Your message dated Sat, 02 Nov 2024 00:50:30 +0000
with message-id <[email protected]>
and subject line Bug#1086272: fixed in gromacs 2024.4-1
has caused the Debian Bug report #1086272,
regarding gromacs: FTBFS with OpenMPI 5 on systems with less than 4 CPUs
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.
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--
1086272: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1086272
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:gromacs
Version: 2024.3-2
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh_testdir
(mkdir -p build/basic; cd build/basic; cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF
-DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now"
-DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL
-DGMX_VERSION_STRING_OF_FORK="Debian-2024.3-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=SSE4.1
-DGMX_MPI=OFF -DGMX_INSTALL_LEGACY_API=ON)
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
[... snipped ...]
87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
87: that with the Verlet scheme, nstlist has no effect on the accuracy of
87: your simulation.
87:
87: Rotation group 0 'system' has 4 atoms
87: Number of degrees of freedom in T-Coupling group rest is 9.00
87: The integrator does not provide a ensemble temperature, there is no system
ensemble temperature
87:
87: NOTE 2 [file
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]:
87: NVE simulation with an initial temperature of zero: will use a Verlet
87: buffer of 10%. Check your energy drift!
87:
87: Enforced rotation: group 0 has 4 reference positions.
87: Reading them from
/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/rotref.0.trr.
87:
87: There were 2 NOTEs
87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log).
87: Reading file
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr,
VERSION 2024.3-Debian_2024.3_2 (single precision)
87: Can not increase nstlist because an NVE ensemble is used
87: Using 1 MPI process
87: Using 2 OpenMP threads
87:
87:
87: WARNING: On rank 0: oversubscribing the recommended max load of 1 logical
CPUs per node with 2 threads.
87: This will cause considerable performance loss.
87:
87: NOTE: Oversubscribing available/permitted CPUs, will not pin threads
87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate'
87: 25 steps, 0.1 ps.
87: Setting the LD random seed to -808458001
87:
87: Generated 1 of the 1 non-bonded parameter combinations
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonA'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonB'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonC'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonD'
87:
87: This run will generate roughly 0 Mb of data
87:
87: Writing final coordinates.
87:
87: Core t (s) Wall t (s) (%)
87: Time: 0.027 0.014 199.6
87: (ns/day) (hour/ns)
87: Performance: 332.120 0.072
87: Opened
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr
as single precision energy file
87:
Reading energy frame 0 time 0.002 Opened
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr
as single precision energy file
87:
Reading energy frame 0 time 0.002
Reading energy frame 1 time 0.012
Reading energy frame 2 time 0.022
Reading energy frame 3 time 0.032
Reading energy frame 4 time 0.042
Reading energy frame 5 time 0.052
Last energy frame read 5 time 0.052
87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (19 ms)
87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8
87: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522
0.801784
87:
87: NOTE 1 [file
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]:
87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
87: that with the Verlet scheme, nstlist has no effect on the accuracy of
87: your simulation.
87:
87: Rotation group 0 'system' has 4 atoms
87: Number of degrees of freedom in T-Coupling group rest is 9.00
87: The integrator does not provide a ensemble temperature, there is no system
ensemble temperature
87:
87: NOTE 2 [file
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]:
87: NVE simulation with an initial temperature of zero: will use a Verlet
87: buffer of 10%. Check your energy drift!
87:
87: Enforced rotation: group 0 has 4 reference positions.
87: Reading them from
/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/rotref.0.trr.
87:
87: There were 2 NOTEs
87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log).
87: Reading file
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr,
VERSION 2024.3-Debian_2024.3_2 (single precision)
87: Can not increase nstlist because an NVE ensemble is used
87: Using 1 MPI process
87: Using 2 OpenMP threads
87:
87:
87: WARNING: On rank 0: oversubscribing the recommended max load of 1 logical
CPUs per node with 2 threads.
87: This will cause considerable performance loss.
87:
87: NOTE: Oversubscribing available/permitted CPUs, will not pin threads
87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate'
87: 25 steps, 0.1 ps.
87: Setting the LD random seed to -1241628743
87:
87: Generated 1 of the 1 non-bonded parameter combinations
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonA'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonB'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonC'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonD'
87:
87: This run will generate roughly 0 Mb of data
87:
87: Writing final coordinates.
87:
87: Core t (s) Wall t (s) (%)
87: Time: 0.028 0.014 199.7
87: (ns/day) (hour/ns)
87: Performance: 320.207 0.075
87: Opened
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr
as single precision energy file
87:
Reading energy frame 0 time 0.002 Opened
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr
as single precision energy file
87:
Reading energy frame 0 time 0.002
Reading energy frame 1 time 0.012
Reading energy frame 2 time 0.022
Reading energy frame 3 time 0.032
Reading energy frame 4 time 0.042
Reading energy frame 5 time 0.052
Last energy frame read 5 time 0.052
87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (19 ms)
87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9
87: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261
0.534522 0.801784
87:
87: NOTE 1 [file
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]:
87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
87: that with the Verlet scheme, nstlist has no effect on the accuracy of
87: your simulation.
87:
87: Rotation group 0 'system' has 4 atoms
87: Number of degrees of freedom in T-Coupling group rest is 9.00
87: The integrator does not provide a ensemble temperature, there is no system
ensemble temperature
87:
87: NOTE 2 [file
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]:
87: NVE simulation with an initial temperature of zero: will use a Verlet
87: buffer of 10%. Check your energy drift!
87:
87: Enforced rotation: group 0 has 4 reference positions.
87: Reading them from
/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/rotref.0.trr.
87:
87: There were 2 NOTEs
87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log).
87: Reading file
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr,
VERSION 2024.3-Debian_2024.3_2 (single precision)
87: Can not increase nstlist because an NVE ensemble is used
87: Using 1 MPI process
87: Using 2 OpenMP threads
87:
87:
87: WARNING: On rank 0: oversubscribing the recommended max load of 1 logical
CPUs per node with 2 threads.
87: This will cause considerable performance loss.
87:
87: NOTE: Oversubscribing available/permitted CPUs, will not pin threads
87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate'
87: 25 steps, 0.1 ps.
87: Setting the LD random seed to 1877078951
87:
87: Generated 1 of the 1 non-bonded parameter combinations
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonA'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonB'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonC'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonD'
87:
87: This run will generate roughly 0 Mb of data
87:
87: Writing final coordinates.
87:
87: Core t (s) Wall t (s) (%)
87: Time: 0.028 0.014 199.7
87: (ns/day) (hour/ns)
87: Performance: 323.100 0.074
87: Opened
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr
as single precision energy file
87:
Reading energy frame 0 time 0.002 Opened
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr
as single precision energy file
87:
Reading energy frame 0 time 0.002
Reading energy frame 1 time 0.012
Reading energy frame 2 time 0.022
Reading energy frame 3 time 0.032
Reading energy frame 4 time 0.042
Reading energy frame 5 time 0.052
Last energy frame read 5 time 0.052
87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (19 ms)
87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10
87: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261
0.534522 0.801784
87:
87: NOTE 1 [file
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]:
87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
87: that with the Verlet scheme, nstlist has no effect on the accuracy of
87: your simulation.
87:
87: Rotation group 0 'system' has 4 atoms
87: Number of degrees of freedom in T-Coupling group rest is 9.00
87: The integrator does not provide a ensemble temperature, there is no system
ensemble temperature
87:
87: NOTE 2 [file
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]:
87: NVE simulation with an initial temperature of zero: will use a Verlet
87: buffer of 10%. Check your energy drift!
87:
87: Enforced rotation: group 0 has 4 reference positions.
87: Reading them from
/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/rotref.0.trr.
87:
87: There were 2 NOTEs
87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log).
87: Reading file
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr,
VERSION 2024.3-Debian_2024.3_2 (single precision)
87: Can not increase nstlist because an NVE ensemble is used
87: Using 1 MPI process
87: Using 2 OpenMP threads
87:
87:
87: WARNING: On rank 0: oversubscribing the recommended max load of 1 logical
CPUs per node with 2 threads.
87: This will cause considerable performance loss.
87:
87: NOTE: Oversubscribing available/permitted CPUs, will not pin threads
87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate'
87: 25 steps, 0.1 ps.
87: Setting the LD random seed to -17337945
87:
87: Generated 1 of the 1 non-bonded parameter combinations
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonA'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonB'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonC'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonD'
87:
87: This run will generate roughly 0 Mb of data
87:
87: Writing final coordinates.
87:
87: Core t (s) Wall t (s) (%)
87: Time: 0.028 0.014 199.7
87: (ns/day) (hour/ns)
87: Performance: 317.579 0.076
87: Opened
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr
as single precision energy file
87:
Reading energy frame 0 time 0.002 Opened
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr
as single precision energy file
87:
Reading energy frame 0 time 0.002
Reading energy frame 1 time 0.012
Reading energy frame 2 time 0.022
Reading energy frame 3 time 0.032
Reading energy frame 4 time 0.042
Reading energy frame 5 time 0.052
Last energy frame read 5 time 0.052
87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (19
ms)
87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11
87: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261
0.534522 0.801784
87:
87: NOTE 1 [file
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]:
87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
87: that with the Verlet scheme, nstlist has no effect on the accuracy of
87: your simulation.
87:
87: Rotation group 0 'system' has 4 atoms
87: Number of degrees of freedom in T-Coupling group rest is 9.00
87: The integrator does not provide a ensemble temperature, there is no system
ensemble temperature
87:
87: NOTE 2 [file
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]:
87: NVE simulation with an initial temperature of zero: will use a Verlet
87: buffer of 10%. Check your energy drift!
87:
87: Enforced rotation: group 0 has 4 reference positions.
87: Reading them from
/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/rotref.0.trr.
87:
87: There were 2 NOTEs
87: Compiled SIMD is SSE4.1, but AVX_512 might be faster (see log).
87: Reading file
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr,
VERSION 2024.3-Debian_2024.3_2 (single precision)
87: Can not increase nstlist because an NVE ensemble is used
87: Using 1 MPI process
87: Using 2 OpenMP threads
87:
87:
87: WARNING: On rank 0: oversubscribing the recommended max load of 1 logical
CPUs per node with 2 threads.
87: This will cause considerable performance loss.
87:
87: NOTE: Oversubscribing available/permitted CPUs, will not pin threads
87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate'
87: 25 steps, 0.1 ps.
87: Setting the LD random seed to -26279941
87:
87: Generated 1 of the 1 non-bonded parameter combinations
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonA'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonB'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonC'
87:
87: Excluding 1 bonded neighbours molecule type 'ArgonD'
87:
87: This run will generate roughly 0 Mb of data
87:
87: Writing final coordinates.
87:
87: Core t (s) Wall t (s) (%)
87: Time: 0.028 0.014 199.7
87: (ns/day) (hour/ns)
87: Performance: 324.039 0.074
87: Opened
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr
as single precision energy file
87:
Reading energy frame 0 time 0.002 Opened
/<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr
as single precision energy file
87:
Reading energy frame 0 time 0.002
Reading energy frame 1 time 0.012
Reading energy frame 2 time 0.022
Reading energy frame 3 time 0.032
Reading energy frame 4 time 0.042
Reading energy frame 5 time 0.052
Last energy frame read 5 time 0.052
87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (19
ms)
87: [----------] 12 tests from RotationWorks/RotationTest (231 ms total)
87:
87: [----------] Global test environment tear-down
87: [==========] 12 tests from 1 test suite ran. (241 ms total)
87: [ PASSED ] 12 tests.
87/91 Test #87: MdrunRotationTests ........................... Passed 0.51
sec
test 88
Start 88: MdrunSimulatorComparison
88: Test command: /<<PKGBUILDDIR>>/build/mpi/bin/mdrun-simulator-comparison-test "-ntomp" "2"
"--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpi/Testing/Temporary/MdrunSimulatorComparison.xml"
88: Working Directory: /<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests
88: Test timeout computed to be: 600
88: [==========] Running 0 tests from 0 test suites.
88: [==========] 0 tests from 0 test suites ran. (0 ms total)
88: [ PASSED ] 0 tests.
88:
88: YOU HAVE 82 DISABLED TESTS
88:
88/91 Test #88: MdrunSimulatorComparison ..................... Passed 0.28
sec
test 89
Start 89: MdrunVirtualSiteTests
89: Test command: /usr/bin/mpiexec "-n" "2" "/<<PKGBUILDDIR>>/build/mpi/bin/mdrun-vsites-test"
"--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpi/Testing/Temporary/MdrunVirtualSiteTests.xml"
89: Working Directory: /<<PKGBUILDDIR>>/build/mpi/src/programs/mdrun/tests
89: Test timeout computed to be: 600
89: --------------------------------------------------------------------------
89: There are not enough slots available in the system to satisfy the 2
89: slots that were requested by the application:
89:
89: /<<PKGBUILDDIR>>/build/mpi/bin/mdrun-vsites-test
89:
89: Either request fewer procs for your application, or make more slots
89: available for use.
89:
89: A "slot" is the PRRTE term for an allocatable unit where we can
89: launch a process. The number of slots available are defined by the
89: environment in which PRRTE processes are run:
89:
89: 1. Hostfile, via "slots=N" clauses (N defaults to number of
89: processor cores if not provided)
89: 2. The --host command line parameter, via a ":N" suffix on the
89: hostname (N defaults to 1 if not provided)
89: 3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.)
89: 4. If none of a hostfile, the --host command line parameter, or an
89: RM is present, PRRTE defaults to the number of processor cores
89:
89: In all the above cases, if you want PRRTE to default to the number
89: of hardware threads instead of the number of processor cores, use the
89: --use-hwthread-cpus option.
89:
89: Alternatively, you can use the --map-by :OVERSUBSCRIBE option to ignore the
89: number of available slots when deciding the number of processes to
89: launch.
89: --------------------------------------------------------------------------
89:
89/91 Test #89: MdrunVirtualSiteTests ........................***Failed 0.02
sec
--------------------------------------------------------------------------
There are not enough slots available in the system to satisfy the 2
slots that were requested by the application:
/<<PKGBUILDDIR>>/build/mpi/bin/mdrun-vsites-test
Either request fewer procs for your application, or make more slots
available for use.
A "slot" is the PRRTE term for an allocatable unit where we can
launch a process. The number of slots available are defined by the
environment in which PRRTE processes are run:
1. Hostfile, via "slots=N" clauses (N defaults to number of
processor cores if not provided)
2. The --host command line parameter, via a ":N" suffix on the
hostname (N defaults to 1 if not provided)
3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.)
4. If none of a hostfile, the --host command line parameter, or an
RM is present, PRRTE defaults to the number of processor cores
In all the above cases, if you want PRRTE to default to the number
of hardware threads instead of the number of processor cores, use the
--use-hwthread-cpus option.
Alternatively, you can use the --map-by :OVERSUBSCRIBE option to ignore the
number of available slots when deciding the number of processes to
launch.
--------------------------------------------------------------------------
test 90
Start 90: EnsembleHistogramPotentialPlugin.ForceCalc
90: Test command: /<<PKGBUILDDIR>>/build/mpi/bin/gmxapi_extension_histogram-test
"--gtest_filter=EnsembleHistogramPotentialPlugin.ForceCalc"
90: Working Directory:
/<<PKGBUILDDIR>>/build/mpi/python_packaging/sample_restraint/tests
90: Test timeout computed to be: 1500
90: Running main() from ./src/external/googletest/googletest/src/gtest_main.cc
90: Note: Google Test filter = EnsembleHistogramPotentialPlugin.ForceCalc
90: [==========] Running 1 test from 1 test suite.
90: [----------] Global test environment set-up.
90: [----------] 1 test from EnsembleHistogramPotentialPlugin
90: [ RUN ] EnsembleHistogramPotentialPlugin.ForceCalc
90: [ OK ] EnsembleHistogramPotentialPlugin.ForceCalc (0 ms)
90: [----------] 1 test from EnsembleHistogramPotentialPlugin (0 ms total)
90:
90: [----------] Global test environment tear-down
90: [==========] 1 test from 1 test suite ran. (0 ms total)
90: [ PASSED ] 1 test.
90/91 Test #90: EnsembleHistogramPotentialPlugin.ForceCalc ... Passed 0.25
sec
test 91
Start 91: EnsembleBoundingPotentialPlugin.ForceCalc
91: Test command: /<<PKGBUILDDIR>>/build/mpi/bin/gmxapi_extension_bounding-test
"--gtest_filter=EnsembleBoundingPotentialPlugin.ForceCalc"
91: Working Directory:
/<<PKGBUILDDIR>>/build/mpi/python_packaging/sample_restraint/tests
91: Test timeout computed to be: 1500
91: Running main() from ./src/external/googletest/googletest/src/gtest_main.cc
91: Note: Google Test filter = EnsembleBoundingPotentialPlugin.ForceCalc
91: [==========] Running 1 test from 1 test suite.
91: [----------] Global test environment set-up.
91: [----------] 1 test from EnsembleBoundingPotentialPlugin
91: [ RUN ] EnsembleBoundingPotentialPlugin.ForceCalc
91: [ OK ] EnsembleBoundingPotentialPlugin.ForceCalc (0 ms)
91: [----------] 1 test from EnsembleBoundingPotentialPlugin (0 ms total)
91:
91: [----------] Global test environment tear-down
91: [==========] 1 test from 1 test suite ran. (0 ms total)
91: [ PASSED ] 1 test.
91/91 Test #91: EnsembleBoundingPotentialPlugin.ForceCalc .... Passed 0.25
sec
81% tests passed, 17 tests failed out of 91
Label Time Summary:
GTest = 71.71 sec*proc (87 tests)
IntegrationTest = 34.63 sec*proc (30 tests)
MpiTest = 22.77 sec*proc (23 tests)
QuickGpuTest = 13.70 sec*proc (20 tests)
SlowGpuTest = 35.28 sec*proc (14 tests)
SlowTest = 23.72 sec*proc (13 tests)
UnitTest = 13.36 sec*proc (44 tests)
Total Test time (real) = 56.29 sec
The following tests FAILED:
2 - GmxapiMpiTests (Failed)
4 - GmxapiInternalsMpiTests (Failed)
14 - TestUtilsMpiUnitTests (Failed)
16 - UtilityMpiUnitTests (Failed)
28 - DomDecMpiTests (Failed)
35 - MdrunUtilityMpiUnitTests (Failed)
67 - MdrunTestsTwoRanks (Failed)
70 - Minimize2RankTests (Failed)
73 - MdrunMpiTests (Failed)
74 - MdrunMultiSimTests (Failed)
75 - MdrunMultiSimReplexTests (Failed)
76 - MdrunMultiSimReplexEquivalenceTests (Failed)
78 - MdrunMpi2RankPmeTests (Failed)
80 - MdrunCoordinationBasicTests2Ranks (Failed)
82 - MdrunCoordinationCouplingTests2Ranks (Failed)
84 - MdrunCoordinationConstraintsTests2Ranks (Failed)
89 - MdrunVirtualSiteTests (Failed)
Errors while running CTest
make: *** [debian/rules:126: build-mpi] Error 8
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202410/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks.
--- End Message ---
--- Begin Message ---
Source: gromacs
Source-Version: 2024.4-1
Done: Nicholas Breen <[email protected]>
We believe that the bug you reported is fixed in the latest version of
gromacs, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nicholas Breen <[email protected]> (supplier of updated gromacs 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 31 Oct 2024 20:23:53 -0700
Source: gromacs
Architecture: source
Version: 2024.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Nicholas Breen <[email protected]>
Closes: 1086272
Changes:
gromacs (2024.4-1) unstable; urgency=medium
.
* New upstream version.
* Update oversubscription environment variable for OpenMPI 5.0.
(Closes: #1086272)
* Remove obsolete workaround for #494046.
* Add chrpath workaround for OpenMPI 5.x RPATH bug, #1085509.
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