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https://git.savannah.gnu.org/git/parallel.git
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Bugfix: Race condition giving segfault rarely
This commit is contained in:
Ole Tange
parent
cf05dae1b1
commit
757dddaf6c
213
src/parallel
213
src/parallel
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@ -150,6 +150,15 @@ B<{6}> will refer to the line with the same line number from the 6th
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file.
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=item B<--arg-file-sep> I<sep-str> (unimplemented)
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Use I<sep-str> instead of B<::::> as separator string between command
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and argument files. Useful if B<::::> is used for something else by the
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command.
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See also: B<::::>.
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=item B<--arg-sep> I<sep-str> (beta testing)
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Use I<sep-str> instead of B<:::> as separator string. Useful if B<:::>
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@ -806,12 +815,12 @@ B<find . -name '*.jpg' | parallel -j +0 convert -geometry 120 {} {.}_thumb.jpg>
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This will generate an uncompressed version of .gz-files next to the .gz-file:
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B<ls *.gz | parallel zcat {} ">>B<"{.}>
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B<parallel zcat {} ">>B<"{.} ::: *.gz>
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Quoting of > is necessary to postpone the redirection. Another
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solution is to quote the whole command:
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B<ls *.gz | parallel "zcat {} >>B<{.}">
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B<parallel "zcat {} >>B<{.}" ::: *.gz>
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Other special shell charaters (such as * ; $ > < | >> <<) also needs
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to be put in quotes, as they may otherwise be interpreted by the shell
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@ -840,12 +849,12 @@ often useful.
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Create a directory for each zip-file and unzip it in that dir:
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B<ls *zip | parallel 'mkdir {.}; cd {.}; unzip ../{}'>
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B<parallel 'mkdir {.}; cd {.}; unzip ../{}' ::: *.zip>
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Recompress all .gz files in current directory using B<bzip2> running 1
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job per CPU core in parallel:
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B<ls *.gz | parallel -j+0 "zcat {} | bzip2 >>B<{.}.bz2 && rm {}">
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B<parallel -j+0 "zcat {} | bzip2 >>B<{.}.bz2 && rm {}" ::: *.gz>
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Convert all WAV files to MP3 using LAME:
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@ -911,11 +920,11 @@ B<-u>.
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Compare the output of:
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B<(echo foss.org.my; echo debian.org; echo freenetproject.org) | parallel traceroute>
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B<parallel traceroute ::: foss.org.my debian.org freenetproject.org>
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to the output of:
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B<(echo foss.org.my; echo debian.org; echo freenetproject.org) | parallel -u traceroute>
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B<parallel -u traceroute ::: foss.org.my debian.org freenetproject.org>
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=head1 EXAMPLE: Keep order of output same as order of input
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@ -935,7 +944,7 @@ If you remove B<-k> some of the lines may come out in the wrong order.
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Another example is B<traceroute>:
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B<(echo foss.org.my; echo debian.org; echo freenetproject.org) | parallel traceroute>
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B<parallel traceroute ::: foss.org.my debian.org freenetproject.org>
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will give traceroute of foss.org.my, debian.org and
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freenetproject.org, but it will be sorted according to which job
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@ -943,7 +952,7 @@ completed first.
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To keep the order the same as input run:
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B<(echo foss.org.my; echo debian.org; echo freenetproject.org) | parallel -k traceroute>
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B<parallel -k traceroute ::: foss.org.my debian.org freenetproject.org>
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This will make sure the traceroute to foss.org.my will be printed
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first.
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@ -954,7 +963,7 @@ first.
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B<grep -r> greps recursively through directories. On multicore CPUs
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GNU B<parallel> can often speed this up.
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find . -type f | parallel -k -j150% -n 1000 -m grep -H -n STRING {}
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B<find . -type f | parallel -k -j150% -n 1000 -m grep -H -n STRING {}>
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This will run 1.5 job per core, and give 1000 arguments to B<grep>.
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@ -1346,7 +1355,7 @@ and the last half of the line is from another process. The example
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B<Parallel grep> cannot be done reliably with B<make -j> because of
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this.
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(Very early versions of GNU Parallel was coincidently implemented
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(Very early versions of GNU B<parallel> were coincidently implemented
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using B<make -j>).
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@ -1382,47 +1391,46 @@ start. GNU B<parallel> only requires one step.
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Here are the examples from B<ppss>'s manual page with the equivalent
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using GNU B<parallel>:
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./ppss.sh standalone -d /path/to/files -c 'gzip '
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B<1> ./ppss.sh standalone -d /path/to/files -c 'gzip '
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find /path/to/files -type f | parallel -j+0 gzip
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B<1> find /path/to/files -type f | parallel -j+0 gzip
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./ppss.sh standalone -d /path/to/files -c 'cp "$ITEM" /destination/dir '
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B<2> ./ppss.sh standalone -d /path/to/files -c 'cp "$ITEM" /destination/dir '
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find /path/to/files -type f | parallel -j+0 cp {} /destination/dir
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B<2> find /path/to/files -type f | parallel -j+0 cp {} /destination/dir
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./ppss.sh standalone -f list-of-urls.txt -c 'wget -q '
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B<3> ./ppss.sh standalone -f list-of-urls.txt -c 'wget -q '
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parallel -a list-of-urls.txt wget -q
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B<3> parallel -a list-of-urls.txt wget -q
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./ppss.sh standalone -f list-of-urls.txt -c 'wget -q "$ITEM"'
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B<4> ./ppss.sh standalone -f list-of-urls.txt -c 'wget -q "$ITEM"'
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parallel -a list-of-urls.txt wget -q {}
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./ppss config -C config.cfg -c 'encode.sh ' -d /source/dir -m 192.168.1.100 -u ppss -k ppss-key.key -S ./encode.sh -n nodes.txt -o /some/output/dir --upload --download
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./ppss deploy -C config.cfg
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B<4> parallel -a list-of-urls.txt wget -q {}
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B<5> ./ppss config -C config.cfg -c 'encode.sh ' -d /source/dir -m
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192.168.1.100 -u ppss -k ppss-key.key -S ./encode.sh -n nodes.txt -o
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/some/output/dir --upload --download ; ./ppss deploy -C config.cfg ;
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./ppss start -C config
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# parallel does not use configs. If you want a different username put it in nodes.txt: user@hostname
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B<5> # parallel does not use configs. If you want a different username put it in nodes.txt: user@hostname
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find source/dir -type f | parallel --sshloginfile nodes.txt --trc {.}.mp3 lame -a {} -o {.}.mp3 --preset standard --quiet
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B<5> find source/dir -type f | parallel --sshloginfile nodes.txt --trc {.}.mp3 lame -a {} -o {.}.mp3 --preset standard --quiet
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./ppss stop -C config.cfg
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B<6> ./ppss stop -C config.cfg
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killall -TERM parallel
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B<6> killall -TERM parallel
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./ppss pause -C config.cfg
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B<7> ./ppss pause -C config.cfg
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Press: CTRL-Z or killall -SIGTSTP parallel
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B<7> Press: CTRL-Z or killall -SIGTSTP parallel
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./ppss continue -C config.cfg
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B<8> ./ppss continue -C config.cfg
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Enter: fg or killall -SIGCONT parallel
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B<8> Enter: fg or killall -SIGCONT parallel
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./ppss.sh status -C config.cfg
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B<9> ./ppss.sh status -C config.cfg
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killall -SIGUSR1 parallel # Not quite equivalent: Only shows the currently running jobs
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B<9> killall -SIGUSR2 parallel
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=head2 DIFFERENCES BETWEEN pexec AND GNU Parallel
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@ -1432,49 +1440,49 @@ B<pexec> is also a tool for running jobs in parallel.
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Here are the examples from B<pexec>'s info page with the equivalent
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using GNU B<parallel>:
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pexec -o sqrt-%s.dat -p "$(seq 10)" -e NUM -n 4 -c -- \
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B<1> pexec -o sqrt-%s.dat -p "$(seq 10)" -e NUM -n 4 -c -- \
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'echo "scale=10000;sqrt($NUM)" | bc'
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seq 10 | parallel -j4 'echo "scale=10000;sqrt({})" | bc > sqrt-{}.dat'
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B<1> seq 10 | parallel -j4 'echo "scale=10000;sqrt({})" | bc > sqrt-{}.dat'
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pexec -p "$(ls myfiles*.ext)" -i %s -o %s.sort -- sort
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B<2> pexec -p "$(ls myfiles*.ext)" -i %s -o %s.sort -- sort
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ls myfiles*.ext | parallel sort {} ">{}.sort"
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B<2> ls myfiles*.ext | parallel sort {} ">{}.sort"
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pexec -f image.list -n auto -e B -u star.log -c -- \
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B<3> pexec -f image.list -n auto -e B -u star.log -c -- \
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'fistar $B.fits -f 100 -F id,x,y,flux -o $B.star'
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parallel -a image.list -j+0 \
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B<3> parallel -a image.list -j+0 \
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'fistar {}.fits -f 100 -F id,x,y,flux -o {}.star' 2>star.log
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pexec -r *.png -e IMG -c -o - -- \
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B<4> pexec -r *.png -e IMG -c -o - -- \
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'convert $IMG ${IMG%.png}.jpeg ; "echo $IMG: done"'
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ls *.png | parallel 'convert {} {.}.jpeg; echo {}: done'
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B<4> ls *.png | parallel 'convert {} {.}.jpeg; echo {}: done'
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pexec -r *.png -i %s -o %s.jpg -c 'pngtopnm | pnmtojpeg'
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B<5> pexec -r *.png -i %s -o %s.jpg -c 'pngtopnm | pnmtojpeg'
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ls *.png | parallel 'pngtopnm < {} | pnmtojpeg > {}.jpg'
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B<5> ls *.png | parallel 'pngtopnm < {} | pnmtojpeg > {}.jpg'
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for p in *.png ; do echo ${p%.png} ; done | \
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B<6> for p in *.png ; do echo ${p%.png} ; done | \
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pexec -f - -i %s.png -o %s.jpg -c 'pngtopnm | pnmtojpeg'
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ls *.png | parallel 'pngtopnm < {} | pnmtojpeg > {.}.jpg'
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B<6> ls *.png | parallel 'pngtopnm < {} | pnmtojpeg > {.}.jpg'
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LIST=$(for p in *.png ; do echo ${p%.png} ; done)
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B<7> LIST=$(for p in *.png ; do echo ${p%.png} ; done)
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pexec -r $LIST -i %s.png -o %s.jpg -c 'pngtopnm | pnmtojpeg'
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ls *.png | parallel 'pngtopnm < {} | pnmtojpeg > {.}.jpg'
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B<7> ls *.png | parallel 'pngtopnm < {} | pnmtojpeg > {.}.jpg'
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pexec -n 8 -r *.jpg -y unix -e IMG -c \
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B<8> pexec -n 8 -r *.jpg -y unix -e IMG -c \
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'pexec -j -m blockread -d $IMG | \
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jpegtopnm | pnmscale 0.5 | pnmtojpeg | \
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pexec -j -m blockwrite -s th_$IMG'
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GNU B<parallel> does not support mutexes directly but uses B<mutex> to
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B<8> GNU B<parallel> does not support mutexes directly but uses B<mutex> to
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do that.
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ls *jpg | parallel -j8 'mutex -m blockread cat {} | jpegtopnm |' \
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B<8> ls *jpg | parallel -j8 'mutex -m blockread cat {} | jpegtopnm |' \
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'pnmscale 0.5 | pnmtojpeg | mutex -m blockwrite cat > th_{}'
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@ -1489,32 +1497,32 @@ the section B<DIFFERENCES BETWEEN xargs AND GNU Parallel>.
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Here are the examples from B<xjobs>'s man page with the equivalent
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using GNU B<parallel>:
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ls -1 *.zip | xjobs unzip
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B<1> ls -1 *.zip | xjobs unzip
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ls *.zip | parallel unzip
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B<1> ls *.zip | parallel unzip
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ls -1 *.zip | xjobs -n unzip
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B<2> ls -1 *.zip | xjobs -n unzip
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ls *.zip | parallel unzip >/dev/null
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B<2> ls *.zip | parallel unzip >/dev/null
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find . -name '*.bak' | xjobs gzip
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B<3> find . -name '*.bak' | xjobs gzip
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find . -name '*.bak' | parallel gzip
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B<3> find . -name '*.bak' | parallel gzip
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ls -1 *.jar | sed 's/\(.*\)/\1 > \1.idx/' | xjobs jar tf
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B<4> ls -1 *.jar | sed 's/\(.*\)/\1 > \1.idx/' | xjobs jar tf
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ls *.jar | parallel jar tf {} '>' {}.idx
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B<4> ls *.jar | parallel jar tf {} '>' {}.idx
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xjobs -s script
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B<5> xjobs -s script
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cat script | parallel
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B<5> cat script | parallel
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mkfifo /var/run/my_named_pipe;
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B<6> mkfifo /var/run/my_named_pipe;
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xjobs -s /var/run/my_named_pipe &
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echo unzip 1.zip >> /var/run/my_named_pipe;
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echo tar cf /backup/myhome.tar /home/me >> /var/run/my_named_pipe
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mkfifo /var/run/my_named_pipe;
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B<6> mkfifo /var/run/my_named_pipe;
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cat /var/run/my_named_pipe | parallel &
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echo unzip 1.zip >> /var/run/my_named_pipe;
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echo tar cf /backup/myhome.tar /home/me >> /var/run/my_named_pipe
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@ -1539,7 +1547,7 @@ using GNU B<parallel>:
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prll -s 'mogrify -flip $1' *.jpg
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ls *.jpg | parallel mogrify -flip
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parallel mogrify -flip ::: *.jpg
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=head2 DIFFERENCES BETWEEN dxargs AND GNU Parallel
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@ -1570,49 +1578,49 @@ B<xapply> can run jobs in parallel on the local computer.
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Here are the examples from B<xapply>'s man page with the equivalent
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using GNU B<parallel>:
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xapply '(cd %1 && make all)' */
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B<1> xapply '(cd %1 && make all)' */
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parallel 'cd {} && make all' ::: */
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B<1> parallel 'cd {} && make all' ::: */
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xapply -f 'diff %1 ../version5/%1' manifest | more
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B<2> xapply -f 'diff %1 ../version5/%1' manifest | more
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parallel diff {} ../version5/{} < manifest | more
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B<2> parallel diff {} ../version5/{} < manifest | more
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xapply -p/dev/null -f 'diff %1 %2' manifest1 checklist1
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B<3> xapply -p/dev/null -f 'diff %1 %2' manifest1 checklist1
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parallel diff {1} {2} :::: manifest1 checklist1
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B<3> parallel diff {1} {2} :::: manifest1 checklist1
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xapply 'indent' *.c
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B<4> xapply 'indent' *.c
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parallel indent ::: *.c
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B<4> parallel indent ::: *.c
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find ~ksb/bin -type f ! -perm -111 -print | xapply -f -v 'chmod a+x' -
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B<5> find ~ksb/bin -type f ! -perm -111 -print | xapply -f -v 'chmod a+x' -
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find ~ksb/bin -type f ! -perm -111 -print | parallel -v chmod a+x
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B<5> find ~ksb/bin -type f ! -perm -111 -print | parallel -v chmod a+x
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find */ -... | fmt 960 1024 | xapply -f -i /dev/tty 'vi' -
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B<6> find */ -... | fmt 960 1024 | xapply -f -i /dev/tty 'vi' -
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sh <(find */ -... | parallel -s 1024 echo vi)
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B<6> sh <(find */ -... | parallel -s 1024 echo vi)
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find ... | xapply -f -5 -i /dev/tty 'vi' - - - - -
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B<7> find ... | xapply -f -5 -i /dev/tty 'vi' - - - - -
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sh <(find ... |parallel -n5 echo vi)
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B<7> sh <(find ... |parallel -n5 echo vi)
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xapply -fn "" /etc/passwd
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B<8> xapply -fn "" /etc/passwd
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parallel -k echo < /etc/passwd
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B<8> parallel -k echo < /etc/passwd
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tr ':' '\012' < /etc/passwd | xapply -7 -nf 'chown %1 %6' - - - - - - -
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B<9> tr ':' '\012' < /etc/passwd | xapply -7 -nf 'chown %1 %6' - - - - - - -
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tr ':' '\012' < /etc/passwd | parallel -N7 chown {1} {6}
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B<9> tr ':' '\012' < /etc/passwd | parallel -N7 chown {1} {6}
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xapply '[ -d %1/RCS ] || echo %1' */
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B<10> xapply '[ -d %1/RCS ] || echo %1' */
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parallel '[ -d {}/RCS ] || echo {}' ::: */
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B<10> parallel '[ -d {}/RCS ] || echo {}' ::: */
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xapply -f '[ -f %1 ] && echo %1' List | ...
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B<11> xapply -f '[ -f %1 ] && echo %1' List | ...
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parallel '[ -f {} ] && echo {}' < List | ...
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B<11> parallel '[ -f {} ] && echo {}' < List | ...
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=head2 DIFFERENCES BETWEEN ClusterSSH AND GNU Parallel
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@ -1805,9 +1813,9 @@ reap_if_needed();
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drain_job_queue();
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cleanup();
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if($::opt_halt_on_error) {
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exit $Global::halt_on_error_exitstatus;
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wait_and_exit $Global::halt_on_error_exitstatus;
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} else {
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exit(min($Global::exitstatus,254));
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wait_and_exit(min($Global::exitstatus,254));
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}
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sub parse_options {
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@ -1832,6 +1840,7 @@ sub parse_options {
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$Global::halt_on_error_exitstatus = 0;
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$Global::total_jobs = 0;
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$Global::arg_sep = ":::";
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$Global::arg_file_sep = ":::";
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Getopt::Long::Configure ("bundling","require_order");
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# Add options from .parallelrc
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@ -1878,6 +1887,7 @@ sub parse_options {
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"progress" => \$::opt_progress,
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"eta" => \$::opt_eta,
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"arg-sep|argsep=s" => \$::opt_arg_sep,
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"arg-file-sep|argfilesep=s" => \$::opt_arg_file_sep,
|
||||
# xargs-compatibility - implemented, man, unittest
|
||||
"max-procs|P=s" => \$::opt_P,
|
||||
"delimiter|d=s" => \$::opt_d,
|
||||
|
|
@ -1926,10 +1936,11 @@ sub parse_options {
|
|||
if(defined $::opt_N and $::opt_N) { $Global::max_number_of_args = $::opt_N; }
|
||||
if(defined $::opt_help) { die_usage(); }
|
||||
if(defined $::opt_arg_sep) { $Global::arg_sep = $::opt_arg_sep; }
|
||||
if(defined $::opt_number_of_cpus) { print no_of_cpus(),"\n"; exit(0); }
|
||||
if(defined $::opt_number_of_cores) { print no_of_cores(),"\n"; exit(0); }
|
||||
if(defined $::opt_max_line_length_allowed) { print real_max_length(),"\n"; exit(0); }
|
||||
if(defined $::opt_version) { version(); exit(0); }
|
||||
if(defined $::opt_arg_file_sep) { $Global::arg_file_sep = $::opt_arg_file_sep; }
|
||||
if(defined $::opt_number_of_cpus) { print no_of_cpus(),"\n"; wait_and_exit(0); }
|
||||
if(defined $::opt_number_of_cores) { print no_of_cores(),"\n"; wait_and_exit(0); }
|
||||
if(defined $::opt_max_line_length_allowed) { print real_max_length(),"\n"; wait_and_exit(0); }
|
||||
if(defined $::opt_version) { version(); wait_and_exit(0); }
|
||||
if(defined $::opt_show_limits) { show_limits(); }
|
||||
if(defined @::opt_sshlogin) { @Global::sshlogin = @::opt_sshlogin; }
|
||||
if(defined $::opt_sshloginfile) { read_sshloginfile($::opt_sshloginfile); }
|
||||
|
|
@ -1968,13 +1979,13 @@ sub parse_options {
|
|||
@ARGV=@new_argv;
|
||||
}
|
||||
|
||||
if(grep /^::::$/o, @ARGV) {
|
||||
if(grep /^$Global::arg_file_sep$/o, @ARGV) {
|
||||
# convert :::: to multiple -a
|
||||
my @new_argv = ();
|
||||
my @argument_files;
|
||||
while(@ARGV) {
|
||||
my $arg = shift @ARGV;
|
||||
if($arg eq "::::") {
|
||||
if($arg eq $Global::arg_file_sep) {
|
||||
@argument_files = @ARGV;
|
||||
@ARGV=();
|
||||
} else {
|
||||
|
|
@ -2082,7 +2093,7 @@ sub open_or_exit {
|
|||
print STDERR "$Global::progname: ".
|
||||
"Cannot open input file `$file': ".
|
||||
"No such file or directory\n";
|
||||
exit(255);
|
||||
wait_and_exit(255);
|
||||
}
|
||||
return $fh;
|
||||
}
|
||||
|
|
@ -2213,7 +2224,7 @@ sub get_multiple_args {
|
|||
. $max_length_of_command_line .
|
||||
") at number $number_of_args: ".
|
||||
(substr($next_arg,0,50))."...\n");
|
||||
exit(255);
|
||||
wait_and_exit(255);
|
||||
}
|
||||
if(defined $quoted_args[0]) {
|
||||
last;
|
||||
|
|
@ -2222,7 +2233,7 @@ sub get_multiple_args {
|
|||
. $max_length_of_command_line .
|
||||
") at number $number_of_args: ".
|
||||
(substr($next_arg,0,50))."...\n");
|
||||
exit(255);
|
||||
wait_and_exit(255);
|
||||
}
|
||||
}
|
||||
if($Global::max_number_of_args and
|
||||
|
|
@ -2504,7 +2515,7 @@ sub processes_available_by_system_limit {
|
|||
# The child takes one process slot
|
||||
# It will be killed later
|
||||
sleep 100000;
|
||||
exit(0);
|
||||
wait_and_exit(0);
|
||||
} else {
|
||||
$max_system_proc_reached = 1;
|
||||
}
|
||||
|
|
@ -3485,7 +3496,7 @@ sub sshcommand_of_sshlogin {
|
|||
} else {
|
||||
debug($master,"\n");
|
||||
`$master`;
|
||||
exit(0);
|
||||
wait_and_exit(0);
|
||||
}
|
||||
}
|
||||
} else {
|
||||
|
|
@ -3725,10 +3736,16 @@ sub reaper {
|
|||
# Usage
|
||||
#
|
||||
|
||||
sub wait_and_exit {
|
||||
# If we do not wait, we sometimes get segfault
|
||||
wait();
|
||||
exit(shift);
|
||||
}
|
||||
|
||||
sub die_usage {
|
||||
# Returns: N/A
|
||||
usage();
|
||||
exit(255);
|
||||
wait_and_exit(255);
|
||||
}
|
||||
|
||||
sub usage {
|
||||
|
|
|
|||
BIN
unittest/input-files/segfault/items-0.xi
Normal file
BIN
unittest/input-files/segfault/items-0.xi
Normal file
Binary file not shown.
16
unittest/input-files/segfault/trysegfault
Executable file
16
unittest/input-files/segfault/trysegfault
Executable file
|
|
@ -0,0 +1,16 @@
|
|||
stdout parallel -i -s28 -0 true from \{\} to x{}y < items-0.xi |egrep -v 'exit|Command|\.\.\.'
|
||||
|
||||
# Fejler
|
||||
#stdout parallel -Di -s28 -0 true from \{\} to x{}y < items-0.xi > /dev/null
|
||||
# stdout parallel -Di -s28 -0 echo from \{\} to x{}y < items-0.xi > /dev/null
|
||||
|
||||
#grep Segmentation /tmp/out && cat >/tmp/:out < /tmp/out
|
||||
|
||||
# Denne fejler: seq 1 100 | parallel --eta trysegfault
|
||||
#stdout stdout /usr/local/bin/parallel -Di -s26 -0 echo from \{\} to x{}y < items-0.xi > /tmp/out;
|
||||
#grep Segmentation /tmp/out && cat >/tmp/:out < /tmp/out
|
||||
|
||||
|
||||
|
||||
#/usr/local/bin/parallel -s26 -0 echo < items-0.xi > /tmp/out
|
||||
|
||||
9
unittest/tests-to-run/test28.sh
Normal file
9
unittest/tests-to-run/test28.sh
Normal file
|
|
@ -0,0 +1,9 @@
|
|||
#!/bin/bash -x
|
||||
|
||||
rsync -Ha --delete input-files/segfault/ tmp/
|
||||
cd tmp
|
||||
|
||||
echo '### Test of segfaulting issue'
|
||||
echo 'This gave /home/tange/bin/stdout: line 3: 20374 Segmentation fault "$@" 2>&1'
|
||||
echo 'before adding wait() before exit'
|
||||
seq 1 300 | stdout parallel ./trysegfault
|
||||
3
unittest/wanted-results/test28
Normal file
3
unittest/wanted-results/test28
Normal file
|
|
@ -0,0 +1,3 @@
|
|||
### Test of segfaulting issue
|
||||
This gave /home/tange/bin/stdout: line 3: 20374 Segmentation fault "$@" 2>&1
|
||||
before adding wait() before exit
|
||||
Loading…
Reference in a new issue