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 amd64because 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: -----------------------]
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