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Don't check job_is_first_task, and allow qconf to fail.
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@brianwalenz
brianwalenz committed Jul 19, 2019
1 parent 48555da commit 56d8be4
Showing 1 changed file with 39 additions and 31 deletions.
70 changes: 39 additions & 31 deletions src/pipelines/canu/Grid_SGE.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -56,27 +56,28 @@ sub detectSGE () {


sub discoverThreadsOption () {
my @env = `qconf -spl`; chomp @env;
my @env = `qconf -spl 2> /dev/null`; chomp @env;
my @thr;
my $bestThr = undef;
my $bestSlots = 0;

my @peErrorList;

foreach my $env (@env) {
my $ns = 0;
my $ar = 0;
my $jf = 0;
my $ar = "unknown";

open(F, "qconf -sp $env |");
open(F, "qconf -sp $env 2> /dev/null |");
while (<F>) {
$ns = $1 if (m/slots\s+(\d+)/); # How many slots can we use?
$ar = 1 if (m/allocation_rule.*pe_slots/); # All slots need to be on a single node.
#$cs = 1 if (m/control_slaves.*FALSE/); # Doesn't apply to pe_slots.
$jf = 1 if (m/job_is_first_task.*TRUE/); # The fisrt task (slot) does actual work.
$ns = $1 if (m/slots\s+(\d+)/); # How many slots can we use?
$ar = $1 if (m/allocation_rule\s+(.*)/);
}
close(F);

next if ($ar == 0);
next if ($jf == 0);
if ($ar ne "\$pe_slots") {
push @peErrorList, "-- WARNING: Parallel Environment '$env' ignored; uses allocation_rule '$ar'\n";
next;
}

push @thr, $env;

Expand All @@ -86,31 +87,44 @@ sub discoverThreadsOption () {
}
}

if (scalar(@thr) == 1) {
if (scalar(@thr) == 0) {
print STDERR "--\n";

foreach my $err (@peErrorList) {
print STDERR $err;
}

print STDERR "--\n";
print STDERR "-- ERROR: No Sun Grid Engine Parallel Environment is using allocation rule '\$pe_threads'.\n";
print STDERR "-- ERROR: Multi-thread execution not supported on this grid.\n";
print STDERR "--\n";

caExit("can't configure for SGE", undef);
}

elsif (scalar(@thr) == 1) {
print STDERR "-- Detected Sun Grid Engine parallel environment '$thr[0]'.\n";
return($thr[0]);
}

if (scalar(@thr) > 1) {
else {
print STDERR "--\n";
print STDERR "-- WARNING: Couldn't determine the SGE parallel environment to run multi-threaded codes.\n";
print STDERR "-- WARNING: Multiple Sun Grid Engine Parallel Environments can run multi-threaded codes.\n";
print STDERR "-- WARNING: Valid choices are:\n";
print STDERR "-- WARNING: $_\n" foreach (@thr);
print STDERR "-- WARNING:\n";
print STDERR "-- WARNING: Using SGE parallel environment '$bestThr'.\n";
print STDERR "-- WARNING: Using Parallel Environment '$bestThr'.\n";
print STDERR "--\n";

return($bestThr);
}

return(undef);
}


sub discoverMemoryOption () {
my @mem;

open(F, "qconf -sc |");
open(F, "qconf -sc 2> /dev/null |");
while (<F>) {
my @vals = split '\s+', $_;

Expand Down Expand Up @@ -152,7 +166,7 @@ sub configureSGE () {
if (!defined($maxArraySize)) {
$maxArraySize = 65535;

open(F, "qconf -sconf |") or caExit("can't run 'qconf' to get SGE config", undef);
open(F, "qconf -sconf 2> /dev/null |") or caExit("can't run 'qconf' to get SGE config", undef);
while (<F>) {
if (m/max_aj_tasks\s+(\d+)/) {
$maxArraySize = $1;
Expand All @@ -179,8 +193,6 @@ sub configureSGE () {
# (it's the one with allocation_rule of $pe_slots),
# Try to figure out the name of the memory resource.

my $configError = 0;

if (!defined(getGlobal("gridEngineResourceOption"))) {
my $thr = discoverThreadsOption();
my $mem = discoverMemoryOption();
Expand All @@ -199,7 +211,7 @@ sub configureSGE () {
print STDERR "-- ERROR: substitute the correct values for THREADS and MEMORY.\n";
print STDERR "--\n";

caExit("can't configure for SGE", undef) if ($configError);
caExit("can't configure for SGE", undef);
}

setGlobal("gridEngineResourceOption", "-pe $thr THREADS -l $mem=MEMORY");
Expand All @@ -226,31 +238,27 @@ sub configureSGE () {
}

# Check that the threads and memory options look sane.
# In particular, check that the PE requested is using allocation_rule $pe_slots, and job_is_first_task.

{
my $opt = getGlobal("gridEngineResourceOption");
my $thr = $1 if ($opt =~ m/-pe\s+(.*)\s+THREADS/);
my $mem = $1 if ($opt =~ m/-l\s+(.*)=MEMORY/);

if (defined($thr)) {
my $ar = 0;
my $jf = 0;
my $ar = "\$pe_slots"; # Default to $pe_slots state for Mick's busted grid config.
my @lines;

open(F, "qconf -sp $thr 2> /dev/null |");
while (<F>) {
push @lines, $_;

$ar = 1 if (m/allocation_rule.*pe_slots/); # All slots need to be on a single node.
$jf = 1 if (m/job_is_first_task.*TRUE/); # The fisrt task (slot) does actual work.
$ar = $1 if (m/^allocation_rule\s+(.*)$/);
}
close(F);

if (($ar == 0) || ($jf == 0)) {
if ($ar ne "\$pe_slots") {
print STDERR "\n";
print STDERR "ERROR: Sun Grid Engine parallel environment '$thr' is using 'allocation_rule' other than '\$pe_slots'.\n" if ($ar == 0);
print STDERR "ERROR: Sun Grid Engine parallel environment '$thr' didn't set 'job_is_first_task'.\n" if ($jf == 0);
print STDERR "ERROR:\n";

if (scalar(@lines) == 0) {
Expand All @@ -268,7 +276,7 @@ sub configureSGE () {
# Set memory-per-job if configured and the user hasn't supplied a value.
# Otherwise, leave it in the default off state.
if (defined($mem) && !defined(getGlobal("gridEngineMemoryPerJob"))) {
open(F, "qconf -sc |");
open(F, "qconf -sc 2> /dev/null |");
while (<F>) {
my @vals = split '\s+', $_;

Expand All @@ -288,15 +296,15 @@ sub configureSGE () {
my %start_shell;

if (getGlobal('gridOptions') !~ m/-S/) {
open(Q, "qconf -sql |");
open(Q, "qconf -sql 2> /dev/null |");
while (<Q>) {
chomp;
my $q = $_;

$start_mode{$q} = "na";
$start_shell{$q} = "na";

open(F, "qconf -sq $q |");
open(F, "qconf -sq $q 2> /dev/null |");
while (<F>) {
$start_mode{$q} = $1 if (m/shell_start_mode\s+(\S+)/);
$start_shell{$q} = $1 if (m/shell\s+(\S+)/);
Expand Down

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