[Debichem-devel] Bug#1006382: apbs: failing autopkgtest on one of ci.d.n amd64 workers

[Paul Gevers]

Source: apbs
Version: 3.0.0+dfsg1-3
Severity: serious
X-Debbugs-CC: debian-ci at lists.debian.org
Tags: sid bookworm
User: debian-ci at 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-ci at 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: -----------------------]
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