mirror of
https://git.savannah.gnu.org/git/parallel.git
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parallel: Use open3(x,x,x,"-") for setpgrp if available.
This commit is contained in:
Ole Tange
parent
58fc7e7c7c
commit
4e90972584
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@ -32,11 +32,10 @@ measure() {
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INNER=$2
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CORES=$3
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VERSION=$4
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GHZ=3.0
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MHZ=1700
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# Force cpuspeed at 1.7GHz - seems to give tighter results
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# forever 'sleep 10;parallel sudo cpufreq-set -f ${GHZ}GHz -c{} ::: {0..7}' &
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# forever 'sleep 10;parallel sudo cpufreq-set -f 1700MHz -c{} ::: {0..7}' &
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forever 'parallel sudo cpufreq-set -g performance -u '$MHZ'MHz -d '$MHZ'MHz -c{} ::: {0..3};sleep 10' &
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PATH=/tmp/bin:$PATH
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cd /tmp/bin
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@ -52,8 +51,11 @@ measure() {
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boxplot(JobRuntime/$INNER*1000~Command,data=jl,las=2,outline=F,
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ylab="milliseconds/job",main="GNU Parallel performance\n$OUTER trials each running $INNER");
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_
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cp /tmp/boxplot.pdf $HOME/tmp/boxplot-j$CORES-${GHZ}ghz-$OUTER-${INNER}v$VERSION.pdf
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cp /tmp/boxplot.pdf $HOME/tmp/boxplot-j$CORES-${MHZ}MHz-$OUTER-${INNER}v$VERSION.pdf
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evince /tmp/boxplot.pdf
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}
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#measure 3000 1000 2 1
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measure 30 10 2 1
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measure 300 100 2 1
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measure 3000 1000 2 1
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@ -227,17 +227,19 @@ GNU Parallel 20160522 ('ttipleaks') <<[stable]>> has been released. It is availa
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Haiku of the month:
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<<>>
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Programs using net
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only spare capacity
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niceload dash dash net
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-- Ole Tange
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New in this release:
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* niceload --net
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*
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* niceload --net pauses the program if the internet connection is overloaded.
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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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* Updated speed comparison between versions https://www.gnu.org/software/parallel/process-time-j2-1700MHz-3000-1000.pdf
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* << kontakt GNU Parallel was used (unfortunately without citation) in: Instrumentation and Trace Analysis for Ad-hoc Python Workflows in Cloud Environments http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7214035>>
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* <<Har angiveligt submittet ny version - afventer opdatering>> GNU Parallel was used (unfortunately without citation) in: MUGBAS: a species free gene-based programme suite for post-GWAS analysis http://www.ncbi.nlm.nih.gov/pubmed/25765345
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@ -254,7 +256,41 @@ for Big Data Applications https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumb
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* <<Citation needed: Introspecting for RSA Key Material to Assist Intrusion Detection http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=7331177&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7331177>>
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* GNU Parallel was cited in: Structure and evolutionary history of a large family of NLR proteins in the zebrafish http://rsob.royalsocietypublishing.org/content/royopenbio/6/4/160009.full.pdf
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* <<Citation needed: 3D-GNOME: an integrated web service for structural modeling of the 3D genome http://nar.oxfordjournals.org/content/early/2016/05/16/nar.gkw437.full.pdf+html>>
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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: Improving computation efficiency by parallel programming http://www.irbis-nbuv.gov.ua/cgi-bin/irbis_nbuv/cgiirbis_64.exe?C21COM=2&I21DBN=UJRN&P21DBN=UJRN&IMAGE_FILE_DOWNLOAD=1&Image_file_name=PDF/ape_2013_3_44.pdf
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* GNU Parallel was cited in: A supernova feedback implementation for the astrophysical simulation software Arepo https://arxiv.org/abs/1604.06071
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* GNU Parallel was cited in: Lorenz-Mie theory for 2D scattering and resonance calculations https://arxiv.org/pdf/1505.07691v2.pdf
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* GNU Parallel was cited in: Host-pathogen co-evolution and the emergence of broadly neutralizing antibodies in chronic infections https://arxiv.org/abs/1512.06296
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* GNU Parallel was cited in: Pacific People, Metabolic Disease and Evolutionary Processes: a mitochondrial DNA study https://otago.ourarchive.ac.nz/handle/10523/6340
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* GNU Parallel was cited in: The effect of domain modeling on efficiency of planning: Lessons from the Nomystery domain http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=7407131
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* GNU Parallel was cited in: Oops, my tests broke the build: An analysis of Travis CI buildswith GitHub https://peerj.com/preprints/1984/
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* GNU Parallel was cited in: Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution http://www.g3journal.org/content/5/5/719.full.pdf+html
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* GNU Parallel was cited in: An Empirical Comparison of Neural Architectures for Reinforcement Learning in Partially Observable Environments http://biorxiv.org/content/biorxiv/early/2016/03/24/022707.full.pdf
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* GNU Parallel was cited in: Functional enrichments of disease variants across thousands of independent loci in eight diseases http://biorxiv.org/content/early/2016/04/11/048066.abstract
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* GNU Parallel was cited in: PleaseTM: Enabling Transaction Conflict Management in Requester-wins Hardware Transactional Memory http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7446072
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* GNU Parallel was cited in: EASE-MM: Sequence-Based Prediction of Mutation-Induced Stability Changes with Feature-Based Multiple Models http://www.sciencedirect.com/science/article/pii/S0022283616000310
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* GNU Parallel was cited in: A new orthology assessment method for phylogenomic data: Unrooted Phylogenetic Orthology http://mbe.oxfordjournals.org/content/early/2016/04/06/molbev.msw069.short https://github.com/ballesterus/UPhO
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* GNU Parallel was cited in: Distinctive Interest Point Selection for Efficient Near-duplicate Image Retrieval http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7459172
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* GNU Parallel was cited in: The Evolution of C Programming Practices: A Study of the Unix Operating System 1973–2015 https://dl.acm.org/citation.cfm?id=2884799 (It has the cutest thumbnail graphs I have ever seen scattered all over the text)
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* GNU Parallel was cited in: StrAuto: Automation and Parallelization of STRUCTURE Analysis http://vchhatre.w3.uvm.edu/download/strauto/strauto_doc.pdf
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* GNU Parallel was cited in: Data processing pipeline for serial femtosecond crystallography at SACLA http://journals.iucr.org/j/issues/2016/03/00/zw5001/index.html
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@ -274,16 +310,24 @@ for Big Data Applications https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumb
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* GNU Parallel was cited in: How attention influences perceptual decision making: Single-trial EEG correlates of drift-diffusion model parameters http://www.cidlab.com/prints/nunez2016attention.pdf
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* GNU Parallel was cited in: Telomere And Proximal Sequence Analysis Using High-Throughput Sequencing Reads http://repository.upenn.edu/edissertations/1460/
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* GNU Parallel was cited in: AT-GIS: Highly Parallel Spatial Query Processing with Associative Transducers http://lsds.doc.ic.ac.uk/sites/default/files/ATGIS-SIGMOD16.pdf
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* GNU Parallel was cited in: PVAIR: Partial Variable Assignment InterpolatoR http://verify.inf.usi.ch/sites/default/files/main-2.pdf
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* GNU Parallel was cited in: Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life http://opus.bath.ac.uk/43955/
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* GNU Parallel was cited in: Shannon: An Information-Optimal de NovoRNA-Seq Assembler http://biorxiv.org/content/biorxiv/early/2016/02/09/039230.full.pdf
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* GNU Parallel was cited in: Adaptive Measure-Theoretic Parameter Estimation for Coastal Ocean Modeling https://repositories.lib.utexas.edu/handle/2152/32435
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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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* GNU Parallel was cited in: Reference genotype and exome data from an Australian Aboriginal population for health-based research http://www.nature.com/articles/sdata201623
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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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* GNU Parallel was cited in: Do aye-ayes echolocate? http://biorxiv.org/content/biorxiv/early/2016/04/11/048165.full.pdf
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* GNU Parallel was cited in: Functional enrichments of disease variants across thousands of independent loci in eight diseases http://biorxiv.org/content/biorxiv/early/2016/04/11/048066.full.pdf
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@ -321,7 +321,7 @@ sub get_options_from_array {
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$opt::load = -1;
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}
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if($opt::net) {
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$opt::nethops ||= 2;
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$opt::nethops ||= 3;
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}
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if($opt::nethops) {
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# niceload -l 0.01 --sensor 'netsensor_script'
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@ -104,7 +104,7 @@ B<--noswap> will set both B<--start-noswap> and B<run-noswap>.
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=item B<--net> (alpha testing)
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Shorthand for B<--nethops 2>.
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Shorthand for B<--nethops 3>.
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=item B<--nethops> I<h> (alpha testing)
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19
src/parallel
19
src/parallel
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@ -7482,7 +7482,7 @@ sub start {
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eval {
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if(not $pid = ::open3($stdin_fh, ">&OUT", ">&ERR", "-")) {
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# Each child gets its own process group to make it safe to killall
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setpgrp(0,0);
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setpgrp(0,0) || ::die_bug("setpgrp failed");
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exec("exec $Global::shell -c ".::shell_quote_scalar_default($command))
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|| ::die_bug("open3-$stdin_fh $command");
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}
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@ -7520,16 +7520,23 @@ sub start {
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}
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sub open3_setpgrp {
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# If the OS supports open3(x,x,x,"-") use that
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# eval { if(not $pid=::open3($i,$o,$e,"-")) { exit } }
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# if $!: external
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# TODO build a selector that works with out side effects
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# Select and run open3_setpgrp_internal/open3_setpgrp_external
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# parallel -j0 --timeout 5 '( (sleep {}) & )& sleep 7' ::: {1..55} &
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# ps -opid,ppid,pgrp,cmd
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# parallel --timeout 6 -q perl -e 'sleep(1);if(fork()){sleep(30)}while(not fork and $t++<30000){ }' ::: 1
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# perl -e 'sleep(1);if(fork()){sleep(3)}while(not fork and time-$^T<8){ }'
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no warnings 'redefine';
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if(1) {
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my ($outfh,$name) = ::tmpfile(SUFFIX => ".tst");
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# Test to see if open3(,,,"-") is supported
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my $script = 'if(not $pid=::open3($i,$o,$e,"-")) { unlink shift }';
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qx{ perl -MIPC::Open3 -e '$script' $name };
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if(-e $name) {
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# Does not support open3(x,x,x,"-")
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unlink($name);
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*open3_setpgrp = \&open3_setpgrp_external;
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} else {
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# Supports open3(x,x,x,"-")
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# This is 0.5 ms faster to run
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*open3_setpgrp = \&open3_setpgrp_internal;
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}
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# The sub is now redefined. Call it
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@ -1272,10 +1272,10 @@ with 'y' or 'Y'. Implies B<-t>.
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=item B<--parens> I<parensstring>
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Use to define start and end parenthesis for B<{= perl expression =}>. The
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Define start and end parenthesis for B<{= perl expression =}>. The
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left and the right parenthesis can be multiple characters and are
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assumed to be the same length. The default is B<{==}> giving
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B<{=> as the start parenthesis and B<=}> as the end parenthesis.
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assumed to be the same length. The default is B<{==}> giving B<{=> as
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the start parenthesis and B<=}> as the end parenthesis.
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Another useful setting is B<,,,,> which would make both parenthesis
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B<,,>:
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@ -1546,7 +1546,7 @@ it possible to define your own replacement strings. GNU B<parallel>'s
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--rpl '{/.} s:.*/::; s:\.[^/.]+$::;'
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--rpl '{.} s:\.[^/.]+$::'
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The <--plus> replacement strings are implemented as:
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The B<--plus> replacement strings are implemented as:
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--rpl '{+/} s:/[^/]*$::'
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--rpl '{+.} s:.*\.::'
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@ -1567,12 +1567,12 @@ of GNU B<parallel>'s internal functions and data structures.
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Here are a few examples:
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Remove 2 extensions (e.g. .tar.gz)
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--rpl '{..} s:\.[^/.]+$::;s:\.[^/.]+$::;'
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Keep only the extension
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--rpl '{ext} s:.*\.::'
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Is the job sequence even or odd?
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--rpl '{odd} $_=$job->seq()%2?"odd":"even"'
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--rpl '{odd} $_ = $job->seq() % 2 ? "odd" : "even"'
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Pad job sequence with leading zeros to get equal width
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--rpl '{0#} $f = "%0".int(1+log(total_jobs())/log(10))."d"; $_=sprintf($f,$job->seq())'
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Job sequence counting from 0
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--rpl '{#0} $_ = $job->seq() - 1'
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See also: B<{= perl expression =}> B<--parens>
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@ -1981,13 +1981,13 @@ Use B<tmux> for output. Start a B<tmux> session and run each job in a
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window in that session. No other output will be produced.
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=item B<--timeout> I<val>
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=item B<--timeout> I<secs>
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Time out for command. If the command runs for longer than I<val>
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Time out for command. If the command runs for longer than I<secs>
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seconds it will get killed with SIGTERM, followed by SIGTERM 200 ms
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later, followed by SIGKILL 200 ms later.
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If I<val> is followed by a % then the timeout will dynamically be
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If I<secs> is followed by a % then the timeout will dynamically be
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computed as a percentage of the median average runtime. Only values
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> 100% will make sense.
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@ -2561,7 +2561,7 @@
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Web site: http://www.gnu.org/software/parallel
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When using programs that use GNU Parallel to process data for publication
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please cite as described in 'parallel --bibtex'.</code></pre>
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please cite as described in 'parallel --citation'.</code></pre>
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<p>In scripts <b>--minversion</b> can be used to ensure the user has at least this version:</p>
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@ -2572,9 +2572,9 @@
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<pre><code> 20160322
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Your version is at least 20130722.</code></pre>
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<p>If using GNU <b>parallel</b> for research the BibTeX citation can be generated using <b>--bibtex</b>:</p>
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<p>If you are using GNU <b>parallel</b> for research the BibTeX citation can be generated using <b>--citation</b>:</p>
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<pre><code> parallel --bibtex</code></pre>
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<pre><code> parallel --citation</code></pre>
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<p>Output:</p>
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@ -2661,10 +2661,10 @@
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<li><p>(Re-)walk through the tutorial if you have not done so in the past year (http://www.gnu.org/software/parallel/parallel_tutorial.html)</p>
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</li>
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<li><p>Give a demo at your local user group/team/colleagues</p>
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<li><p>Give a demo at your local user group/your team/your colleagues</p>
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</li>
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<li><p>Post the intro videos and the tutorial on Reddit, Diaspora*, forums, blogs, Identi.ca, Google+, Twitter, Facebook, Linkedin, mailing lists</p>
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<li><p>Post the intro videos and the tutorial on Reddit, Diaspora*, forums, blogs, Identi.ca, Google+, Twitter, Facebook, Linkedin, and mailing lists</p>
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</li>
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<li><p>Request or write a review for your favourite blog or magazine (especially if you do something cool with GNU <b>parallel</b>)</p>
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@ -2679,7 +2679,7 @@
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<ul>
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<li><p>Please cite GNU <b>parallel</b> in you publications (use <b>--bibtex</b>)</p>
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<li><p>Please cite GNU <b>parallel</b> in you publications (use <b>--citation</b>)</p>
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</li>
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</ul>
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@ -2603,7 +2603,7 @@ Output:
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Web site: http://www.gnu.org/software/parallel
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When using programs that use GNU Parallel to process data for publication
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please cite as described in 'parallel --bibtex'.
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please cite as described in 'parallel --citation'.
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In scripts B<--minversion> can be used to ensure the user has at least
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this version:
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@ -2615,10 +2615,10 @@ Output:
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20160322
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Your version is at least 20130722.
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If using GNU B<parallel> for research the BibTeX citation can be
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generated using B<--bibtex>:
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If you are using GNU B<parallel> for research the BibTeX citation can be
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generated using B<--citation>:
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parallel --bibtex
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parallel --citation
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Output:
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@ -2714,13 +2714,13 @@ If you like GNU B<parallel>:
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=item *
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Give a demo at your local user group/team/colleagues
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Give a demo at your local user group/your team/your colleagues
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=item *
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Post the intro videos and the tutorial on Reddit, Diaspora*,
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forums, blogs, Identi.ca, Google+, Twitter, Facebook, Linkedin,
|
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mailing lists
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and mailing lists
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=item *
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@ -2739,7 +2739,7 @@ If you use GNU B<parallel> for research:
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=item *
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Please cite GNU B<parallel> in you publications (use B<--bibtex>)
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Please cite GNU B<parallel> in you publications (use B<--citation>)
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=back
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@ -16,7 +16,7 @@ S_POLAR=`parallel -k echo -S 1/{}.polarhome.com ::: $P`
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# 20150414 --timeout 80 -> 40
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# 20151219 --retries 5 -> 2
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TIMEOUT=10
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RETRIES=2
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RETRIES=4
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echo '### Tests on polarhome machines'
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echo 'Setup on polarhome machines'
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@ -1269,7 +1269,7 @@ please cite as described in 'parallel --citation'.
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parallel --minversion VERSION && echo Your version is at least VERSION.
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VERSION
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Your version is at least VERSION.
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parallel --bibtex
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parallel --citation
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Academic tradition requires you to cite works you base your article on.
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When using programs that use GNU Parallel to process data for publication
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please cite:
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