mirror of
https://git.savannah.gnu.org/git/parallel.git
synced 2024-11-25 23:47:53 +00:00
Fixed: bug #36139: --load causes parallel not to finish
This commit is contained in:
Ole Tange
parent
27c776acb5
commit
f4f5fdd6c6
|
|
@ -181,9 +181,22 @@ for stable long-term use.
|
|||
|
||||
New in this release:
|
||||
|
||||
* Article: Computational and experimental analyses of
|
||||
retrotransposon-associated minisatellite DNAs in the soybean genome.
|
||||
http://www.biomedcentral.com/content/supplementary/1471-2105-13-s2-s13-s1.pdf
|
||||
|
||||
* Blog post: GNU parallel - the best thing since sliced bread.
|
||||
https://arrayal.wordpress.com/2012/03/27/gnu-parallel-the-best-thing-since-sliced-bread/
|
||||
|
||||
* Blog post: GNU Parallel makes everything faster.
|
||||
http://compbiously.blogspot.com/2012/03/gnu-parallel-makes-everything-faster.html
|
||||
|
||||
* Blog post (German): Howto: GNU parallel.
|
||||
http://d24m.de/2012/04/05/howto-gnu-parallel/
|
||||
|
||||
* Blog post: Running in Parallel
|
||||
http://interactivity.ifactory.com/2012/04/running-in-parallel/
|
||||
|
||||
* Bug fixes and man page updates.
|
||||
|
||||
|
||||
|
|
|
|||
93
src/parallel
93
src/parallel
|
|
@ -42,7 +42,6 @@ if(not $ENV{SHELL}) {
|
|||
$SIG{TERM} = sub {}; # Dummy until jobs really start
|
||||
open $Global::original_stderr, ">&STDERR" or ::die_bug("Can't dup STDERR: $!");
|
||||
|
||||
do_not_reap();
|
||||
parse_options();
|
||||
my $number_of_args;
|
||||
if($Global::max_number_of_args) {
|
||||
|
|
@ -159,10 +158,10 @@ start_more_jobs();
|
|||
if($::opt_pipe) {
|
||||
spreadstdin(@fhlist);
|
||||
}
|
||||
reap_if_needed();
|
||||
::debug("Start draining\n");
|
||||
drain_job_queue();
|
||||
::debug("Done draining\n");
|
||||
reaper();
|
||||
cleanup();
|
||||
if($Global::semaphore) {
|
||||
$sem->release();
|
||||
|
|
@ -225,7 +224,6 @@ sub spreadstdin {
|
|||
for my $in (@fhlist) {
|
||||
while(!$force_one_time_through++ or read($in,substr($buf,length $buf,0),$::opt_blocksize)) {
|
||||
# substr above = append to $buf
|
||||
reap_if_needed(); # Re-enable reaping after read() (Bug#33352)
|
||||
if($::opt_r) {
|
||||
# Remove empty lines
|
||||
$buf=~s/^\s*\n//gm;
|
||||
|
|
@ -267,12 +265,11 @@ sub spreadstdin {
|
|||
$i += length $recend; # find the actual splitting location
|
||||
my $record = $header.substr($buf,0,$i);
|
||||
substr($buf,0,$i) = "";
|
||||
::debug("Read record: ".length($record)."\n");
|
||||
# ::debug("Read record: ".length($record)."\n");
|
||||
write_record_to_pipe(\$record,$recstart,$recend);
|
||||
}
|
||||
}
|
||||
}
|
||||
do_not_reap(); # Disable reaping before read($in) (Bug#33352)
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -309,7 +306,6 @@ sub flush_and_close_pipes {
|
|||
do {
|
||||
$flush_done = 1;
|
||||
# Make sure everything is written to the jobs
|
||||
do_not_reap();
|
||||
for my $job (values %Global::running) {
|
||||
if($job->remaining()) {
|
||||
if($job->complete_write()) {
|
||||
|
|
@ -319,16 +315,12 @@ sub flush_and_close_pipes {
|
|||
$flush_done = 0;
|
||||
}
|
||||
}
|
||||
reap_if_needed();
|
||||
usleep($sleep);
|
||||
$sleep *= 1.1; # exponential back off
|
||||
$sleep = ::reap_usleep($sleep);
|
||||
} while (not $flush_done);
|
||||
do_not_reap();
|
||||
for my $job (values %Global::running) {
|
||||
my $fh = $job->stdin();
|
||||
close $fh;
|
||||
}
|
||||
reap_if_needed();
|
||||
}
|
||||
|
||||
sub write_record_to_pipe {
|
||||
|
|
@ -346,7 +338,6 @@ sub write_record_to_pipe {
|
|||
my $sleep = 0.00001; # 0.00001 ms - better performance on highend
|
||||
write_record: while(1) {
|
||||
# Sorting according to sequence is necessary for -k to work
|
||||
do_not_reap(); # If Global::running is changed the for loop has a race condition
|
||||
for my $job (sort { $a->seq() <=> $b->seq() } values %Global::running) {
|
||||
::debug("Looking at ",$job->seq(),"-",$job->remaining(),"-",$job->datawritten(),"\n");
|
||||
if($job->remaining()) {
|
||||
|
|
@ -371,13 +362,10 @@ sub write_record_to_pipe {
|
|||
}
|
||||
}
|
||||
}
|
||||
# Force reaping as sigchild is sometimes forgotten;
|
||||
if(not reaper()) {
|
||||
usleep($sleep);
|
||||
$sleep = ($sleep < 1000) ? ($sleep * 1.1) : ($sleep); # exponential back off
|
||||
}
|
||||
}
|
||||
reap_if_needed();
|
||||
# Maybe this should be in an if statement: if sleep > 0.001: start more
|
||||
start_more_jobs(); # These jobs may not be started because of loadavg
|
||||
$sleep = ::reap_usleep($sleep);
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
|
|
@ -1166,7 +1154,7 @@ sub start_another_job {
|
|||
debug("Command to run on '".$job->sshlogin()."': '".$job->replaced()."'\n");
|
||||
if($job->start()) {
|
||||
$Global::running{$job->pid()} = $job;
|
||||
debug("Started as seq ".$job->seq(),"\n");
|
||||
debug("Started as seq ",$job->seq()," pid:",$job->pid(),"\n");
|
||||
return 1;
|
||||
} else {
|
||||
# If interactive says: Dont run the job, then skip it and run the next
|
||||
|
|
@ -1184,9 +1172,7 @@ sub drain_job_queue {
|
|||
# Returns: N/A
|
||||
$Private::first_completed ||= time;
|
||||
if($::opt_progress) {
|
||||
do_not_reap();
|
||||
print $Global::original_stderr init_progress();
|
||||
reap_if_needed();
|
||||
}
|
||||
my $last_header="";
|
||||
my $sleep = 0.2;
|
||||
|
|
@ -1195,9 +1181,6 @@ sub drain_job_queue {
|
|||
debug("jobs running: ", $Global::total_running, "==", scalar
|
||||
keys %Global::running," slots: ", $Global::max_jobs_running,
|
||||
" Memory usage:".my_memory_usage()." ");
|
||||
$sleep = ($sleep < 1000) ? ($sleep * 1.1) : ($sleep);
|
||||
usleep($sleep);
|
||||
do_not_reap();
|
||||
if($::opt_pipe) {
|
||||
# When using --pipe sometimes file handles are not closed properly
|
||||
for my $job (values %Global::running) {
|
||||
|
|
@ -1214,16 +1197,11 @@ sub drain_job_queue {
|
|||
print $Global::original_stderr "\r",$progress{'status'};
|
||||
}
|
||||
# Sometimes SIGCHLD is not registered, so force reaper
|
||||
if(reaper()) {
|
||||
# Child finished this time around: Reset sleep time
|
||||
$sleep = 0.2;
|
||||
}
|
||||
reap_if_needed();
|
||||
$sleep = ::reap_usleep($sleep);
|
||||
}
|
||||
if(not $Global::JobQueue->empty()) {
|
||||
start_more_jobs(); # These jobs may not be started because of loadavg
|
||||
$sleep = ($sleep < 1000) ? ($sleep * 1.1) : ($sleep);
|
||||
usleep($sleep);
|
||||
$sleep = ::reap_usleep($sleep);
|
||||
}
|
||||
} while ($Global::total_running > 0
|
||||
or
|
||||
|
|
@ -1633,47 +1611,22 @@ sub start_no_new_jobs {
|
|||
$Global::start_no_new_jobs++;
|
||||
}
|
||||
|
||||
sub count_sig_child {
|
||||
# Returns: N/A
|
||||
$Global::sig_child_caught++;
|
||||
}
|
||||
|
||||
sub do_not_reap {
|
||||
# This will postpone SIGCHILD for sections that cannot be distracted by a dying child
|
||||
# (Racecondition)
|
||||
# Returns: N/A
|
||||
$SIG{CHLD} = \&count_sig_child;
|
||||
}
|
||||
|
||||
sub reap_if_needed {
|
||||
# Do the postponed SIGCHILDs if any and re-install normal reaper for SIGCHILD
|
||||
# (Racecondition)
|
||||
# Returns: N/A
|
||||
if($Global::sig_child_caught) {
|
||||
$Global::sig_child_caught = 0;
|
||||
reaper();
|
||||
}
|
||||
$SIG{CHLD} = \&reaper;
|
||||
}
|
||||
|
||||
sub reaper {
|
||||
# A job finished.
|
||||
# Print the output.
|
||||
# Start another job
|
||||
# Returns: N/A
|
||||
do_not_reap();
|
||||
$Private::reaperlevel++;
|
||||
my $stiff;
|
||||
my $children_reaped = 0;
|
||||
debug("Reaper called $Private::reaperlevel ");
|
||||
debug("Reaper called ");
|
||||
while (($stiff = waitpid(-1, &WNOHANG)) > 0) {
|
||||
$children_reaped++;
|
||||
if($Global::sshmaster{$stiff}) {
|
||||
# This is one of the ssh -M: ignore
|
||||
next;
|
||||
}
|
||||
# Ignore processes that we did not start
|
||||
my $job = $Global::running{$stiff};
|
||||
# '-a <(seq 10)' will give us a pid not in %Global::running
|
||||
$job or next;
|
||||
$job->set_exitstatus($? >> 8);
|
||||
$job->set_exitsignal($? & 127);
|
||||
|
|
@ -1732,9 +1685,7 @@ sub reaper {
|
|||
delete $Global::running{$stiff};
|
||||
start_more_jobs();
|
||||
}
|
||||
reap_if_needed();
|
||||
debug("Reaper exit $Private::reaperlevel\n");
|
||||
$Private::reaperlevel--;
|
||||
debug("Reaper exit\n");
|
||||
return $children_reaped;
|
||||
}
|
||||
|
||||
|
|
@ -1931,6 +1882,21 @@ sub hostname {
|
|||
return $Private::hostname;
|
||||
}
|
||||
|
||||
sub reap_usleep {
|
||||
# Reap dead children.
|
||||
# If no children: Sleep specified amount with exponential backoff
|
||||
# Returns:
|
||||
# 0.00001 if children reaped (0.00001 ms works best on highend)
|
||||
# $ms*1.1 if no children reaped
|
||||
my $ms = shift;
|
||||
if(reaper()) {
|
||||
return 0.00001;
|
||||
} else {
|
||||
usleep($ms);
|
||||
return (($ms < 1000) ? ($ms * 1.1) : ($ms)); # exponential back off
|
||||
}
|
||||
}
|
||||
|
||||
sub usleep {
|
||||
# Sleep this many milliseconds.
|
||||
my $secs = shift;
|
||||
|
|
@ -2244,7 +2210,7 @@ sub loadavg {
|
|||
$update_loadavg_file = 1;
|
||||
}
|
||||
if($update_loadavg_file) {
|
||||
::debug("Updating loadavg file".$self->{'loadavg_file'});
|
||||
::debug("Updating loadavg file".$self->{'loadavg_file'}."\n");
|
||||
$self->{'last_loadavg_update'} = time;
|
||||
-e $ENV{'HOME'}."/.parallel" or mkdir $ENV{'HOME'}."/.parallel";
|
||||
-e $ENV{'HOME'}."/.parallel/tmp" or mkdir $ENV{'HOME'}."/.parallel/tmp";
|
||||
|
|
@ -2372,7 +2338,6 @@ sub processes_available_by_system_limit {
|
|||
my $time = time;
|
||||
my %fh;
|
||||
my @children;
|
||||
::do_not_reap();
|
||||
|
||||
# Reserve filehandles
|
||||
# perl uses 7 filehandles for something?
|
||||
|
|
|
|||
|
|
@ -1,15 +1,13 @@
|
|||
#!/bin/bash
|
||||
|
||||
echo '### Test --joblog with exitval'
|
||||
parallel --joblog /tmp/parallel_test_joblog 'sleep {} && echo foo' ::: 100 2>/dev/null &
|
||||
sleep 1
|
||||
echo '### Test --joblog with exitval and Test --joblog with signal'
|
||||
parallel --joblog /tmp/parallel_joblog_exitval 'sleep {} && echo foo' ::: 100 2>/dev/null &
|
||||
parallel --joblog /tmp/parallel_joblog_signal 'sleep {}' ::: 100 2>/dev/null &
|
||||
sleep 0.5
|
||||
killall -6 sleep
|
||||
grep -q 134 /tmp/parallel_test_joblog && echo OK
|
||||
sleep 0.1
|
||||
grep -q 134 /tmp/parallel_joblog_exitval && echo exitval OK
|
||||
grep -q '[^0-9]6[^0-9]' /tmp/parallel_joblog_signal && echo signal OK
|
||||
|
||||
echo '### Test --joblog with signal'
|
||||
parallel --joblog /tmp/parallel_test_joblog 'sleep {}' ::: 100 2>/dev/null &
|
||||
sleep 1
|
||||
killall -6 sleep
|
||||
grep -q '[^0-9]6[^0-9]' /tmp/parallel_test_joblog && echo OK
|
||||
rm /tmp/parallel_joblog_exitval /tmp/parallel_joblog_signal
|
||||
|
||||
rm /tmp/parallel_test_joblog
|
||||
|
|
|
|||
20
testsuite/tests-to-run/test66.sh
Normal file
20
testsuite/tests-to-run/test66.sh
Normal file
|
|
@ -0,0 +1,20 @@
|
|||
#!/bin/bash
|
||||
|
||||
echo "### Test : as delimiter. This can be confusing for uptime ie. --load";
|
||||
parallel -k --load 100% -d : echo ::: a:b:c
|
||||
|
||||
export PARALLEL="--load 100%"
|
||||
echo PARALLEL=$PARALLEL
|
||||
|
||||
for i in $(seq 2 10); do
|
||||
i2=$[i*i]
|
||||
seq $i2 | parallel -j0 --load 100% -kX echo {} |wc
|
||||
seq 1 ${i2}0000 | nice parallel -kj20 --recend "\n" --spreadstdin gzip -9 | zcat | sort -n | md5sum
|
||||
done
|
||||
|
||||
echo "### Test if --load blocks. Bug.";
|
||||
seq 1 1000 | parallel -kj2 --load 100% --recend "\n" --spreadstdin gzip -9 | zcat | sort -n | md5sum
|
||||
seq 1 1000 | parallel -kj0 --load 100% --recend "\n" --spreadstdin gzip -9 | zcat | sort -n | md5sum
|
||||
|
||||
seq 1 1000000 | parallel -kj0 --recend "\n" --spreadstdin gzip -9 | zcat | sort -n | md5sum
|
||||
seq 1 1000000 | nice parallel -kj20 --recend "\n" --spreadstdin gzip -9 | zcat | sort -n | md5sum
|
||||
|
|
@ -1,4 +1,3 @@
|
|||
### Test --joblog with exitval
|
||||
OK
|
||||
### Test --joblog with signal
|
||||
OK
|
||||
### Test --joblog with exitval and Test --joblog with signal
|
||||
exitval OK
|
||||
signal OK
|
||||
|
|
|
|||
28
testsuite/wanted-results/test66
Normal file
28
testsuite/wanted-results/test66
Normal file
|
|
@ -0,0 +1,28 @@
|
|||
### Test : as delimiter. This can be confusing for uptime ie. --load
|
||||
a
|
||||
b
|
||||
c
|
||||
PARALLEL=--load 100%
|
||||
4 4 8
|
||||
1c0f34fee7176dc367bead8f96cba6bc -
|
||||
9 9 18
|
||||
fa364205fcf6665c6f3e6cb868f65fd6 -
|
||||
16 16 39
|
||||
6f5db0373227d2281dc26b1bf63b4027 -
|
||||
25 25 66
|
||||
17e914b4a407dccd370c13173865deb1 -
|
||||
36 36 99
|
||||
5ee21398ecde0f3ea9b6093fbaf5a3c2 -
|
||||
49 49 138
|
||||
2af8be7306df18164a68e30e427217e0 -
|
||||
64 64 183
|
||||
f78c5b3d13146c60c9b586f51d05a4ae -
|
||||
81 81 234
|
||||
c88e1757ddc619efd9ee507a7702b53c -
|
||||
100 100 292
|
||||
8a7095c1c23bfadc311fe6b16d950582 -
|
||||
### Test if --load blocks. Bug.
|
||||
53d025127ae99ab79e8502aae2d9bea6 -
|
||||
53d025127ae99ab79e8502aae2d9bea6 -
|
||||
8a7095c1c23bfadc311fe6b16d950582 -
|
||||
8a7095c1c23bfadc311fe6b16d950582 -
|
||||
Loading…
Reference in a new issue