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Feature/jstassi/#75 #76 updates #85

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Feature/jstassi/#75 #76 updates #85

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29c3cef
Updates to use logical directory path for FVROOT rather than physical…
gmao-jstassi Apr 16, 2021
84d0179
Added -partition and -qos options to script
gmao-jstassi Apr 16, 2021
b7cea8e
Merge branch 'develop' into feature/jstassi/#75-#76-updates
mathomp4 Apr 19, 2021
25c1651
Merge branch 'develop' into feature/jstassi/#75-#76-updates
mathomp4 Apr 19, 2021
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2 changes: 1 addition & 1 deletion parallel_build.csh
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ if ($name != $name:t) then
set scriptname = $name:t
cd $name:h
endif
set srcdir = `pwd`
set srcdir = `pwd -L`
setenv ESMADIR $srcdir

# Save the original argv because I'm not a good
Expand Down
46 changes: 38 additions & 8 deletions src/Applications/GEOSdas_App/fvsetup
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Expand Up @@ -341,7 +341,7 @@
# 25Jul2017 Holdaway Added resource files associated with NGGPS FV3 tlm/adjoint, sens and svec
# 19Jul2018 Wargan Additions for OMPS
#-------------------------------------------------------------------------
use Cwd qw(cwd);
use Cwd qw(abs_path cwd);
use English;
use Env; # make env vars readily available
use File::Basename qw(basename dirname);
Expand Down Expand Up @@ -379,7 +379,7 @@ my ($gocart_tracers, $radcor, $emiss, $lsmodel_flag, $rroute_flag);
my ($agcm_rst_flg, $sensdeg, %setupfile, @otherheaders);
my ($checkFLG, $dbqueue, $runjobFLG, $saveFLG, $stopFLG);
my (@fvprompt, @fvANS1, @fvANS2, $fvsetupflags);
my ($fvhome, $fvroot, $fvbin, $checkID, $siteID);
my ($fvhome, $fvroot, $fvbin, $bindir, $pwdL, $pwdP, $checkID, $siteID);
my ($remNODE, $remID);
my ($qsub);
my ($acqloc);
Expand All @@ -394,12 +394,42 @@ system clear;
get_runtime_values();
$ENV{"PATH"} = $FindBin::Bin .":$ENV{PATH}";

# FVROOT is directory above bin dir where binaries have been installed
# --------------------------------------------------------------------
$fvroot = dirname($FindBin::Bin);
$fvroot =~ s|/u/.realmounts/share|/share|; # for portability across
# NAS machines
$fvbin = "$fvroot/bin";
# FVROOT is directory above fvbin where binaries have been installed
# ------------------------------------------------------------------
$fvbin = $FindBin::Bin; # absolute path of fvbin

chomp($pwdL = `pwd -L`); # logical path of calling program
chomp($pwdP = `pwd -P`); # physical (absolute) path of calling program

# if fvsetup is called from local directory
#------------------------------------------
if ($pwdP eq $FindBin::Bin) { $fvbin = $pwdL }

# if fvsetup is called from remote directory
#-------------------------------------------
else {
$bindir = dirname($0);

# remove single-dot (".") path segments
#--------------------------------------
while ($bindir =~ m|^\./|) { $bindir =~ s|^\./|| }
while ($bindir =~ m|/\./|) { $bindir =~ s|/\./|/| }
while ($bindir =~ m|/\.$|) { $bindir =~ s|/\.$|| }

# remove leading double-dot ("..") path segments
#-----------------------------------------------
while ($bindir =~ m|^\.\.|) {
$bindir =~ s|^\.\.||;
$pwdL = dirname($pwdL);
$bindir =~ s|^/||;
}

# determine path of fvbin
#------------------------
$bindir = "$pwdL/$bindir" unless $bindir =~ m|^/|;
$fvbin = $bindir if -e $bindir and abs_path($bindir) eq $fvbin;
}
$fvroot = dirname($fvbin);
$fvetc = "$fvroot/etc";
$user = getpwuid($<) unless ($user = $ENV{"USER"});

Expand Down
63 changes: 35 additions & 28 deletions src/Applications/GEOSdas_App/monthly.yyyymm.pl.tmpl
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Expand Up @@ -58,10 +58,10 @@ my ($EXPID, $FVHOME, $PBS_BIN, $account, $listdir, $mnthlyRC);
my ($numnodes_mm, $numnodes_mp, $plotHISTrc, $qcmd, $rundir);
my ($script, $siteID, $workdir, $yyyymm, %newrc, %JOBID);
my ($walltime_cl, $walltime_mm, $walltime_mp, $walltime_pf);
my ($MONTHLY_PARTITION, $MONTHLY_QOS);
my ($partition, $qos);

#$MONTHLY_PARTITION = "preops";
#$MONTHLY_QOS = "dastest";
#$partition = "preops";
#$qos = "dastest";

my %valid = ( "fetch" => 1,
"means" => 1,
Expand Down Expand Up @@ -115,6 +115,9 @@ sub init {
"finish_plots" => \$finish,
"nopush" => \$nopush,

"partition=s" => \$partition,
"qos=s" => \$qos,

"rc|mrc=s" => \$mnthlyRC,
"newrc:s" => \@newrc,

Expand Down Expand Up @@ -381,7 +384,7 @@ sub fetch_calc_tar_and_clean {
sub fetch_inputs {
my (%opts, $filestring, $ftype, $htype, $do_dmput, $do_tar);
my ($tmpl, $prefetch_j, $jobname, $outfile);
my ($job_name, $time, $output, $partition, $vFLG);
my ($job_name, $time, $output, $parFLG, $vFLG);
my (%value, @deps, $dependFLG, $cmd);

# input arguments
Expand All @@ -405,14 +408,14 @@ sub fetch_inputs {
$job_name = "SBATCH --job-name=$jobname";
$time = "SBATCH --time=$walltime_pf";
$output = "SBATCH --output=$outfile";
$partition = "SBATCH --partition=datamove";
$parFLG = "SBATCH --partition=datamove";
$vFLG = "--export=outfile=$outfile";
}
else {
$job_name = "PBS -N $jobname";
$time = "PBS -l walltime=$walltime_pf";
$output = "PBS -o $outfile";
$partition = "";
$parFLG = "";
$vFLG = "-v outfile=$outfile";
}

Expand All @@ -421,7 +424,7 @@ sub fetch_inputs {
$value{"__TIME__"} = $time;
$value{"__ACCOUNT__"} = $account;
$value{"__OUTPUT__"} = $output;
$value{"__PARTITION__"} = $partition;
$value{"__PARTITION__"} = $parFLG;

$value{"__FILESTRING__"} = $filestring;
$value{"__HOURTYPE__"} = $htype;
Expand Down Expand Up @@ -488,8 +491,8 @@ sub calc_monthly_means {
$nodes = "SBATCH --nodes=$numnodes_mm";
$per_node = "SBATCH --tasks-per-node=$tasks_per_node";
$vFLG = "--export=outfile=$outfile";
$parFLG = "SBATCH --partition=$MONTHLY_PARTITION" if $MONTHLY_PARTITION;
$qosFLG = "SBATCH --qos=$MONTHLY_QOS" if $MONTHLY_QOS;
$parFLG = "SBATCH --partition=$partition" if $partition;
$qosFLG = "SBATCH --qos=$qos" if $qos;
}
else {
$job_name = "PBS -N $jobname";
Expand Down Expand Up @@ -549,7 +552,7 @@ sub calc_monthly_means {
sub tar_and_clean_inputs {
my (%opts, $filestring, $ftype, $do_tar, $lastFLG);
my ($tmpl, $tarandclean_j, $jobname, $outfile);
my ($job_name, $time, $output, $partition, $vFLG);
my ($job_name, $time, $output, $parFLG, $vFLG);
my (%value, $walltime, @deps, $dependFLG, $cmd);

# input arguments
Expand All @@ -572,14 +575,14 @@ sub tar_and_clean_inputs {
$job_name = "SBATCH --job-name=$jobname";
$time = "SBATCH --time=$walltime_cl";
$output = "SBATCH --output=$outfile";
$partition = "SBATCH --partition=datamove";
$parFLG = "SBATCH --partition=datamove";
$vFLG = "--export=outfile=$outfile";
}
else {
$job_name = "PBS -N $jobname ";
$time = "PBS -l walltime=$walltime_cl";
$output = "PBS -o $outfile";
$partition = "";
$parFLG = "";
$vFLG = "-v outfile=$outfile";
}

Expand All @@ -588,7 +591,7 @@ sub tar_and_clean_inputs {
$value{"__TIME__"} = $time;
$value{"__ACCOUNT__"} = $account;
$value{"__OUTPUT__"} = $output;
$value{"__PARTITION__"} = $partition;
$value{"__PARTITION__"} = $parFLG;

$value{"__FILESTRING__"} = $filestring;
$value{"__YYYYMM__"} = $yyyymm;
Expand Down Expand Up @@ -733,7 +736,7 @@ sub archive_monthly_files {
#=======================================================================
sub monthly_plots {
my ($tmpl, $transfer_csh, $plots_j, $jobname, $outfile);
my ($job_name, $nodes, $time, $output, $partition);
my ($job_name, $nodes, $time, $output, $parFLG);
my (%value, @deps, $dependFLG, $vFLG, $cmd);

# create plots transfer job script
Expand All @@ -747,14 +750,14 @@ sub monthly_plots {
$job_name = "SBATCH --job-name=$jobname";
$time = "SBATCH --time=$walltime_cl";
$output = "SBATCH --output=$outfile";
$partition = "SBATCH --partition=datamove";
$parFLG = "SBATCH --partition=datamove";
$vFLG = "--export=outfile=$outfile";
}
else {
$job_name = "PBS -N $jobname";
$time = "PBS -l walltime=$walltime_cl";
$output = "PBS -o $outfile";
$partition = "";
$parFLG = "";
$vFLG = "-v outfile=$outfile";
}

Expand All @@ -763,7 +766,7 @@ sub monthly_plots {
$value{"__TIME__"} = $time;
$value{"__ACCOUNT__"} = $account;
$value{"__OUTPUT__"} = $output;
$value{"__PARTITION__"} = $partition;
$value{"__PARTITION__"} = $parFLG;

$value{"__TRANSFER__"} = basename($transfer_csh);
$value{"__RUNDIR__"} = $rundir;
Expand Down Expand Up @@ -1038,21 +1041,25 @@ purpose: calculate means, tar inputs, and/or produce plots for monthly data
usage: $script [process options] [plot option] [other options]

process options (see Notes below)
-means calculate monthly means
-tar tar input files
-plots produce monthly plots from monthly means
-finish_plots finish monthly plots job which stopped before completion
-means calculate monthly means
-tar tar input files
-plots produce monthly plots from monthly means
-finish_plots finish monthly plots job which stopped before completion

plot option (only valid when used with -plots or -finish_plots)
-nopush do not transfer gif files to Web server after plotting
-nopush do not transfer gif files to Web server after plotting

slurm directive options
-partition partition send monthly means jobs to specified partition
-qos qos send monthly means jobs to specified qos

other options
-rc mnthlyRC name of monthly rc file [run/monthly.rc]
-newrc [n] re-create resource files prior to any other processing
if n==1, then write new monthly rc file
if n==2, then write new plots HISTORY.rc_tmpl
if no value for n is given, then n==1,2
-h print usage information
-rc mnthlyRC name of monthly rc file [run/monthly.rc]
-newrc [n] re-create resource files prior to any other processing
if n==1, then write new monthly rc file
if n==2, then write new plots HISTORY.rc_tmpl
if no value for n is given, then n==1,2
-h print usage information

Notes:
1. Plots cannot be produced unless monthly means are calculated
Expand Down