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: -----------------------]