diff --git a/doc/release_new_version b/doc/release_new_version index 94f72ce4..4a924c36 100644 --- a/doc/release_new_version +++ b/doc/release_new_version @@ -198,45 +198,33 @@ cc:Sandro Cazzaniga , Ryoichiro Suzuki , Jesse Alama -Subject: GNU Parallel 20130722 ('Engelbart') released +Subject: GNU Parallel 20130822 ('Compostela') released -GNU Parallel 20130722 ('Engelbart') has been released. It is +GNU Parallel 20130822 ('Compostela') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/ New in this release: -* --round-robin with --pipe will write all blocks to already running - jobs. - -* --env can now transfer Bash function for remote execution. That is - pretty cool! - * New signing key. Due to recommendations from NIST http://www.keylength.com/en/4/ the signing key was changed from 1024D/4000g/ID:FFFFFFF1 to 9888R/ID:88888888. -* GNU Parallel was used (unfortunately with improper citation) in: - Understanding the Impact of E-Commerce Software on the Adoption of Structured Data on the Web - http://link.springer.com/chapter/10.1007/978-3-642-38366-3_9#page-1 +* Agalma: an automated phylogenomics workflow + http://arxiv.org/pdf/1307.6432 -* GNU Parallel was used (unfortunately with improper citation) in: - CWI at TREC 2012, KBA track and Session Track - http://trec.nist.gov/pubs/trec21/papers/CWI.kba.session.final.pdf +* Aligning to unique regions + http://davetang.org/muse/2013/07/22/aligning-to-unique-regions/ -* Mitigation of Adverse Effects Caused by Shock Wave Boundary Layer - Interactions through Optimal Wall Shaping. - http://arc.aiaa.org/doi/abs/10.2514/6.2013-2653 +* Top 10 scripting tricks for basic bioinformatics + http://students.washington.edu/bowmanjs/wordpress/?p=873 -* Using GNU parallel to convert images. - http://www.brunokim.com.br/blog/?p=18 +* Using GNU Parallel to speed up and simplify data analyzes + http://www.sergeymarkov.com/blog/2013/07/using-gnu-parallel-to-speed-up-and-simplify-data-analyzes/ -* A quick way to parallelize. - http://timotheepoisot.fr/2013/07/08/parallel/ +* Compression of files in parallel using GNU parallel + http://codextechnicanum.blogspot.dk/2013/07/compression-of-files-in-parallel-using.html -* GNU Parallel 20130522 ('Rana Plaza') 发布，并行作业执行. - http://www.open-open.com/news/view/371301 - -* Quite a few bug fixes and man page updates. +* Bug fixes and man page updates. = About GNU Parallel = diff --git a/src/parallel b/src/parallel index da026ab6..693f956a 100755 --- a/src/parallel +++ b/src/parallel @@ -448,7 +448,7 @@ sub spreadstdin { } } if($something_written) { - $sleep = $sleep/2; + $sleep = $sleep/2+0.001; } $sleep = ::reap_usleep($sleep); } @@ -523,7 +523,7 @@ sub write_record_to_pipe { substr($$record_ref,$endpos,length $$record_ref) = ""; # Remove rec_sep if($opt::remove_rec_sep) { - remove_rec_sep($record_ref,$recstart,$recend); + Job::remove_rec_sep($record_ref,$recstart,$recend); } $job->write($header_ref); $job->write($record_ref); @@ -727,7 +727,7 @@ sub get_options_from_array { sub parse_options { # Returns: N/A # Defaults: - $Global::version = 20130722; + $Global::version = 20130730; $Global::progname = 'parallel'; $Global::infinity = 2**31; $Global::debug = 0; @@ -1547,7 +1547,7 @@ sub drain_job_queue { # These jobs may not be started because of loadavg # or too little time between each ssh login. if(start_more_jobs() > 0) { - $sleep = $sleep/2; + $sleep = $sleep/2+0.001; } } # Sometimes SIGCHLD is not registered, so force reaper @@ -4482,7 +4482,7 @@ sub print { my $in_fd = $self->fd($fdno); if(not $in_fd) { if(not $Job::file_descriptor_warning_printed{$fdno}++) { - ::warning("File descriptor $fdno not defined\n"); + # ::warning("File descriptor $fdno not defined\n"); } next; } @@ -6062,5 +6062,5 @@ sub mkdir_or_die { # Keep perl -w happy $opt::x = $Semaphore::timeout = $Semaphore::wait = $opt::shebang = $Global::no_more_file_handles_warned = -0; +$Job::file_descriptor_warning_printed = 0; diff --git a/src/sql.texi b/src/sql.texi index a9df36c8..63720c3f 100644 --- a/src/sql.texi +++ b/src/sql.texi @@ -329,7 +329,7 @@ Use GNU @strong{parallel}'s @strong{--colsep} to separate columns: @section Retry if the connection fails @anchor{Retry if the connection fails} -If the access to the database fails occationally @strong{--retries} can help +If the access to the database fails occasionally @strong{--retries} can help make sure the query succeeds: @strong{sql --retries 5 :myalias 'SELECT * FROM really_big_foo;'} diff --git a/testsuite/tests-to-run/parallel-local4.sh b/testsuite/tests-to-run/parallel-local4.sh index 630fce82..804ab61f 100644 --- a/testsuite/tests-to-run/parallel-local4.sh +++ b/testsuite/tests-to-run/parallel-local4.sh @@ -22,6 +22,9 @@ echo '### -l -n with pipe' echo '### bug #39360: --joblog does not work with --pipe' seq 100 | parallel --joblog - --pipe wc | tr '0-9' 'X' +echo '### bug #39572: --tty and --joblog do not work' + seq 1 | parallel --joblog - -u true | tr '0-9' 'X' + echo '### How do we deal with missing $HOME' unset HOME; stdout perl -w $(which parallel) echo ::: 1 2 3 diff --git a/testsuite/wanted-results/parallel-local4 b/testsuite/wanted-results/parallel-local4 index 64d5c185..9729b2af 100644 --- a/testsuite/wanted-results/parallel-local4 +++ b/testsuite/wanted-results/parallel-local4 @@ -93,6 +93,11 @@ echo '### bug #39360: --joblog does not work with --pipe' Seq Host Starttime Runtime Send Receive Exitval Signal Command X : XXXXXXXXXX.XXX X.XXX X X X X wc XXX XXX XXX +echo '### bug #39572: --tty and --joblog do not work' +### bug #39572: --tty and --joblog do not work + seq 1 | parallel --joblog - -u true | tr '0-9' 'X' +Seq Host Starttime Runtime Send Receive Exitval Signal Command +X : XXXXXXXXXX.XXX X.XXX X X X X true X echo '### How do we deal with missing $HOME' ### How do we deal with missing $HOME unset HOME; stdout perl -w $(which parallel) echo ::: 1 2 3 diff --git a/testsuite/wanted-results/parallel-polarhome b/testsuite/wanted-results/parallel-polarhome index 29d6e36b..73166af3 100644 --- a/testsuite/wanted-results/parallel-polarhome +++ b/testsuite/wanted-results/parallel-polarhome @@ -33,7 +33,7 @@ redhat.polarhome.com Works on redhat.polarhome.com hpux.polarhome.com Works on hpux.polarhome.com qnx.polarhome.com Works on qnx.polarhome.com qnx.polarhome.com parallel: Warning: Cannot figure out number of CPU cores. Using 1. -irix.polarhome.com Unknown open() mode '>&=' at bin/parallel line 1316. +irix.polarhome.com Unknown open() mode '>&=' at bin/parallel line 1318. openindiana.polarhome.com Works on openindiana.polarhome.com openindiana.polarhome.com parallel: Warning: Cannot figure out number of CPU cores. Using 1. suse.polarhome.com Works on suse.polarhome.com @@ -46,3 +46,5 @@ centos.polarhome.com Works on centos.polarhome.com miros.polarhome.com Works on miros.polarhome.com hurd.polarhome.com Works on hurd.polarhome.com minix.polarhome.com Works on minix.polarhome.com +raspberrypi.polarhome.com Works on raspberrypi.polarhome.com +raspberrypi.polarhome.com parallel: Warning: Cannot figure out number of CPU cores. Using 1.