."&& MEMLIMIT=\$(( (\$MEM * 95) / ($ENV{CRUNCH_NODE_SLOTS} * 100) )) "
."&& let SWAPLIMIT=\$MEMLIMIT+\$SWAP "
.q{&& declare -a VOLUMES=() }
- .q{&& if which crunchrunner >/dev/null ; then VOLUMES+=("--volume=$(which crunchrunner):/usr/local/bin/crunchrunner") ; fi }
- .q{&& if test -f /etc/ssl/certs/ca-certificates.crt ; then VOLUMES+=("--volume=/etc/ssl/certs/ca-certificates.crt:/etc/arvados/ca-certificates.crt") ; }
- .q{elif test -f /etc/pki/tls/certs/ca-bundle.crt ; then VOLUMES+=("--volume=/etc/pki/tls/certs/ca-bundle.crt:/etc/arvados/ca-certificates.crt") ; fi };
+ .q{&& if which crunchrunner >/dev/null ; then VOLUMES+=("--volume=$(which crunchrunner):/usr/local/bin/crunchrunner:ro") ; fi }
+ .q{&& if test -f /etc/ssl/certs/ca-certificates.crt ; then VOLUMES+=("--volume=/etc/ssl/certs/ca-certificates.crt:/etc/arvados/ca-certificates.crt:ro") ; }
+ .q{elif test -f /etc/pki/tls/certs/ca-bundle.crt ; then VOLUMES+=("--volume=/etc/pki/tls/certs/ca-bundle.crt:/etc/arvados/ca-certificates.crt:ro") ; fi };
$command .= "&& exec arv-mount --read-write --mount-by-pdh=by_pdh --mount-tmp=tmp --crunchstat-interval=10 --allow-other $arv_file_cache \Q$keep_mnt\E --exec ";
$ENV{TASK_KEEPMOUNT} = "$keep_mnt/by_pdh";
my $line = $1;
substr $jobstep[$jobstepidx]->{stderr}, 0, 1+length($line), "";
Log ($jobstepidx, "stderr $line");
- if ($line =~ /srun: error: (SLURM job $ENV{SLURM_JOB_ID} has expired|Unable to confirm allocation for job $ENV{SLURM_JOB_ID})/) {
- # whoa.
+ if ($line =~ /srun: error: (SLURM job $ENV{SLURM_JOB_ID} has expired|Unable to confirm allocation for job $ENV{SLURM_JOB_ID})/i) {
+ # If the allocation is revoked, we can't possibly continue, so mark all
+ # nodes as failed. This will cause the overall exit code to be
+ # EX_RETRY_UNLOCKED instead of failure so that crunch_dispatch can re-run
+ # this job.
$main::please_freeze = 1;
+ foreach my $st (@slot) {
+ $st->{node}->{fail_count}++;
+ }
}
- elsif ($line =~ /srun: error: (Node failure on|Aborting, .*\bio error\b)/) {
+ elsif ($line =~ /srun: error: .*?\b(Node failure on|Aborting, .*?\bio error\b)/i) {
$jobstep[$jobstepidx]->{tempfail} = 1;
if (defined($job_slot_index)) {
$slot[$job_slot_index]->{node}->{fail_count}++;
ban_node_by_slot($job_slot_index);
}
}
- elsif ($line =~ /srun: error: (Unable to create job step|.*: Communication connection failure)/) {
+ elsif ($line =~ /srun: error: (Unable to create job step|.*?: Communication connection failure)/i) {
$jobstep[$jobstepidx]->{tempfail} = 1;
ban_node_by_slot($job_slot_index) if (defined($job_slot_index));
}
close($log_pipe_in);
my $logger_failed = 0;
- my $read_result = log_writer_read_output(120);
+ my $read_result = log_writer_read_output(600);
if ($read_result == -1) {
$logger_failed = -1;
Log (undef, "timed out reading from 'arv-put'");
}
}
}
- if (defined($filename) and ($filename =~ /^([0-9A-Fa-f]{64})\.tar$/)) {
+ if (defined($filename) and ($filename =~ /^((?:sha256:)?[0-9A-Fa-f]{64})\.tar$/)) {
return ($streamname, $1);
} else {
return (undef, undef);