[Debichem-devel] Bug#897191: pymol: autopkgtest times out with new version while succeeded in the past
Paul Gevers
elbrus at debian.org
Sun Apr 29 20:21:51 BST 2018
Source: pymol
Version: 2.1.0+dfsg-1
Severity: normal
User: debian-ci at lists.debian.org
Usertags: regression timeout
With the upload of version 2.1.0+dfsg-1 of pymol, the autopkgtest¹
started to fail due to it timing out (> 11 hours) on 4 of the tests and
additionally due to unexpected output to stderr (see the relevant part
of the log copied below). Previous versions only required a couple of
minutes. Therefore I assume a lot of tests got added (albeit no note in
the changelog about that), otherwise it is really worth it to try and
find out why it now takes so much longer.
A note about time outs. Time outs can often be worked around by
splitting a test into multiple autopkgtest because each gets its own
timeout. On the other hand, is 11 hours or more really worth it?
Couldn't a limited set of the test be run?
Output to stderr normally causes a test to fail. One can overrule that
by add allow-stderr to the test Restrictions if the output is expected
and to be ignored.
Don't hesitate to ask for help for the Debian CI team if you need help
solving this issue.
Paul
PS: I don't want to threaten, but if the time out isn't going to be
fixed soon, we'll probably add pymol to the ci.d.n blacklist.
¹ https://ci.debian.net/packages/p/pymol/unstable/amd64/
² debian-ci at lists.debian.org
autopkgtest [10:06:31]: test command1: sh
debian/tests/call-pymol-scripts examples/ \
"(start_pymol)|(xmlrpc01)|(sd_annotate)|(povray01)|(contact)|(dali)|(density)|(groel_es)|(packing)|(packsurf)|(ref_frame)|(ribosome)|(ss_xfer)|(multiclip_ray)"
autopkgtest [10:06:31]: test command1: [-----------------------
Search pymol scripts in
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src/examples...
Processing new directory
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src/examples
Run 'pymol -c
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src/examples/chempy/generate_mmff.py'...
[31;1mnot ok - line 'PyMOL: normal program termination.' was not found
in pymol output[0m
Run 'pymol -c
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src/examples/chempy/generate_amber.py'...
[31;1mnot ok - line 'PyMOL: normal program termination.' was not found
in pymol output[0m
autopkgtest [12:53:11]: ERROR: timed out on command "su -s /bin/bash
debci -c set -e; export USER=`id -nu`; . /etc/profile >/dev/null 2>&1 ||
true; . ~/.profile >/dev/null 2>&1 || true;
buildtree="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src"; mkdir
-p -m 1777 --
"/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command1-artifacts"; export
AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command1-artifacts";
export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755
"/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp"; export
AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp";
export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive;
export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=8; unset LANGUAGE
LC_CTYPE LC_NUMERIC LC_TIME LC_COLLATE LC_MONETARY LC_MESSAGES
LC_PAPER LC_NAME LC_ADDRESS LC_TELEPHONE LC_MEASUREMENT
LC_IDENTIFICATION LC_ALL;rm -f /tmp/autopkgtest_script_pid; set -C; echo
$$ > /tmp/autopkgtest_script_pid; set +C; trap "rm -f
/tmp/autopkgtest_script_pid" EXIT INT QUIT PIPE; cd "$buildtree"; touch
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command1-stdout
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command1-stderr; bash -ec 'sh
debian/tests/call-pymol-scripts examples/ \
"(start_pymol)|(xmlrpc01)|(sd_annotate)|(povray01)|(contact)|(dali)|(density)|(groel_es)|(packing)|(packsurf)|(ref_frame)|(ribosome)|(ss_xfer)|(multiclip_ray)"'
2> >(tee -a /tmp/autopkgtest-lxc.abr4cnnf/downtmp/command1-stderr >&2) >
>(tee -a /tmp/autopkgtest-lxc.abr4cnnf/downtmp/command1-stdout);" (kind:
test)
autopkgtest [12:53:12]: test command1: -----------------------]
autopkgtest [12:53:12]: test command1: - - - - - - - - - - results - -
- - - - - - - -
command1 FAIL timed out
autopkgtest [12:53:12]: test command1: - - - - - - - - - - stderr - - -
- - - - - - -
[31;1mnot ok - line 'PyMOL: normal program termination.' was not found
in pymol output[0m
[31;1mnot ok - line 'PyMOL: normal program termination.' was not found
in pymol output[0m
autopkgtest [12:53:45]: test command2: [-----------------------
Search pymol scripts in
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src/data/demo...
Processing new directory
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src/data/demo
autopkgtest [15:40:26]: ERROR: timed out on command "su -s /bin/bash
debci -c set -e; export USER=`id -nu`; . /etc/profile >/dev/null 2>&1 ||
true; . ~/.profile >/dev/null 2>&1 || true;
buildtree="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src"; mkdir
-p -m 1777 --
"/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command2-artifacts"; export
AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command2-artifacts";
export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755
"/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp"; export
AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp";
export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive;
export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=8; unset LANGUAGE
LC_CTYPE LC_NUMERIC LC_TIME LC_COLLATE LC_MONETARY LC_MESSAGES
LC_PAPER LC_NAME LC_ADDRESS LC_TELEPHONE LC_MEASUREMENT
LC_IDENTIFICATION LC_ALL;rm -f /tmp/autopkgtest_script_pid; set -C; echo
$$ > /tmp/autopkgtest_script_pid; set +C; trap "rm -f
/tmp/autopkgtest_script_pid" EXIT INT QUIT PIPE; cd "$buildtree"; touch
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command2-stdout
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command2-stderr; bash -ec 'sh
debian/tests/call-pymol-scripts data/demo' 2> >(tee -a
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command2-stderr >&2) > >(tee -a
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command2-stdout);" (kind: test)
autopkgtest [15:40:26]: test command2: -----------------------]
autopkgtest [15:40:26]: test command2: - - - - - - - - - - results - -
- - - - - - - -
command2 FAIL timed out
autopkgtest [15:41:40]: test command4: sh
debian/tests/call-pymol-scripts /usr/share/pymol/examples \
"(cookbook/)|(xmlrpc01)|(sd_annotate)|(povray01)"
autopkgtest [15:41:40]: test command4: [-----------------------
Search pymol scripts in /usr/share/pymol/examples...
Processing new directory /usr/share/pymol/examples
Run 'pymol -c /usr/share/pymol/examples/chempy/generate_mmff.py'...
[31;1mnot ok - line 'PyMOL: normal program termination.' was not found
in pymol output[0m
Run 'pymol -c /usr/share/pymol/examples/chempy/generate_amber.py'...
[31;1mnot ok - line 'PyMOL: normal program termination.' was not found
in pymol output[0m
Skip /usr/share/pymol/examples/cookbook/scenes2movie.pml
Skip /usr/share/pymol/examples/cookbook/packsurf.pml
Skip /usr/share/pymol/examples/cookbook/packing.pml
Skip /usr/share/pymol/examples/cookbook/multiclip_ray.pml
Skip /usr/share/pymol/examples/cookbook/ss_xfer.pml
Skip /usr/share/pymol/examples/cookbook/seq_match_sele.pml
Skip /usr/share/pymol/examples/cookbook/contact.pml
Skip /usr/share/pymol/examples/cookbook/area_diff.pml
Skip /usr/share/pymol/examples/cookbook/ref_frame.pml
autopkgtest [18:28:20]: ERROR: timed out on command "su -s /bin/bash
debci -c set -e; export USER=`id -nu`; . /etc/profile >/dev/null 2>&1 ||
true; . ~/.profile >/dev/null 2>&1 || true;
buildtree="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src"; mkdir
-p -m 1777 --
"/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command4-artifacts"; export
AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command4-artifacts";
export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755
"/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp"; export
AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp";
export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive;
export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=8; unset LANGUAGE
LC_CTYPE LC_NUMERIC LC_TIME LC_COLLATE LC_MONETARY LC_MESSAGES
LC_PAPER LC_NAME LC_ADDRESS LC_TELEPHONE LC_MEASUREMENT
LC_IDENTIFICATION LC_ALL;rm -f /tmp/autopkgtest_script_pid; set -C; echo
$$ > /tmp/autopkgtest_script_pid; set +C; trap "rm -f
/tmp/autopkgtest_script_pid" EXIT INT QUIT PIPE; cd "$buildtree"; touch
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command4-stdout
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command4-stderr; bash -ec 'sh
debian/tests/call-pymol-scripts /usr/share/pymol/examples \
"(cookbook/)|(xmlrpc01)|(sd_annotate)|(povray01)"' 2> >(tee -a
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command4-stderr >&2) > >(tee -a
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command4-stdout);" (kind: test)
autopkgtest [18:28:21]: test command4: -----------------------]
autopkgtest [18:28:21]: test command4: - - - - - - - - - - results - -
- - - - - - - -
command4 FAIL timed out
autopkgtest [18:28:21]: test command4: - - - - - - - - - - stderr - - -
- - - - - - -
[31;1mnot ok - line 'PyMOL: normal program termination.' was not found
in pymol output[0m
[31;1mnot ok - line 'PyMOL: normal program termination.' was not found
in pymol output[0m
autopkgtest [18:28:52]: test command5: sh
debian/tests/call-pymol-scripts /usr/share/pymol/examples/cookbook
multiclip_ray
autopkgtest [18:28:52]: test command5: [-----------------------
Search pymol scripts in /usr/share/pymol/examples/cookbook...
Processing new directory /usr/share/pymol/examples/cookbook
autopkgtest [21:15:32]: ERROR: timed out on command "su -s /bin/bash
debci -c set -e; export USER=`id -nu`; . /etc/profile >/dev/null 2>&1 ||
true; . ~/.profile >/dev/null 2>&1 || true;
buildtree="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src"; mkdir
-p -m 1777 --
"/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command5-artifacts"; export
AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command5-artifacts";
export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755
"/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp"; export
AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp";
export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive;
export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=8; unset LANGUAGE
LC_CTYPE LC_NUMERIC LC_TIME LC_COLLATE LC_MONETARY LC_MESSAGES
LC_PAPER LC_NAME LC_ADDRESS LC_TELEPHONE LC_MEASUREMENT
LC_IDENTIFICATION LC_ALL;rm -f /tmp/autopkgtest_script_pid; set -C; echo
$$ > /tmp/autopkgtest_script_pid; set +C; trap "rm -f
/tmp/autopkgtest_script_pid" EXIT INT QUIT PIPE; cd "$buildtree"; touch
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command5-stdout
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command5-stderr; bash -ec 'sh
debian/tests/call-pymol-scripts /usr/share/pymol/examples/cookbook
multiclip_ray' 2> >(tee -a
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command5-stderr >&2) > >(tee -a
/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command5-stdout);" (kind: test)
autopkgtest [21:15:32]: test command5: -----------------------]
autopkgtest [21:15:32]: test command5: - - - - - - - - - - results - -
- - - - - - - -
command5 FAIL timed out
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