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Fixed bug #46819: --wd is ignored for --nonall.

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This commit is contained in:
Ole Tange 2016-01-06 16:22:30 +01:00
parent 582164930a
commit 37fd9adb7b
6 changed files with 40 additions and 22 deletions
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12
doc/release_new_version
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@ -241,6 +241,8 @@ New in this release:
* man parallel_tutorial has been given an overhaul. * man parallel_tutorial has been given an overhaul.
* --workdir now accepts replacementstrings.
* << 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>> * << 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>>
* <<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 * <<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
@ -257,12 +259,18 @@ for Big Data Applications https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumb
* <<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>> * <<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>>
* GNU Parallel is used in LAST: http://last.cbrc.jp/
* GNU Parallel was cited in: Possum - A Framework for Three-Dimensional Reconstruction of Brain Images rfom Serial Sections http://link.springer.com/article/10.1007/s12021-015-9286-1 * GNU Parallel was cited in: Possum - A Framework for Three-Dimensional Reconstruction of Brain Images rfom Serial Sections http://link.springer.com/article/10.1007/s12021-015-9286-1
* GNU Parallel was cited in: A Genetic Algorithm for the selection of structural MRI features for classification of Mild Cognitive Impairment and Alzheimer's Disease http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?tp=&arnumber=7359909&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7359909
* GNU Parallel was cited in: The Effect of Domain Modeling on Performance of Planning Algorithms http://isaim2016.cs.virginia.edu/papers/ISAIM2016_Bartak_Vodrazka.pdf
* Plotting time tables for jobs run by GNU Parallel https://github.com/ziotom78/plot_joblog
* GNU Parallel was used in: Mission Impossible: you have 1 minute to analyze the Ebola Genome https://www.biostars.org/p/119397 * GNU Parallel was used in: Mission Impossible: you have 1 minute to analyze the Ebola Genome https://www.biostars.org/p/119397
* GNU Parallel is used in LAST: http://last.cbrc.jp/
* Distributed Log Search Using GNU Parallel http://blog.codehate.com/post/134320079974/distributed-log-search-using-gnu-parallel * Distributed Log Search Using GNU Parallel http://blog.codehate.com/post/134320079974/distributed-log-search-using-gnu-parallel
* Bug fixes and man page updates. * Bug fixes and man page updates.

4
src/parallel
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@ -3208,6 +3208,7 @@ sub onall {
((defined $opt::retries) ? "--retries ".$opt::retries : ""), ((defined $opt::retries) ? "--retries ".$opt::retries : ""),
((defined $opt::timeout) ? "--timeout ".$opt::timeout : ""), ((defined $opt::timeout) ? "--timeout ".$opt::timeout : ""),
((defined $opt::ungroup) ? "-u" : ""), ((defined $opt::ungroup) ? "-u" : ""),
((defined $opt::workdir) ? "--wd ".$opt::workdir : ""),
(@Global::transfer_files ? map { "--tf ".::shell_quote_scalar($_) } (@Global::transfer_files ? map { "--tf ".::shell_quote_scalar($_) }
@Global::transfer_files : ""), @Global::transfer_files : ""),
(@Global::ret_files ? map { "--return ".::shell_quote_scalar($_) } (@Global::ret_files ? map { "--return ".::shell_quote_scalar($_) }
@ -9737,6 +9738,7 @@ sub new {
"pg" => "Pg", "pg" => "Pg",
"postgres" => "Pg", "postgres" => "Pg",
"postgresql" => "Pg", "postgresql" => "Pg",
"csv" => "CSV",
"oracle" => "Oracle", "oracle" => "Oracle",
"ora" => "Oracle"); "ora" => "Oracle");
my $driver = $driveralias{$options{'databasedriver'}} || my $driver = $driveralias{$options{'databasedriver'}} ||
@ -9840,7 +9842,7 @@ sub parse_dburl {
if($url=~m!(?:sql:)? # You can prefix with 'sql:' if($url=~m!(?:sql:)? # You can prefix with 'sql:'
((?:oracle|ora|mysql|pg|postgres|postgresql)(?:s|ssl|)| ((?:oracle|ora|mysql|pg|postgres|postgresql)(?:s|ssl|)|
(?:sqlite|sqlite2|sqlite3)):// # Databasedriver ($1) (?:sqlite|sqlite2|sqlite3|csv)):// # Databasedriver ($1)
(?: (?:
([^:@/][^:@]*|) # Username ($2) ([^:@/][^:@]*|) # Username ($2)
(?: (?:

34
src/parallel.pod
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@ -322,7 +322,7 @@ shell quote a string
=item Z<> B<total_jobs()> =item Z<> B<total_jobs()>
number of jobs in total (alpha testing) number of jobs in total (beta testing)
=back =back
@ -452,9 +452,9 @@ It is compatible with B<zenity>:
2> >(zenity --progress --auto-kill) | wc 2> >(zenity --progress --auto-kill) | wc
=item B<--basefile> I<file> (alpha testing) =item B<--basefile> I<file> (beta testing)
=item B<--bf> I<file> (alpha testing) =item B<--bf> I<file> (beta testing)
I<file> will be transferred to each sshlogin before a jobs is I<file> will be transferred to each sshlogin before a jobs is
started. It will be removed if B<--cleanup> is active. The file may be started. It will be removed if B<--cleanup> is active. The file may be
@ -540,7 +540,7 @@ Implies B<--pipe> unless B<--pipepart> is used.
See also B<--fifo>. See also B<--fifo>.
=item B<--cleanup> (alpha testing) =item B<--cleanup> (beta testing)
Remove transferred files. B<--cleanup> will remove the transferred Remove transferred files. B<--cleanup> will remove the transferred
files on the remote computer after processing is done. files on the remote computer after processing is done.
@ -1060,9 +1060,9 @@ the same syntax as B<--jobs>, so I<100%> for one per CPU is a valid
setting. Only difference is 0 which is interpreted as 0.01. setting. Only difference is 0 which is interpreted as 0.01.
=item B<--controlmaster> (alpha testing) =item B<--controlmaster> (beta testing)
=item B<-M> (alpha testing) =item B<-M> (beta testing)
Use ssh's ControlMaster to make ssh connections faster. Useful if jobs Use ssh's ControlMaster to make ssh connections faster. Useful if jobs
run remote and are very fast to run. This is disabled for sshlogins run remote and are very fast to run. This is disabled for sshlogins
@ -1100,7 +1100,7 @@ See also B<-X> for context replace. If in doubt use B<-X> as that will
most likely do what is needed. most likely do what is needed.
=item B<--memfree> I<size> (beta testing) =item B<--memfree> I<size>
Minimum memory free when starting another job. The I<size> can be Minimum memory free when starting another job. The I<size> can be
postfixed with K, M, G, T, P, k, m, g, t, or p which would multiply postfixed with K, M, G, T, P, k, m, g, t, or p which would multiply
@ -1161,9 +1161,9 @@ of each job is saved in a file and the filename is then printed.
See also: B<--results> See also: B<--results>
=item B<--pipe> (alpha testing) =item B<--pipe> (beta testing)
=item B<--spreadstdin> (alpha testing) =item B<--spreadstdin> (beta testing)
Spread input to jobs on stdin (standard input). Read a block of data Spread input to jobs on stdin (standard input). Read a block of data
from stdin (standard input) and give one block of data as input to one from stdin (standard input) and give one block of data as input to one
@ -1524,7 +1524,7 @@ the joblog.
See also B<--joblog>, B<--resume>, B<--resume-failed>. See also B<--joblog>, B<--resume>, B<--resume-failed>.
=item B<--retries> I<n> (alpha testing) =item B<--retries> I<n> (beta testing)
If a job fails, retry it on another computer on which it has not If a job fails, retry it on another computer on which it has not
failed. Do this I<n> times. If there are fewer than I<n> computers in failed. Do this I<n> times. If there are fewer than I<n> computers in
@ -1533,7 +1533,7 @@ useful if some jobs fail for no apparent reason (such as network
failure). failure).
=item B<--return> I<filename> (alpha testing) =item B<--return> I<filename> (beta testing)
Transfer files from remote computers. B<--return> is used with Transfer files from remote computers. B<--return> is used with
B<--sshlogin> when the arguments are files on the remote computers. When B<--sshlogin> when the arguments are files on the remote computers. When
@ -2050,14 +2050,14 @@ Print the job to be run on stderr (standard error).
See also B<-v>, B<-p>. See also B<-v>, B<-p>.
=item B<--transfer> (alpha testing) =item B<--transfer> (beta testing)
Transfer files to remote computers. Shorthand for: B<--transferfile {}>. Transfer files to remote computers. Shorthand for: B<--transferfile {}>.
=item B<--transferfile> I<filename> (alpha testing) =item B<--transferfile> I<filename> (beta testing)
=item B<--tf> I<filename> (alpha testing) =item B<--tf> I<filename> (beta testing)
B<--transferfile> is used with B<--sshlogin> to transfer files to the B<--transferfile> is used with B<--sshlogin> to transfer files to the
remote computers. The files will be transferred using B<rsync> and remote computers. The files will be transferred using B<rsync> and
@ -2187,9 +2187,9 @@ Use B<-v> B<-v> to print the wrapping ssh command when running remotely.
Print the version GNU B<parallel> and exit. Print the version GNU B<parallel> and exit.
=item B<--workdir> I<mydir> =item B<--workdir> I<mydir> (alpha testing)
=item B<--wd> I<mydir> =item B<--wd> I<mydir> (alpha testing)
Files transferred using B<--transferfile> and B<--return> will be Files transferred using B<--transferfile> and B<--return> will be
relative to I<mydir> on remote computers, and the command will be relative to I<mydir> on remote computers, and the command will be
@ -2211,6 +2211,8 @@ To see the difference try:
parallel --wd . -S server pwd ::: "" parallel --wd . -S server pwd ::: ""
parallel --wd ... -S server pwd ::: "" parallel --wd ... -S server pwd ::: ""
I<mydir> can contain GNU B<parallel>'s replacement strings.
=item B<--wait> =item B<--wait>

3
testsuite/tests-to-run/parallel-local-ssh6.sh
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@ -81,4 +81,7 @@ echo '### Test --wd {= =}';
parallel --workdir '{= $_=uc($_) =}' -S $SSHLOGIN2 touch ::: wd1 wd2; parallel --workdir '{= $_=uc($_) =}' -S $SSHLOGIN2 touch ::: wd1 wd2;
ssh $SSHLOGIN2 ls -d WD1 WD2 ssh $SSHLOGIN2 ls -d WD1 WD2
echo '### Test --nonall --wd';
parallel --workdir /tmp -S $SSHLOGIN2 --nonall pwd
EOF EOF

6
testsuite/wanted-results/parallel-local-ssh5
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@ -93,11 +93,11 @@ OK
# Test gl. parallel med --ssh lsh: Hvilke fejler? brug dem. Også hvis de fejler # Test gl. parallel med --ssh lsh: Hvilke fejler? brug dem. Også hvis de fejler
echo '### bug #45025: --pipe --retries does not reschedule on other host' echo '### bug #45025: --pipe --retries does not reschedule on other host'
### bug #45025: --pipe --retries does not reschedule on other host ### bug #45025: --pipe --retries does not reschedule on other host
seq 1 300030| stdout parallel -k --retries 2 -S a.a,: --pipe 'wc;hostname' seq 1 300030| stdout parallel -k --retries 2 -S a.a,: --pipe 'wc;hostname' | perl -pe 's/'`hostname`'/localhost-:/'
parallel: Warning: Could not figure out number of cpus on a.a (). Using 1. parallel: Warning: Could not figure out number of cpus on a.a (). Using 1.
165668 165668 1048571 165668 165668 1048571
aspire localhost-:
134362 134362 940534 134362 134362 940534
aspire localhost-:
stdout parallel --retries 2 --roundrobin echo ::: should fail stdout parallel --retries 2 --roundrobin echo ::: should fail
parallel: Error: --retries cannot be combined with --roundrobin. parallel: Error: --retries cannot be combined with --roundrobin.

3
testsuite/wanted-results/parallel-local-ssh6
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@ -114,3 +114,6 @@ echo '### Test --wd {= =}'; ssh csh@lo rm -rf WD1 WD2; mkdir -p $HOME/mydir;
### Test --wd {= =} ### Test --wd {= =}
WD1 WD1
WD2 WD2
echo '### Test --nonall --wd'; parallel --workdir /tmp -S csh@lo --nonall pwd
### Test --nonall --wd
/tmp