Your message dated Tue, 31 May 2022 07:49:07 +0000
with message-id <e1nvwcl-0002ss...@fasolo.debian.org>
and subject line Bug#1006382: fixed in apbs 3.4.1-2
has caused the Debian Bug report #1006382,
regarding apbs: failing autopkgtest on one of ci.d.n amd64 workers
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
1006382: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1006382
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: apbs
Version: 3.0.0+dfsg1-3
Severity: serious
X-Debbugs-CC: debian...@lists.debian.org
Tags: sid bookworm
User: debian...@lists.debian.org
Usertags: flaky
Dear maintainer(s),
I looked at the results of the autopkgtest of you package on amd64
because it showed up as regressions (due to timeout) for multiple
packages. I recently replaced one of our amd64 hosts and it seems that
all jobs that were scheduled on that host since then fail, while the
other workers (including the other architectures) are OK. The host is
rather powerful: 56 CPU's, 384 GB RAM. Looking at the text in the log it
seems the test is finished, but doesn't close properly. I suspect a race
condition.
Don't hesitate to contact us at debian...@lists.debian.org if you need
help debugging this issue.
Paul
https://ci.debian.net/packages/a/apbs/testing/amd64/
https://ci.debian.net/data/autopkgtest/testing/amd64/a/apbs/19529862/log.gz
----------------------------------------
CALCULATION #5 (rna): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 19.4227 A
Current memory usage: 208.541 MB total, 428.140 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 97 x 129
Grid spacings: 0.708 x 0.572 x 0.643
Grid lengths: 45.332 x 54.950 x 82.263
Grid center: (13.822, 5.283, 8.258)
Multigrid levels: 4
Molecule ID: 3
Nonlinear traditional PBE
Single Debye-Huckel sphere boundary conditions
2 ion species (0.025 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.025 M concentration
2.000 A-radius, -1.000 e-charge, 0.025 M concentration
Solute dielectric: 4.000
Solvent dielectric: 80.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Total electrostatic energy = 2.329205982055E+04 kJ/mol
Calculating forces...
----------------------------------------
CALCULATION #6 (rna): MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (2 A) for exclusion function
Debye length: 19.4227 A
Current memory usage: 208.541 MB total, 428.140 MB high water
Using cubic spline charge discretization.
Grid dimensions: 65 x 97 x 129
Grid spacings: 0.708 x 0.545 x 0.534
Grid lengths: 45.332 x 52.323 x 68.390
Grid center: (13.822, 5.283, 8.258)
Multigrid levels: 4
Molecule ID: 3
Nonlinear traditional PBE
Boundary conditions from focusing
2 ion species (0.025 M ionic strength):
2.000 A-radius, 1.000 e-charge, 0.025 M concentration
2.000 A-radius, -1.000 e-charge, 0.025 M concentration
Solute dielectric: 4.000
Solvent dielectric: 80.000
Using "molecular" surface definition; no smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Ion charge density to be written to qdens-rna-0.025.dx
Ion number density to be written to ndens-rna-0.025.dx
Total electrostatic energy = 2.653636629928E+04 kJ/mol
Calculating forces...
Writing charge density to qdens-rna-0.025-PE0.dx
Writing number density to ndens-rna-0.025-PE0.dx
----------------------------------------
PRINT STATEMENTS
print energy 1 (complex) - 2 (peptide) - 3 (rna) end
Local net energy (PE 0) = 8.674116429351E+01 kJ/mol
Global net ELEC energy = 8.674116429351E+01 kJ/mol
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying 3 molecules
Final memory usage: 0.001 MB total, 428.140 MB high water
Thanks for using APBS!
autopkgtest [13:12:07]: 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.tstul8x9/downtmp/build.FHv/src"; mkdir
-p -m 1777 --
"/tmp/autopkgtest-lxc.tstul8x9/downtmp/test-apbs-artifacts"; export
AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.tstul8x9/downtmp/test-apbs-artifacts";
export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755
"/tmp/autopkgtest-lxc.tstul8x9/downtmp/autopkgtest_tmp"; export
AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.tstul8x9/downtmp/autopkgtest_tmp";
export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive;
export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=56; 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"; chmod
+x
/tmp/autopkgtest-lxc.tstul8x9/downtmp/build.FHv/src/debian/tests/test-apbs;
touch /tmp/autopkgtest-lxc.tstul8x9/downtmp/test-apbs-stdout
/tmp/autopkgtest-lxc.tstul8x9/downtmp/test-apbs-stderr;
/tmp/autopkgtest-lxc.tstul8x9/downtmp/build.FHv/src/debian/tests/test-apbs
2> >(tee -a /tmp/autopkgtest-lxc.tstul8x9/downtmp/test-apbs-stderr >&2)
> >(tee -a /tmp/autopkgtest-lxc.tstul8x9/downtmp/test-apbs-stdout);"
(kind: test)
autopkgtest [13:12:07]: test test-apbs: -----------------------]
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: apbs
Source-Version: 3.4.1-2
Done: Drew Parsons <dpars...@debian.org>
We believe that the bug you reported is fixed in the latest version of
apbs, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1006...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <dpars...@debian.org> (supplier of updated apbs package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 31 May 2022 02:52:47 +0200
Source: apbs
Architecture: source
Version: 3.4.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Closes: 979339 1006382 1008726
Changes:
apbs (3.4.1-2) unstable; urgency=medium
.
* Team upload.
* Build-Depends-Indep: python3-yaml (to build docs)
* add specific copyright entries for FETK components
punc/src/pmg (GPL) and punc/src/vf2c (AT&T)
* patch FETK punc component vf2c/uninit.c to not run __mips block on
linux
* don't double-up bin dir in path for apbs tools. Closes: #979339.
* debian/rules: run build-time tests after dh_auto_install
* FETK is now provided (built against system SuperLU), and debci
tests pass. Closes: #1006382, #1008726.
Checksums-Sha1:
3e73492bbe130f6525c0950512f2b399cbdaceda 2639 apbs_3.4.1-2.dsc
9aa10d8ef734ac5ee65538f9207220548b3afed3 20287852 apbs_3.4.1-2.debian.tar.xz
Checksums-Sha256:
dc4c8d42b8e3db875bb195a630eb10c065af8e5b4167674f6c858f9ac2c3e485 2639
apbs_3.4.1-2.dsc
66c7f9549abeb20cd76f3b1d80f1dc85a809559d15fcb5e00bc6937be1eeb0e0 20287852
apbs_3.4.1-2.debian.tar.xz
Files:
373fdfab5204e5e7da4a044295dc35d3 2639 science optional apbs_3.4.1-2.dsc
74b2b3406bc62b43bcdbd0c09042125f 20287852 science optional
apbs_3.4.1-2.debian.tar.xz
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