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Fixed bug #45993: --wd ... should also work when run locally.

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This commit is contained in:
Ole Tange 2015-09-25 01:29:34 +02:00
parent d3b5e26c1a
commit 51f5363211
4 changed files with 74 additions and 21 deletions
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5
doc/release_new_version
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@ -232,6 +232,11 @@ New in this release:
* <<Afventer updateret publisering>> GNU Parallel was used in: Large Scale Author Name Disambiguation in Digital Libraries http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?tp=&arnumber=7004487&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7004487
* <<kontaktet 2015-06-22 Afventer svar fra journal>> GNU Parallel was used (unfortunately with wrong citation) in: TADSim: Discrete Event-Based Performance Prediction for Temperature-Accelerated Dynamics http://vruehle.de/publications/2015c.pdf
http://www.researchgate.net/profile/Christoph_Junghans/publication/276178326_TADSim_Discrete_Event-Based_Performance_Prediction_for_Temperature-Accelerated_Dynamics/links/55562b6708ae980ca60c8369.pdf
* GNU Parallel was cited in: Roary: rapid large-scale prokaryote pan genome analysis http://bioinformatics.oxfordjournals.org/content/early/2015/08/05/bioinformatics.btv421.full.pdf+html
* GNU Parallel is used in TraitAR: https://testpypi.python.org/pypi/traitar/0.1.4
* Bug fixes and man page updates.

52
src/parallel
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@ -3503,6 +3503,23 @@ sub show_limits {
sub __GENERIC_COMMON_FUNCTION__ {}
sub mkdir_or_die {
# If dir is not executable: die
my $dir = shift;
my @dir_parts = split(m:/:,$dir);
my ($ddir,$part);
while(defined ($part = shift @dir_parts)) {
$part eq "" and next;
$ddir .= "/".$part;
-d $ddir and next;
mkdir $ddir;
}
if(not -x $dir) {
::error("Cannot write to $dir: $!");
::wait_and_exit(255);
}
}
sub tmpfile {
# Create tempfile as $TMPDIR/parXXXXX
# Returns:
@ -6710,6 +6727,16 @@ sub sshlogin_wrap {
$ENV{'PARALLEL_SEQ'} = $self->seq();
$ENV{'PARALLEL_PID'} = $$;
if($serverlogin eq ":") {
if($opt::workdir) {
# Create workdir if needed. Then cd to it.
my $wd = $self->workdir();
if($opt::workdir eq "." or $opt::workdir eq "...") {
# If $wd does not start with '/': Prepend $HOME
$wd =~ s:^([^/]):$ENV{'HOME'}/$1:;
}
::mkdir_or_die($wd);
$command = "cd ".::shell_quote_scalar($wd)." || exit 255; ".$command;
}
if(@opt::env) {
# Prepend with environment setter, which sets functions in zsh
my ($csh_friendly,$envset,$bashfuncset) = env_as_eval();
@ -6973,7 +7000,7 @@ sub workdir {
$workdir = $opt::workdir;
# Rsync treats /./ special. We dont want that
$workdir =~ s:/\./:/:g; # Remove /./
$workdir =~ s:/+$::; # Remove ending / if any
$workdir =~ s:(.)/+$:$1:; # Remove ending / if any
$workdir =~ s:^\./::g; # Remove starting ./ if any
}
} else {
@ -9289,9 +9316,9 @@ sub new {
$id =~ s/([^-_a-z0-9])/unpack("H*",$1)/ige; # Convert non-word chars to hex
$id = "id-".$id; # To distinguish it from a process id
my $parallel_dir = $ENV{'HOME'}."/.parallel";
-d $parallel_dir or mkdir_or_die($parallel_dir);
-d $parallel_dir or ::mkdir_or_die($parallel_dir);
my $parallel_locks = $parallel_dir."/semaphores";
-d $parallel_locks or mkdir_or_die($parallel_locks);
-d $parallel_locks or ::mkdir_or_die($parallel_locks);
my $lockdir = "$parallel_locks/$id";
my $lockfile = $lockdir.".lock";
if($count < 1) { ::die_bug("semaphore-count: $count"); }
@ -9400,7 +9427,7 @@ sub atomic_link_if_count_less_than {
my $nlinks = $self->nlinks();
::debug("sem","$nlinks<$self->{'count'} ");
if($nlinks < $self->{'count'}) {
-d $self->{'lockdir'} or mkdir_or_die($self->{'lockdir'});
-d $self->{'lockdir'} or ::mkdir_or_die($self->{'lockdir'});
if(not -e $self->{'idfile'}) {
open (my $fh, ">", $self->{'idfile'}) or
::die_bug("write_idfile: $self->{'idfile'}");
@ -9492,23 +9519,6 @@ sub unlock {
::debug("run", "unlocked\n");
}
sub mkdir_or_die {
# If dir is not writable: die
my $dir = shift;
my @dir_parts = split(m:/:,$dir);
my ($ddir,$part);
while(defined ($part = shift @dir_parts)) {
$part eq "" and next;
$ddir .= "/".$part;
-d $ddir and next;
mkdir $ddir;
}
if(not -w $dir) {
::error("Cannot write to $dir: $!");
::wait_and_exit(255);
}
}
# Keep perl -w happy
$opt::x = $Semaphore::timeout = $Semaphore::wait =

12
testsuite/tests-to-run/parallel-local-0.3s.sh
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@ -218,6 +218,18 @@ parallel --dryrun --joblog - echo ::: Only_this
echo '**'
echo 'bug #45993: --wd ... should also work when run locally'
parallel --wd /bi 'pwd; echo $OLDPWD; echo' ::: fail
parallel --wd /bin 'pwd; echo $OLDPWD; echo' ::: OK
parallel --wd / 'pwd; echo $OLDPWD; echo' ::: OK
parallel --wd /tmp 'pwd; echo $OLDPWD; echo' ::: OK
parallel --wd ... 'pwd; echo $OLDPWD; echo' ::: OK | perl -pe 's/\d+/0/g'
parallel --wd . 'pwd; echo $OLDPWD; echo' ::: OK
echo '**'
EOF
echo '### 1 .par file from --files expected'
find /tmp{/*,}/*.{par,tms,tmx} 2>/dev/null -mmin -10 | wc -l

26
testsuite/wanted-results/parallel-local-0.3s
View file

@ -451,5 +451,31 @@ parallel --dryrun --joblog - echo ::: Only_this
echo Only_this
echo '**'
**
echo 'bug #45993: --wd ... should also work when run locally'
bug #45993: --wd ... should also work when run locally
parallel --wd /bi 'pwd; echo $OLDPWD; echo' ::: fail
parallel: Error: Cannot write to /bi: No such file or directory
parallel --wd /bin 'pwd; echo $OLDPWD; echo' ::: OK
/bin
/home/tange/privat/parallel/testsuite
OK
parallel --wd / 'pwd; echo $OLDPWD; echo' ::: OK
/
/home/tange/privat/parallel/testsuite
OK
parallel --wd /tmp 'pwd; echo $OLDPWD; echo' ::: OK
/tmp
/home/tange/privat/parallel/testsuite
OK
parallel --wd ... 'pwd; echo $OLDPWD; echo' ::: OK | perl -pe 's/\d+/0/g'
/home/tange/.parallel/tmp/aspire-0-0
/home/tange/privat/parallel/testsuite
OK
parallel --wd . 'pwd; echo $OLDPWD; echo' ::: OK
/home/tange/privat/parallel/testsuite
/home/tange/privat/parallel/testsuite
OK
echo '**'
**
### 1 .par file from --files expected
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