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testsuite: env_parallel expanded.
This commit is contained in:
Ole Tange
parent
68a48146ea
commit
f38d7fe29f
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@ -219,29 +219,26 @@ cc:Tim Cuthbertson <tim3d.junk@gmail.com>,
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Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
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Jesse Alama <jesse.alama@gmail.com>
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Subject: GNU Parallel 20160622 ('Orlando') released <<[stable]>>
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Subject: GNU Parallel 20160722 ('Brexit') released <<[stable]>>
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GNU Parallel 20160622 ('Orlando') <<[stable]>> has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
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GNU Parallel 20160722 ('Brexit') <<[stable]>> has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
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<<No new functionality was introduced so this is a good candidate for a stable release.>>
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Haiku of the month:
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Does path on remote
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not include GNU Parallel?
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Try --env PATH.
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<<>>
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-- Ole Tange
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New in this release:
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* $PATH can now be exported using --env PATH. Useful if GNU Parallel is not in your path on remote machines.
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* env_parallel is now ready for wider testing. It is still beta quality.
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* If --block is left out, --pipepart will use a block size that will result in 10 jobs per jobslot.
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* env_parallel is heavily modified for all shells and testing has been increased.
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* The cookie from 2016-01-04 was won by Morgan Rodgers on the 2016-06-06 after 5 months.
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* Vote for GNU Parallel's community ad on https://meta.askubuntu.com/questions/14925/community-promotion-ads-2016/15046#15046
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* Selectively choosing what to export using --env now works for env_parallel (bash, csh, fish, ksh, pdksh, tcsh, zsh).
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* <<Possibly http://link.springer.com/chapter/10.1007%2F978-3-319-22053-6_46>>
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@ -269,21 +266,31 @@ for Big Data Applications https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumb
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* <<link No citation: Next-generation TCP for ns-3 simulator http://www.sciencedirect.com/science/article/pii/S1569190X15300939>>
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* GNU Parallel was cited in: Genotypic Resistance Tests Sequences Reveal the Role of Marginalized Populations in HIV-1 Transmission in Switzerland http://www.nature.com/articles/srep27580
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* <<No citation: Argumentation Models for Cyber Attribution http://arxiv.org/pdf/1607.02171.pdf>>
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* GNU Parallel was cited in: A Deep-Learning Approach for Operation of an Automated Realtime Flare Forecast https://arxiv.org/pdf/1606.01587.pdf
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* <<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>>
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* Unix parallel: Populating all the USB sticks http://www.markhneedham.com/blog/2016/06/01/unix-parallel-populating-all-the-usb-sticks/
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* GNU Parallel was cited in: HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment http://www.bioone.org/doi/full/10.3732/apps.1600016
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* GNU Parallel is a fantastic utility https://www.dray.be/parallel/
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* GNU Parallel was cited in: StrAuto - Automation and Parallelization of STRUCTURE Analysis http://www.crypticlineage.net/download/strauto/strauto_doc.pdf
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* Combining a large number of VCF files https://gtamazian.com/2016/06/16/combining-a-large-number-of-vcf-files/
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* GNU Parallel was cited in: Tools and techniques for computational reproducibility http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0135-4
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* Useful Scraping Techniques http://blog.apps.npr.org/2016/06/17/scraping-tips.html
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* GNU Parallel was cited in: FlashPCA: fast sparse canonical correlation analysis of genomic data http://biorxiv.org/content/biorxiv/suppl/2016/04/06/047217.DC1/047217-1.pdf
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* Tools of the trade http://onox.com.br/2015/05/tools-of-the-trade/#more-198
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* GNU Parallel was cited in: Computational Design of DNA-Binding Proteins http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16
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* Armslist scraper https://github.com/nprapps/armslist-scraper/
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* GNU Parallel was cited in: Math Indexer and Searcher under the Hood: Fine-tuning Query Expansion and Unification Strategies http://research.nii.ac.jp/ntcir/workshop/OnlineProceedings12/pdf/ntcir/MathIR/05-NTCIR12-MathIR-RuzickaM.pdf
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* GNU Parallel was cited in: The Evolution and Fate of Super-Chandrasekhar Mass White Dwarf Merger Remnants http://arxiv.org/pdf/1606.02300.pdf
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* GNU Parallel was cited in: Evaluation of Coastal Scatterometer Products https://mdc.coaps.fsu.edu/scatterometry/meeting/docs/2016/Thu_AM/coastal-poster.pdf
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* GNU Parallel was used in: https://github.com/splitice/bulkdnsblcheck
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* The iconv slurp misfeature http://www.openfusion.net/linux/iconv_slurp_misfeature
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* แบบว่า CPU เหลือ https://veer66.wordpress.com/2016/06/15/gnu-parallel/
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* Bug fixes and man page updates.
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@ -52,12 +52,12 @@ env_parallel() {
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}
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if(grep { /^_$/ } @envvar) {
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if(not open(IN, "<", "$ENV{HOME}/.parallel/ignored_vars")) {
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print STDERR "parallel: Error: ",
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"Run \"parallel --record-env\" in a clean environment first.\n";
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print STDERR "parallel: Error: ",
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"Run \"parallel --record-env\" in a clean environment first.\n";
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} else {
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chomp(@ignored_vars = <IN>);
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$vars = join "|",map { quotemeta $_ } @ignored_vars;
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print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
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chomp(@ignored_vars = <IN>);
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$vars = join "|",map { quotemeta $_ } "env_parallel", @ignored_vars;
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print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
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}
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}
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' -- "$@"
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@ -87,7 +87,7 @@ env_parallel() {
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local _variable_NAMES="$(compgen -A variable |
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grep -E "^$_grep_REGEXP"\$ | grep -vE "^$_ignore_UNDERSCORE"\$ |
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grep -vFf <(readonly) |
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egrep -v '^(BASHOPTS|BASHPID|EUID|GROUPS|FUNCNAME|DIRSTACK|_|PIPESTATUS|PPID|SHELLOPTS|UID|USERNAME|BASH_[A-Z_]+)$')"
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grep -Ev '^(BASHOPTS|BASHPID|EUID|GROUPS|FUNCNAME|DIRSTACK|_|PIPESTATUS|PPID|SHELLOPTS|UID|USERNAME|BASH_[A-Z_]+)$')"
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local _list_variable_VALUES="typeset -p $_variable_NAMES"
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if [[ "$_variable_NAMES" = "" ]] ; then
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# no variables selected
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@ -57,12 +57,12 @@ else
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}
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if(grep { /^_$/ } @envvar) {
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if(not open(IN, "<", "$ENV{HOME}/.parallel/ignored_vars")) {
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print STDERR "parallel: Error: ",
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"Run 'parallel --record-env' in a clean environment first.\n";
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print STDERR "parallel: Error: ",
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"Run \"parallel --record-env\" in a clean environment first.\n";
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} else {
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chomp(@ignored_vars = <IN>);
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$vars = join "|",map { quotemeta $_ } @ignored_vars;
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print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
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chomp(@ignored_vars = <IN>);
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$vars = join "|",map { quotemeta $_ } "env_parallel", @ignored_vars;
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print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
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}
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}
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'EOF'
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@ -46,7 +46,8 @@ function env_parallel
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begin;
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set _grep_REGEXP (
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begin;
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perl -e 'for(@ARGV){
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perl -e '
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for(@ARGV){
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/^_$/ and $next_is_env = 0;
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$next_is_env and push @envvar, split/,/, $_;
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$next_is_env = /^--env$/;
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@ -66,12 +67,12 @@ function env_parallel
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}
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if(grep { /^_$/ } @envvar) {
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if(not open(IN, "<", "$ENV{HOME}/.parallel/ignored_vars")) {
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print STDERR "parallel: Error: ",
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print STDERR "parallel: Error: ",
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"Run \"parallel --record-env\" in a clean environment first.\n";
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} else {
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chomp(@ignored_vars = <IN>);
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$vars = join "|",map { quotemeta $_ } @ignored_vars;
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print $vars ? "($vars)" : "(nO,VaRs)";
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$vars = join "|",map { quotemeta $_ } "env_parallel", @ignored_vars;
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print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
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}
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}
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' -- $argv;
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@ -52,12 +52,12 @@ env_parallel() {
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}
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if(grep { /^_$/ } @envvar) {
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if(not open(IN, "<", "$ENV{HOME}/.parallel/ignored_vars")) {
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print STDERR "parallel: Error: ",
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"Run \"parallel --record-env\" in a clean environment first.\n";
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print STDERR "parallel: Error: ",
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"Run \"parallel --record-env\" in a clean environment first.\n";
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} else {
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chomp(@ignored_vars = <IN>);
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$vars = join "|",map { quotemeta $_ } @ignored_vars;
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print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
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chomp(@ignored_vars = <IN>);
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$vars = join "|",map { quotemeta $_ } "env_parallel", @ignored_vars;
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print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
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}
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}
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' -- "$@"
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@ -86,7 +86,7 @@ env_parallel() {
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# Grep variable names
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_variable_NAMES="$(typeset +p | perl -pe 's/^typeset .. //' |
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grep -E "^$_grep_REGEXP"\$ | grep -vE "^$_ignore_UNDERSCORE"\$ |
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egrep -v '^(PIPESTATUS)$')"
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grep -Ev '^(PIPESTATUS)$')"
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_list_variable_VALUES="typeset -p $_variable_NAMES"
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if [[ "$_variable_NAMES" = "" ]] ; then
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# no variables selected
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@ -52,12 +52,12 @@ env_parallel() {
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}
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if(grep { /^_$/ } @envvar) {
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if(not open(IN, "<", "$ENV{HOME}/.parallel/ignored_vars")) {
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print STDERR "parallel: Error: ",
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"Run \"parallel --record-env\" in a clean environment first.\n";
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print STDERR "parallel: Error: ",
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"Run \"parallel --record-env\" in a clean environment first.\n";
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} else {
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chomp(@ignored_vars = <IN>);
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$vars = join "|",map { quotemeta $_ } @ignored_vars;
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print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
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chomp(@ignored_vars = <IN>);
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$vars = join "|",map { quotemeta $_ } "env_parallel", @ignored_vars;
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print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
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}
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}
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' -- "$@"
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@ -15,25 +15,36 @@ B<env_parallel> [options for GNU Parallel]
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=head1 DESCRIPTION
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B<env_parallel> is a shell function that exports the current
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environment to GNU Parallel.
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environment to GNU B<parallel>.
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If the shell function is not loaded, a dummy script will be run
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instead that explains how to install the function.
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B<env_parallel> is alpha quality and not production ready.
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B<env_parallel> is beta quality and not production ready.
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B<env_parallel> is 0.1 sec slower at startup than pure GNU
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B<parallel>, and takes up to 15 ms to start a job.
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=head2 Environment space
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B<env_parallel> only works if the size of the current environment is
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smaller than the maximal length of a command and smaller than half of
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the max if running remotely. E.g. The max size of Bash's command is
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128 KB, so B<env_parallel> will fail if B<set | wc -c> is bigger than
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128 KB. Technically the limit is in execve(1) which IPC::open3 uses.
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By default B<env_parallel> will export all environment variables,
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arrays, aliases, functions and shell options (see details for the
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individual shells below).
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But this only works if the size of the current environment is smaller
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than the maximal length of a command and smaller than half of the max
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if running remotely. E.g. The max size of Bash's command is 128 KB, so
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B<env_parallel> will fail if B<set | wc -c> is bigger than 128
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KB. Technically the limit is in execve(1) which IPC::open3 uses.
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Bash completion functions are well-known for taking up well over 128
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KB of environment space and the primary reason for causing
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B<env_parallel> to fail.
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Instead you can use B<--env> to specify which variables, arrays,
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aliases and functions to export as this will only export those with
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the given name.
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=head1 OPTIONS
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@ -93,6 +104,268 @@ E.g. by doing:
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=back
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=head2 csh
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B<--env> is supported to export only the variable, alias, function, or
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array with the given name. Multiple B<--env>s can be given.
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B<env_parallel> for B<csh> breaks B<$PARALLEL>, so do not use
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B<$PARALLEL>.
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Installation
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Put this in $HOME/.cshrc:
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source `which env_parallel.csh`
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E.g. by doing:
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echo 'source `which env_parallel.csh`' >> $HOME/.cshrc
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=over 8
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=item aliases
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alias myecho echo
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env_parallel myecho ::: test
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env_parallel -S server myecho ::: test
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env_parallel --env myecho myecho ::: work
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env_parallel --env myecho -S server myecho ::: work
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=item functions
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Not supported by B<csh>.
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=item variables
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set myvar=test
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env_parallel echo "\$myvar" ::: test
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env_parallel -S csh@server echo "\$myvar" ::: test
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env_parallel --env myvar echo '$myvar' ::: work
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env_parallel --env myvar -S server echo '$myvar' ::: work
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=item arrays with no special chars
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set myarray=(foo bar baz)
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env_parallel echo "\${myarray\[\{\}\]}" ::: 1 2 3
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env_parallel -S csh@server echo "\${myarray\[\{\}\]}" ::: 1 2 3
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env_parallel -k --env myarray echo \$'{myarray[{}]}' ::: 1 2 3
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env_parallel -k --env myarray -S server echo \$'{myarray[{}]}' ::: 1 2 3
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=back
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=head2 fish
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B<--env> is supported to export only the variable, alias, function, or
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array with the given name. Multiple B<--env>s can be given.
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Installation
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Put this in $HOME/.config/fish/config.fish:
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source (which env_parallel.fish)
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E.g. by doing:
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echo 'source (which env_parallel.fish)' >> $HOME/.config/fish/config.fish
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=over 8
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=item aliases
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alias myecho 'echo aliases'
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env_parallel myecho ::: work
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env_parallel -S server myecho ::: work
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env_parallel --env myecho myecho ::: work
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env_parallel --env myecho -S server myecho ::: work
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=item functions
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function myfunc
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echo functions $argv
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end
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env_parallel myfunc ::: work
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env_parallel -S server myfunc ::: work
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env_parallel --env myfunc myfunc ::: work
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env_parallel --env myfunc -S server myfunc ::: work
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=item variables
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set myvar variables
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env_parallel echo '$myvar' ::: work
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env_parallel -S server echo '$myvar' ::: work
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env_parallel --env myvar echo '$myvar' ::: work
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env_parallel --env myvar -S server echo '$myvar' ::: work
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=item arrays
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set myarray arrays work, too
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env_parallel -k echo '$myarray[{}]' ::: 1 2 3
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env_parallel -k -S server echo '$myarray[{}]' ::: 1 2 3
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env_parallel -k --env myarray echo '$myarray[{}]' ::: 1 2 3
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env_parallel -k --env myarray -S server echo '$myarray[{}]' ::: 1 2 3
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=back
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=head2 ksh
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B<--env> is supported to export only the variable, alias, function, or
|
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array with the given name. Multiple B<--env>s can be given.
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|
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Installation
|
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|
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Put this in $HOME/.kshrc:
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|
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source `which env_parallel.ksh`
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|
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E.g. by doing:
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|
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echo 'source `which env_parallel.ksh`' >> $HOME/.kshrc
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=over 8
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=item aliases
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|
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alias myecho='echo aliases'
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env_parallel myecho ::: work
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env_parallel -S server myecho ::: work
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env_parallel --env myecho myecho ::: work
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env_parallel --env myecho -S server myecho ::: work
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=item functions
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myfunc() { echo functions $*; }
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env_parallel myfunc ::: work
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env_parallel -S server myfunc ::: work
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env_parallel --env myfunc myfunc ::: work
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env_parallel --env myfunc -S server myfunc ::: work
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=item variables
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myvar=variables
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env_parallel echo '$myvar' ::: work
|
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env_parallel -S server echo '$myvar' ::: work
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env_parallel --env myvar echo '$myvar' ::: work
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env_parallel --env myvar -S server echo '$myvar' ::: work
|
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|
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=item arrays
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myarray=(arrays work, too)
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env_parallel -k echo '${myarray[{}]}' ::: 0 1 2
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env_parallel -k -S server echo '${myarray[{}]}' ::: 0 1 2
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env_parallel -k --env myarray echo '${myarray[{}]}' ::: 0 1 2
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env_parallel -k --env myarray -S server echo '${myarray[{}]}' ::: 0 1 2
|
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|
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=back
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=head2 pdksh
|
||||
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B<--env> is supported to export only the variable, alias, function, or
|
||||
array with the given name. Multiple B<--env>s can be given.
|
||||
|
||||
Installation
|
||||
|
||||
Put this in $HOME/.profile:
|
||||
|
||||
source `which env_parallel.pdksh`
|
||||
|
||||
E.g. by doing:
|
||||
|
||||
echo 'source `which env_parallel.pdksh`' >> $HOME/.profile
|
||||
|
||||
=over 8
|
||||
|
||||
=item aliases
|
||||
|
||||
alias myecho="echo aliases";
|
||||
env_parallel myecho ::: work;
|
||||
env_parallel -S server myecho ::: work;
|
||||
env_parallel --env myecho myecho ::: work;
|
||||
env_parallel --env myecho -S server myecho ::: work
|
||||
|
||||
=item functions
|
||||
|
||||
myfunc() { echo functions $*; };
|
||||
env_parallel myfunc ::: work;
|
||||
env_parallel -S server myfunc ::: work;
|
||||
env_parallel --env myfunc myfunc ::: work;
|
||||
env_parallel --env myfunc -S server myfunc ::: work
|
||||
|
||||
=item variables
|
||||
|
||||
myvar=variables;
|
||||
env_parallel echo "\$myvar" ::: work;
|
||||
env_parallel -S server echo "\$myvar" ::: work;
|
||||
env_parallel --env myvar echo "\$myvar" ::: work;
|
||||
env_parallel --env myvar -S server echo "\$myvar" ::: work
|
||||
|
||||
=item arrays
|
||||
|
||||
myarray=(arrays work, too);
|
||||
env_parallel -k echo "\${myarray[{}]}" ::: 0 1 2;
|
||||
env_parallel -k -S server echo "\${myarray[{}]}" ::: 0 1 2;
|
||||
env_parallel -k --env myarray echo "\${myarray[{}]}" ::: 0 1 2;
|
||||
env_parallel -k --env myarray -S server echo "\${myarray[{}]}" ::: 0 1 2
|
||||
|
||||
=back
|
||||
|
||||
|
||||
=head2 tcsh
|
||||
|
||||
B<--env> is supported to export only the variable, alias, function, or
|
||||
array with the given name. Multiple B<--env>s can be given.
|
||||
|
||||
B<env_parallel> for B<tcsh> breaks B<$PARALLEL>, so do not use
|
||||
B<$PARALLEL>.
|
||||
|
||||
Installation
|
||||
|
||||
Put this in $HOME/.tcshrc:
|
||||
|
||||
source `which env_parallel.tcsh`
|
||||
|
||||
E.g. by doing:
|
||||
|
||||
echo 'source `which env_parallel.tcsh`' >> $HOME/.tcshrc
|
||||
|
||||
=over 8
|
||||
|
||||
=item aliases
|
||||
|
||||
alias myecho 'echo aliases'
|
||||
env_parallel myecho ::: work
|
||||
env_parallel -S server myecho ::: work
|
||||
env_parallel --env myecho myecho ::: work
|
||||
env_parallel --env myecho -S server myecho ::: work
|
||||
|
||||
=item functions
|
||||
|
||||
Not supported by B<tcsh>.
|
||||
|
||||
=item variables
|
||||
|
||||
set myvar=variables
|
||||
env_parallel echo '$myvar' ::: work
|
||||
env_parallel -S server echo '$myvar' ::: work
|
||||
env_parallel --env myvar echo '$myvar' ::: work
|
||||
env_parallel --env myvar -S server echo '$myvar' ::: work
|
||||
|
||||
=item arrays with no special chars
|
||||
|
||||
set myarray=(arrays work, too)
|
||||
env_parallel -k echo \$'{myarray[{}]}' ::: 1 2 3
|
||||
env_parallel -k -S server echo \$'{myarray[{}]}' ::: 1 2 3
|
||||
env_parallel -k --env myarray echo \$'{myarray[{}]}' ::: 1 2 3
|
||||
env_parallel -k --env myarray -S server echo \$'{myarray[{}]}' ::: 1 2 3
|
||||
|
||||
=back
|
||||
|
||||
|
||||
=head2 Zsh
|
||||
|
||||
B<--env> is supported to export only the variable, alias, function, or
|
||||
|
|
@ -144,248 +417,6 @@ E.g. by doing:
|
|||
|
||||
=back
|
||||
|
||||
=head2 fish
|
||||
|
||||
Installation
|
||||
|
||||
Put this in $HOME/.config/fish/config.fish:
|
||||
|
||||
source (which env_parallel.fish)
|
||||
|
||||
E.g. by doing:
|
||||
|
||||
echo 'source (which env_parallel.fish)' >> $HOME/.config/fish/config.fish
|
||||
|
||||
=over 8
|
||||
|
||||
=item aliases
|
||||
|
||||
alias myecho 'echo aliases'
|
||||
env_parallel myecho ::: work
|
||||
env_parallel -S server myecho ::: work
|
||||
env_parallel --env myecho myecho ::: work
|
||||
env_parallel --env myecho -S server myecho ::: work
|
||||
|
||||
=item functions
|
||||
|
||||
function myfunc
|
||||
echo functions $argv
|
||||
end
|
||||
env_parallel myfunc ::: work
|
||||
env_parallel -S server myfunc ::: work
|
||||
env_parallel --env myfunc myfunc ::: work
|
||||
env_parallel --env myfunc -S server myfunc ::: work
|
||||
|
||||
=item variables
|
||||
|
||||
set myvar variables
|
||||
env_parallel echo '$myvar' ::: work
|
||||
env_parallel -S server echo '$myvar' ::: work
|
||||
env_parallel --env myvar echo '$myvar' ::: work
|
||||
env_parallel --env myvar -S server echo '$myvar' ::: work
|
||||
|
||||
=item arrays
|
||||
|
||||
set myarray arrays work, too
|
||||
env_parallel -k echo '$myarray[{}]' ::: 1 2 3
|
||||
env_parallel -k -S server echo '$myarray[{}]' ::: 1 2 3
|
||||
env_parallel -k --env myarray echo '$myarray[{}]' ::: 1 2 3
|
||||
env_parallel -k --env myarray -S server echo '$myarray[{}]' ::: 1 2 3
|
||||
|
||||
=back
|
||||
|
||||
=head2 ksh
|
||||
|
||||
Installation
|
||||
|
||||
Put this in $HOME/.kshrc:
|
||||
|
||||
source `which env_parallel.ksh`
|
||||
|
||||
E.g. by doing:
|
||||
|
||||
echo 'source `which env_parallel.ksh`' >> $HOME/.kshrc
|
||||
|
||||
=over 8
|
||||
|
||||
=item aliases
|
||||
|
||||
alias myecho='echo aliases'
|
||||
env_parallel myecho ::: work
|
||||
env_parallel -S server myecho ::: work
|
||||
env_parallel --env myecho myecho ::: work
|
||||
env_parallel --env myecho -S server myecho ::: work
|
||||
|
||||
=item functions
|
||||
|
||||
myfunc() { echo functions $*; }
|
||||
env_parallel myfunc ::: work
|
||||
env_parallel -S server myfunc ::: work
|
||||
env_parallel --env myfunc myfunc ::: work
|
||||
env_parallel --env myfunc -S server myfunc ::: work
|
||||
|
||||
=item variables
|
||||
|
||||
myvar=variables
|
||||
env_parallel echo '$myvar' ::: work
|
||||
env_parallel -S server echo '$myvar' ::: work
|
||||
env_parallel --env myvar echo '$myvar' ::: work
|
||||
env_parallel --env myvar -S server echo '$myvar' ::: work
|
||||
|
||||
=item arrays
|
||||
|
||||
myarray=(arrays work, too)
|
||||
env_parallel -k echo '${myarray[{}]}' ::: 0 1 2
|
||||
env_parallel -k -S server echo '${myarray[{}]}' ::: 0 1 2
|
||||
env_parallel -k --env myarray echo '${myarray[{}]}' ::: 0 1 2
|
||||
env_parallel -k --env myarray -S server echo '${myarray[{}]}' ::: 0 1 2
|
||||
|
||||
=back
|
||||
|
||||
=head2 pdksh
|
||||
|
||||
Installation
|
||||
|
||||
Put this in $HOME/.profile:
|
||||
|
||||
source `which env_parallel.pdksh`
|
||||
|
||||
E.g. by doing:
|
||||
|
||||
echo 'source `which env_parallel.pdksh`' >> $HOME/.profile
|
||||
|
||||
=over 8
|
||||
|
||||
=item aliases
|
||||
|
||||
alias myecho="echo aliases";
|
||||
env_parallel myecho ::: work;
|
||||
env_parallel -S server myecho ::: work;
|
||||
env_parallel --env myecho myecho ::: work;
|
||||
env_parallel --env myecho -S server myecho ::: work
|
||||
|
||||
=item functions
|
||||
|
||||
myfunc() { echo functions $*; };
|
||||
env_parallel myfunc ::: work;
|
||||
env_parallel -S server myfunc ::: work;
|
||||
env_parallel --env myfunc myfunc ::: work;
|
||||
env_parallel --env myfunc -S server myfunc ::: work
|
||||
|
||||
=item variables
|
||||
|
||||
myvar=variables;
|
||||
env_parallel echo "\$myvar" ::: work;
|
||||
env_parallel -S server echo "\$myvar" ::: work;
|
||||
env_parallel --env myvar echo "\$myvar" ::: work;
|
||||
env_parallel --env myvar -S server echo "\$myvar" ::: work
|
||||
|
||||
=item arrays
|
||||
|
||||
myarray=(arrays work, too);
|
||||
env_parallel -k echo "\${myarray[{}]}" ::: 0 1 2;
|
||||
env_parallel -k -S server echo "\${myarray[{}]}" ::: 0 1 2;
|
||||
env_parallel -k --env myarray echo "\${myarray[{}]}" ::: 0 1 2;
|
||||
env_parallel -k --env myarray -S server echo "\${myarray[{}]}" ::: 0 1 2
|
||||
|
||||
=back
|
||||
|
||||
=head2 csh
|
||||
|
||||
B<env_parallel> for B<csh> breaks B<$PARALLEL>, so do not use
|
||||
B<$PARALLEL>.
|
||||
|
||||
Installation
|
||||
|
||||
Put this in $HOME/.cshrc:
|
||||
|
||||
source `which env_parallel.csh`
|
||||
|
||||
E.g. by doing:
|
||||
|
||||
echo 'source `which env_parallel.csh`' >> $HOME/.cshrc
|
||||
|
||||
=over 8
|
||||
|
||||
=item aliases
|
||||
|
||||
alias myecho echo
|
||||
env_parallel myecho ::: test
|
||||
env_parallel -S server myecho ::: test
|
||||
env_parallel --env myecho myecho ::: work
|
||||
env_parallel --env myecho -S server myecho ::: work
|
||||
|
||||
=item functions
|
||||
|
||||
Not supported by B<csh>.
|
||||
|
||||
=item variables
|
||||
|
||||
set myvar=test
|
||||
env_parallel echo "\$myvar" ::: test
|
||||
env_parallel -S csh@server echo "\$myvar" ::: test
|
||||
env_parallel --env myvar echo '$myvar' ::: work
|
||||
env_parallel --env myvar -S server echo '$myvar' ::: work
|
||||
|
||||
|
||||
=item arrays with no special chars
|
||||
|
||||
set myarray=(foo bar baz)
|
||||
env_parallel echo "\${myarray\[\{\}\]}" ::: 1 2 3
|
||||
env_parallel -S csh@server echo "\${myarray\[\{\}\]}" ::: 1 2 3
|
||||
env_parallel -k --env myarray echo \$'{myarray[{}]}' ::: 1 2 3
|
||||
env_parallel -k --env myarray -S server echo \$'{myarray[{}]}' ::: 1 2 3
|
||||
|
||||
=back
|
||||
|
||||
=head2 tcsh
|
||||
|
||||
B<env_parallel> for B<tcsh> breaks B<$PARALLEL>, so do not use
|
||||
B<$PARALLEL>.
|
||||
|
||||
Installation
|
||||
|
||||
Put this in $HOME/.tcshrc:
|
||||
|
||||
source `which env_parallel.tcsh`
|
||||
|
||||
E.g. by doing:
|
||||
|
||||
echo 'source `which env_parallel.tcsh`' >> $HOME/.tcshrc
|
||||
|
||||
=over 8
|
||||
|
||||
=item aliases
|
||||
|
||||
alias myecho 'echo aliases'
|
||||
env_parallel myecho ::: work
|
||||
env_parallel -S server myecho ::: work
|
||||
env_parallel --env myecho myecho ::: work
|
||||
env_parallel --env myecho -S server myecho ::: work
|
||||
|
||||
=item functions
|
||||
|
||||
Not supported by B<tcsh>.
|
||||
|
||||
=item variables
|
||||
|
||||
set myvar=variables
|
||||
env_parallel echo '$myvar' ::: work
|
||||
env_parallel -S server echo '$myvar' ::: work
|
||||
env_parallel --env myvar echo '$myvar' ::: work
|
||||
env_parallel --env myvar -S server echo '$myvar' ::: work
|
||||
|
||||
=item arrays with no special chars
|
||||
|
||||
set myarray=(arrays work, too)
|
||||
env_parallel -k echo \$'{myarray[{}]}' ::: 1 2 3
|
||||
env_parallel -k -S server echo \$'{myarray[{}]}' ::: 1 2 3
|
||||
env_parallel -k --env myarray echo \$'{myarray[{}]}' ::: 1 2 3
|
||||
env_parallel -k --env myarray -S server echo \$'{myarray[{}]}' ::: 1 2 3
|
||||
|
||||
=back
|
||||
|
||||
|
||||
|
||||
=head1 EXIT STATUS
|
||||
|
||||
|
|
@ -530,7 +561,10 @@ B<env_parallel> uses GNU B<parallel>.
|
|||
|
||||
=head1 SEE ALSO
|
||||
|
||||
B<parallel>(1), B<bash>(1), B<ksh>(1), B<zsh>(1), B<ksh>(1),
|
||||
B<pdksh>(1)
|
||||
B<parallel>(1),
|
||||
|
||||
B<bash>(1), B<csh>(1), B<fish>(1), B<ksh>(1), B<pdksh>(1) B<tcsh>(1),
|
||||
B<zsh>(1).
|
||||
|
||||
|
||||
=cut
|
||||
|
|
|
|||
|
|
@ -57,12 +57,12 @@ else
|
|||
}
|
||||
if(grep { /^_$/ } @envvar) {
|
||||
if(not open(IN, "<", "$ENV{HOME}/.parallel/ignored_vars")) {
|
||||
print STDERR "parallel: Error: ",
|
||||
"Run 'parallel --record-env' in a clean environment first.\n";
|
||||
print STDERR "parallel: Error: ",
|
||||
"Run \"parallel --record-env\" in a clean environment first.\n";
|
||||
} else {
|
||||
chomp(@ignored_vars = <IN>);
|
||||
$vars = join "|",map { quotemeta $_ } @ignored_vars;
|
||||
print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
|
||||
chomp(@ignored_vars = <IN>);
|
||||
$vars = join "|",map { quotemeta $_ } "env_parallel", @ignored_vars;
|
||||
print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
|
||||
}
|
||||
}
|
||||
'EOF'
|
||||
|
|
|
|||
|
|
@ -52,12 +52,12 @@ env_parallel() {
|
|||
}
|
||||
if(grep { /^_$/ } @envvar) {
|
||||
if(not open(IN, "<", "$ENV{HOME}/.parallel/ignored_vars")) {
|
||||
print STDERR "parallel: Error: ",
|
||||
"Run \"parallel --record-env\" in a clean environment first.\n";
|
||||
print STDERR "parallel: Error: ",
|
||||
"Run \"parallel --record-env\" in a clean environment first.\n";
|
||||
} else {
|
||||
chomp(@ignored_vars = <IN>);
|
||||
$vars = join "|",map { quotemeta $_ } @ignored_vars;
|
||||
print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
|
||||
chomp(@ignored_vars = <IN>);
|
||||
$vars = join "|",map { quotemeta $_ } "env_parallel", @ignored_vars;
|
||||
print $vars ? "($vars)" : "(,,nO,,VaRs,,)";
|
||||
}
|
||||
}
|
||||
' -- "$@"
|
||||
|
|
@ -86,11 +86,11 @@ env_parallel() {
|
|||
unset _function_NAMES
|
||||
|
||||
# Grep variable names
|
||||
# The egrep -v is crap and should be better
|
||||
# The grep -Ev is crap and should be better
|
||||
_variable_NAMES="$(print -l ${(k)parameters} |
|
||||
grep -E "^$_grep_REGEXP"\$ | grep -vE "^$_ignore_UNDERSCORE"\$ |
|
||||
egrep -v '^([-?#!$*@_0]|zsh_eval_context|ZSH_EVAL_CONTEXT|LINENO|IFS|commands|functions|options|aliases|EUID|EGID|UID|GID)$' |
|
||||
egrep -v 'terminfo|funcstack|galiases|keymaps|parameters|jobdirs|dirstack|functrace|funcsourcetrace|zsh_scheduled_events|dis_aliases|dis_reswords|dis_saliases|modules|reswords|saliases|widgets|userdirs|historywords|nameddirs|termcap|dis_builtins|dis_functions|jobtexts|funcfiletrace|dis_galiases|builtins|history|jobstates'
|
||||
grep -Ev '^([-?#!$*@_0]|zsh_eval_context|ZSH_EVAL_CONTEXT|LINENO|IFS|commands|functions|options|aliases|EUID|EGID|UID|GID)$' |
|
||||
grep -Ev 'terminfo|funcstack|galiases|keymaps|parameters|jobdirs|dirstack|functrace|funcsourcetrace|zsh_scheduled_events|dis_aliases|dis_reswords|dis_saliases|modules|reswords|saliases|widgets|userdirs|historywords|nameddirs|termcap|dis_builtins|dis_functions|jobtexts|funcfiletrace|dis_galiases|builtins|history|jobstates'
|
||||
)"
|
||||
_list_variable_VALUES="typeset -p "$(echo $_variable_NAMES|xargs)" |
|
||||
grep -aFvf <(typeset -pr)
|
||||
|
|
|
|||
|
|
@ -3734,7 +3734,7 @@ sub citation {
|
|||
" url = {http://www.gnu.org/s/parallel},",
|
||||
" year = {2011},",
|
||||
" pages = {42-47},",
|
||||
" doi = {10.5281/zenodo.16303}",
|
||||
" doi = {http://dx.doi.org/10.5281/zenodo.16303}",
|
||||
"}",
|
||||
"",
|
||||
"(Feel free to use \\nocite{Tange2011a})",
|
||||
|
|
|
|||
|
|
@ -266,6 +266,14 @@ shell quote a string
|
|||
|
||||
number of jobs in total
|
||||
|
||||
=item Z<> B<$job->slot()>
|
||||
|
||||
slot number of job
|
||||
|
||||
=item Z<> B<$job->seq()>
|
||||
|
||||
sequence number of job
|
||||
|
||||
=back
|
||||
|
||||
Example:
|
||||
|
|
@ -1476,7 +1484,7 @@ sequence numbers in B<--joblog> then the input, the command, and
|
|||
B<--joblog> all have to remain unchanged; otherwise GNU B<parallel>
|
||||
may run wrong commands.
|
||||
|
||||
See also B<--joblog>, B<--results>, B<--resume-failed>.
|
||||
See also B<--joblog>, B<--results>, B<--resume-failed>, B<--retries>.
|
||||
|
||||
|
||||
=item B<--resume-failed>
|
||||
|
|
@ -1489,7 +1497,7 @@ numbers in B<--joblog> then the input, the command, and B<--joblog>
|
|||
all have to remain unchanged; otherwise GNU B<parallel> may run wrong
|
||||
commands.
|
||||
|
||||
See also B<--joblog>, B<--resume>.
|
||||
See also B<--joblog>, B<--resume>, B<--retry-failed>, B<--retries>.
|
||||
|
||||
|
||||
=item B<--retry-failed>
|
||||
|
|
@ -1497,10 +1505,66 @@ See also B<--joblog>, B<--resume>.
|
|||
Retry all failed jobs in joblog. By reading B<--joblog> GNU
|
||||
B<parallel> will figure out the failed jobs and run those again.
|
||||
|
||||
B<--retry-failed> ignore the command and arguments: It only looks at
|
||||
the joblog.
|
||||
B<--retry-failed> ignores the command and arguments on the command
|
||||
line: It only looks at the joblog.
|
||||
|
||||
See also B<--joblog>, B<--resume>, B<--resume-failed>.
|
||||
B<Differences between --resume, --resume-failed, --retry-failed>
|
||||
|
||||
In this example B<exit {= $_%=2 =}> will cause every other job to fail.
|
||||
|
||||
timeout -k 1 4 parallel --joblog log -j10 'sleep {}; exit {= $_%=2 =}' ::: {10..1}
|
||||
|
||||
4 jobs completed. 2 failed:
|
||||
|
||||
Seq [...] Exitval Signal Command
|
||||
10 [...] 1 0 sleep 1; exit 1
|
||||
9 [...] 0 0 sleep 2; exit 0
|
||||
8 [...] 1 0 sleep 3; exit 1
|
||||
7 [...] 0 0 sleep 4; exit 0
|
||||
|
||||
B<--resume> does not care about the Exitval, but only looks at Seq. If
|
||||
the Seq is run, it will not be run again. So if needed, you can change
|
||||
the command for the seqs not run yet:
|
||||
|
||||
parallel --resume --joblog log -j10 'sleep .{}; exit {= $_%=2 =}' ::: {10..1}
|
||||
|
||||
Seq [...] Exitval Signal Command
|
||||
[... as above ...]
|
||||
1 [...] 0 0 sleep .10; exit 0
|
||||
6 [...] 1 0 sleep .5; exit 1
|
||||
5 [...] 0 0 sleep .6; exit 0
|
||||
4 [...] 1 0 sleep .7; exit 1
|
||||
3 [...] 0 0 sleep .8; exit 0
|
||||
2 [...] 1 0 sleep .9; exit 1
|
||||
|
||||
B<--resume-failed> cares about the Exitval, but also only looks at Seq
|
||||
to figure out which commands to run. Again this means you can change
|
||||
the command, but not the arguments. It will run the failed seqs and
|
||||
the seqs not yet run:
|
||||
|
||||
parallel --resume-failed --joblog log -j10 'echo {};sleep .{}; exit {= $_%=3 =}' ::: {10..1}
|
||||
|
||||
Seq [...] Exitval Signal Command
|
||||
[... as above ...]
|
||||
10 [...] 1 0 echo 1;sleep .1; exit 1
|
||||
8 [...] 0 0 echo 3;sleep .3; exit 0
|
||||
6 [...] 2 0 echo 5;sleep .5; exit 2
|
||||
4 [...] 1 0 echo 7;sleep .7; exit 1
|
||||
2 [...] 0 0 echo 9;sleep .9; exit 0
|
||||
|
||||
B<--retry-failed> cares about the Exitval, but takes the command from
|
||||
the joblog. It ignores any arguments or commands given on the command
|
||||
line:
|
||||
|
||||
parallel --retry-failed --joblog log -j10 this part is ignored
|
||||
|
||||
Seq [...] Exitval Signal Command
|
||||
[... as above ...]
|
||||
10 [...] 1 0 echo 1;sleep .1; exit 1
|
||||
6 [...] 2 0 echo 5;sleep .5; exit 2
|
||||
4 [...] 1 0 echo 7;sleep .7; exit 1
|
||||
|
||||
See also B<--joblog>, B<--resume>, B<--resume-failed>, B<--retries>.
|
||||
|
||||
|
||||
=item B<--retries> I<n>
|
||||
|
|
@ -1609,6 +1673,8 @@ Here are a few examples:
|
|||
--rpl '{0#} $f = "%0".int(1+log(total_jobs())/log(10))."d"; $_=sprintf($f,$job->seq())'
|
||||
Job sequence counting from 0
|
||||
--rpl '{#0} $_ = $job->seq() - 1'
|
||||
Job slot counting from 2
|
||||
--rpl '{%1} $_ = $job->slot() + 1'
|
||||
|
||||
See also: B<{= perl expression =}> B<--parens>
|
||||
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@ par_tmp_full() {
|
|||
# Assume /tmp/shm is easy to fill up
|
||||
export SHM=/tmp/shm/parallel
|
||||
mkdir -p $SHM
|
||||
sudo umount -l $SHM
|
||||
sudo umount -l $SHM 2>/dev/null
|
||||
sudo mount -t tmpfs -o size=10% none $SHM
|
||||
|
||||
echo "### Test --tmpdir running full. bug #40733 was caused by this"
|
||||
|
|
|
|||
|
|
@ -62,13 +62,13 @@ par_bash_underscore aliases in and arrays in functions work
|
|||
par_bash_underscore aliases in and arrays in functions work
|
||||
par_bash_underscore aliases in functions work
|
||||
par_bash_underscore aliases in functions work
|
||||
par_bash_underscore /bin/bash: line 139: myecho: command not found
|
||||
par_bash_underscore /bin/bash: line 70: myecho: command not found
|
||||
par_bash_underscore OK if no myecho ^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
par_bash_underscore /bin/bash: line 139: myecho: command not found
|
||||
par_bash_underscore /bin/bash: line 70: myecho: command not found
|
||||
par_bash_underscore OK if no myecho ^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
par_bash_underscore /bin/bash: line 136: myfunc: command not found
|
||||
par_bash_underscore /bin/bash: line 68: myfunc: command not found
|
||||
par_bash_underscore OK if no myfunc ^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
par_bash_underscore /bin/bash: line 136: myfunc: command not found
|
||||
par_bash_underscore /bin/bash: line 68: myfunc: command not found
|
||||
par_bash_underscore OK if no myfunc ^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
par_csh_funky 3 arg alias_works
|
||||
par_csh_funky myvar works
|
||||
|
|
@ -274,13 +274,13 @@ par_ksh_underscore aliases in and arrays in functions work
|
|||
par_ksh_underscore aliases in and arrays in functions work
|
||||
par_ksh_underscore aliases in functions work
|
||||
par_ksh_underscore aliases in functions work
|
||||
par_ksh_underscore /usr/bin/ksh[193]: myecho: not found [No such file or directory]
|
||||
par_ksh_underscore /usr/bin/ksh[113]: myecho: not found [No such file or directory]
|
||||
par_ksh_underscore OK if no myecho ^^^^^^^^^^^^^^^^^
|
||||
par_ksh_underscore /usr/bin/ksh[193]: myecho: not found [No such file or directory]
|
||||
par_ksh_underscore /usr/bin/ksh[113]: myecho: not found [No such file or directory]
|
||||
par_ksh_underscore OK if no myecho ^^^^^^^^^^^^^^^^^
|
||||
par_ksh_underscore /usr/bin/ksh: line 193: myfunc: not found
|
||||
par_ksh_underscore /usr/bin/ksh: line 113: myfunc: not found
|
||||
par_ksh_underscore OK if no myfunc ^^^^^^^^^^^^^^^^^
|
||||
par_ksh_underscore /usr/bin/ksh: line 193: myfunc: not found
|
||||
par_ksh_underscore /usr/bin/ksh: line 113: myfunc: not found
|
||||
par_ksh_underscore OK if no myfunc ^^^^^^^^^^^^^^^^^
|
||||
par_pdksh_funky 3 arg alias_works
|
||||
par_pdksh_funky function_works
|
||||
|
|
|
|||
Loading…
Reference in a new issue