mirror of
https://git.savannah.gnu.org/git/parallel.git
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testsuite: Changes due to changed environment and code.
This commit is contained in:
Ole Tange
parent
e3d00f03f6
commit
b44e91df26
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@ -4,7 +4,7 @@
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Check that documentation is updated (compare to web):
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Fixet for 20160922
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Fixet for 20161022
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git diff last-release-commit
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Unmodified beta since last version => production
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Unmodified alpha since last version => beta
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@ -219,9 +219,9 @@ 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 20160922 ('Christiania') released <<[stable]>>
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Subject: GNU Parallel 20161022 ('Matthew') released <<[stable]>>
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GNU Parallel 20160922 ('Christiania') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
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GNU Parallel 20161022 ('Matthew') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
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<<No new functionality was introduced so this is a good candidate for a stable release.>>
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@ -263,25 +263,11 @@ for Big Data Applications https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumb
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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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* parcat - cat files or fifos in parallel
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* GNU Parallel was cited in: Efficiently parallelized modeling of tightly focused, large bandwidth laser pulses https://arxiv.org/pdf/1609.08146v1.pdf
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* GNU Parallel was cited in: Velocity: A Netflow Based Optimized Geo-IP Lookup Tool https://mospace.umsystem.edu/xmlui/bitstream/handle/10355/50842/Thesis_2016_Pakhare.pdf?sequence=1&isAllowed=y
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* How to crunch lots of geodata in parallel http://blog.faraday.io/how-to-crunch-lots-of-geodata-in-parallel/
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* GNU Parallel was cited in: Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011931/
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* GNU Parallel is used in Gene Set Omic Analysis: https://bitbucket.org/srp33/gsoa
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* Using GNU Parallel and ImageMagick for Conversions https://blog.fractalcomic.com/tutorials/using-gnu-parallel-and-imagemagick-for-conversions/
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* Training in GNU Parallel http://www.cism.ucl.ac.be/Services/Formations/parcomp.pdf
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* Chown Ceph OSD data directory using GNU Parallel http://blog.widodh.nl/2016/08/chown-ceph-osd-data-directory-using-gnu-parallel/
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* FastGBS uses GNU Parallel https://bitbucket.org/jerlar73/fastgbs
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* dDocent: A guide to ddRAD sequencing https://ddocent.wordpress.com/ddocent-pipeline-user-guide/
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* SOFTWARE GNU Parallel http://msi-riss.readthedocs.io/en/latest/software/gnu-parallel.html
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* GNU parallel is my new toaster http://amedee.me/gnu-parallel-is-my-new-toaster/index.html
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* Bug fixes and man page updates.
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@ -24,7 +24,7 @@
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use strict;
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use Getopt::Long;
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$Global::progname="niceload";
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$Global::version = 20160922;
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$Global::version = 20160924;
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Getopt::Long::Configure("bundling","require_order");
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get_options_from_array(\@ARGV) || die_usage();
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if($opt::version) {
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@ -559,7 +559,9 @@ If the strings B<{=> and B<=}> cause problems they can be replaced with B<--pare
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parallel --parens ,,,, echo ',, s:\.[^.]+$::;s:\.[^.]+$::; ,,' ::: foo.tar.gz
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Output: Same as above.
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Output:
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foo
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To define a shorthand replacement string use B<--rpl>:
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@ -635,7 +637,7 @@ Output:
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foo bar
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If shorthand defined using B<--rpl> starts with B<{> it can be used as
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If a shorthand defined using B<--rpl> starts with B<{> it can be used as
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a positional replacement string, too:
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parallel --rpl '{..} s:\.[^.]+$::;s:\.[^.]+$::;' echo '{2..} {1}' ::: bar ::: foo.tar.gz
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2
src/sql
2
src/sql
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@ -566,7 +566,7 @@ $Global::Initfile && unlink $Global::Initfile;
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exit ($err);
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sub parse_options {
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$Global::version = 20160922;
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$Global::version = 20160924;
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$Global::progname = 'sql';
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# This must be done first as this may exec myself
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@ -83,6 +83,10 @@ echo '### exported function to csh but with PARALLEL_SHELL=bash'
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stdout parallel --env doit -S csh@lo doit ::: not_OK;
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PARALLEL_SHELL=bash parallel --env doit -S csh@lo doit ::: OK
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echo '### bug #49404: "Max jobs to run" does not equal the number of jobs specified when using GNU Parallel on remote server?'
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echo should give 12 running jobs
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stdout parallel -S 16/lo --progress true ::: {1..12} | grep /.12
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EOF
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@ -13,7 +13,7 @@ test -n "" \
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-exec chmod u+rwx,go+rx {} \; -o \
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! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \
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! -type d ! -perm -400 -exec chmod a+r {} \; -o \
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! -type d ! -perm -444 -exec /bin/bash /home/tange/privat/parallel/install-sh -c -m a+r {} {} \; \
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! -type d ! -perm -444 -exec /bin/bash /mnt/4tb/home/tange/privat/parallel/install-sh -c -m a+r {} {} \; \
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|| chmod -R a+r "parallel-00000000"
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tardir=parallel-00000000 && ${TAR-tar} chof - "$tardir" | GZIP=--best gzip -c >parallel-00000000.tar.gz
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make[0]: Leaving directory '/mnt/4tb/home/tange/privat/parallel'
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@ -297,23 +297,23 @@ bug #45993: --wd ... should also work when run locally
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parallel: Error: Cannot change into non-executable dir /bi: No such file or directory
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parallel --wd /bin 'pwd; echo $OLDPWD; echo' ::: OK
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/bin
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/home/tange/privat/parallel/testsuite
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/mnt/4tb/home/tange/privat/parallel/testsuite
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OK
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parallel --wd / 'pwd; echo $OLDPWD; echo' ::: OK
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/
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/home/tange/privat/parallel/testsuite
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/mnt/4tb/home/tange/privat/parallel/testsuite
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OK
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parallel --wd /tmp 'pwd; echo $OLDPWD; echo' ::: OK
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/tmp
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/home/tange/privat/parallel/testsuite
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/mnt/4tb/home/tange/privat/parallel/testsuite
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OK
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parallel --wd ... 'pwd; echo $OLDPWD; echo' ::: OK | perl -pe 's/\d+/0/g'
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/home/tange/.parallel/tmp/aspire-0-0
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/home/tange/privat/parallel/testsuite
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/mnt/0tb/home/tange/.parallel/tmp/aspire-0-0
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/mnt/0tb/home/tange/privat/parallel/testsuite
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OK
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parallel --wd . 'pwd; echo $OLDPWD; echo' ::: OK
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/home/tange/privat/parallel/testsuite
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/home/tange/privat/parallel/testsuite
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/mnt/4tb/home/tange/privat/parallel/testsuite
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/mnt/4tb/home/tange/privat/parallel/testsuite
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OK
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echo '**'
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**
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@ -3,8 +3,8 @@ par_mem_leak ### test for mem leak
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par_mem_leak no mem leak detected
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par_outside_file_handle_limit 2>&1
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par_outside_file_handle_limit ### Test Force outside the file handle limit, 2009-02-17 Gave fork error
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par_outside_file_handle_limit parallel: Warning: Only enough file handles to run 252 jobs in parallel.
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par_outside_file_handle_limit parallel: Warning: Running 'parallel -j0 -N 252 --pipe parallel -j0' or
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par_outside_file_handle_limit parallel: Warning: Only enough file handles to run 251 jobs in parallel.
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par_outside_file_handle_limit parallel: Warning: Running 'parallel -j0 -N 251 --pipe parallel -j0' or
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par_outside_file_handle_limit parallel: Warning: raising ulimit -n or /etc/security/limits.conf may help.
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par_outside_file_handle_limit Start
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par_outside_file_handle_limit end
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@ -1,7 +1,7 @@
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echo '### bug #46214: Using --pipepart doesnt spawn multiple jobs in version 20150922'
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### bug #46214: Using --pipepart doesnt spawn multiple jobs in version 20150922
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seq 1000000 > /tmp/num1000000; stdout parallel --pipepart --progress -a /tmp/num1000000 --block 10k -j0 true |grep 1:local
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1:local / 8 / 252
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1:local / 8 / 251
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echo '**'
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**
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testhalt() { echo '### testhalt --halt '$1; (yes 0 | head -n 10; seq 10) | stdout parallel -kj4 --halt $1 'sleep {= $_=$_*0.3+1 =}; exit {}'; echo $?; (seq 10; yes 0 | head -n 10) | stdout parallel -kj4 --halt $1 'sleep {= $_=$_*0.3+1 =}; exit {}'; echo $?; }; export -f testhalt; parallel -kj0 testhalt ::: now,fail=0 now,fail=1 now,fail=2 now,fail=30% now,fail=70% soon,fail=0 soon,fail=1 soon,fail=2 soon,fail=30% soon,fail=70% now,success=0 now,success=1 now,success=2 now,success=30% now,success=70% soon,success=0 soon,success=1 soon,success=2 soon,success=30% now,success=70%
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@ -55,7 +55,7 @@ echo '**'
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make[1]: Entering directory '/mnt/4tb/home/tange/privat/parallel/testsuite'
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# Make sure we can reach the virtual machines
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#sudo ifconfig wlp13s0:0 192.168.1.72 || sudo ifconfig wlan0:0 192.168.1.72
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sudo ifconfig enp14s0 192.168.1.72 || sudo ifconfig eth0:0 192.168.1.72
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sudo ifconfig enp14s0:0 192.168.1.72 || sudo ifconfig eth0:0 192.168.1.72
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# If they are already running: Don't fail
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VBoxManage startvm CentOS3-root:centos3 || VBoxManage controlvm CentOS3-root:centos3 resume || true
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Waiting for VM "CentOS3-root:centos3" to power on...
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@ -63,4 +63,5 @@ VM "CentOS3-root:centos3" has been successfully started.
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VBoxManage startvm RedHat9-root:redhat9 || VBoxManage controlvm RedHat9-root:redhat9 resume || true
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Waiting for VM "RedHat9-root:redhat9" to power on...
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VM "RedHat9-root:redhat9" has been successfully started.
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parallel 'ping {} | read' ::: redhat9.tange.dk centos3.tange.dk
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make[1]: Leaving directory '/mnt/4tb/home/tange/privat/parallel/testsuite'
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@ -20,22 +20,22 @@ echo '### bug #41805: Idea: propagate --env for parallel --number-of-cores'
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** test_zsh
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FOO=test_zsh parallel --env FOO,HOME -S zsh@lo -N0 env ::: "" |sort|egrep 'FOO|^HOME'
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FOO=test_zsh
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HOME=/home/tange
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HOME=/mnt/4tb/home/tange
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echo '** test_zsh_filter'
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** test_zsh_filter
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FOO=test_zsh_filter parallel --filter-hosts --env FOO,HOME -S zsh@lo -N0 env ::: "" |sort|egrep 'FOO|^HOME'
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FOO=test_zsh_filter
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HOME=/home/tange
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HOME=/mnt/4tb/home/tange
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echo '** test_csh'
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** test_csh
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FOO=test_csh parallel --env FOO,HOME -S csh@lo -N0 env ::: "" |sort|egrep 'FOO|^HOME'
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FOO=test_csh
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HOME=/home/tange
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HOME=/mnt/4tb/home/tange
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echo '** test_csh_filter'
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** test_csh_filter
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FOO=test_csh_filter parallel --filter-hosts --env FOO,HOME -S csh@lo -N0 env ::: "" |sort|egrep 'FOO|^HOME'
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FOO=test_csh_filter
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HOME=/home/tange
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HOME=/mnt/4tb/home/tange
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echo '** bug #41805 done'
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** bug #41805 done
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echo '### Deal with long command lines on remote servers'
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@ -122,6 +122,12 @@ echo '### exported function to csh but with PARALLEL_SHELL=bash'
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doit() { echo "$1"; }; export -f doit; stdout parallel --env doit -S csh@lo doit ::: not_OK; PARALLEL_SHELL=bash parallel --env doit -S csh@lo doit ::: OK
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CSH/TCSH DO NOT SUPPORT newlines IN VARIABLES/FUNCTIONS. Unset doit
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OK
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echo '### bug #49404: "Max jobs to run" does not equal the number of jobs specified when using GNU Parallel on remote server?'
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### bug #49404: "Max jobs to run" does not equal the number of jobs specified when using GNU Parallel on remote server?
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echo should give 12 running jobs
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should give 12 running jobs
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stdout parallel -S 16/lo --progress true ::: {1..12} | grep /.12
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1:lo / 16 / 12
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bug #47695: How to set $PATH on remote?
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* Documentation: https://help.ubuntu.com
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@ -187,12 +187,10 @@ echo '### Test stdin goes to first command only'
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### Test stdin goes to first command only
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echo via cat |parallel --arg-sep .--- -kv .--- 'cat' 'echo b'
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cat
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via cat
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echo b
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b
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echo via cat |parallel -kv ::: 'cat' 'echo b'
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cat
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via cat
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echo b
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b
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echo '### Bug made 4 5 go before 1 2 3'
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@ -1,13 +1,13 @@
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bug #46120: Suspend should suspend (at least local) children
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1024 SHA256:SXgag2Z2L91JsrT5WjNBcARD1EpyCCj4JctVJ6Zpzm0 /home/tange/.ssh/id_dsa (DSA)
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8192 SHA256:lYn04AefJq/5r0e4FftceviJ7JVnq9NGKY3CW9XMpO8 /home/tange/.ssh/id_rsa (RSA)
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4096 SHA256:jUQ9ysfprs7UOckttjjVb+j3qikUmKWDEWC+eEJkbDQ /home/tange/.ssh/id_rsa_openindiana (RSA)
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1024 SHA256:SXgag2Z2L91JsrT5WjNBcARD1EpyCCj4JctVJ6Zpzm0 /mnt/4tb/home/tange/.ssh/id_dsa (DSA)
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8192 SHA256:lYn04AefJq/5r0e4FftceviJ7JVnq9NGKY3CW9XMpO8 /mnt/4tb/home/tange/.ssh/id_rsa (RSA)
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4096 SHA256:jUQ9ysfprs7UOckttjjVb+j3qikUmKWDEWC+eEJkbDQ /mnt/4tb/home/tange/.ssh/id_rsa_openindiana (RSA)
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stdout /usr/bin/time -f CPUTIME=%U parallel --timeout 5 burnP6 ::: 1 | grep -q CPUTIME=1
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Zero=OK 0
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1024 SHA256:SXgag2Z2L91JsrT5WjNBcARD1EpyCCj4JctVJ6Zpzm0 /home/tange/.ssh/id_dsa (DSA)
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8192 SHA256:lYn04AefJq/5r0e4FftceviJ7JVnq9NGKY3CW9XMpO8 /home/tange/.ssh/id_rsa (RSA)
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4096 SHA256:jUQ9ysfprs7UOckttjjVb+j3qikUmKWDEWC+eEJkbDQ /home/tange/.ssh/id_rsa_openindiana (RSA)
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1024 SHA256:SXgag2Z2L91JsrT5WjNBcARD1EpyCCj4JctVJ6Zpzm0 /mnt/4tb/home/tange/.ssh/id_dsa (DSA)
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8192 SHA256:lYn04AefJq/5r0e4FftceviJ7JVnq9NGKY3CW9XMpO8 /mnt/4tb/home/tange/.ssh/id_rsa (RSA)
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4096 SHA256:jUQ9ysfprs7UOckttjjVb+j3qikUmKWDEWC+eEJkbDQ /mnt/4tb/home/tange/.ssh/id_rsa_openindiana (RSA)
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echo 1 | stdout /usr/bin/time -f CPUTIME=%U parallel --timeout 5 burnP6 | grep -q CPUTIME=1
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Zero=OK 0
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@ -161,7 +161,7 @@ num8
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num_%header
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tsv-file.tsv
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foo
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/home/tange/privat/parallel/testsuite/tmp
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/mnt/4tb/home/tange/privat/parallel/testsuite/tmp
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my_func() {
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echo in my_func $1
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}
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@ -760,34 +760,34 @@ Unknown option: :::
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Unknown option: green
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env_parallel only works if it is a function. Do the below and restart your shell.
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bash: Put this in /home/tange/.bashrc: . /usr/local/bin/env_parallel.bash
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E.g. by doing: echo '. /usr/local/bin/env_parallel.bash' >> /home/tange/.bashrc
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bash: Put this in /mnt/4tb/home/tange/.bashrc: . /usr/local/bin/env_parallel.bash
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E.g. by doing: echo '. /usr/local/bin/env_parallel.bash' >> /mnt/4tb/home/tange/.bashrc
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Supports: aliases, functions, variables, arrays
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zsh: Put this in /home/tange/.zshrc: . /usr/local/bin/env_parallel.zsh
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E.g. by doing: echo '. /usr/local/bin/env_parallel.zsh' >> /home/tange/.zshenv
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zsh: Put this in /mnt/4tb/home/tange/.zshrc: . /usr/local/bin/env_parallel.zsh
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E.g. by doing: echo '. /usr/local/bin/env_parallel.zsh' >> /mnt/4tb/home/tange/.zshenv
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Supports: functions, variables, arrays
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fish: Put this in /home/tange/.config/fish/config.fish:
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fish: Put this in /mnt/4tb/home/tange/.config/fish/config.fish:
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. (which env_parallel.fish)
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E.g. by doing:
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echo '. (which env_parallel.fish)' >> /home/tange/.config/fish/config.fish
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echo '. (which env_parallel.fish)' >> /mnt/4tb/home/tange/.config/fish/config.fish
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Supports: aliases, functions, variables, arrays
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ksh: Put this in /home/tange/.kshrc: source /usr/local/bin/env_parallel.ksh
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E.g. by doing: echo 'source /usr/local/bin/env_parallel.ksh' >> /home/tange/.kshrc
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ksh: Put this in /mnt/4tb/home/tange/.kshrc: source /usr/local/bin/env_parallel.ksh
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E.g. by doing: echo 'source /usr/local/bin/env_parallel.ksh' >> /mnt/4tb/home/tange/.kshrc
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Supports: aliases, functions, variables, arrays
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pdksh: Put this in /home/tange/.profile: source /usr/local/bin/env_parallel.pdksh
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E.g. by doing: echo '. /usr/local/bin/env_parallel.pdksh' >> /home/tange/.profile
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pdksh: Put this in /mnt/4tb/home/tange/.profile: source /usr/local/bin/env_parallel.pdksh
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E.g. by doing: echo '. /usr/local/bin/env_parallel.pdksh' >> /mnt/4tb/home/tange/.profile
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Supports: aliases, functions, variables, arrays
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csh: Put this in /home/tange/.cshrc: source /usr/local/bin/env_parallel.csh
|
||||
E.g. by doing: echo 'source /usr/local/bin/env_parallel.csh' >> /home/tange/.cshrc
|
||||
csh: Put this in /mnt/4tb/home/tange/.cshrc: source /usr/local/bin/env_parallel.csh
|
||||
E.g. by doing: echo 'source /usr/local/bin/env_parallel.csh' >> /mnt/4tb/home/tange/.cshrc
|
||||
Supports: aliases, variables, arrays with no special chars
|
||||
|
||||
tcsh: Put this in /home/tange/.tcshrc: source /usr/local/bin/env_parallel.tcsh
|
||||
E.g. by doing: echo 'source /usr/local/bin/env_parallel.tcsh' >> /home/tange/.tcshrc
|
||||
tcsh: Put this in /mnt/4tb/home/tange/.tcshrc: source /usr/local/bin/env_parallel.tcsh
|
||||
E.g. by doing: echo 'source /usr/local/bin/env_parallel.tcsh' >> /mnt/4tb/home/tange/.tcshrc
|
||||
Supports: aliases, variables, arrays with no special chars
|
||||
|
||||
To install in all shells run:
|
||||
|
|
|
|||
|
|
@ -56,7 +56,7 @@ Error:
|
|||
sql [-hnr] [--table-size] [--db-size] [-p pass-through] [-s string] dburl [command]
|
||||
### Test dburl :
|
||||
Error:
|
||||
: is not defined in /home/tange/.sql/aliases /home/tange/.dburl.aliases /etc/sql/aliases /usr/local/bin/dburl.aliases /usr/local/bin/dburl.aliases.dist
|
||||
: is not defined in /mnt/4tb/home/tange/.sql/aliases /mnt/4tb/home/tange/.dburl.aliases /etc/sql/aliases /usr/local/bin/dburl.aliases /usr/local/bin/dburl.aliases.dist
|
||||
|
||||
sql [-hnr] [--table-size] [--db-size] [-p pass-through] [-s string] dburl [command]
|
||||
### Test oracle with multiple arguments on the command line
|
||||
|
|
|
|||
Loading…
Reference in a new issue