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parcat: Small fixup.

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testsuite: Fixups for --line-buffer/--files.
This commit is contained in:
Ole Tange 2016-09-23 00:57:30 +02:00
parent a4ddcbf8bc
commit 74e35933f4
11 changed files with 173 additions and 38 deletions
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27
doc/release_new_version
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@ -219,18 +219,15 @@ cc:Tim Cuthbertson <tim3d.junk@gmail.com>,
Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
Jesse Alama <jesse.alama@gmail.com>
Subject: GNU Parallel 20160922 ('Umbria') released <<[stable]>>
Subject: GNU Parallel 20160922 ('Christiania') released <<[stable]>>
GNU Parallel 20160922 ('Umbria') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
GNU Parallel 20160922 ('Christiania') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
<<No new functionality was introduced so this is a good candidate for a stable release.>>
Haiku of the month:
Want to monitor
many job outputs at once:
--tmuxpane
--ole-tange
-- Ole Tange
New in this release:
@ -266,8 +263,26 @@ for Big Data Applications https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumb
* <<Possible: http://link.springer.com/article/10.1007/s12021-015-9290-5 http://link.springer.com/protocol/10.1007/978-1-4939-3578-9_14>>
* parcat - cat files or fifos in parallel
* GNU Parallel was cited in: Velocity: A Netflow Based Optimized Geo-IP Lookup Tool https://mospace.umsystem.edu/xmlui/bitstream/handle/10355/50842/Thesis_2016_Pakhare.pdf?sequence=1&isAllowed=y
* GNU Parallel was cited in: Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011931/
* GNU Parallel is used in Gene Set Omic Analysis: https://bitbucket.org/srp33/gsoa
* Using GNU Parallel and ImageMagick for Conversions https://blog.fractalcomic.com/tutorials/using-gnu-parallel-and-imagemagick-for-conversions/
* Training in GNU Parallel http://www.cism.ucl.ac.be/Services/Formations/parcomp.pdf
* Chown Ceph OSD data directory using GNU Parallel http://blog.widodh.nl/2016/08/chown-ceph-osd-data-directory-using-gnu-parallel/
* FastGBS uses GNU Parallel https://bitbucket.org/jerlar73/fastgbs
* dDocent: A guide to ddRAD sequencing https://ddocent.wordpress.com/ddocent-pipeline-user-guide/
* SOFTWARE GNU Parallel http://msi-riss.readthedocs.io/en/latest/software/gnu-parallel.html
* Bug fixes and man page updates.
GNU Parallel - For people who live life in the parallel lane.

4
src/parallel.pod
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@ -264,11 +264,11 @@ shell quote a string
number of jobs in total
=item Z<> B<$job->slot()>
=item Z<> B<$job->>B<slot()>
slot number of job
=item Z<> B<$job->seq()>
=item Z<> B<$job->>B<seq()>
sequence number of job

18
src/parcat Normal file → Executable file
View file

@ -32,15 +32,8 @@ GNU B<parcat> is part of GNU B<parallel>. Report bugs to <bug-parallel@gnu.org>.
=head1 AUTHOR
When using GNU B<sql> for a publication please cite:
O. Tange (2011): GNU SQL - A Command Line Tool for Accessing Different
Databases Using DBURLs, ;login: The USENIX Magazine, April 2011:29-32.
Copyright (C) 2008,2009,2010 Ole Tange http://ole.tange.dk
Copyright (C) 2010,2011 Ole Tange, http://ole.tange.dk and Free
Software Foundation, Inc.
Copyright (C) 2016 Ole Tange, http://ole.tange.dk and Free Software
Foundation, Inc.
=head1 LICENSE
@ -203,14 +196,12 @@ sub producer {
}
my $s = IO::Select->new();
my %fhr;
my %buffer;
sub add_file {
my $fd = shift;
open(my $fh, "<&=", $fd) || die;
$s->add($fh);
$fhr{$fh}++;
# Tell the producer now opened here and can be released
$okq->enqueue($fd);
# Initialize the buffer
@ -236,9 +227,9 @@ my (@ready,$file,$rv,$buf);
do {
# Wait until at least one file is opened
add_files_block();
while($q->pending or keys %fhr) {
while($q->pending or keys %buffer) {
add_files();
while(keys %fhr) {
while(keys %buffer) {
@ready = $s->can_read(0.01);
if(not @ready) {
add_files();
@ -252,7 +243,6 @@ do {
} else {
# This file is done
$s->remove($file);
delete $fhr{$file};
print @{$buffer{$file}};
delete $buffer{$file};
# Closing the $file causes it to block

3
testsuite/Makefile
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@ -58,7 +58,7 @@ startvm:
# If they are already running: Don't fail
VBoxManage startvm CentOS3-root:centos3 || VBoxManage controlvm CentOS3-root:centos3 resume || true
VBoxManage startvm RedHat9-root:redhat9 || VBoxManage controlvm RedHat9-root:redhat9 resume || true
parallel ping -c 3 ::: redhat9.tange.dk centos3.tange.dk oracle11.tange.dk
parallel 'ping {} | read' ::: redhat9.tange.dk centos3.tange.dk
stopvm:
# || true - because this should not fail if the VM is not running
@ -73,6 +73,7 @@ startdb:
#echo shutdown abort | sudo su - oracle -c "sqlplus / as sysdba"
sudo parallel /etc/init.d/{} status '||' /etc/init.d/{} restart ::: postgresql mysql # oracle-xe
VBoxManage startvm OracleXE || true
parallel 'ping {} | read' ::: oracle11.tange.dk
clean:
rm -rf input-files/random_dirs_no_newline

2
testsuite/tests-to-run/parallel-local-0.3s.sh
View file

@ -643,7 +643,7 @@ echo '**'
echo '### bug #48658: --linebuffer --files'
parallel --files --linebuffer 'sleep .1;seq {};sleep .1' ::: {1..10} | wc -l
stdout parallel --files --linebuffer 'sleep .1;seq {};sleep .1' ::: {1..10} | wc -l
echo '**'

12
testsuite/tests-to-run/parallel-local-100s.sh
View file

@ -33,23 +33,21 @@ measure() {
# Input:
# $1 = iterations
# $2 = sleep 1 sec for every $2
seq $1 |
stdout time -v parallel -u sleep '{= $_=$_%'$2'?0:1 =}' |
grep Maximum | field 6;
seq $1 | ramusage parallel -u sleep '{= $_=$_%'$2'?0:1 =}'
}
export -f measure
no_mem_leak() {
# Return false if leaking
max1000=$(parallel measure {} 100000 ::: 1000 1000 1000 1000 |
max1000=$(parallel measure {} 100000 ::: 1000 1000 1000 1000 1000 1000 1000 1000 |
sort -n | tail -n 1)
min30000=$(parallel measure {} 100000 ::: 30000 30000 30000 30000 |
min30000=$(parallel measure {} 100000 ::: 30000 30000 30000 |
sort -n | head -n 1)
if [ $max1000 -gt $min30000 ] ; then
# Make sure there are a few sleeps
max1000=$(parallel measure {} 100 ::: 1000 1000 1000 1000 |
max1000=$(parallel measure {} 100 ::: 1000 1000 1000 1000 1000 1000 1000 1000 |
sort -n | tail -n 1)
min30000=$(parallel measure {} 100 ::: 30000 30000 30000 30000 |
min30000=$(parallel measure {} 100 ::: 30000 30000 30000 |
sort -n | head -n 1)
if [ $max1000 -gt $min30000 ] ; then
echo $max1000 -gt $min30000 = no leak

14
testsuite/tests-to-run/parallel-local-1s.sh
View file

@ -82,6 +82,20 @@ echo 'bug #41613: --compress --line-buffer no newline';
perl -e 'print "It worked"'| parallel --pipe --compress --line-buffer cat; echo
echo 'bug #48658: --linebuffer --files';
doit() { parallel --files --linebuffer --compress-program $1 seq ::: 100000 | wc -l ; };
export -f doit;
parallel -k doit ::: zstd pzstd clzip lz4 lzop pigz pxz gzip plzip pbzip2 lzma xz lzip bzip2 lbzip2 lrz
doit() { parallel --results /tmp/par48658$1 --linebuffer --compress-program $1 seq ::: 100000 | wc -l ; rm -rf "/tmp/par48658$1"; };
export -f doit;
parallel -k doit ::: zstd pzstd clzip lz4 lzop pigz pxz gzip plzip pbzip2 lzma xz lzip bzip2 lbzip2 lrz
doit() { parallel --linebuffer --compress-program $1 seq ::: 100000 | wc -l ; };
export -f doit;
parallel -k doit ::: zstd pzstd clzip lz4 lzop pigz pxz gzip plzip pbzip2 lzma xz lzip bzip2 lbzip2 lrz
echo '**'
echo "### Test -I";

48
testsuite/wanted-results/parallel-install
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@ -119,18 +119,32 @@ Warning: pod2html not found. Using old parallel_tutorial.html
rm -f ./pod2htm*
pod2texi --output=./parallel.texi ./parallel.pod \
|| echo "Warning: pod2texi not found. Using old parallel.texi"
/bin/bash: pod2texi: command not found
Warning: pod2texi not found. Using old parallel.texi
pod2texi --output=./env_parallel.texi ./env_parallel.pod \
|| echo "Warning: pod2texi not found. Using old env_parallel.texi"
/bin/bash: pod2texi: command not found
Warning: pod2texi not found. Using old env_parallel.texi
pod2texi --output=./sem.texi ./sem.pod \
|| echo "Warning: pod2texi not found. Using old sem.texi"
/bin/bash: pod2texi: command not found
Warning: pod2texi not found. Using old sem.texi
pod2texi --output=./sql.texi ./sql \
|| echo "Warning: pod2texi not found. Using old sql.texi"
/bin/bash: pod2texi: command not found
Warning: pod2texi not found. Using old sql.texi
pod2texi --output=./niceload.texi ./niceload.pod \
|| echo "Warning: pod2texi not found. Using old niceload.texi"
/bin/bash: pod2texi: command not found
Warning: pod2texi not found. Using old niceload.texi
pod2texi --output=./parallel_tutorial.texi ./parallel_tutorial.pod \
|| echo "Warning: pod2texi not found. Using old parallel_tutorial.texi"
/bin/bash: pod2texi: command not found
Warning: pod2texi not found. Using old parallel_tutorial.texi
pod2texi --output=./parallel_design.texi ./parallel_design.pod \
|| echo "Warning: pod2texi not found. Using old parallel_design.texi"
/bin/bash: pod2texi: command not found
Warning: pod2texi not found. Using old parallel_design.texi
pod2pdf --output-file ./parallel.pdf ./parallel.pod --title "GNU Parallel" \
|| echo "Warning: pod2pdf not found. Using old parallel.pdf"
/bin/bash: pod2pdf: command not found
@ -161,7 +175,7 @@ pod2pdf --output-file ./parallel_design.pdf ./parallel_design.pod --title "GNU P
Warning: pod2pdf not found. Using old parallel_design.pdf
make[0]: Entering directory '/tmp/parallel-00000000/src'
/bin/mkdir -p '/usr/local/bin'
/usr/bin/install -c parallel sql niceload env_parallel env_parallel.bash env_parallel.zsh env_parallel.fish env_parallel.ksh env_parallel.pdksh env_parallel.csh env_parallel.tcsh '/usr/local/bin'
/usr/bin/install -c parallel sql niceload parcat env_parallel env_parallel.bash env_parallel.zsh env_parallel.fish env_parallel.ksh env_parallel.pdksh env_parallel.csh env_parallel.tcsh '/usr/local/bin'
make install-exec-hook
make[0]: Entering directory '/tmp/parallel-00000000/src'
rm /usr/local/bin/sem || true
@ -209,6 +223,34 @@ pod2html --title "GNU Parallel tutorial" ./parallel_tutorial.pod > ./parallel_tu
/bin/bash: pod2html: command not found
Warning: pod2html not found. Using old parallel_tutorial.html
rm -f ./pod2htm*
pod2texi --output=./parallel.texi ./parallel.pod \
|| echo "Warning: pod2texi not found. Using old parallel.texi"
/bin/bash: pod2texi: command not found
Warning: pod2texi not found. Using old parallel.texi
pod2texi --output=./env_parallel.texi ./env_parallel.pod \
|| echo "Warning: pod2texi not found. Using old env_parallel.texi"
/bin/bash: pod2texi: command not found
Warning: pod2texi not found. Using old env_parallel.texi
pod2texi --output=./sem.texi ./sem.pod \
|| echo "Warning: pod2texi not found. Using old sem.texi"
/bin/bash: pod2texi: command not found
Warning: pod2texi not found. Using old sem.texi
pod2texi --output=./sql.texi ./sql \
|| echo "Warning: pod2texi not found. Using old sql.texi"
/bin/bash: pod2texi: command not found
Warning: pod2texi not found. Using old sql.texi
pod2texi --output=./niceload.texi ./niceload.pod \
|| echo "Warning: pod2texi not found. Using old niceload.texi"
/bin/bash: pod2texi: command not found
Warning: pod2texi not found. Using old niceload.texi
pod2texi --output=./parallel_tutorial.texi ./parallel_tutorial.pod \
|| echo "Warning: pod2texi not found. Using old parallel_tutorial.texi"
/bin/bash: pod2texi: command not found
Warning: pod2texi not found. Using old parallel_tutorial.texi
pod2texi --output=./parallel_design.texi ./parallel_design.pod \
|| echo "Warning: pod2texi not found. Using old parallel_design.texi"
/bin/bash: pod2texi: command not found
Warning: pod2texi not found. Using old parallel_design.texi
pod2pdf --output-file ./parallel.pdf ./parallel.pod --title "GNU Parallel" \
|| echo "Warning: pod2pdf not found. Using old parallel.pdf"
/bin/bash: pod2pdf: command not found
@ -238,7 +280,7 @@ pod2pdf --output-file ./parallel_design.pdf ./parallel_design.pod --title "GNU P
/bin/bash: pod2pdf: command not found
Warning: pod2pdf not found. Using old parallel_design.pdf
/bin/mkdir -p '/usr/local/share/doc/parallel'
/usr/bin/install -c -m 644 parallel.html env_parallel.html sem.html sql.html niceload.html parallel_tutorial.html parallel_design.html parallel.texi env_parallel.texi sem.texi sql.texi niceload.texi parallel_tutorial.texi parallel_design.texi parallel.pdf env_parallel.pdf sem.pdf sql.pdf niceload.pdf parallel_tutorial.pdf parallel_design.pdf '/usr/local/share/doc/parallel'
/usr/bin/install -c -m 644 parallel.html env_parallel.html sem.html sql.html niceload.html parallel_tutorial.html parallel_design.html parcat.html parallel.texi env_parallel.texi sem.texi sql.texi niceload.texi parallel_tutorial.texi parallel_design.texi parcat.texi parallel.pdf env_parallel.pdf sem.pdf sql.pdf niceload.pdf parallel_tutorial.pdf parallel_design.pdf parcat.pdf '/usr/local/share/doc/parallel'
pod2man --release='00000000' --center='parallel' \
--section=1 ./parallel.pod > ./parallel.1n \
&& mv ./parallel.1n ./parallel.1 \
@ -282,7 +324,7 @@ pod2man --release='00000000' --center='parallel' \
/bin/bash: pod2man: command not found
Warning: pod2man not found. Using old parallel_design.7
/bin/mkdir -p '/usr/local/share/man/man1'
/usr/bin/install -c -m 644 parallel.1 env_parallel.1 sem.1 sql.1 niceload.1 '/usr/local/share/man/man1'
/usr/bin/install -c -m 644 parallel.1 env_parallel.1 sem.1 sql.1 niceload.1 parcat.1 '/usr/local/share/man/man1'
/bin/mkdir -p '/usr/local/share/man/man7'
/usr/bin/install -c -m 644 parallel_tutorial.7 parallel_design.7 '/usr/local/share/man/man7'
make[0]: Leaving directory '/tmp/parallel-00000000/src'

4
testsuite/wanted-results/parallel-local-0.3s
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@ -1761,9 +1761,9 @@ echo '**'
**
echo '### bug #48658: --linebuffer --files'
### bug #48658: --linebuffer --files
parallel --files --linebuffer 'sleep .1;seq {};sleep .1' ::: {1..10} | wc -l
stdout parallel --files --linebuffer 'sleep .1;seq {};sleep .1' ::: {1..10} | wc -l
10
echo '**'
**
### 1 .par file from --files expected
0
10

54
testsuite/wanted-results/parallel-local-1s
View file

@ -74,8 +74,6 @@ parallel: Error: false failed.
(parallel --files --tag --line-buffer --compress-program false echo \;sleep 1\;ls ::: /no-existing; echo $?) | tail -n1
1
parallel: Error: false failed.
parallel: Error: false failed.
parallel: Error: false failed.
parallel: Error: false failed.
parallel --tag --compress-program false echo \;ls ::: /no-existing; echo $?
1
@ -236,6 +234,58 @@ ls: cannot access '/OK-if-missing-file': No such file or directory
echo 'bug #41613: --compress --line-buffer no newline'; perl -e 'print "It worked"'| parallel --pipe --compress --line-buffer cat; echo
bug #41613: --compress --line-buffer no newline
It worked
echo 'bug #48658: --linebuffer --files'; doit() { parallel --files --linebuffer --compress-program $1 seq ::: 100000 | wc -l ; }; export -f doit; parallel -k doit ::: zstd pzstd clzip lz4 lzop pigz pxz gzip plzip pbzip2 lzma xz lzip bzip2 lbzip2 lrz
bug #48658: --linebuffer --files
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doit() { parallel --results /tmp/par48658$1 --linebuffer --compress-program $1 seq ::: 100000 | wc -l ; rm -rf "/tmp/par48658$1"; }; export -f doit; parallel -k doit ::: zstd pzstd clzip lz4 lzop pigz pxz gzip plzip pbzip2 lzma xz lzip bzip2 lbzip2 lrz
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doit() { parallel --linebuffer --compress-program $1 seq ::: 100000 | wc -l ; }; export -f doit; parallel -k doit ::: zstd pzstd clzip lz4 lzop pigz pxz gzip plzip pbzip2 lzma xz lzip bzip2 lbzip2 lrz
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echo '**'
**
echo "### Test -I"; seq 1 10 | parallel -k 'seq 1 {} | parallel -k -I :: echo {} ::'

25
testsuite/wanted-results/parallel-tutorial
View file

@ -350,6 +350,31 @@ pre- A-post
pre-A -post
parallel --trim lr echo pre-{}-post ::: ' A '
pre-A-post
parallel echo \={} ::: zsh bash ls
=zsh
=bash
=ls
parallel 'set a="{}"; if( { test -d "$a" } ) echo "$a is a dir"' ::: *
/bin/bash: -c: line 0: syntax error near unexpected token `)'
/bin/bash: -c: line 0: `set a="abc-file"; if( { test -d "$a" } ) echo "$a is a dir"'
/bin/bash: -c: line 0: syntax error near unexpected token `)'
/bin/bash: -c: line 0: `set a="abc0-file"; if( { test -d "$a" } ) echo "$a is a dir"'
/bin/bash: -c: line 0: syntax error near unexpected token `)'
/bin/bash: -c: line 0: `set a="abc_-file"; if( { test -d "$a" } ) echo "$a is a dir"'
/bin/bash: -c: line 0: syntax error near unexpected token `)'
/bin/bash: -c: line 0: `set a="def-file"; if( { test -d "$a" } ) echo "$a is a dir"'
/bin/bash: -c: line 0: syntax error near unexpected token `)'
/bin/bash: -c: line 0: `set a="num1000000"; if( { test -d "$a" } ) echo "$a is a dir"'
/bin/bash: -c: line 0: syntax error near unexpected token `)'
/bin/bash: -c: line 0: `set a="num128"; if( { test -d "$a" } ) echo "$a is a dir"'
/bin/bash: -c: line 0: syntax error near unexpected token `)'
/bin/bash: -c: line 0: `set a="num30000"; if( { test -d "$a" } ) echo "$a is a dir"'
/bin/bash: -c: line 0: syntax error near unexpected token `)'
/bin/bash: -c: line 0: `set a="num8"; if( { test -d "$a" } ) echo "$a is a dir"'
/bin/bash: -c: line 0: syntax error near unexpected token `)'
/bin/bash: -c: line 0: `set a="num_%header"; if( { test -d "$a" } ) echo "$a is a dir"'
/bin/bash: -c: line 0: syntax error near unexpected token `)'
/bin/bash: -c: line 0: `set a="tsv-file.tsv"; if( { test -d "$a" } ) echo "$a is a dir"'
parallel --tag echo foo-{} ::: A B C
A foo-A
B foo-B