=TRUE,pattern="ens.0001.PRIOR")
#move_files = first_files[ (!first_files %in% noremove_files) & (!first_files %in% prior_files)]
#if(length(move_files) > 0)
# {
# for(k in 1:length(move_files))
# {
# newfilenm = gsub(".nc",".PRIOR.nc",move_files[k])
# file.copy(move_files[k],newfilenm)
# file.remove(move_files[k])
# }
# }
#remove_files = modelfiles[!modelfiles %in% first_files]
#file.remove(remove_files)
}