canu: Add job-limits feature for SLURM

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat May 26 09:15:11 2018 -0500
Changeset:	578a570d4a1b138a3d2902a891b78e111af890f2

Modified Files:
	canu/distinfo
	canu/patches/patch-pipelines_canu_Execution.pm
Added Files:
	canu/patches/patch-pipelines_canu_Defaults.pm

Log Message:
canu: Add job-limits feature for SLURM

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=578a570d4a1b138a3d2902a891b78e111af890f2

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 canu/distinfo                                  |  3 ++-
 canu/patches/patch-pipelines_canu_Defaults.pm  | 12 ++++++++++++
 canu/patches/patch-pipelines_canu_Execution.pm | 17 ++++++++++++-----
 3 files changed, 26 insertions(+), 6 deletions(-)

diffs:
diff --git a/canu/distinfo b/canu/distinfo
index 8bf866d7f9..0cc03f7fef 100644
--- a/canu/distinfo
+++ b/canu/distinfo
@@ -4,4 +4,5 @@ SHA1 (canu-1.7.tar.gz) = aaaafd8516be5e4d725af407bc84b3c6f178b2ac
 RMD160 (canu-1.7.tar.gz) = bd394bb6dcebd43d2793ca1aa9bd60ec6be75beb
 SHA512 (canu-1.7.tar.gz) = dbc1dca4df4117521143843bb781227f4dfde5ba7068e47b51ccf9e9dba45eb2629b5773531e4f362f1df05eab3f1a62088c5fa231d3624af23f11d97e7a4edf
 Size (canu-1.7.tar.gz) = 2533016 bytes
-SHA1 (patch-pipelines_canu_Execution.pm) = 4f9d343e03cc802b90616844cb331b78793bd368
+SHA1 (patch-pipelines_canu_Defaults.pm) = e6136febb18e50c90f4935248ee84c0d18199fb1
+SHA1 (patch-pipelines_canu_Execution.pm) = 265a8a9794a879bc80624921ecb6ebf6e4a40b53
diff --git a/canu/patches/patch-pipelines_canu_Defaults.pm b/canu/patches/patch-pipelines_canu_Defaults.pm
new file mode 100644
index 0000000000..aba13962c4
--- /dev/null
+++ b/canu/patches/patch-pipelines_canu_Defaults.pm
@@ -0,0 +1,12 @@
+--- pipelines/canu/Defaults.pm.orig	2018-02-27 13:46:07 UTC
++++ pipelines/canu/Defaults.pm
+@@ -637,6 +637,9 @@ sub setExecDefaults ($$) {
+     my $tag         = shift @_;
+     my $name        = shift @_;
+ 
++    $global{"slurmArrayConcurrentTasks"}  = undef;
++    $synops{"slurmArrayConcurrentTasks"}  = "Max tasks that can run at once";
++
+     $global{"gridOptions${tag}"}   = undef;
+     $synops{"gridOptions${tag}"}   = "Grid engine options applied to $name jobs";
+ 
diff --git a/canu/patches/patch-pipelines_canu_Execution.pm b/canu/patches/patch-pipelines_canu_Execution.pm
index c6859316fb..5b709d0eb8 100644
--- a/canu/patches/patch-pipelines_canu_Execution.pm
+++ b/canu/patches/patch-pipelines_canu_Execution.pm
@@ -1,9 +1,6 @@
-$NetBSD$
-
-# Eliminate assumptions about install dir name
---- pipelines/canu/Execution.pm.orig	2017-04-17 19:32:38.000000000 +0000
+--- pipelines/canu/Execution.pm.orig	2018-02-27 13:46:07 UTC
 +++ pipelines/canu/Execution.pm
-@@ -293,10 +293,6 @@ sub skipStage ($$@) {
+@@ -303,10 +303,6 @@ sub skipStage ($$@) {
  sub getInstallDirectory () {
      my $installDir = $FindBin::RealBin;
  
@@ -14,3 +11,13 @@ $NetBSD$
      return($installDir);
  }
  
+@@ -727,6 +723,9 @@ sub buildGridArray ($$$$) {
+ 
+     $opt =~ s/ARRAY_NAME/$name/g;        #  Replace ARRAY_NAME with 'job name'
+     $opt =~ s/ARRAY_JOBS/$bgn-$end/g;    #  Replace ARRAY_JOBS with 'bgn-end'
++    if ( defined(getGlobal("slurmArrayConcurrentTasks")) ) {
++        $opt = $opt . '%' . getGlobal("slurmArrayConcurrentTasks");
++    }
+ 
+     return($opt, $off);
+ }