Qstat & QA submission updates.

Author: olsonanl

service-scripts/p3x-qstat.pl

@@ -46,7 +46,9 @@ =head1 DESCRIPTION
 				    ["compute-node|N=s\@" => "Limit results to the given compute node", { default => [] }],
 				    ["slurm" => "Interpret job IDs as Slurm job IDs"],
 				    ["count" => "Print a count of matching records only"],
+				    ["sort-by-ram" => "Sort by memory used"],
 				    ["n-jobs|n=i" => "Limit to the given number of jobs", { default => 50 } ],
+				    ["show-inactive-jobs" => "Include inactive cluster jobs"],
 				    ["parsable" => "Generate tab-delimited output"],
 				    ["no-header" => "Skip printing header"],
 				    ["help|h" => "Show this help message."],
@@ -58,7 +60,7 @@ =head1 DESCRIPTION
 my $dbh = DBI->connect("dbi:mysql:" . sched_db_name . ";host=" . sched_db_host . ";port=$port",
 		       sched_db_user, sched_db_pass);
 $dbh or die "Cannot connect to database: " . $DBI::errstr;
-$dbh->do(qq(SET time_zone = "+00:00"));
+# $dbh->do(qq(SET time_zone = "+00:00"));
 
 
 #
@@ -132,6 +134,10 @@ =head1 DESCRIPTION
 }
 
 my @sort = ('t.submit_time DESC');
+if ($opt->sort_by_ram)
+{
+    unshift(@sort, 'cj.maxrss DESC');
+}
 my $sort = join(", ", @sort);
 
 my @ids;
@@ -195,7 +201,10 @@ =head1 DESCRIPTION
     push(@conds, "$field IN ($vals)");
 }
 
-push(@conds, "te.active = 1 or te.active IS NULL");
+if (!$opt->show_inactive_jobs)
+{
+    push(@conds, "te.active = 1 or te.active IS NULL");
+}
 
 my $cond = join(" AND ", map { "($_)" } @conds);
 
@@ -231,7 +240,7 @@ =head1 DESCRIPTION
 	     IF(finish_time != DEFAULT(finish_time) AND start_time != DEFAULT(start_time), timediff(finish_time, start_time), '') as elap,
 	     t.output_path, t.output_file, t.params,
 	     t.req_memory, t.req_cpu, t.req_runtime, t.user_metadata,
-	     cj.job_id, cj.job_status, cj.maxrss, cj.cluster_id, cj.nodelist
+	     cj.job_id, cj.job_status, cj.maxrss, cj.cluster_id, cj.nodelist, te.active
 	     $full_condition
 	     ORDER BY $sort
 	     $limit
@@ -283,6 +292,11 @@ =head1 DESCRIPTION
     push(@cols, { title => "User metadata" });
 }
 
+if ($opt->show_inactive_jobs)
+{
+    push(@cols, { title => "Cjob active" });
+}
+
 push(@cols, map { { title => $_ } } @{$opt->show_parameter});
 push(@cols, map { { title => $_ } } @{$opt->show_count});
 
@@ -374,6 +388,7 @@ =head1 DESCRIPTION
     push(@row, $task->{output_file}) if $opt->show_output_file;
     push(@row, $task->{output_path}) if $opt->show_output_path;
     push(@row, $task->{user_metadata}) if $opt->show_user_metadata;
+    push(@row, $task->{active}) if $opt->show_inactive_jobs;
 
     for my $p (@{$opt->show_parameter})
     {

service-scripts/p3x-run-qa.pl

@@ -290,7 +290,18 @@ sub submit_job
     push(@cmd, '--reservation', $opt->reservation) if $opt->reservation;
     push(@cmd, '--constraint', $opt->constraint) if $opt->constraint;
     push(@cmd, "--user-metadata", $opt->user_metadata) if $opt->user_metadata;
-    push(@cmd, "--preflight", $_) foreach @{$opt->preflight};
+
+    #
+    # Hack
+    #
+    my @preflight = @{$opt->preflight};
+    
+    if ($app eq 'MetagenomeBinning')
+    {
+	@preflight = ("memory=48000", "runtime=21600");
+    }
+    
+    push(@cmd, "--preflight", $_) foreach @preflight;
     push(@cmd, $app, $params);
 
     my $out;