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parallel: Fixed bug #59893: --halt soon doesn't work with --delay.
This commit is contained in:
Ole Tange
parent
f539554727
commit
b210039626
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@ -14,6 +14,15 @@ that it is cited. The citation notice makes users aware of this.
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See also: https://lists.gnu.org/archive/html/parallel/2013-11/msg00006.html
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The funding of free software is hard. There does not seem to be a
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single solution that just works:
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* https://stackoverflow.blog/2021/01/07/open-source-has-a-funding-problem/
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* https://www.slideshare.net/NadiaEghbal/consider-the-maintainer
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* https://www.youtube.com/watch?v=vTsc1m78BUk
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* https://blog.licensezero.com/2019/08/24/process-of-elimination.html
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* https://www.numfocus.org/blog/why-is-numpy-only-now-getting-funded/
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> Is the citation notice compatible with GPLv3?
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@ -95,6 +104,7 @@ refer to peer-reviewed articles - others do not:
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* https://www.open-mpi.org/papers/
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* https://www.tensorflow.org/about/bib
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* http://www.fon.hum.uva.nl/paul/praat.html
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* https://github.com/UnixJunkie/PAR/blob/master/README
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> I do not like the notice. Can I fork GNU Parallel and remove it?
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@ -1,5 +1,8 @@
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Quote of the month:
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Try GNU parallel it's awesome, and exactly the thing you are looking for. It allows you to set number of processes running among many things. I use it a lot, and can't recommend it enough.
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-- mapettheone@reddit
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It's really quite amazing how powerful and flexible it is
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-- schwanengesang @tensegrist@twitter
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@ -192,7 +192,7 @@ from:tange@gnu.org
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to:parallel@gnu.org, bug-parallel@gnu.org
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stable-bcc: Jesse Alama <jessealama@fastmail.fm>
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Subject: GNU Parallel 20210122 ('Capitol Riots') released <<[stable]>>
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Subject: GNU Parallel 20210122 ('Ask/Capitol Riots') released <<[stable]>>
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GNU Parallel 20210122 ('') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
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@ -206,6 +206,11 @@ Quote of the month:
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<<>>
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New in this release:
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* $PARALLEL_ARGHOSTGROUPS and the replacement string {agrp} will give the hostgroup given on the argument when using --hostgroup.
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* Handy time functions for {= =}: yyyy_mm_dd_hh_mm_ss() yyyy_mm_dd_hh_mm() yyyy_mm_dd() yyyymmddhhmmss() yyyymmddhhmm() yyyymmdd()
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<<>>
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@ -215,6 +220,10 @@ News about GNU Parallel:
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https://www.codenong.com/25172209/
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https://qiita.com/hana_shin/items/53c3c78525c9c758ae7c
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https://canvas.stanford.edu/courses/133091
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<<>>
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Get the book: GNU Parallel 2018 http://www.lulu.com/shop/ole-tange/gnu-parallel-2018/paperback/product-23558902.html
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17
src/parallel
17
src/parallel
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@ -10624,16 +10624,15 @@ sub set_exitsignal($$) {
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} elsif($Global::halt_success) {
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$Global::halt_exitstatus = 0;
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}
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if($Global::halt_when eq "soon"
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and
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(scalar(keys %Global::running) > 0
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or
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$Global::max_jobs_running == 1)) {
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::status
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("$Global::progname: Starting no more jobs. ".
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"Waiting for ". (keys %Global::running).
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" jobs to finish.");
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if($Global::halt_when eq "soon") {
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$Global::start_no_new_jobs ||= 1;
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if(scalar(keys %Global::running) > 0) {
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# Only warn if there are more jobs running
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::status
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("$Global::progname: Starting no more jobs. ".
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"Waiting for ". (keys %Global::running).
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" jobs to finish.");
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}
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}
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return($Global::halt_when);
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}
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@ -322,6 +322,10 @@ perl quote a string
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do not quote current replacement string
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=item Z<> B<hash(val)>
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compute B::hash(val)
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=item Z<> B<total_jobs()>
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number of jobs in total
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@ -2201,7 +2201,9 @@ is sendt to stdout (standard output) and prepended with e:.
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For short jobs with little output B<par> is 20% faster than GNU
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B<parallel> and 60% slower than B<xargs>.
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http://savannah.nongnu.org/projects/par (Last checked: 2019-02)
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https://github.com/UnixJunkie/PAR
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https://savannah.nongnu.org/projects/par (Last checked: 2019-02)
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=head2 DIFFERENCES BETWEEN fd AND GNU Parallel
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@ -2555,15 +2557,17 @@ output to stderr (this can be prevented with -q)
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scanme.nmap.org 443
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EOF
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cat /tmp/host-port.txt | \
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runp -q -p 'netcat -v -w2 -z' 2>&1 | egrep '(succeeded!|open)$'
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1$ cat /tmp/host-port.txt |
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runp -q -p 'netcat -v -w2 -z' 2>&1 | egrep '(succeeded!|open)$'
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# --colsep is needed to split the line
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cat /tmp/host-port.txt | \
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parallel --colsep ' ' netcat -v -w2 -z 2>&1 | egrep '(succeeded!|open)$'
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1$ cat /tmp/host-port.txt |
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parallel --colsep ' ' netcat -v -w2 -z 2>&1 |
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egrep '(succeeded!|open)$'
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# or use uq for unquoted:
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cat /tmp/host-port.txt | \
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parallel netcat -v -w2 -z {=uq=} 2>&1 | egrep '(succeeded!|open)$'
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1$ cat /tmp/host-port.txt |
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parallel netcat -v -w2 -z {=uq=} 2>&1 |
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egrep '(succeeded!|open)$'
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https://github.com/jreisinger/runp (Last checked: 2020-04)
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@ -2603,11 +2607,11 @@ seconds (compared to 10 seconds with GNU B<parallel>).
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=head3 Examples as GNU Parallel
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1$ papply gzip *.txt
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1$ parallel gzip ::: *.txt
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2$ papply "convert %F %n.jpg" *.png
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2$ parallel convert {} {.}.jpg ::: *.png
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@ -2633,18 +2637,18 @@ composed commands.
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=head3 Examples as GNU Parallel
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1$ S="/tmp/example_socket"
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1$ ID=myid
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2$ async -s="$S" server --start
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2$ # GNU Parallel does not need a server to run
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3$ for i in {1..20}; do
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# prints command output to stdout
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async -s="$S" cmd -- bash -c "sleep 1 && echo test $i"
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done
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3$ for i in {1..20}; do
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# prints command output to stdout
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sem --id "$ID" -j100% "sleep 1 && echo test $i"
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@ -2653,38 +2657,38 @@ composed commands.
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# use -u or --line-buffer
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sem --id "$ID" -j100% --line-buffer "sleep 1 && echo test $i"
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done
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4$ # wait until all commands are finished
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async -s="$S" wait
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4$ sem --id "$ID" --wait
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5$ # configure the server to run four commands in parallel
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async -s="$S" server -j4
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5$ export PARALLEL=-j4
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6$ mkdir "/tmp/ex_dir"
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for i in {21..40}; do
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# redirects command output to /tmp/ex_dir/file*
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async -s="$S" cmd -o "/tmp/ex_dir/file$i" -- \
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bash -c "sleep 1 && echo test $i"
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done
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6$ mkdir "/tmp/ex_dir"
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for i in {21..40}; do
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# redirects command output to /tmp/ex_dir/file*
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sem --id "$ID" --result '/tmp/my-ex/file-{=$_=""=}'"$i" \
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"sleep 1 && echo test $i"
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done
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7$ sem --id "$ID" --wait
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7$ async -s="$S" wait
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8$ # stops server
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async -s="$S" server --stop
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8$ # GNU Parallel does not need to stop a server
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@ -2709,23 +2713,199 @@ name (%IN) can be put in the command line. You can only use %IN once.
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It can also run full command lines in parallel (like: B<cat file |
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parallel>).
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=head3 EXAMPLES FROM pardi test.sh
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1$ time pardi -v -c 100 -i data/decoys.smi -ie .smi -oe .smi \
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-o data/decoys_std_pardi.smi \
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-w '(standardiser -i %IN -o %OUT 2>&1) > /dev/null'
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1$ cat data/decoys.smi |
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time parallel -N 100 --pipe --cat \
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'(standardiser -i {} -o {#} 2>&1) > /dev/null; cat {#}; rm {#}' \
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> data/decoys_std_pardi.smi
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2$ pardi -n 1 -i data/test_in.types -o data/test_out.types \
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-d 'r:^#atoms:' -w 'cat %IN > %OUT'
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2$ cat data/test_in.types | parallel -n 1 -k --pipe --cat \
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--regexp --recstart '^#atoms' 'cat {}' > data/test_out.types
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3$ pardi -c 6 -i data/test_in.types -o data/test_out.types \
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-d 'r:^#atoms:' -w 'cat %IN > %OUT'
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3$ cat data/test_in.types | parallel -n 6 -k --pipe --cat \
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--regexp --recstart '^#atoms' 'cat {}' > data/test_out.types
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4$ pardi -i data/decoys.mol2 -o data/still_decoys.mol2 \
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-d 's:@<TRIPOS>MOLECULE' -w 'cp %IN %OUT'
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4$ cat data/decoys.mol2 |
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parallel -n 1 --pipe --cat --recstart '@<TRIPOS>MOLECULE' \
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'cp {} {#}; cat {#}; rm {#}' > data/still_decoys.mol2
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5$ pardi -i data/decoys.mol2 -o data/decoys2.mol2 \
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-d b:10000 -w 'cp %IN %OUT' --preserve
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5$ cat data/decoys.mol2 |
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parallel -k --pipe --block 10k --recend '' --cat \
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'cat {} > {#}; cat {#}; rm {#}' > data/decoys2.mol2
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https://github.com/UnixJunkie/pardi (Last checked: 2021-01)
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=head2 DIFFERENCES BETWEEN bthread AND GNU Parallel
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Summary (see legend above):
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- - - I4 - - -
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- - - - - M6
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O1 - O3 - - - O7 O8 - -
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E1 - - - - - -
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- - - - - - - - -
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- -
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B<bthread> takes around 1 sec per MB of output. The maximal output
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line length is 1073741759.
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You cannot quote space in the command, so you cannot run composed
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commands like B<sh -c "echo a; echo b">.
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https://gitlab.com/netikras/bthread (Last checked: 2021-01)
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=head2 DIFFERENCES BETWEEN simple_gpu_scheduler AND GNU Parallel
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Summary (see legend above):
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I1 - - - - - I7
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M1 - - - - M6
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- O2 O3 - - O6 - N/A N/A O10
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E1 - - - - - -
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- - - - - - - - -
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- -
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=head3 EXAMPLES FROM simple_gpu_scheduler MANUAL
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1$ simple_gpu_scheduler --gpus 0 1 2 < gpu_commands.txt
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1$ parallel -j3 --shuf \
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CUDA_VISIBLE_DEVICES='{=1 $_=slot()-1 =} {=uq;=}' < gpu_commands.txt
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2$ simple_hypersearch "python3 train_dnn.py --lr {lr} --batch_size {bs}" \
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-p lr 0.001 0.0005 0.0001 -p bs 32 64 128 |
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simple_gpu_scheduler --gpus 0,1,2
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2$ parallel --header : --shuf -j3 -v \
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CUDA_VISIBLE_DEVICES='{=1 $_=slot()-1 =}' \
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python3 train_dnn.py --lr {lr} --batch_size {bs} \
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::: lr 0.001 0.0005 0.0001 ::: bs 32 64 128
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3$ simple_hypersearch \
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"python3 train_dnn.py --lr {lr} --batch_size {bs}" \
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--n-samples 5 -p lr 0.001 0.0005 0.0001 -p bs 32 64 128 |
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simple_gpu_scheduler --gpus 0,1,2
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3$ parallel --header : --shuf \
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CUDA_VISIBLE_DEVICES='{=1 $_=slot()-1; seq() > 5 and skip() =}' \
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python3 train_dnn.py --lr {lr} --batch_size {bs} \
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::: lr 0.001 0.0005 0.0001 ::: bs 32 64 128
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4$ touch gpu.queue
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tail -f -n 0 gpu.queue | simple_gpu_scheduler --gpus 0,1,2 &
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echo "my_command_with | and stuff > logfile" >> gpu.queue
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4$ touch gpu.queue
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tail -f -n 0 gpu.queue |
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parallel -j3 CUDA_VISIBLE_DEVICES='{=1 $_=slot()-1 =} {=uq;=}' &
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# Needed to fill job slots once
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seq 3 | parallel echo true >> gpu.queue
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# Add jobs
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echo "my_command_with | and stuff > logfile" >> gpu.queue
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# Needed to flush output from completed jobs
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seq 3 | parallel echo true >> gpu.queue
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https://github.com/ExpectationMax/simple_gpu_scheduler (Last checked:
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2021-01)
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=head2 DIFFERENCES BETWEEN parasweep AND GNU Parallel
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B<parasweep> is a Python module for facilitating parallel parameter
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sweeps.
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A B<parasweep> job will normally take a text file as input. The text
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file contains arguments for the job. Some of these arguments will be
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fixed and some of them will be changed by B<parasweep>.
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It does this by having a template file such as template.txt:
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Xval: {x}
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Yval: {y}
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FixedValue: 9
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# x with 2 decimals
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DecimalX: {x:.2f}
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TenX: ${x*10}
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RandomVal: {r}
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and from this template it generates the file to be used by the job by
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replacing the replacement strings.
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Being a Python module B<parasweep> integrates tighter with Python than
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GNU B<parallel>. You get the parameters directly in a Python data
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structure. With GNU B<parallel> you can use the JSON or CSV output
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format to get something similar, but you would have to read the
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output.
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B<parasweep> has a filtering method to ignore parameter combinations
|
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you do not need.
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Instead of calling the jobs directly, B<parasweep> can use Python's
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Distributed Resource Management Application API to make jobs run with
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different cluster software.
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=head3 Future support in GNU Parallel
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|
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B<Future> versions of GNU B<parallel> may support templates
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with replacement strings. Such as:
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|
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Xval: {x}
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Yval: {y}
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FixedValue: 9
|
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# x with 2 decimals
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DecimalX: {=x $_=sprintf("%.2f",$_) =}
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TenX: {=x $_=$_*10 =}
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RandomVal: {= $_=rand() =}
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that can be used like:
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parallel --header : --tmpl my.tmpl {#}.t myprog {#}.t ::: x 1 2 3 ::: y 1 2 3
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Filtering may also be supported as:
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parallel --filter '{1} > {2}' echo ::: 1 2 3 ::: 1 2 3
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which will basically do:
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parallel echo '{= $arg[1] > $arg[2] and skip() =}' ::: 1 2 3 ::: 1 2 3
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|
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https://github.com/eviatarbach/parasweep (Last checked: 2021-01)
|
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=head2 Todo
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||||
|
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https://reposhub.com/python/command-line-tools/Akianonymus-parallel-bash.html
|
||||
|
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https://github.com/Nukesor/pueue
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|
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PASH: Light-touch Data-Parallel Shell Processing
|
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|
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https://arxiv.org/pdf/2012.15443.pdf KumQuat
|
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|
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https://arxiv.org/pdf/2007.09436.pdf
|
||||
|
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https://github.com/UnixJunkie/PAR (Same as http://savannah.nongnu.org/projects/par above?)
|
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|
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https://gitlab.com/netikras/bthread
|
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|
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https://github.com/JeiKeiLim/simple_distribute_job
|
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|
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https://github.com/Akianonymus/parallel-bash
|
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|
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https://github.com/reggi/pkgrun
|
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|
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https://github.com/benoror/better-npm-run - not obvious how to use
|
||||
|
|
@ -2738,29 +2918,6 @@ https://github.com/flesler/parallel
|
|||
|
||||
https://github.com/Julian/Verge
|
||||
|
||||
https://github.com/ExpectationMax/simple_gpu_scheduler
|
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simple_gpu_scheduler --gpus 0 1 2 < gpu_commands.txt
|
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parallel -j3 --shuf CUDA_VISIBLE_DEVICES='{=1 $_=slot()-1 =} {=uq;=}' < gpu_commands.txt
|
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|
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simple_hypersearch "python3 train_dnn.py --lr {lr} --batch_size {bs}" -p lr 0.001 0.0005 0.0001 -p bs 32 64 128 | simple_gpu_scheduler --gpus 0,1,2
|
||||
parallel --header : --shuf -j3 -v CUDA_VISIBLE_DEVICES='{=1 $_=slot()-1 =}' python3 train_dnn.py --lr {lr} --batch_size {bs} ::: lr 0.001 0.0005 0.0001 ::: bs 32 64 128
|
||||
|
||||
simple_hypersearch "python3 train_dnn.py --lr {lr} --batch_size {bs}" --n-samples 5 -p lr 0.001 0.0005 0.0001 -p bs 32 64 128 | simple_gpu_scheduler --gpus 0,1,2
|
||||
parallel --header : --shuf CUDA_VISIBLE_DEVICES='{=1 $_=slot()-1; seq() > 5 and skip() =}' python3 train_dnn.py --lr {lr} --batch_size {bs} ::: lr 0.001 0.0005 0.0001 ::: bs 32 64 128
|
||||
|
||||
touch gpu.queue
|
||||
tail -f -n 0 gpu.queue | simple_gpu_scheduler --gpus 0,1,2 &
|
||||
echo "my_command_with | and stuff > logfile" >> gpu.queue
|
||||
|
||||
touch gpu.queue
|
||||
tail -f -n 0 gpu.queue | parallel -j3 CUDA_VISIBLE_DEVICES='{=1 $_=slot()-1 =} {=uq;=}' &
|
||||
# Needed to fill job slots once
|
||||
seq 3 | parallel echo true >> gpu.queue
|
||||
# Add jobs
|
||||
echo "my_command_with | and stuff > logfile" >> gpu.queue
|
||||
# Needed to flush output from completed jobs
|
||||
seq 3 | parallel echo true >> gpu.queue
|
||||
|
||||
|
||||
=head1 TESTING OTHER TOOLS
|
||||
|
||||
|
|
|
|||
|
|
@ -4,6 +4,12 @@
|
|||
# Each should be taking 3-10s and be possible to run in parallel
|
||||
# I.e.: No race conditions, no logins
|
||||
|
||||
par_delay_halt_soon() {
|
||||
echo "bug #59893: --halt soon doesn't work with --delay"
|
||||
seq 0 10 |
|
||||
stdout parallel --delay 1 -uj2 --halt soon,fail=1 'sleep 0.{};echo {};exit {}'
|
||||
}
|
||||
|
||||
par_show_limits() {
|
||||
echo '### Test --show-limits'
|
||||
(
|
||||
|
|
|
|||
|
|
@ -60,6 +60,11 @@ par_compute_command_len a_b_c_d
|
|||
par_compute_command_len
|
||||
par_delay ### Test --delay
|
||||
par_delay More than 3.3 secs: OK
|
||||
par_delay_halt_soon bug #59893: --halt soon doesn't work with --delay
|
||||
par_delay_halt_soon 0
|
||||
par_delay_halt_soon 1
|
||||
par_delay_halt_soon parallel: This job failed:
|
||||
par_delay_halt_soon sleep 0.1;echo 1;exit 1
|
||||
par_delay_human_readable a
|
||||
par_delay_human_readable b
|
||||
par_delay_human_readable c
|
||||
|
|
|
|||
Loading…
Reference in a new issue