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Bug#1006382: apbs: failing autopkgtest on one of ci.d.n amd64 workers



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