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parallel: Allow for empty loadavg file. This can happen on NFS.
Passes testsuite.
This commit is contained in:
Ole Tange
parent
fc6ad919d3
commit
0b8e949cbb
2
README
2
README
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@ -30,7 +30,7 @@ For security reasons it is recommended you use your package manager to
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install. But if you cannot do that then you can use this 10 seconds
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installation.
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The 10 seconds installation will try do to a full installation; if
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The 10 seconds installation will try to do a full installation; if
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that fails, a personal installation; if that fails, a minimal
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installation.
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@ -220,8 +220,14 @@ New in this release:
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* GNU Parallel was cited in:
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* GNU Parallel was cited in: Parallel Execution of Structural Mechanic Tasks with Use of Small Supercomputers http://www.sciencedirect.com/science/article/pii/S1877705817324815
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https://support.ehelp.edu.au/support/solutions/articles/6000089713-tips-for-running-jobs-on-your-vm#parallel
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https://pzelasko.github.io/posts/speed-up-ml-model-development-with-gnu-parallel
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http://tdhopper.com/blog/2017/Jun/07/parallelizing-a-python-function-for-the-extremely-lazy/
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<<Citation not OK: BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing https://www.nature.com/articles/s41598-017-01703-6>>
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<<Wrong citation https://iris.sissa.it/retrieve/handle/20.500.11767/36149/10823/And%C3%B2_tesi.pdf>>
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32
src/parallel
32
src/parallel
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@ -5279,6 +5279,7 @@ sub loadavg_too_high {
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awk '{print $2,$1}' };
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$dummy="echo S COMMAND;echo R dummy";
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%ps=(
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# TODO Find better code for AIX
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'aix' => "uptime",
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'cygwin' => $cygwin,
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'darwin' => $bsd,
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@ -5327,19 +5328,24 @@ sub loadavg {
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local $/; # $/ = undef => slurp whole file
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my $load_out = <$load_fh>;
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close $load_fh;
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# Count lines starting with D,O,R but command does not start with [
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my $load =()= ($load_out=~/(^\s?[DOR]\S* +(?=[^\[])\S)/gm);
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if($load > 0) {
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# load is overestimated by 1
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$self->{'loadavg'} = $load - 1;
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::debug("load", "New loadavg: ", $self->{'loadavg'},"\n");
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} elsif ($load_out=~/average: (\d+.\d+)/) {
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# AIX does not support instant load average
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# 04:11AM up 21 days, 12:55, 1 user, load average: 1.85, 1.57, 1.55
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$self->{'loadavg'} = $1;
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} else {
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::die_bug("loadavg_invalid_content: " .
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$self->{'loadavg_file'} . "\n$load_out");
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if($load_out =~ /\S/) {
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# Content can be empty if ~/ is on NFS
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# due to reading being non-atomic.
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#
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# Count lines starting with D,O,R but command does not start with [
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my $load =()= ($load_out=~/(^\s?[DOR]\S* +(?=[^\[])\S)/gm);
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if($load > 0) {
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# load is overestimated by 1
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$self->{'loadavg'} = $load - 1;
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::debug("load", "New loadavg: ", $self->{'loadavg'},"\n");
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} elsif ($load_out=~/average: (\d+.\d+)/) {
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# AIX does not support instant load average
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# 04:11AM up 21 days, 12:55, 1 user, load average: 1.85, 1.57, 1.55
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$self->{'loadavg'} = $1;
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} else {
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::die_bug("loadavg_invalid_content: " .
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$self->{'loadavg_file'} . "\n$load_out");
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}
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}
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$update_loadavg_file = 1;
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} else {
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@ -1933,21 +1933,21 @@ inputsource.
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Like this:
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#!/usr/bin/parallel --shebang -r traceroute
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#!/usr/bin/parallel --shebang -r wget
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qubes-os.org
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debian.org
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freenetproject.org
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https://ftpmirror.gnu.org/parallel/parallel-20120822.tar.bz2
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https://ftpmirror.gnu.org/parallel/parallel-20130822.tar.bz2
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https://ftpmirror.gnu.org/parallel/parallel-20140822.tar.bz2
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B<--shebang> must be set as the first option.
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On FreeBSD B<env> is needed:
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#!/usr/bin/env -S parallel --shebang -r traceroute
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#!/usr/bin/env -S parallel --shebang -r wget
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qubes-os.org
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debian.org
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freenetproject.org
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https://ftpmirror.gnu.org/parallel/parallel-20120822.tar.bz2
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https://ftpmirror.gnu.org/parallel/parallel-20130822.tar.bz2
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https://ftpmirror.gnu.org/parallel/parallel-20140822.tar.bz2
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There are many limitations of shebang (#!) depending on your operating
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system. See details on http://www.in-ulm.de/~mascheck/various/shebang/
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@ -2406,7 +2406,7 @@ care about the output. Compare these:
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'sleep {};echo -n start{};sleep {};echo {}end'
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It also disables B<--tag>. GNU B<parallel> outputs faster with
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B<-u>. Compare the speed of these:
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B<-u>. Compare the speeds of these:
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parallel seq ::: 300000000 >/dev/null
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parallel -u seq ::: 300000000 >/dev/null
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@ -3106,11 +3106,12 @@ printed as soon as possible you can use B<-u>.
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Compare the output of:
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parallel traceroute ::: qubes-os.org debian.org freenetproject.org
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parallel --line-buffer traceroute ::: \
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qubes-os.org debian.org freenetproject.org
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parallel -u traceroute ::: qubes-os.org debian.org freenetproject.org
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parallel wget --limit-rate=100k \
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https://ftpmirror.gnu.org/parallel/parallel-20{}0822.tar.bz2 ::: {12..16}
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parallel --line-buffer wget --limit-rate=100k \
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https://ftpmirror.gnu.org/parallel/parallel-20{}0822.tar.bz2 ::: {12..16}
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parallel -u wget --limit-rate=100k \
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https://ftpmirror.gnu.org/parallel/parallel-20{}0822.tar.bz2 ::: {12..16}
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=head1 EXAMPLE: Tag output lines
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@ -3118,13 +3119,15 @@ GNU B<parallel> groups the output lines, but it can be hard to see
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where the different jobs begin. B<--tag> prepends the argument to make
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that more visible:
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parallel --tag traceroute ::: \
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qubes-os.org debian.org freenetproject.org
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parallel --tag wget --limit-rate=100k \
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https://ftpmirror.gnu.org/parallel/parallel-20{}0822.tar.bz2 \
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::: {12..16}
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B<--tag> works with B<--line-buffer> but not with B<-u>:
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parallel --tag --line-buffer traceroute \
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::: qubes-os.org debian.org freenetproject.org
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parallel --tag --line-buffer wget --limit-rate=100k \
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https://ftpmirror.gnu.org/parallel/parallel-20{}0822.tar.bz2 \
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::: {12..16}
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Check the uptime of the servers in I<~/.parallel/sshloginfile>:
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@ -14,7 +14,8 @@ seq 1 3 | parallel -k --interactive "sleep 0.1; echo opt--interactive"
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_EOF
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chmod 755 /tmp/parallel-script-for-expect
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expect -b - <<_EOF
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(
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expect -b - <<_EOF
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spawn /tmp/parallel-script-for-expect
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expect "echo opt-p 1"
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send "y\n"
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@ -32,8 +33,10 @@ expect "opt--interactive 1"
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expect "echo opt--interactive 3"
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send "y\n"
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expect "opt--interactive 3"
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send "\n"
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_EOF
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echo
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echo
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) | perl -ne '/\S/ and print'
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}
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par_k() {
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@ -44,16 +47,6 @@ par_k() {
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echo "echo end") | stdout parallel -k -j0
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}
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par_sigterm() {
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echo '### Test SIGTERM'
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parallel -k -j5 sleep 10';' echo ::: {1..99} >/tmp/parallel$$ 2>&1 &
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A=$!
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sleep 19; kill -TERM $A
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wait
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sort /tmp/parallel$$
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rm /tmp/parallel$$
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}
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par_pipepart_spawn() {
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echo '### bug #46214: Using --pipepart doesnt spawn multiple jobs in version 20150922'
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seq 1000000 > /tmp/num1000000;
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@ -316,7 +309,7 @@ par_plus_dyn_repl() {
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par_slow_total_jobs() {
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echo 'bug #51006: Slow total_jobs() eats job'
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(echo a; sleep 6; echo b; sleep 6; seq 2) |
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(echo a; sleep 7; echo b; sleep 7; seq 2) |
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parallel -k echo '{=total_jobs()=}'
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}
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@ -4,6 +4,16 @@
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# Each should be taking 30-100s and be possible to run in parallel
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# I.e.: No race conditions, no logins
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par_sigterm() {
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echo '### Test SIGTERM'
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parallel -k -j5 sleep 15';' echo ::: {1..99} >/tmp/parallel$$ 2>&1 &
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A=$!
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sleep 29; kill -TERM $A
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wait
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sort /tmp/parallel$$
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rm /tmp/parallel$$
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}
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par_race_condition1() {
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echo '### Test race condition on 8 CPU (my laptop)'
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seq 1 5000000 > /tmp/parallel_race_cond
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@ -268,8 +268,7 @@ par_interactive sleep 0.1; echo opt--interactive 1 ?...y
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par_interactive sleep 0.1; echo opt--interactive 2 ?...n
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par_interactive sleep 0.1; echo opt--interactive 3 ?...y
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par_interactive opt--interactive 1
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par_interactive opt--interactive 3
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par_interactive
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par_interactive opt--interactive 3
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par_k ### Test -k
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par_k parallel: Warning: Only enough file handles to run 9 jobs in parallel.
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par_k parallel: Warning: Running 'parallel -j0 -N 9 --pipe parallel -j0' or
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@ -914,24 +913,6 @@ par_results_csv 9,:,999.999,999.999,0,6,0,0,"echo 23 12",23,12,"23 12
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par_results_csv ",
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par_round_robin_blocks bug #49664: --round-robin does not complete
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par_round_robin_blocks 8
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par_sigterm ### Test SIGTERM
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par_sigterm 1
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par_sigterm 10
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par_sigterm 2
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par_sigterm 3
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par_sigterm 4
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par_sigterm 5
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par_sigterm 6
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par_sigterm 7
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par_sigterm 8
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par_sigterm 9
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par_sigterm parallel: SIGTERM received. No new jobs will be started.
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par_sigterm parallel: Waiting for these 5 jobs to finish. Send SIGTERM again to stop now.
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par_sigterm parallel: sleep 10; echo 10
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par_sigterm parallel: sleep 10; echo 6
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par_sigterm parallel: sleep 10; echo 7
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par_sigterm parallel: sleep 10; echo 8
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par_sigterm parallel: sleep 10; echo 9
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par_slow_total_jobs bug #51006: Slow total_jobs() eats job
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par_slow_total_jobs parallel: Warning: Reading 2 arguments took longer than 10 seconds.
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par_slow_total_jobs a
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@ -20,6 +20,24 @@ par_race_condition1 7
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par_race_condition1 8
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par_race_condition1 9
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par_race_condition1 10
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par_sigterm ### Test SIGTERM
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par_sigterm 1
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par_sigterm 10
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par_sigterm 2
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par_sigterm 3
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par_sigterm 4
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par_sigterm 5
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par_sigterm 6
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par_sigterm 7
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par_sigterm 8
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par_sigterm 9
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par_sigterm parallel: SIGTERM received. No new jobs will be started.
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par_sigterm parallel: Waiting for these 5 jobs to finish. Send SIGTERM again to stop now.
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par_sigterm parallel: sleep 15; echo 10
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par_sigterm parallel: sleep 15; echo 6
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par_sigterm parallel: sleep 15; echo 7
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par_sigterm parallel: sleep 15; echo 8
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par_sigterm parallel: sleep 15; echo 9
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par_tmp_full ### Test --tmpdir running full. bug #40733 was caused by this
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par_tmp_full parallel: Error: Output is incomplete. Cannot append to buffer file in /tmp/shm/parallel. Is the disk full?
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par_tmp_full parallel: Error: Change $TMPDIR with --tmpdir or use --compress.
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@ -42,6 +42,7 @@ hpux.polarhome.com Error in tempfile() using /XXXXXXXX.arg: Could not create tem
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hpux.polarhome.com OK
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copy_and_test qnx.polarhome.com
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qnx.polarhome.com ### Run the test on qnx.polarhome.com
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qnx.polarhome.com parallel: Warning: Cannot figure out number of CPU cores. Using 1.
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copy_and_test debian-ppc.polarhome.com
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debian-ppc.polarhome.com ### Run the test on debian-ppc.polarhome.com
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debian-ppc.polarhome.com Works on debian-ppc.polarhome.com
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@ -166,6 +167,7 @@ netbsd.polarhome.com
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openbsd.polarhome.com
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openindiana
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pidora
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qnx
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raspbian
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redhat.polarhome.com
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scosysv.polarhome.com
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@ -195,6 +197,7 @@ netbsd.polarhome.com Missing name for redirect.
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openbsd.polarhome.com bash only A
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openindiana.polarhome.com bash only A
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pidora.polarhome.com bash only A
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qnx.polarhome.com /bin/sh: syntax error: `(' unexpected
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raspbian.polarhome.com bash only A
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redhat.polarhome.com bash only A
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scosysv.polarhome.com bash only A
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