Index: trunk/ippScripts/scripts/sc_prepare_camera.pl
===================================================================
--- trunk/ippScripts/scripts/sc_prepare_camera.pl	(revision 37125)
+++ trunk/ippScripts/scripts/sc_prepare_camera.pl	(revision 37833)
@@ -1,3 +1,5 @@
 #! /usr/bin/env perl
+
+# generate the input & output files lists and commands for a single camRun
 
 use Carp;
@@ -16,21 +18,14 @@
 use Pod::Usage qw( pod2usage );
 
-
 # Hard coded values
-# my $remote_root   = '/scratch3/watersc1/';  # Far side destination base location
-my $remote_root   = '/lustre/scratch1/turquoise/watersc1/ps1/'; # Far side destination base location
-$remote_root = '/scratch3/watersc1/';
-my $threads       = 2;                      # How many threads are we going to use?
-my $job_cost      = 1700 / 60 / 60;         # Estimate of how long a job runs, in hours.
-my $proc_per_node = 24;                     # processors per node
-my $min_nodes     = 1;                      # smallest allocation to ask for
-my $max_nodes     = 1000;                   # largest allocation to ask for
-my $min_time      = 1;                      # shortest allocation to ask for
-my $max_time      = 8;                      # longest allocation to ask for
-my $remote_hostname= "LANL/Mustang";         # Name of the remote node.
-my @return_component_list = ("DBINFO.EXP", "PSASTRO.CONFIG", "PSASTRO.OUTPUT", "LOG.EXP", "PSASTRO.STATS");
+# my $remote_root   = '/lustre/scratch1/turquoise/watersc1/ps1/'; # Far side destination base location
+my $remote_root     = '/scratch3/watersc1/';  # Far side destination base location
+my $remote_hostname = "LANL/Mustang";         # Name of the remote node.
+my $threads_req     = 0;                      # How many threads are we going to use?
+
+my $fail_state = "prep_fail";
+
 # Look for programs we need
 my $missing_tools;
-
 my $remotetool = can_run('remotetool') or (warn "Can't find remotetool" and $missing_tools = 1);
 my $camtool    = can_run('camtool') or (warn "Can't find camtool" and $missing_tools = 1);
@@ -41,7 +36,8 @@
 }
 
-my ($remote_id,$cam_id,,$camera,$dbname,$verbose,$path_base,$no_update);
+my ($remote_id,$cam_id,$camera,$dbname,$verbose,$path_base,$no_update);
 GetOptions(
     'remote_id=s'    => \$remote_id,
+    'cam_id=s'       => \$cam_id,
     'camera|c=s'     => \$camera,
     'dbname|d=s'     => \$dbname,
@@ -52,35 +48,18 @@
 
 pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2 ) if @ARGV;
-pod2usage( -msg => "Required options: --remote_id --camera --dbname --path_base", -exitval => 3) unless
+pod2usage( -msg => "Required options: --remote_id --cam_id --camera --dbname --path_base", -exitval => 3) unless
     defined($remote_id) and
+    defined($cam_id) and
     defined($camera) and
     defined($path_base) and
     defined($dbname);
-my $ipprc = PS::IPP::Config->new( $camera ) or my_die( "Unable to set up", $remote_id);
+
+my $ipprc = PS::IPP::Config->new( $camera ) or &my_die( "Unable to set up", $remote_id, $cam_id, $PS_EXIT_CONFIG_ERROR, $fail_state);
 
 my $mdcParser = PS::IPP::Metadata::Config->new; # Parser for metadata config files
 
-#
-# Step 1: Get a list of the components that make up this remoteRun
-
-# SHould this call listrun to ensure we're in state new?
-my $rt_cmd = "$remotetool -listcomponent -remote_id $remote_id";
-$rt_cmd   .= " -dbname $dbname " if defined($dbname);
-
-my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
-    run(command => $rt_cmd, verbose => $verbose);
-unless ($success) {
-    $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
-    &my_die("Unable to run remotetool to determine stage parameters.",
-            $remote_id,$error_code);
-}
-my $compData = $mdcParser->parse(join "", @$stdout_buf) or
-    &my_die("Unable to determine component information.",
-            $remote_id,$PS_EXIT_PROG_ERROR);
-my $compData2= parse_md_list($compData);
-
-#
-# Step 1b: Open output files
-my $uri_command = $path_base . ".cmd";
+my @return_component_list = ("DBINFO.EXP", "PSASTRO.CONFIG", "PSASTRO.OUTPUT", "LOG.EXP", "PSASTRO.STATS");
+
+# STEP 0: Open output files
 my $uri_transfer= $path_base . ".transfer";
 my $uri_check   = $path_base . ".check";
@@ -89,5 +68,4 @@
 my $uri_return  = $path_base . ".return";
 
-my $disk_command = $ipprc->file_resolve($uri_command,1);
 my $disk_transfer= $ipprc->file_resolve($uri_transfer,1);
 my $disk_check   = $ipprc->file_resolve($uri_check,1);
@@ -96,93 +74,84 @@
 my $disk_return  = $ipprc->file_resolve($uri_return,1);
 
-my (undef, $remote_config) = uri_convert($uri_config); # Needs to be done after we've created it.
-
-open(TRANSFER, ">$disk_transfer")  || &my_die("Couldn't open file? $disk_transfer",$remote_id,$PS_EXIT_SYS_ERROR);
-open(CHECK,    ">$disk_check")  || &my_die("Couldn't open file? $disk_check",$remote_id,$PS_EXIT_SYS_ERROR);
-open(CONFIG,   ">$disk_config")  || &my_die("Couldn't open file? $disk_config",$remote_id,$PS_EXIT_SYS_ERROR);
-open(GENERATE, ">$disk_generate") || &my_die("Couldn't open file? $disk_generate",$remote_id,$PS_EXIT_SYS_ERROR);
-open(RETURN,   ">$disk_return") || &my_die("Couldn't open file? $disk_return", $remote_id, $PS_EXIT_SYS_ERROR);
+my (undef, $remote_config) = &uri_convert($uri_config); # Needs to be done after we've created it.
+
+open(TRANSFER, ">$disk_transfer")  || &my_die("Couldn't open file? $disk_transfer",$remote_id, $cam_id, $PS_EXIT_SYS_ERROR, $fail_state);
+open(CHECK,    ">$disk_check")     || &my_die("Couldn't open file? $disk_check",   $remote_id, $cam_id, $PS_EXIT_SYS_ERROR, $fail_state);
+open(CONFIG,   ">$disk_config")    || &my_die("Couldn't open file? $disk_config",  $remote_id, $cam_id, $PS_EXIT_SYS_ERROR, $fail_state);
+open(GENERATE, ">$disk_generate")  || &my_die("Couldn't open file? $disk_generate",$remote_id, $cam_id, $PS_EXIT_SYS_ERROR, $fail_state);
+open(RETURN,   ">$disk_return")    || &my_die("Couldn't open file? $disk_return",  $remote_id, $cam_id, $PS_EXIT_SYS_ERROR, $fail_state);
 my %file_filter = ();
 
-#
-# Step 2: Iterate over all componenets in this remote run.
 my $job_index = 0;
-my @pre_commands = ();
-my @main_commands = ();
-my @post_commands = ();
-
-foreach my $compEntry (@$compData2) {
-    my $cam_id = $compEntry->{stage_id};
-
-# Get exposure level information from the camRun we're working from.
-    
+
+# STEP 1: Get exposure level information for this camRun
+my ($workdir,$exp_tag,$reduction);
+{
     my $command = "$camtool -pendingexp -cam_id $cam_id ";
     $command   .= " -dbname $dbname " if defined($dbname);
-    
+
     my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
         run(command => $command, verbose => 0);
     unless ($success) {
         $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
-        
-        &my_die("Unable to run camtool to determine stage parameters.",
-                $cam_id,$error_code);
-    }
-
-    my $camData = $mdcParser->parse(join "", @$stdout_buf) or
-	&my_die("Unable to determine cam component information.",
-		$cam_id,$PS_EXIT_PROG_ERROR);
-    my $camData2= parse_md_list($camData);
-    my $camEntry = ${ $camData2 }[0];
-    
-    my $workdir = $camEntry->{workdir};
-    my $exp_tag = $camEntry->{exp_tag};
+
+        &my_die("Unable to run camtool to determine stage parameters.", $remote_id, $cam_id, $error_code, $fail_state);
+    }
+
+    my $MDlist = $mdcParser->parse(join "", @$stdout_buf) or
+        &my_die("Unable to determine cam component information.", $remote_id, $cam_id, $PS_EXIT_PROG_ERROR, $fail_state);
+    my $metadata = parse_md_list($MDlist);
+    my $camEntry = $metadata->[0];
+
+    $workdir   = $camEntry->{workdir};
+    $exp_tag   = $camEntry->{exp_tag};
+    $reduction = $camEntry->{reduction};
+    $reduction = 'DEFAULT' unless defined $reduction;
     unless (defined($workdir)) {
-	while( my ($k, $v) = each %$camEntry ) {
-	    print "key: $k, value: $v.\n";
-	}
-
-	print "%{ $camEntry }\n";
-	die;
-    }
-    my $ipp_outroot = "${workdir}/${exp_tag}/${exp_tag}.cm.${cam_id}";
-    my $remote_outroot = uri_local_to_remote($ipp_outroot);
-
-
-#
+        while( my ($k, $v) = each %$camEntry ) {
+            print "key: $k, value: $v.\n";
+        }
+        print "%{ $camEntry }\n";
+        die;
+    }
+}
+
+my $ipp_outroot = "${workdir}/${exp_tag}/${exp_tag}.cm.${cam_id}";
+my $remote_outroot = uri_local_to_remote($ipp_outroot);
+
 # Step 3: Iterate over the sub-components
-
-    my $reg_command = "$camtool -pendingimfile -cam_id $cam_id ";
-    $reg_command   .= " -dbname $dbname " if defined($dbname);
-
-    ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
-	run(command => $reg_command, verbose => 0);
+{
+    my $command = "$camtool -pendingimfile -cam_id $cam_id ";
+    $command   .= " -dbname $dbname " if defined($dbname);
+
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+        run(command => $command, verbose => 0);
     unless ($success) {
-	$error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
-        &my_die("Unable to run camtool -pendingimfile ",
-                $cam_id,$error_code);
-    }
-    
+        $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+        &my_die("Unable to run camtool -pendingimfile ", $remote_id, $cam_id, $error_code, $fail_state);
+    }
 
     # We don't actually care about the input cam data other than to know which mask files to instantiate.
-    my $inpData = $mdcParser->parse(join "", @$stdout_buf) or
-	&my_die("Unable to determine cam component information.",
-		$cam_id, $PS_EXIT_PROG_ERROR);
-    my $inpData2=parse_md_list($inpData);
-    my $chipProto= ${ $inpData2 }[0];
+    my $MDlist = $mdcParser->parse(join "", @$stdout_buf) or
+        &my_die("Unable to determine cam component information.", $remote_id, $cam_id, $PS_EXIT_PROG_ERROR, $fail_state);
+
+    my $metadata = parse_md_list($MDlist);
+    my $chipProto = $metadata->[0];
     my $chip_path = $chipProto->{path_base};
-    my $remote_chip_path = uri_local_to_remote( $chip_path );
+    my $remote_chip_path = &uri_local_to_remote( $chip_path );
     my $pre_cmd_cmfs = "ls -1 ${remote_chip_path}*.cmf > ${remote_outroot}.cmflist";
     my $pre_cmd_masks= "ls -1 ${remote_chip_path}*.mk.fits > ${remote_outroot}.masklist";
 
-    my $reduction = 'DEFAULT' unless defined $camEntry->{reduction};
-    my $recipe_psastro = $ipprc->reduction($reduction, 'PSASTRO'); # Recipe to use                                                                          
+    my $recipe_psastro = $ipprc->reduction($reduction, 'PSASTRO'); # Recipe to use
+    if ($recipe_psastro eq "") {
+        &my_die("Unable to determine PSASTRO recipe", $cam_id, $PS_EXIT_PROG_ERROR);
+    }
 
     my $psastro_command = " psastro -list ${remote_outroot}.cmflist ";
     $psastro_command   .= " -masklist ${remote_outroot}.masklist ${remote_outroot} ";
-#    $psastro_command   .= " -refmasklist ${remote_outroot}.masklist ${remote_outroot} "; # This is used to do edge calculations.  It should probably be smart enough to know that it can just use the masks I just specified, but it's not.
-    # Uncomment when remote psastro supports this
+#   $psastro_command   .= " -refmasklist ${remote_outroot}.masklist ${remote_outroot} ";
+    $psastro_command   .= " -refmasklist /turquoise/usr/projects/ps1/watersc1/references/gpc1.refmask.list ";
     $psastro_command   .= " -kh-correct /turquoise/usr/projects/ps1/watersc1/references/khcorrect.20140606.v0.fits ";
-    $psastro_command   .= " -refmasklist /turquoise/usr/projects/ps1/watersc1/references/gpc1.refmask.list ";
-#    $psastro_command   .= " -astrommodel /turquoise/usr/projects/ps1/watersc1/references/gpc1.20080909.asm ";
+#   $psastro_command   .= " -astrommodel /turquoise/usr/projects/ps1/watersc1/references/gpc1.20080909.asm ";
     $psastro_command   .= " -astrommodel /turquoise/usr/projects/ps1/watersc1/references/gpc1.20140505.asm ";
     $psastro_command   .= " -recipe PSASTRO $recipe_psastro ";
@@ -190,7 +159,8 @@
     $psastro_command   .= " -dumpconfig ${remote_outroot}.psastro.mdc -stats ${remote_outroot}.stats ";
     $psastro_command   .= " -recipe PPSTATS CAMSTATS ";
-    
+
     my $camtool_post_cmd = "camtool -cam_id $cam_id -addprocessedexp -uri UNKNOWN ";
-    $camtool_post_cmd  .=  " -dbname $dbname " if defined $dbname;                                                                                                            $camtool_post_cmd  .=  " -path_base $ipp_outroot -hostname $remote_hostname -dtime_script 0 ";
+    $camtool_post_cmd  .=  " -dbname $dbname " if defined $dbname;
+    $camtool_post_cmd  .=  " -path_base $ipp_outroot -hostname $remote_hostname -dtime_script 0 ";
     my $post_cmd_echo = " echo -n \"$camtool_post_cmd\" > ${remote_outroot}.dbinfo ";
     my $post_cmd_SfM  = " ppStatsFromMetadata ${remote_outroot}.stats - CAMERA_EXP_FPA >> ${remote_outroot}.dbinfo ";
@@ -201,14 +171,14 @@
     # Determine which output files need to be returned
     foreach my $component(@return_component_list) {
-	my $filename = $ipprc->filename($component,$ipp_outroot);
-	my ($ipp_disk, $remote_disk) = uri_to_outputs_for_return( $filename);
-	my $remote_outroot_dir = dirname($ipp_disk);
-	print CONFIG " && mkdir -p ${remote_root}/tmp/${remote_outroot_dir} && ln -sf $remote_disk ${remote_root}/tmp/${ipp_disk} && touch $remote_disk ";
-    }
-    foreach my $chipInfo (@{ $inpData2 }) {
-	my $filename = $ipprc->filename("PSASTRO.OUTPUT.MASK",$ipp_outroot,$chipInfo->{class_id});
-	my ($ipp_disk, $remote_disk) = uri_to_outputs_for_return( $filename);
-	my $remote_outroot_dir = dirname($ipp_disk);
-	print CONFIG " && mkdir -p ${remote_root}/tmp/${remote_outroot_dir} && ln -sf $remote_disk ${remote_root}/tmp/${ipp_disk} && touch $remote_disk ";
+        my $filename = $ipprc->filename($component,$ipp_outroot);
+        my ($ipp_disk, $remote_disk) = &uri_to_outputs_for_return( $filename);
+        my $remote_outroot_dir = dirname($ipp_disk);
+        print CONFIG " && mkdir -p ${remote_root}/tmp/${remote_outroot_dir} && ln -sf $remote_disk ${remote_root}/tmp/${ipp_disk} && touch $remote_disk ";
+    }
+    foreach my $chipInfo (@{ $metadata }) {
+        my $filename = $ipprc->filename("PSASTRO.OUTPUT.MASK",$ipp_outroot,$chipInfo->{class_id});
+        my ($ipp_disk, $remote_disk) = &uri_to_outputs_for_return( $filename);
+        my $remote_outroot_dir = dirname($ipp_disk);
+        print CONFIG " && mkdir -p ${remote_root}/tmp/${remote_outroot_dir} && ln -sf $remote_disk ${remote_root}/tmp/${ipp_disk} && touch $remote_disk ";
     }
     print CONFIG "\n";
@@ -220,48 +190,14 @@
 close(GENERATE);
 
-#
-# Construct the moab command last, so we can use the job_index counter to estimate resources.  Somehow.
-my $proc_need = $job_index * $threads;       # how many total processors do we need?
-my $node_need = $proc_need / $proc_per_node; # this equals how many nodes?
-my $time_need = $job_index * $job_cost;      # How many seconds will this take?
-
-my $fill_factor = 0.8;  # This is the factor of how much of the time allocation we'd like to fill
-my ($time_req,$node_req);
-if ($node_need * $job_cost < $fill_factor * $min_nodes * $min_time) {
-    $time_req = $min_time;
-    $node_req = $min_nodes;
-}
-elsif ($node_need * $job_cost > $fill_factor * $max_nodes * $max_time) {
-    $time_req = $max_time;
-    $node_req = $max_nodes;
-    print STDERR "You've requested the construction of a bundle that appears to need $node_need nodes and $job_cost time per job.  This exceeds the max limits ($max_nodes, $max_time).  Using those max values instead.  Good luck.\n";
-}
-else {
-    $time_req = int(($node_need * $job_cost) / ($fill_factor * $max_nodes)) + 1;
-    $node_req = int(($node_need * $job_cost) / ($fill_factor * $time_req)) + 1;
-}
-$time_req += 1; # Safety addition.
-
-open(COMMAND,  ">$disk_command") || &my_die("Couldn't open file? $disk_command",$remote_id,$PS_EXIT_SYS_ERROR);
-print COMMAND "#!/bin/tcsh\n";
-print COMMAND "##### Moab controll lines\n";
-print COMMAND "#MSUB -l nodes=${node_req}:ppn=${proc_per_node},walltime=${time_req}:00:00\n"; ## CHECK RESOURCES
-print COMMAND "#MSUB -j oe\n";
-print COMMAND "#MSUB -V\n";
-print COMMAND "#MSUB -o ${remote_root}cam.${remote_id}.out\n";
-print COMMAND "date\n";
-print COMMAND 'srun -n $SLURM_JOB_NUM_NODES -m cyclic -l /bin/hostname | sort -n | awk \'{printf "%s\n", $2}\' > hosts.${SLURM_JOB_ID}' . "\n";
-print COMMAND "${remote_root}/stask_chip.py $remote_config " . 'hosts.${SLURM_JOB_ID} 1' . "\n";
-print COMMAND "date\n";
-close(COMMAND);
-
 unless($no_update) {
-    my $command = "remotetool -updaterun -remote_id $remote_id ";
-    $command .= " -set_state pending ";
-    $command .= " -dbname $dbname " if defined $dbname;
-
+    my $command = "remotetool -updatecomponent -remote_id $remote_id -stage_id $cam_id ";
+    $command   .= " -set_jobs $job_index";
+    $command   .= " -set_path_base $path_base";
+    $command   .= " -set_state prep_done";
+    $command   .= " -dbname $dbname " if defined $dbname;
     system($command);
 }
 
+exit (0);
 
 ## Common SC routines
@@ -271,7 +207,7 @@
     my $ipp_disk= $ipprc->file_resolve( $neb_uri );
     my $remote_disk = $ipp_disk;
-    
+
     unless(defined($ipp_disk)) {
-        my_die();
+        &my_die( "Unable to generate file for $neb_uri ", $remote_id, $cam_id, $PS_EXIT_SYS_ERROR, $fail_state);
     }
 
@@ -287,7 +223,7 @@
     my $ipp_disk= $ipprc->file_resolve( $neb_uri , 1);
     my $remote_disk = $ipp_disk;
-    
+
     unless(defined($ipp_disk)) {
-        my_die();
+        &my_die( "Unable to generate file for $neb_uri ", $remote_id, $cam_id, $PS_EXIT_SYS_ERROR, $fail_state);
     }
 
@@ -302,5 +238,5 @@
     my $neb_uri = shift;
     my ($ipp_disk, $remote_disk) = uri_convert( $neb_uri );
-    
+
     unless (exists($file_filter{$neb_uri})) {
         $file_filter{$neb_uri} = 1;
@@ -332,5 +268,5 @@
     return($remote_uri);
 }
- 
+
 sub uri_remote_to_local { #(local_neb_uri) = uri_remote_to_local(remote_uri);
     # This needs to replace the remote root directory with the nebulous tag.
@@ -338,5 +274,5 @@
     $remote_uri =~ s%${remote_root}%%;
     my $local_uri  = "neb:///" . $remote_uri;
-    
+
     return($local_uri);
 }
@@ -345,5 +281,6 @@
 sub my_die { # exit with status; my_die(message,stage_id,exit_code,exit_status);
     my $msg = shift;
-    my $id  = shift;
+    my $remote_id  = shift;
+    my $stage_id  = shift;
     my $exit_code = shift;
     my $exit_state = shift;
@@ -352,8 +289,7 @@
 
     carp($msg);
-    
-    if (defined $id and not $no_update) {
-        my $command = "remotetool -updaterun -remote_id $id";
-        $command .= " -fault $exit_code " if defined $exit_code;
+
+    if (defined $remote_id and defined $stage_id and not $no_update) {
+        my $command = "remotetool -updatecomponent -remote_id $remote_id -stage_id $stage_id";
         $command .= " -set_state $exit_state " if defined $exit_state;
         $command .= " -dbname $dbname " if defined $dbname;