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env_parallel.bash: Initial release of parset.

Browse source 
parallel: Bugfix in some --plus dynamic replacement strings.
parallel: Deal better with commands containing newlines in --joblog.
parallel: Bugfix for --load in csh.
parallel_alternatives.pod: More comparison to rush-parallel.
This commit is contained in:
Ole Tange 2017-04-15 00:00:21 +02:00
parent 685018f532
commit 253c94786f
10 changed files with 637 additions and 79 deletions
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6
doc/release_new_version
View file

@ -195,7 +195,7 @@ to:parallel@gnu.org, bug-parallel@gnu.org
Subject: GNU Parallel 20170422 ('Санкт-Петербу́рг') released <<[stable]>>
GNU Parallel 20170422 ('Санкт-Петербу́рг') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
GNU Parallel 20170422 ('Stockholm/London/Санкт-Петербу́рг') <<[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.>>
@ -221,6 +221,10 @@ https://github.com/lucascbeyeler/zmbackup
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0174575
https://www.slideshare.net/sharatsc/data-science-at-the-command-line
http://www.jianshu.com/p/67b0665490ac
* <<Possibly http://link.springer.com/chapter/10.1007%2F978-3-319-22053-6_46>>
* <<Possibly http://link.springer.com/article/10.1007/s12021-015-9290-5>>

50
src/Makefile.am
View file

@ -11,18 +11,21 @@ install-exec-hook:
if DOCUMENTATION
man_MANS = parallel.1 env_parallel.1 sem.1 sql.1 niceload.1 \
parallel_tutorial.7 parallel_design.7 parallel_alternatives.7 \
parcat.1
parcat.1 parset.1
doc_DATA = parallel.html env_parallel.html sem.html sql.html niceload.html \
parallel_tutorial.html parallel_design.html parallel_alternatives.html \
parcat.html \
parallel.texi env_parallel.texi sem.texi sql.texi niceload.texi \
parallel_tutorial.texi parallel_design.texi parallel_alternatives.texi \
parcat.texi \
parcat.texi parset.texi \
parallel.pdf env_parallel.pdf sem.pdf sql.pdf niceload.pdf \
parallel_tutorial.pdf parallel_design.pdf parallel_alternatives.pdf \
parcat.pdf
parcat.pdf parset.pdf
endif
parset: parset.pod
cp parset.pod parset
# Build documentation file if the tool to build exists.
# Otherwise: Use the distributed version
parallel.1: parallel.pod
@ -80,6 +83,12 @@ parcat.1: parcat
&& mv $(srcdir)/parcat.1n $(srcdir)/parcat.1 \
|| echo "Warning: pod2man not found. Using old parcat.1"
parset.1: parset
pod2man --release='$(PACKAGE_VERSION)' --center='$(PACKAGE_NAME)' \
--section=1 $(srcdir)/parset > $(srcdir)/parset.1n \
&& mv $(srcdir)/parset.1n $(srcdir)/parset.1 \
|| echo "Warning: pod2man not found. Using old parset.1"
parallel.html: parallel.pod
pod2html --title "GNU Parallel" $(srcdir)/parallel.pod > $(srcdir)/parallel.htmln \
&& mv $(srcdir)/parallel.htmln $(srcdir)/parallel.html \
@ -142,6 +151,13 @@ parcat.html: parcat niceload.html
|| echo "Warning: pod2html not found. Using old parcat.html"
rm -f $(srcdir)/pod2htm*
# Depending on niceload.html to avoid stupid pod2html race condition
parset.html: parset parcat.html
pod2html --title "GNU parset" $(srcdir)/parset > $(srcdir)/parset.htmln \
&& mv $(srcdir)/parset.htmln $(srcdir)/parset.html \
|| echo "Warning: pod2html not found. Using old parset.html"
rm -f $(srcdir)/pod2htm*
parallel.texi: parallel.pod
pod2texi --output=$(srcdir)/parallel.texi $(srcdir)/parallel.pod \
|| echo "Warning: pod2texi not found. Using old parallel.texi"
@ -178,6 +194,10 @@ parcat.texi: parcat
pod2texi --output=$(srcdir)/parcat.texi $(srcdir)/parcat \
|| echo "Warning: pod2texi not found. Using old parcat.texi"
parset.texi: parset
pod2texi --output=$(srcdir)/parset.texi $(srcdir)/parset \
|| echo "Warning: pod2texi not found. Using old parset.texi"
parallel.pdf: parallel.pod
pod2pdf --output-file $(srcdir)/parallel.pdf $(srcdir)/parallel.pod --title "GNU Parallel" \
|| echo "Warning: pod2pdf not found. Using old parallel.pdf"
@ -214,26 +234,30 @@ parcat.pdf: parcat
pod2pdf --output-file $(srcdir)/parcat.pdf $(srcdir)/parcat --title "GNU parcat" \
|| echo "Warning: pod2pdf not found. Using old parcat.pdf"
parset.pdf: parset
pod2pdf --output-file $(srcdir)/parset.pdf $(srcdir)/parset --title "GNU parset" \
|| echo "Warning: pod2pdf not found. Using old parset.pdf"
sem: parallel
ln -fs parallel sem
DISTCLEANFILES = parallel.1 env_parallel.1 sem.1 sql.1 niceload.1 \
parallel_tutorial.7 parallel_design.7 parallel_alternatives.7 \
parcat.1 \
parcat.1 parset.1 \
parallel.html env_parallel.html sem.html sql.html niceload.html \
parallel_tutorial.html parallel_design.html parallel_alternatives.html \
parcat.html \
parcat.html parset.html \
parallel.texi env_parallel.texi sem.texi sql.texi niceload.texi \
parallel_tutorial.texi parallel_design.texi parallel_alternatives.texi \
parcat.texi \
parcat.texi parset.texi \
parallel.pdf env_parallel.pdf sem.pdf sql.pdf niceload.pdf \
parallel_tutorial.pdf parallel_design.pdf parallel_alternatives.pdf \
parcat.pdf
parcat.pdf parset.pdf
EXTRA_DIST = parallel sem sql niceload parcat env_parallel \
env_parallel.ash env_parallel.bash env_parallel.csh \
env_parallel.dash env_parallel.fish env_parallel.ksh \
env_parallel.pdksh env_parallel.sh env_parallel.tcsh \
env_parallel.zsh sem.pod parallel.pod env_parallel.pod \
niceload.pod parallel_tutorial.pod parallel_design.pod \
EXTRA_DIST = parallel sem sql niceload parcat parset env_parallel \
env_parallel.ash env_parallel.bash env_parallel.csh \
env_parallel.dash env_parallel.fish env_parallel.ksh \
env_parallel.pdksh env_parallel.sh env_parallel.tcsh \
env_parallel.zsh sem.pod parallel.pod env_parallel.pod \
niceload.pod parallel_tutorial.pod parallel_design.pod \
parallel_alternatives.pod $(DISTCLEANFILES)

50
src/Makefile.in
View file

@ -237,37 +237,37 @@ bin_SCRIPTS = parallel sql niceload parcat env_parallel \
@DOCUMENTATION_TRUE@man_MANS = parallel.1 env_parallel.1 sem.1 sql.1 niceload.1 \
@DOCUMENTATION_TRUE@ parallel_tutorial.7 parallel_design.7 parallel_alternatives.7 \
@DOCUMENTATION_TRUE@ parcat.1
@DOCUMENTATION_TRUE@ parcat.1 parset.1
@DOCUMENTATION_TRUE@doc_DATA = parallel.html env_parallel.html sem.html sql.html niceload.html \
@DOCUMENTATION_TRUE@ parallel_tutorial.html parallel_design.html parallel_alternatives.html \
@DOCUMENTATION_TRUE@ parcat.html \
@DOCUMENTATION_TRUE@ parallel.texi env_parallel.texi sem.texi sql.texi niceload.texi \
@DOCUMENTATION_TRUE@ parallel_tutorial.texi parallel_design.texi parallel_alternatives.texi \
@DOCUMENTATION_TRUE@ parcat.texi \
@DOCUMENTATION_TRUE@ parcat.texi parset.texi \
@DOCUMENTATION_TRUE@ parallel.pdf env_parallel.pdf sem.pdf sql.pdf niceload.pdf \
@DOCUMENTATION_TRUE@ parallel_tutorial.pdf parallel_design.pdf parallel_alternatives.pdf \
@DOCUMENTATION_TRUE@ parcat.pdf
@DOCUMENTATION_TRUE@ parcat.pdf parset.pdf
DISTCLEANFILES = parallel.1 env_parallel.1 sem.1 sql.1 niceload.1 \
parallel_tutorial.7 parallel_design.7 parallel_alternatives.7 \
parcat.1 \
parcat.1 parset.1 \
parallel.html env_parallel.html sem.html sql.html niceload.html \
parallel_tutorial.html parallel_design.html parallel_alternatives.html \
parcat.html \
parcat.html parset.html \
parallel.texi env_parallel.texi sem.texi sql.texi niceload.texi \
parallel_tutorial.texi parallel_design.texi parallel_alternatives.texi \
parcat.texi \
parcat.texi parset.texi \
parallel.pdf env_parallel.pdf sem.pdf sql.pdf niceload.pdf \
parallel_tutorial.pdf parallel_design.pdf parallel_alternatives.pdf \
parcat.pdf
parcat.pdf parset.pdf
EXTRA_DIST = parallel sem sql niceload parcat env_parallel \
env_parallel.ash env_parallel.bash env_parallel.csh \
env_parallel.dash env_parallel.fish env_parallel.ksh \
env_parallel.pdksh env_parallel.sh env_parallel.tcsh \
env_parallel.zsh sem.pod parallel.pod env_parallel.pod \
niceload.pod parallel_tutorial.pod parallel_design.pod \
EXTRA_DIST = parallel sem sql niceload parcat parset env_parallel \
env_parallel.ash env_parallel.bash env_parallel.csh \
env_parallel.dash env_parallel.fish env_parallel.ksh \
env_parallel.pdksh env_parallel.sh env_parallel.tcsh \
env_parallel.zsh sem.pod parallel.pod env_parallel.pod \
niceload.pod parallel_tutorial.pod parallel_design.pod \
parallel_alternatives.pod $(DISTCLEANFILES)
all: all-am
@ -611,6 +611,9 @@ install-exec-hook:
rm $(DESTDIR)$(bindir)/sem || true
$(LN_S) parallel $(DESTDIR)$(bindir)/sem
parset: parset.pod
cp parset.pod parset
# Build documentation file if the tool to build exists.
# Otherwise: Use the distributed version
parallel.1: parallel.pod
@ -667,6 +670,12 @@ parcat.1: parcat
&& mv $(srcdir)/parcat.1n $(srcdir)/parcat.1 \
|| echo "Warning: pod2man not found. Using old parcat.1"
parset.1: parset
pod2man --release='$(PACKAGE_VERSION)' --center='$(PACKAGE_NAME)' \
--section=1 $(srcdir)/parset > $(srcdir)/parset.1n \
&& mv $(srcdir)/parset.1n $(srcdir)/parset.1 \
|| echo "Warning: pod2man not found. Using old parset.1"
parallel.html: parallel.pod
pod2html --title "GNU Parallel" $(srcdir)/parallel.pod > $(srcdir)/parallel.htmln \
&& mv $(srcdir)/parallel.htmln $(srcdir)/parallel.html \
@ -729,6 +738,13 @@ parcat.html: parcat niceload.html
|| echo "Warning: pod2html not found. Using old parcat.html"
rm -f $(srcdir)/pod2htm*
# Depending on niceload.html to avoid stupid pod2html race condition
parset.html: parset parcat.html
pod2html --title "GNU parset" $(srcdir)/parset > $(srcdir)/parset.htmln \
&& mv $(srcdir)/parset.htmln $(srcdir)/parset.html \
|| echo "Warning: pod2html not found. Using old parset.html"
rm -f $(srcdir)/pod2htm*
parallel.texi: parallel.pod
pod2texi --output=$(srcdir)/parallel.texi $(srcdir)/parallel.pod \
|| echo "Warning: pod2texi not found. Using old parallel.texi"
@ -765,6 +781,10 @@ parcat.texi: parcat
pod2texi --output=$(srcdir)/parcat.texi $(srcdir)/parcat \
|| echo "Warning: pod2texi not found. Using old parcat.texi"
parset.texi: parset
pod2texi --output=$(srcdir)/parset.texi $(srcdir)/parset \
|| echo "Warning: pod2texi not found. Using old parset.texi"
parallel.pdf: parallel.pod
pod2pdf --output-file $(srcdir)/parallel.pdf $(srcdir)/parallel.pod --title "GNU Parallel" \
|| echo "Warning: pod2pdf not found. Using old parallel.pdf"
@ -801,6 +821,10 @@ parcat.pdf: parcat
pod2pdf --output-file $(srcdir)/parcat.pdf $(srcdir)/parcat --title "GNU parcat" \
|| echo "Warning: pod2pdf not found. Using old parcat.pdf"
parset.pdf: parset
pod2pdf --output-file $(srcdir)/parset.pdf $(srcdir)/parset --title "GNU parset" \
|| echo "Warning: pod2pdf not found. Using old parset.pdf"
sem: parallel
ln -fs parallel sem

120
src/env_parallel.bash
View file

@ -169,3 +169,123 @@ env_parallel() {
unset PARALLEL_ENV;
return $_parallel_exit_CODE
}
_parset() {
# $1 = variable NAME
# If ${"$1"} is an array: Then put the output into variables with those names
# else put the output into an array named ${"$1"}
# e.g.:
# # Create array named myvar
# parset myvar echo ::: {1..10}
# echo ${myvar[5]}
#
# # Put output into $var_a $var_b $var_c
# varnames=(var_a var_b var_c)
# parset -a varnames echo ::: {1..3}
# echo $var_c
#
# # Put output into $var_a2 $var_b2 $var_c2
# varname=var_a2,var_b2,var_c2
# parset -a varname echo ::: {1..3}
# echo $var_c2
#
# # Put output into $var_a3 $var_b3 $var_c3
# varname="var_a3 var_b3 var_c3"
# parset -a varname echo ::: {1..3}
# echo $var_c3
# Variable name to store in
local _parset_vname
local _parset_vnames
# Array to fetch names from
local _parset_aname
_parset_vname="$1"
_parset_aname="_nO_sUch_vAr"
shift
if [[ "-a" == "$_parset_vname" ]] ; then
# Option -a given
echo '-a given'
_parset_vname="$1"
_parset_aname="$1"
shift
if [[ "$(declare -p $_parset_vname 2>/dev/null)" =~ "declare -a" ]]; then
# OK
true
else
# error
echo "$_parset_vname" must be an array
return 1
fi
else
local _parset_splitable
_parset_splitable="$(eval echo '$'$_parset_vname)"
if echo "$_parset_splitable" | grep -E ',| ' >/dev/null ; then
# Split on , and space
_parset_vnames=( $(perl -e 'print map { s/,| /\n/g; $_ } @ARGV' "$_parset_splitable" ) )
_parset_aname="_parset_vnames"
echo first ${_parset_vnames[0]}
else
# _parset_vname should be used as an array
true
fi
fi
if [[ "$(declare -p $_parset_aname 2>/dev/null)" =~ "declare -a" ]]; then
# vname refers to an array
# The array elements refers to variable names to put output into
eval $(
parallel --files "$@" |
perl -pe 'chop;$_="\"\`cat $_; rm $_\`\"\n"' |
parallel echo {2}={1} :::: - :::+ $(eval echo '${'$_parset_aname'[@]}')
)
unset _parset_aname
else
# Put output into array ${$_parset_vname}
eval $_parset_vname="( $( parallel --files "$@" |
perl -pe 'chop;$_="\"\`cat $_; rm $_\`\" "' ) )"
fi
}
parset() {
# If $1 contains ',' or space:
# Split on , to get the destination variable names
# If $1 is a single destination variable name:
# Treat it as the name of an array
#
# # Create array named myvar
# parset myvar echo ::: {1..10}
# echo ${myvar[5]}
#
# # Put output into $var_a $var_b $var_c
# varnames=(var_a var_b var_c)
# parset "${varnames[*]}" echo ::: {1..3}
# echo $var_c
#
# # Put output into $var_a4 $var_b4 $var_c4
# parset "var_a4 var_b4 var_c4" echo ::: {1..3}
# echo $var_c4
_parset_name="$1"
shift
if echo "$_parset_name" | grep -E ',| ' >/dev/null ; then
# $1 contains , or space
# Split on , or space to get the names
eval "$(
# Compute results into files
parallel --files "$@" |
# var1=`cat tmpfile1; rm tmpfile1`
# var2=`cat tmpfile2; rm tmpfile2`
parallel -q echo {2}='`cat {1}; rm {1}`' :::: - :::+ $(
echo "$_parset_name" |
perl -pe 's/,/ /g'
)
)"
else
# $1 contains no space or ,
# => $1 is the name of the array to put data into
eval $_parset_name="( $( parallel --files "$@" |
perl -pe 'chop;$_="\"\`cat $_; rm $_\`\" "' ) )"
fi
}

109
src/parallel
View file

@ -1362,7 +1362,7 @@ sub check_invalid_option_combinations {
sub init_globals {
# Defaults:
$Global::version = 20170331;
$Global::version = 20170404;
$Global::progname = 'parallel';
$Global::infinity = 2**31;
$Global::debug = 0;
@ -1399,25 +1399,25 @@ sub init_globals {
# {##} = number of jobs
'{##}' => '$_=total_jobs()',
# Bash ${a:-myval}
'{:-(.+?)}' => '$_ ||= $$1',
'{:-([^}]+?)}' => '$_ ||= $$1',
# Bash ${a:2}
'{:(\d+?)}' => 'substr($_,0,$$1) = ""',
# Bash ${a:2:3}
'{:(\d+?):(\d+?)}' => '$_ = substr($_,$$1,$$2);',
# Bash ${a#bc}
'{#([^#].*?)}' => 's/^$$1//;',
'{#([^#][^}]*?)}' => 's/^$$1//;',
# Bash ${a%def}
'{%(.+?)}' => 's/$$1$//;',
'{%([^}]+?)}' => 's/$$1$//;',
# Bash ${a/def/ghi} ${a/def/}
'{/(.+?)/(.*?)}' => 's/$$1/$$2/;',
'{/([^}]+?)/([^}]*?)}' => 's/$$1/$$2/;',
# Bash ${a^a}
'{^(.+?)}' => 's/^($$1)/uc($1)/e;',
'{^([^}]+?)}' => 's/^($$1)/uc($1)/e;',
# Bash ${a^^a}
'{^^(.+?)}' => 's/($$1)/uc($1)/eg;',
'{^^([^}]+?)}' => 's/($$1)/uc($1)/eg;',
# Bash ${a,A}
'{,(.+?)}' => 's/^($$1)/lc($1)/e;',
'{,([^}]+?)}' => 's/^($$1)/lc($1)/e;',
# Bash ${a,,A}
'{,,(.+?)}' => 's/($$1)/lc($1)/eg;',
'{,,([^}]+?)}' => 's/($$1)/lc($1)/eg;',
);
# Modifiable copy of %Global::replace
%Global::rpl = %Global::replace;
@ -1646,32 +1646,38 @@ sub open_joblog {
if($opt::resume || $opt::resume_failed || $opt::retry_failed) {
if(open(my $joblog_fh, "<", $opt::joblog)) {
# Read the joblog
$append = <$joblog_fh>; # If there is a header: Open as append later
# If there is a header: Open as append later
$append = <$joblog_fh>;
my $joblog_regexp;
if($opt::retry_failed) {
# Make a regexp that only matches commands with exit+signal=0
# 4 host 1360490623.067 3.445 1023 1222 0 0 command
$joblog_regexp='^(\d+)(?:\t[^\t]+){5}\t0\t0\t';
my @group;
while(<$joblog_fh>) {
if(/$joblog_regexp/o) {
# This is 30% faster than set_job_already_run($1);
vec($Global::job_already_run,($1||0),1) = 1;
$Global::total_completed++;
$group[$1-1] = "true";
} elsif(/(\d+)\s+\S+(\s+[-0-9.]+){6}\s+(.*)$/) {
$group[$1-1] = $3
} else {
chomp;
::error("Format of '$opt::joblog' is wrong: $_");
::wait_and_exit(255);
{
local $/="\n";
while(<$joblog_fh>) {
if(/$joblog_regexp/o) {
# This is 30% faster than set_job_already_run($1);
vec($Global::job_already_run,($1||0),1) = 1;
$Global::total_completed++;
$group[$1-1] = "true";
} elsif(/(\d+)\s+\S+(\s+[-0-9.]+){6}\s+(.*)$/) {
# Grab out the command
$group[$1-1] = $3;
} else {
chomp;
::error("Format of '$opt::joblog' is wrong: $_");
::wait_and_exit(255);
}
}
}
if(@group) {
my ($outfh,$name) = ::tmpfile(SUFFIX => ".arg");
unlink($name);
# Put args into argfile
print $outfh map { $_,$/ } @group;
# Replace \0 with ' ' as used in print_joblog()
print $outfh map { s/\0/ /g; $_,$/ } @group;
seek $outfh, 0, 0;
exit_if_disk_full();
# Set filehandle to -a
@ -2756,13 +2762,15 @@ sub progress {
$status = $eta .
join(" ",map
{
my $completed = ($Global::host{$_}->jobs_completed()||0);
my $running = $Global::host{$_}->jobs_running();
my $time = $completed ? (time-$^T)/($completed) : "0";
sprintf("%s:%d/%d/%d%%/%.1fs ",
$workerno{$_}, $running, $completed,
($running+$completed)*100
/ $Global::total_started, $time);
if($Global::total_started) {
my $completed = ($Global::host{$_}->jobs_completed()||0);
my $running = $Global::host{$_}->jobs_running();
my $time = $completed ? (time-$^T)/($completed) : "0";
sprintf("%s:%d/%d/%d%%/%.1fs ",
$workerno{$_}, $running, $completed,
($running+$completed)*100
/ $Global::total_started, $time);
}
} @workers);
}
if(length $status > $termcols) {
@ -2770,13 +2778,17 @@ sub progress {
$header = "Computer:jobs running/jobs completed/%of started jobs";
$status = $eta .
join(" ",map
{ sprintf("%s:%d/%d/%d%%",
$sshlogin{$_},
$Global::host{$_}->jobs_running(),
($Global::host{$_}->jobs_completed()||0),
($Global::host{$_}->jobs_running()+
($Global::host{$_}->jobs_completed()||0))*100
/ $Global::total_started) }
{
if($Global::total_started) {
sprintf("%s:%d/%d/%d%%",
$sshlogin{$_},
$Global::host{$_}->jobs_running(),
($Global::host{$_}->jobs_completed()||0),
($Global::host{$_}->jobs_running()+
($Global::host{$_}->jobs_completed()||0))*100
/ $Global::total_started)
}
}
@workers);
}
if(length $status > $termcols) {
@ -2784,13 +2796,17 @@ sub progress {
$header = "Computer:jobs running/jobs completed/%of started jobs";
$status = $eta .
join(" ",map
{ sprintf("%s:%d/%d/%d%%",
$workerno{$_},
$Global::host{$_}->jobs_running(),
($Global::host{$_}->jobs_completed()||0),
($Global::host{$_}->jobs_running()+
($Global::host{$_}->jobs_completed()||0))*100
/ $Global::total_started) }
{
if($Global::total_started) {
sprintf("%s:%d/%d/%d%%",
$workerno{$_},
$Global::host{$_}->jobs_running(),
($Global::host{$_}->jobs_completed()||0),
($Global::host{$_}->jobs_running()+
($Global::host{$_}->jobs_completed()||0))*100
/ $Global::total_started)
}
}
@workers);
}
if(length $status > $termcols) {
@ -5258,7 +5274,8 @@ sub loadavg_too_high {
);
print `$ps{$^O}`;
});
$cmd = "perl -e ".::shell_quote_scalar($ps);
# The command is too long for csh, so base64_wrap the command
$cmd = Job::base64_wrap($ps);
}
return $cmd;
}
@ -8673,6 +8690,8 @@ sub print_joblog {
# Verbose level > 1: Print the rsync and stuff
$cmd = "@command";
}
# Newlines makes it hard to parse the joblog
$cmd =~ s/\n/\0/g;
print $Global::joblog
join("\t", $self->seq(), $self->sshlogin()->string(),
$self->starttime(), sprintf("%10.3f",$self->runtime()),

15
src/parallel.pod
View file

@ -1816,20 +1816,23 @@ Here are a few examples:
--rpl '{#0} $_ = seq() - 1'
Job slot counting from 2
--rpl '{%1} $_ = slot() + 1'
Remove all extensions
--rpl '{:} s:(\.[^/]+)*$::'
You can have dynamic replacement strings by including parenthesis in
the replacement string and adding a regular expression between the
parenthesis. The matching string will be inserted as $$1:
parallel --rpl '{%(.*?)} s/$$1//' echo {%.tar.gz} ::: my.tar.gz
parallel --rpl '{:%(.+?)} s:$$1(\.[^/]+)*$::' \
echo {:%_file} ::: my_file.tar.gz
parallel -n3 --rpl '{/:%(.*?)} s:.*/(.*)$$1(\.[^/]+)*$:$1:' \
echo job {#}: {2} {2.} {3/:%_1} ::: a/b.c c/d.e f/g_1.h.i
You can even use multiple matches:
parallel --rpl '{@(\d+)\S(\d+)\S(\d+)}
if($$3 > 31) { ($$1,$$2,$$3) = ($$3,$$2,$$1) }
if($$2 > 12) { ($$1,$$2,$$3) = ($$1,$$3,$$2) }
$$1 = ($$1%100 + 1900); $_="$$1-$$2-$$3"
' echo {@99-12-31} {@12.31.99} {@31/12-1999} ::: a
parallel --rpl '{/(.+?)/(.*?)} s/$$1/$$2/;'
echo {/replacethis/withthis} {/b/C} ::: a_replacethis_b
parallel --rpl '{(.*?)/(.*?)} $_="$$2$_$$1"' \
echo {swap/these} ::: -middle-
@ -4116,7 +4119,7 @@ the currently running jobs are finished before exiting.
=item $PARALLEL_HOME
Dir where GNU B<parallel> stores config files, semaphores, and caches
information between invocations. Default: $HOME/.parallel
information between invocations. Default: $HOME/.parallel.
=item $PARALLEL_PID

67
src/parallel_alternatives.pod
View file

@ -862,6 +862,73 @@ report this, but finishes with success - thereby risking data loss.
Rush (https://github.com/shenwei356/rush) is written in Go and based
on gargs.
Rush has some string manipulations that can be emulated by putting
this into ~/.parallel/config (% is used instead of ^):
--rpl '{:} s:(\.[^/]+)*$::'
--rpl '{:%([^}]+?)} s:$$1(\.[^/]+)*$::'
--rpl '{/:%([^}]*?)} s:.*/(.*)$$1(\.[^/]+)*$:$1:'
--rpl '{/:} s:(.*/)?([^/.]+)(\.[^/]+)*$:$2:'
Here are the examples from B<rush>'s website:
B<1> seq 1 10 | rush echo {}
B<1> seq 1 10 | parallel echo {}
B<2> seq 1 10 | rush 'echo {}' -k
B<2> seq 1 10 | parallel -k 'echo {}'
B<3> seq 1 | rush 'sleep 2; echo {}' -t 1
B<3> seq 1 | parallel --timeout 1 'sleep 2; echo {}'
B<4> seq 1 | rush 'python script.py' -r 3
B<4> seq 1 | parallel --retries 4 'python script.py'
B<5> echo dir/file_1.txt.gz | rush 'echo {/} {%} {^_1.txt.gz}'
B<5> echo dir/file_1.txt.gz | parallel --plus 'echo {//} {/} {%_1.txt.gz}'
B<6> echo dir.d/file.txt.gz | rush 'echo {.} {:} {%.} {%:}'
B<6> echo dir.d/file.txt.gz | parallel 'echo {.} {:} {/.} {/:}'
B<7> echo 12 file.txt dir/s_1.fq.gz | rush 'echo job {#}: {2} {2.} {3%:^_1}'
B<7> echo 12 file.txt dir/s_1.fq.gz | parallel --colsep ' ' 'echo job {#}: {2} {2.} {3/:%_1}'
B<8> echo a=b=c | rush 'echo {1} {2} {3}' -d =
B<8> echo a=b=c | parallel --colsep = 'echo {1} {2} {3}'
B<9> echo a=b=c | rush -D "=" -k 'echo {}'
B<9> echo -n a=b=c | parallel -d "=" -k 'echo {}'
B<9a> echo abc | rush -D "" -k 'echo {}'
B<9a> echo -n abc | parallel --pipe --recend '' --block 1 -k parallel echo
B<10> seq 1 | rush 'echo Hello, {fname} {lname}!' -v fname=Wei -v lname=Shen
B<10> seq 1 | parallel -N0 'fname=Wei; lname=Shen; echo Hello, ${fname} ${lname}!'
B<11> echo read_1.fq.gz | rush -v p={:^_1} 'echo {p} {p}_2.fq.gz'
B<11> echo read_1.fq.gz | parallel 'p={:%_1}; echo ${p} ${p}_2.fq.gz'
B<12> seq 1 3 | rush 'sleep {}; echo {}' -c -t 2
B<12> seq 1 3 | parallel --joblog mylog --timeout 2 'sleep {}; echo {}'
B<12> Followed by:
B<12> seq 1 3 | parallel --joblog mylog --retry-failed 'sleep {}; echo {}'
=head2 DIFFERENCES BETWEEN machma AND GNU Parallel

231
src/parset.pod Normal file
View file

@ -0,0 +1,231 @@
#!/usr/bin/perl -w
=encoding utf8
=head1 NAME
parset - set shell variables in parallel
=head1 SYNOPSIS
B<parset> I<variablename> [options for GNU Parallel]
=head1 DESCRIPTION
B<parset> is a shell function that puts the output from GNU
B<parallel> into shell variables.
The B<parset> function is defined as part of B<env_parallel>.
If I<variablename> is a single variable name, this will be treated as
the destination variable and made to an array.
If I<variablename> contains multiple names separated by ',' or space,
the names will be the destination variables.
=head1 OPTIONS
Same as GNU B<parallel>.
=head1 SUPPORTED SHELLS
=head2 Bash
=head3 Examples
Put output into B<myarray>:
parset myarray seq 3 ::: 4 5 6
echo "${myarray[1]}"
Put output into vars B<$seq, $pwd, $ls>:
parset "seq pwd ls" ::: "seq 10" pwd ls
echo "$ls"
Put output into vars B<$seq, $pwd, $ls>:
into_vars=(seq pwd ls)
parset "${into_vars[*]}" ::: "seq 10" pwd ls
echo "$ls"
The commands to run can be an array:
cmd=("echo '<<joe \"double space\" cartoon>>'" "pwd")
parset data ::: "${cmd[@]}"
echo "${data[0]}"
echo "${data[1]}"
You cannot pipe into B<parset>, but must use a tempfile:
seq 10 > parallel_input
parset res echo :::: parallel_input
echo "${res[0]}"
echo "${res[9]}"
=head3 Installation
Put this in B<$HOME/.bashrc>:
. `which env_parallel.bash`
E.g. by doing:
echo '. `which env_parallel.bash`' >> $HOME/.bashrc
=head1 EXIT STATUS
Same as GNU B<parallel>.
=head1 AUTHOR
When using GNU B<parallel> for a publication please cite:
O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login:
The USENIX Magazine, February 2011:42-47.
This helps funding further development; and it won't cost you a cent.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
Copyright (C) 2007-10-18 Ole Tange, http://ole.tange.dk
Copyright (C) 2008,2009,2010 Ole Tange, http://ole.tange.dk
Copyright (C) 2010,2011,2012,2013,2014,2015,2016,2017 Ole Tange,
http://ole.tange.dk and Free Software Foundation, Inc.
Parts of the manual concerning B<xargs> compatibility is inspired by
the manual of B<xargs> from GNU findutils 4.4.2.
=head1 LICENSE
Copyright (C) 2016
Ole Tange and Free Software Foundation, Inc.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
at your option any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
=head2 Documentation license I
Permission is granted to copy, distribute and/or modify this documentation
under the terms of the GNU Free Documentation License, Version 1.3 or
any later version published by the Free Software Foundation; with no
Invariant Sections, with no Front-Cover Texts, and with no Back-Cover
Texts. A copy of the license is included in the file fdl.txt.
=head2 Documentation license II
You are free:
=over 9
=item B<to Share>
to copy, distribute and transmit the work
=item B<to Remix>
to adapt the work
=back
Under the following conditions:
=over 9
=item B<Attribution>
You must attribute the work in the manner specified by the author or
licensor (but not in any way that suggests that they endorse you or
your use of the work).
=item B<Share Alike>
If you alter, transform, or build upon this work, you may distribute
the resulting work only under the same, similar or a compatible
license.
=back
With the understanding that:
=over 9
=item B<Waiver>
Any of the above conditions can be waived if you get permission from
the copyright holder.
=item B<Public Domain>
Where the work or any of its elements is in the public domain under
applicable law, that status is in no way affected by the license.
=item B<Other Rights>
In no way are any of the following rights affected by the license:
=over 2
=item *
Your fair dealing or fair use rights, or other applicable
copyright exceptions and limitations;
=item *
The author's moral rights;
=item *
Rights other persons may have either in the work itself or in
how the work is used, such as publicity or privacy rights.
=back
=back
=over 9
=item B<Notice>
For any reuse or distribution, you must make clear to others the
license terms of this work.
=back
A copy of the full license is included in the file as cc-by-sa.txt.
=head1 DEPENDENCIES
B<env_parallel> uses GNU B<parallel>.
=head1 SEE ALSO
B<parallel>(1),
B<bash>(1), B<csh>(1), B<fish>(1), B<ksh>(1), B<pdksh>(1) B<tcsh>(1),
B<zsh>(1).
=cut

35
testsuite/tests-to-run/parallel-local-1s.sh
View file

@ -196,6 +196,41 @@ par_result_replace() {
rm -rf /tmp/par_*_49983-*
}
par_parset() {
echo '### test parset'
. `which env_parallel.bash`
echo 'Put output into $myarray'
parset myarray seq 3 ::: 4 5 6
echo "${myarray[1]}"
echo 'Put output into vars $seq, $pwd, $ls'
parset "seq pwd ls" ::: "seq 10" pwd ls
echo "$seq"
echo 'Put output into vars $seq, $pwd, $ls':
into_vars=(seq pwd ls)
parset "${into_vars[*]}" ::: "seq 5" pwd ls
echo "$seq"
echo 'The commands to run can be an array'
cmd=("echo '<<joe \"double space\" cartoon>>'" "pwd")
parset data ::: "${cmd[@]}"
echo "${data[0]}"
echo "${data[1]}"
echo 'You cannot pipe into parset, but must use a tempfile'
seq 10 > parallel_input
parset res echo :::: parallel_input
echo "${res[0]}"
echo "${res[9]}"
echo 'Commands with newline require -0'
parset var -0 ::: 'echo "line1
line2"' 'echo "command2"'
echo "${var[0]}"
}
export -f $(compgen -A function | grep par_)
compgen -A function | grep par_ | sort |

33
testsuite/wanted-results/parallel-local-1s
View file

@ -4,7 +4,7 @@ echo "### BUG: The length for -X is not close to max (131072)"; seq 1 60000 |
seq 1 60000 | parallel -X echo a{}b{}c |head -n 1 |wc
1 5644 65514
seq 1 60000 | parallel -X echo |head -n 1 |wc
1 12771 65520
1 12770 65514
seq 1 60000 | parallel -X echo a{}b{}c {} |head -n 1 |wc
1 8098 65512
seq 1 60000 | parallel -X echo {}aa{} |head -n 1 |wc
@ -453,6 +453,37 @@ par_failing_compressor parallel: Error: cat;false failed.
par_failing_compressor parallel -k -k -k -k --compress --compress-program cat\;false --decompress-program cat\;false echo ::: C=cat\;false,D=cat\;false
par_failing_compressor C=cat;false,D=cat;false
par_failing_compressor parallel: Error: cat;false failed.
par_parset ### test parset
par_parset Put output into $myarray
par_parset 3
par_parset 4
par_parset 5
par_parset Put output into vars $seq, $pwd, $ls
par_parset 1
par_parset 2
par_parset 3
par_parset 4
par_parset 5
par_parset 6
par_parset 7
par_parset 8
par_parset 9
par_parset 10
par_parset Put output into vars $seq, $pwd, $ls:
par_parset 1
par_parset 2
par_parset 3
par_parset 4
par_parset 5
par_parset The commands to run can be an array
par_parset <<joe "double space" cartoon>>
par_parset ~/privat/parallel/testsuite
par_parset You cannot pipe into parset, but must use a tempfile
par_parset 1
par_parset 10
par_parset Commands with newline require -0
par_parset line1
par_parset line2
par_result ### Test --results
par_result I III
par_result I IIII