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testsuite: Fixup of polarhome and added X.Xs.sh.

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This commit is contained in:
Ole Tange 2013-12-19 02:19:19 +01:00
parent fbfd7d3bf7
commit bfb01e89df
18 changed files with 176 additions and 125 deletions
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3
NEWS
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@ -19,8 +19,7 @@
* --transfer and --basefile support paths relative to the --workdir by * --transfer and --basefile support paths relative to the --workdir by
inserting /./ into the path. inserting /./ into the path.
* GNU Parallel was used (unfortunately with improper citation) in: * GNU Parallel was cited in: 'fastphylo: Fast tools for phylogenetics'
'fastphylo: Fast tools for phylogenetics'
http://www.biomedcentral.com/1471-2105/14/334/abstract http://www.biomedcentral.com/1471-2105/14/334/abstract
* Using GNU parallel * Using GNU parallel

15
doc/release_new_version
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@ -244,12 +244,12 @@ New in this release:
Analysis Pipeline for Discovery of Human Genetic Variation Analysis Pipeline for Discovery of Human Genetic Variation
http://www.google.com/patents/US20130311106 http://www.google.com/patents/US20130311106
* Encrypt and decrypt in parallel with GPG
http://blog.tkassembled.com/412/encrypt-and-decrypt-in-parallel-with-gpg/
* Using GNU Parallel to create a SVM classifier * Using GNU Parallel to create a SVM classifier
http://ivanyu.me/blog/2013/12/01/parallel/ http://ivanyu.me/blog/2013/12/01/parallel/
* Mon make à moi (French)
http://www.slideshare.net/lindenb/mon-make-moi-tout-sauf-galaxy
* Parallel xz compression * Parallel xz compression
http://anthon.home.xs4all.nl/rants/2013/parallel_xz/ http://anthon.home.xs4all.nl/rants/2013/parallel_xz/
@ -262,9 +262,18 @@ New in this release:
* Gnu Parallel for fun and profit * Gnu Parallel for fun and profit
https://gist.github.com/celoyd/f7eb55ad69c9b33fd8c3 https://gist.github.com/celoyd/f7eb55ad69c9b33fd8c3
* Parallelization of Exploitation
http://rantsideasstuff.com/parallelization-of-exploitation/
* Running assemblies in parallel
https://khmer-protocols.readthedocs.org/en/v0.8.3/metagenomics/4-assemble.html
* Procesando la contabilidad del PP * Procesando la contabilidad del PP
http://www.neorazorx.com/2013/07/procesando-la-contabilidad-del-pp.html http://www.neorazorx.com/2013/07/procesando-la-contabilidad-del-pp.html
* Mon make à moi (French)
http://www.slideshare.net/lindenb/mon-make-moi-tout-sauf-galaxy
* Bug fixes and man page updates. * Bug fixes and man page updates.

2
src/parallel.pod
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@ -3619,7 +3619,7 @@ B<seq>, B<cat>, B<echo>, and B<sleep> can reproduce most errors. If
your example requires large files, see if you can make them by your example requires large files, see if you can make them by
something like B<seq 1000000> > B<file> or B<yes | head -n 10000000> > something like B<seq 1000000> > B<file> or B<yes | head -n 10000000> >
B<file>. If your example requires remote execution, see if you can B<file>. If your example requires remote execution, see if you can
use B<localhost>. use B<localhost> - maybe using another login.
=item * =item *

19
testsuite/tests-to-run/parallel-local-0.3s.sh Normal file
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@ -0,0 +1,19 @@
#!/bin/bash
# Simple jobs that never fails
# Each should be taking 0.3-1s and be possible to run in parallel
# I.e.: No race conditions, no logins
cat <<'EOF' | sed -e 's/;$/; /;s/$SERVER1/'$SERVER1'/;s/$SERVER2/'$SERVER2'/' | stdout parallel -k -j4 -L1
echo '### Test exit val - true';
echo true | parallel;
echo $?
echo '**'
echo '### Test exit val - false';
echo false | parallel;
echo $?
echo '**'
EOF

23
testsuite/tests-to-run/parallel-local-100s.sh Normal file
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@ -0,0 +1,23 @@
#!/bin/bash
# Simple jobs that never fails
# Each should be taking >100s and be possible to run in parallel
# I.e.: No race conditions, no logins
cat <<'EOF' | sed -e 's/;$/; /;s/$SERVER1/'$SERVER1'/;s/$SERVER2/'$SERVER2'/' | stdout parallel -k -j4 -L1
echo '### Test if we can deal with output > 4 GB'
## echo | niceload --io 10 parallel -q perl -e '"\$a=\"x\"x1000000;for(0..4300){print \$a}"' | md5sum
echo | parallel -q perl -e '$a="x"x1000000;for(0..4300){print $a}' | md5sum
echo '**'
echo "### Test Force outside the file handle limit, 2009-02-17 Gave fork error"
(echo echo Start; seq 1 20000 | perl -pe 's/^/true /'; echo echo end) | stdout parallel -uj 0 | egrep -v 'processes took|adjusting'
echo '**'
echo '### Test of --retries on unreachable host'
seq 2 | stdout parallel -k --retries 2 -v -S 4.3.2.1,: echo
echo '**'
EOF

7
testsuite/tests-to-run/parallel-local-10s.sh Normal file
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@ -0,0 +1,7 @@
#!/bin/bash
# Simple jobs that never fails
# Each should be taking 10-30s and be possible to run in parallel
# I.e.: No race conditions, no logins
cat <<'EOF' | sed -e 's/;$/; /;s/$SERVER1/'$SERVER1'/;s/$SERVER2/'$SERVER2'/' | stdout parallel -k -j4 -L1
EOF

19
testsuite/tests-to-run/parallel-local-30s.sh Normal file
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@ -0,0 +1,19 @@
#!/bin/bash
# Simple jobs that never fails
# Each should be taking 30-100s and be possible to run in parallel
# I.e.: No race conditions, no logins
cat <<'EOF' | sed -e 's/;$/; /;s/$SERVER1/'$SERVER1'/;s/$SERVER2/'$SERVER2'/' | stdout parallel -k -j4 -L1
echo '### Test race condition on 8 CPU (my laptop)';
seq 1 5000000 > /tmp/parallel_test;
seq 1 10 | parallel -k "cat /tmp/parallel_test | parallel --pipe --recend '' -k gzip >/dev/null; echo {}"
echo '**'
echo "### Test --tmpdir running full. bug #40733 was caused by this"
stdout parallel -j1 --tmpdir /run/shm cat /dev/zero ::: dummy
echo '**'
EOF

43
testsuite/tests-to-run/parallel-local11.sh → testsuite/tests-to-run/parallel-local-3s.sh Executable file → Normal file
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@ -1,48 +1,9 @@
#!/bin/bash #!/bin/bash
# Simple jobs that never fails # Simple jobs that never fails
# Each should be taking 100s and be possible to run in parallel # Each should be taking 3-10s and be possible to run in parallel
# I.e.: No race conditions, no logins # I.e.: No race conditions, no logins
cat <<'EOF' | sed -e 's/;$/; /;s/$SERVER1/'$SERVER1'/;s/$SERVER2/'$SERVER2'/' | stdout parallel -k -j4 -L1 cat <<'EOF' | sed -e 's/;$/; /;s/$SERVER1/'$SERVER1'/;s/$SERVER2/'$SERVER2'/' | stdout parallel -k -j4 -L1
echo '### Test if we can deal with output > 4 GB'
## echo | niceload --io 10 parallel -q perl -e '"\$a=\"x\"x1000000;for(0..4300){print \$a}"' | md5sum
echo | parallel -q perl -e '$a="x"x1000000;for(0..4300){print $a}' | md5sum
echo '**'
echo "### Test --tmpdir running full. bug #40733 was caused by this"
stdout parallel -j1 --tmpdir /run/shm cat /dev/zero ::: dummy
echo '**'
echo "### Test Force outside the file handle limit, 2009-02-17 Gave fork error"
(echo echo Start; seq 1 20000 | perl -pe 's/^/true /'; echo echo end) | stdout parallel -uj 0 | egrep -v 'processes took|adjusting'
echo '**'
echo '### Test of --retries on unreachable host'
seq 2 | stdout parallel -k --retries 2 -v -S 4.3.2.1,: echo
echo '**'
echo '### Test race condition on 8 CPU (my laptop)';
seq 1 5000000 > /tmp/parallel_test;
seq 1 10 | parallel -k "cat /tmp/parallel_test | parallel --pipe --recend '' -k gzip >/dev/null; echo {}"
echo '**'
echo '### Test exit val - true';
echo true | parallel;
echo $?
echo '**'
echo '### Test exit val - false';
echo false | parallel;
echo $?
echo '**'
echo '### Test --halt-on-error 0'; echo '### Test --halt-on-error 0';
(echo "sleep 1;true"; echo "sleep 2;false";echo "sleep 3;true") | parallel -j10 --halt-on-error 0; (echo "sleep 1;true"; echo "sleep 2;false";echo "sleep 3;true") | parallel -j10 --halt-on-error 0;
echo $?; echo $?;
@ -80,6 +41,4 @@ echo '**'
echo '### Test slow arguments generation - https://savannah.gnu.org/bugs/?32834'; echo '### Test slow arguments generation - https://savannah.gnu.org/bugs/?32834';
seq 1 3 | parallel -j1 "sleep 2; echo {}" | parallel -kj2 echo seq 1 3 | parallel -j1 "sleep 2; echo {}" | parallel -kj2 echo
EOF EOF

2
testsuite/tests-to-run/parallel-local105.sh
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@ -1,6 +1,6 @@
#!/bin/bash #!/bin/bash
TMP=/tmp/parallel_local105 TMP=/run/shm/parallel_local105
rm -rf $TMP 2>/dev/null rm -rf $TMP 2>/dev/null
mkdir -p $TMP mkdir -p $TMP
tar -C $TMP -xf input-files/random_dirs_with_newline.tar.bz2 tar -C $TMP -xf input-files/random_dirs_with_newline.tar.bz2

8
testsuite/tests-to-run/parallel-local15.sh
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@ -1,7 +1,9 @@
#!/bin/bash #!/bin/bash
rsync -Ha --delete input-files/testdir/ /tmp/parallel_$$ TMP=/run/shm/parallel_$$
cd /tmp/parallel_$$
rsync -Ha --delete input-files/testdir/ $TMP/
cd $TMP/
echo echo test of cat pipe sh | parallel -j 50 2>&1 echo echo test of cat pipe sh | parallel -j 50 2>&1
find . -name '*.jpg' | parallel -j +0 convert -geometry 120 {} {//}/thumb_{/} find . -name '*.jpg' | parallel -j +0 convert -geometry 120 {} {//}/thumb_{/}
@ -25,4 +27,4 @@ find . -type f | parallel -qv --group perl -ne '/^\S+\s+\S+$/ and print $ARGV,"\
EOF EOF
cd - cd -
rm -rf /tmp/parallel_$$ rm -rf $TMP/

2
testsuite/tests-to-run/parallel-local2.sh
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@ -27,7 +27,7 @@ echo "bug #38441: CPU usage goes to 100% if load is higher than --load at first
echo '### Test slow arguments generation - https://savannah.gnu.org/bugs/?32834' echo '### Test slow arguments generation - https://savannah.gnu.org/bugs/?32834'
seq 1 3 | parallel -j1 "sleep 2; echo {}" | parallel -kj2 echo seq 1 3 | parallel -j1 "sleep 2; echo {}" | parallel -kj2 echo
echo '### Test too slow spawning - TODO THIS CURRENTLY DOES NOT OVERLOAD' echo '### Test too slow spawning'
# Let the commands below run during high load # Let the commands below run during high load
seq `parallel --number-of-cores` | parallel -j200% -N0 timeout -k 25 26 burnP6 & seq `parallel --number-of-cores` | parallel -j200% -N0 timeout -k 25 26 burnP6 &
sleep 1; sleep 1;

17
testsuite/tests-to-run/parallel-polarhome.sh
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@ -13,17 +13,14 @@ POLAR=`parallel -k echo {}.polarhome.com ::: $P`
echo '### Tests on polarhome machines' echo '### Tests on polarhome machines'
echo 'Setup on polarhome machines' echo 'Setup on polarhome machines'
stdout parallel -kj0 ssh -oLogLevel=quiet {} mkdir -p bin ::: $POLAR & stdout parallel -kj0 ssh -oLogLevel=quiet {} mkdir -p bin ::: $POLAR &
# scp to each polarhome machine do not work. Use cat
copy_to_host() { copy_and_test() {
H=$1 H=$1
# scp to each polarhome machine do not work. Use cat
# Avoid the stupid /etc/issue.net banner with -oLogLevel=quiet # Avoid the stupid /etc/issue.net banner with -oLogLevel=quiet
ssh -oLogLevel=quiet $H rm -f bin/parallel echo '### Run the test on '$H
cat `which parallel` | ssh -oLogLevel=quiet $H 'cat > bin/parallel; chmod 755 bin/parallel' cat `which parallel` | ssh -oLogLevel=quiet $H 'cat > bin/p.tmp && chmod 755 bin/p.tmp && mv bin/p.tmp bin/parallel; bin/perl bin/parallel echo Works on ::: '$H
} }
export -f copy_to_host export -f copy_and_test
stdout parallel -j0 --timeout 20 --tag -kj0 -v copy_to_host {} ::: $POLAR stdout parallel -j0 -k --timeout 80 --delay 0.1 --tag -v copy_and_test {} ::: $POLAR
# Now test
echo '### Run the test on polarhome machines'
stdout parallel -j0 --argsep // -k --tag ssh -oLogLevel=quiet {} bin/perl bin/parallel -k echo Works on ::: {} // $POLAR

6
testsuite/wanted-results/parallel-local-0.3s Normal file
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@ -0,0 +1,6 @@
### Test exit val - true
0
**
### Test exit val - false
1
**

17
testsuite/wanted-results/parallel-local-100s Normal file
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@ -0,0 +1,17 @@
### Test if we can deal with output > 4 GB
46a318993dfc8e2afd71ff2bc6f605f1 -
**
### Test Force outside the file handle limit, 2009-02-17 Gave fork error
parallel: Warning: Only enough file handles to run 506 jobs in parallel.
Raising ulimit -n or /etc/security/limits.conf may help.
Start
end
**
### Test of --retries on unreachable host
ssh: connect to host 4.3.2.1 port 22: Connection timed out
parallel: Warning: Could not figure out number of cpus on 4.3.2.1 (). Using 1.
echo 1
1
echo 2
2
**

16
testsuite/wanted-results/parallel-local-30s Normal file
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@ -0,0 +1,16 @@
### Test race condition on 8 CPU (my laptop)
1
2
3
4
5
6
7
8
9
10
**
### Test --tmpdir running full. bug #40733 was caused by this
parallel: Error: Output is incomplete. Cannot append to buffer file in $TMPDIR. Is the disk full?
parallel: Error: Change $TMPDIR with --tmpdir.
**

39
testsuite/wanted-results/parallel-local11 → testsuite/wanted-results/parallel-local-3s
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@ -1,42 +1,3 @@
### Test if we can deal with output > 4 GB
46a318993dfc8e2afd71ff2bc6f605f1 -
**
### Test --tmpdir running full. bug #40733 was caused by this
parallel: Error: Output is incomplete. Cannot append to buffer file in $TMPDIR. Is the disk full?
parallel: Error: Change $TMPDIR with --tmpdir.
**
### Test Force outside the file handle limit, 2009-02-17 Gave fork error
parallel: Warning: Only enough file handles to run 506 jobs in parallel.
Raising ulimit -n or /etc/security/limits.conf may help.
Start
end
**
### Test of --retries on unreachable host
ssh: connect to host 4.3.2.1 port 22: Connection timed out
parallel: Warning: Could not figure out number of cpus on 4.3.2.1 (). Using 1.
echo 1
1
echo 2
2
**
### Test race condition on 8 CPU (my laptop)
1
2
3
4
5
6
7
8
9
10
**
### Test exit val - true
0
**
### Test exit val - false
1
**
### Test --halt-on-error 0 ### Test --halt-on-error 0
1 1
2 2

5
testsuite/wanted-results/parallel-local2
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@ -5,6 +5,5 @@ Less than 1 secs user time: OK
1 1
2 2
3 3
### Test too slow spawning - TODO THIS CURRENTLY DOES NOT OVERLOAD ### Test too slow spawning
parallel: Warning: Only enough file handles to run 506 jobs in parallel. OK
Raising ulimit -n or /etc/security/limits.conf may help.

58
testsuite/wanted-results/parallel-polarhome
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@ -1,43 +1,61 @@
### Tests on polarhome machines ### Tests on polarhome machines
Setup on polarhome machines Setup on polarhome machines
copy_to_host freebsd.polarhome.com copy_and_test freebsd.polarhome.com
copy_to_host solaris.polarhome.com freebsd.polarhome.com ### Run the test on freebsd.polarhome.com
copy_to_host openbsd.polarhome.com
copy_to_host netbsd.polarhome.com
copy_to_host debian.polarhome.com
copy_to_host aix.polarhome.com
copy_to_host redhat.polarhome.com
copy_to_host hpux.polarhome.com
copy_to_host qnx.polarhome.com
copy_to_host openindiana.polarhome.com
copy_to_host suse.polarhome.com
copy_to_host mandriva.polarhome.com
copy_to_host ubuntu.polarhome.com
copy_to_host scosysv.polarhome.com
copy_to_host unixware.polarhome.com
copy_to_host dragonfly.polarhome.com
copy_to_host centos.polarhome.com
copy_to_host miros.polarhome.com
copy_to_host hurd.polarhome.com
### Run the test on polarhome machines
freebsd.polarhome.com Works on freebsd.polarhome.com freebsd.polarhome.com Works on freebsd.polarhome.com
copy_and_test solaris.polarhome.com
solaris.polarhome.com ### Run the test on solaris.polarhome.com
solaris.polarhome.com Works on solaris.polarhome.com solaris.polarhome.com Works on solaris.polarhome.com
copy_and_test openbsd.polarhome.com
openbsd.polarhome.com ### Run the test on openbsd.polarhome.com
openbsd.polarhome.com Works on openbsd.polarhome.com openbsd.polarhome.com Works on openbsd.polarhome.com
copy_and_test netbsd.polarhome.com
netbsd.polarhome.com ### Run the test on netbsd.polarhome.com
netbsd.polarhome.com Works on netbsd.polarhome.com netbsd.polarhome.com Works on netbsd.polarhome.com
copy_and_test debian.polarhome.com
debian.polarhome.com ### Run the test on debian.polarhome.com
debian.polarhome.com Works on debian.polarhome.com debian.polarhome.com Works on debian.polarhome.com
copy_and_test aix.polarhome.com
aix.polarhome.com ### Run the test on aix.polarhome.com
aix.polarhome.com Works on aix.polarhome.com aix.polarhome.com Works on aix.polarhome.com
copy_and_test redhat.polarhome.com
redhat.polarhome.com ### Run the test on redhat.polarhome.com
redhat.polarhome.com Works on redhat.polarhome.com redhat.polarhome.com Works on redhat.polarhome.com
copy_and_test hpux.polarhome.com
hpux.polarhome.com ### Run the test on hpux.polarhome.com
hpux.polarhome.com Works on hpux.polarhome.com hpux.polarhome.com Works on hpux.polarhome.com
copy_and_test qnx.polarhome.com
qnx.polarhome.com ### Run the test on qnx.polarhome.com
qnx.polarhome.com Works on qnx.polarhome.com qnx.polarhome.com Works on qnx.polarhome.com
qnx.polarhome.com parallel: Warning: Cannot figure out number of CPU cores. Using 1. qnx.polarhome.com parallel: Warning: Cannot figure out number of CPU cores. Using 1.
copy_and_test openindiana.polarhome.com
openindiana.polarhome.com ### Run the test on openindiana.polarhome.com
openindiana.polarhome.com Works on openindiana.polarhome.com openindiana.polarhome.com Works on openindiana.polarhome.com
openindiana.polarhome.com parallel: Warning: Cannot figure out number of CPU cores. Using 1. openindiana.polarhome.com parallel: Warning: Cannot figure out number of CPU cores. Using 1.
copy_and_test suse.polarhome.com
suse.polarhome.com ### Run the test on suse.polarhome.com
suse.polarhome.com Works on suse.polarhome.com suse.polarhome.com Works on suse.polarhome.com
copy_and_test mandriva.polarhome.com
mandriva.polarhome.com ### Run the test on mandriva.polarhome.com
mandriva.polarhome.com Works on mandriva.polarhome.com mandriva.polarhome.com Works on mandriva.polarhome.com
copy_and_test ubuntu.polarhome.com
ubuntu.polarhome.com ### Run the test on ubuntu.polarhome.com
ubuntu.polarhome.com Works on ubuntu.polarhome.com ubuntu.polarhome.com Works on ubuntu.polarhome.com
copy_and_test scosysv.polarhome.com
scosysv.polarhome.com ### Run the test on scosysv.polarhome.com
scosysv.polarhome.com Works on scosysv.polarhome.com scosysv.polarhome.com Works on scosysv.polarhome.com
copy_and_test unixware.polarhome.com
unixware.polarhome.com ### Run the test on unixware.polarhome.com
unixware.polarhome.com Works on unixware.polarhome.com unixware.polarhome.com Works on unixware.polarhome.com
copy_and_test dragonfly.polarhome.com
dragonfly.polarhome.com ### Run the test on dragonfly.polarhome.com
dragonfly.polarhome.com Works on dragonfly.polarhome.com dragonfly.polarhome.com Works on dragonfly.polarhome.com
copy_and_test centos.polarhome.com
centos.polarhome.com ### Run the test on centos.polarhome.com
centos.polarhome.com Works on centos.polarhome.com centos.polarhome.com Works on centos.polarhome.com
copy_and_test miros.polarhome.com
miros.polarhome.com ### Run the test on miros.polarhome.com
miros.polarhome.com Works on miros.polarhome.com miros.polarhome.com Works on miros.polarhome.com
copy_and_test hurd.polarhome.com
hurd.polarhome.com ### Run the test on hurd.polarhome.com
hurd.polarhome.com Works on hurd.polarhome.com hurd.polarhome.com Works on hurd.polarhome.com