[gmx-users] 2018 installation make check errors, probably CUDA related
Szilárd Páll
pall.szilard at gmail.com
Fri Mar 23 11:45:29 CET 2018
Hi,
Please provide the output of unit tests with 2018.1, it has improved
the error reporting targeting exactly these types of errors.
Cheers,
--
Szilárd
On Thu, Mar 22, 2018 at 5:44 PM, Tresadern, Gary [RNDBE]
<gtresade at its.jnj.com> wrote:
> Hi Mark,
> Thanks, I tried 2018-1 and was hopeful it would solve the problem as I'd seen comment of funny findGpus() behavior whilst googling to fix this. Unfortunately I still have the same problem. I've spent the day trying to pin down the nvidia-smi settings, I have the persistence on and the daemon running to restart at reboot, I have clocked up the K40 to 3004,875, but these are minor issues. Something more fundamental is must be going wrong. I'm out of ideas at this point, I must have tried the rebuild 3 dozen times in last ten days or so.
>
> Cheers
> Gary
>
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Mark Abraham
> Sent: Wednesday, 21 March 2018 17:03
> To: gmx-users at gromacs.org
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [EXTERNAL] Re: [gmx-users] 2018 installation make check errors, probably CUDA related
>
> Hi,
>
> Please try 2018.1 and let us know, as some issues that look like these have been resolved.
>
> Thanks,
>
> Mark
>
>
>
>>> Cheers
>>> Gary
>>>
>>>
>>>
>>>
>>> wrndbeberhel13 :~> nvidia-smi
>>> Wed Mar 21 16:25:23 2018
>>>
>>> +-----------------------------------------------------------------------------+
>>> | NVIDIA-SMI 390.42 Driver Version: 390.42
>>> |
>>>
>>> |-------------------------------+----------------------+----------------------+
>>> | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr.
>>> ECC |
>>> | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util
>>> Compute M. |
>>>
>>> |===============================+======================+======================|
>>> | 0 Quadro K4200 On | 00000000:03:00.0 On |
>>> N/A |
>>> | 30% 36C P8 15W / 110W | 71MiB / 4036MiB | 0% E.
>>> Process |
>>>
>>> +-------------------------------+----------------------+----------------------+
>>> | 1 Tesla K40c On | 00000000:81:00.0 Off |
>>> 2 |
>>> | 23% 40C P8 22W / 235W | 0MiB / 11441MiB | 0% E.
>>> Process |
>>>
>>> +-------------------------------+----------------------+----------------------+
>>>
>>>
>>> +-----------------------------------------------------------------------------+
>>> | Processes: GPU
>>> Memory |
>>> | GPU PID Type Process name Usage
>>> |
>>>
>>> |=============================================================================|
>>> | 0 7891 G /usr/bin/Xorg
>>> 69MiB |
>>>
>>> +-----------------------------------------------------------------------------+
>>>
>>> -----Original Message-----
>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
>>> Tresadern, Gary [RNDBE]
>>> Sent: Saturday, 17 March 2018 16:46
>>> To: 'gromacs.org_gmx-users at maillist.sys.kth.se' <
>>> gromacs.org_gmx-users at maillist.sys.kth.se>
>>> Subject: [EXTERNAL] Re: [gmx-users] 2018 installation make check
>>> errors, probably CUDA related
>>>
>>> Hi,
>>>
>>> I am unable to pass the make check tests for a 2018 build. I had a
>>> working build earlier in the week, but since we updated the cuda
>>> toolkit and nvidia driver it now fails.
>>> Below are some details of the installation procedure.
>>> I tried manually setting variables such as CUDA_VISIBLE_DEVICES but
>>> that also didn't help.
>>> I am running out of ideas, if you have any tips please let me know.
>>>
>>> Thanks
>>> Gary
>>>
>>> bash-4.1$ su softinst
>>> bash-4.1$ scl enable devtoolset-2 bash bash-4.1$ which cmake
>>> /usr/local/bin/cmake bash-4.1$ cmake --version cmake version 3.6.2
>>> CMake suite maintained and supported by Kitware (kitware.com/cmake).
>>> bash-4.1$ gcc --version
>>> gcc (GCC) 4.8.2 20140120 (Red Hat 4.8.2-15) Copyright (C) 2013 Free
>>> Software Foundation, Inc.
>>> This is free software; see the source for copying conditions. There
>>> is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
>>> PARTICULAR PURPOSE.
>>> bash-4.1$ ls /usr/local/cuda-9.1/
>>> bin/ extras/ lib64/ libnvvp/
>>> nsightee_plugins/ nvvm/ samples/ src/
>>> tools/ doc/ include/ libnsight/
>>> LICENSE nvml/ README share/
>>> targets/ version.txt bash-4.1$ ls /usr/local/cuda-9.1/bin/
>>> bin2c cuda-gdb
>>> fatbinary nvcc.profile nvvp
>>> computeprof cuda-gdbserver
>>> gpu-library-advisor nvdisasm ptxas
>>> crt/ cuda-install-samples-9.1.sh
>>> nsight nvlink cudafe
>>> cuda-memcheck nsight_ee_plugins_manage.sh
>>> nvprof
>>> cudafe++ cuobjdump
>>> nvcc
>>> cudafe++nvprune
>>> bash-4.1$ export PATH=$PATH:/usr/local/bin/ bash-4.1$ export
>>> CUDA_HOME=/usr/local/cuda-9.1/ bash-4.1$ export
>>> PATH=$PATH:/usr/lib64/mpich/bin/ bash-4.1$ export
>>> LD_LIBRARY_PATH="/usr/local/cuda-9.1/lib64/:${LD_LIBRARY_PATH}"
>>> bash-4.1$ export
>>> LD_LIBRARY_PATH="/usr/local/cuda-9.1/lib64:/usr/local/cuda-9.1/targets/x86_64-linux/lib/:${LD_LIBRARY_PATH}"
>>> bash-4.1$ export
>>> LD_LIBRARY_PATH=/usr/lib64/openmpi-1.10/lib/openmpi/:$LD_LIBRARY_PATH
>>> bash-4.1$ export
>>> MPI_CXX_INCLUDE_PATH=/usr/include/openmpi-1.10-x86_64/openmpi/ompi/mp
>>> i/cxx/ bash-4.1$ export PATH=$PATH:/usr/lib64/openmpi-1.10/bin/
>>>
>>> bash-4.1$ cmake .. -DGMX_BUILD_OWN_FFTW=ON
>>> -DREGRESSIONTEST_DOWNLOAD=ON
>>> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.1/ -DGMX_GPU=on
>>> -DCMAKE_INSTALL_PREFIX=/prd/pkgs/gromacs/gromacs-2018/ -DGMX_MPI=on
>>> bash-4.1$ make bash-4.1$ make check Test project /prd/pkgs/gromacs/gromacs-2018/build
>>> Start 1: TestUtilsUnitTests
>>> 1/39 Test #1: TestUtilsUnitTests ............... Passed 0.41 sec
>>> Start 2: TestUtilsMpiUnitTests
>>> 2/39 Test #2: TestUtilsMpiUnitTests ............ Passed 0.29 sec
>>> Start 3: MdlibUnitTest
>>> 3/39 Test #3: MdlibUnitTest .................... Passed 0.24 sec
>>> Start 4: AppliedForcesUnitTest
>>> 4/39 Test #4: AppliedForcesUnitTest ............ Passed 0.22 sec
>>> Start 5: ListedForcesTest
>>> 5/39 Test #5: ListedForcesTest ................. Passed 0.25 sec
>>> Start 6: CommandLineUnitTests
>>> 6/39 Test #6: CommandLineUnitTests ............. Passed 0.29 sec
>>> Start 7: EwaldUnitTests
>>> 7/39 Test #7: EwaldUnitTests ...................***Failed 0.92 sec
>>> [==========] Running 257 tests from 10 test cases.
>>> [----------] Global test environment set-up.
>>>
>>> -------------------------------------------------------
>>> Program: ewald-test, version 2018
>>> Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 735)
>>> Function: void findGpus(gmx_gpu_info_t*)
>>>
>>> Assertion failed:
>>> Condition: cudaSuccess == cudaPeekAtLastError() Should be cudaSuccess
>>>
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS website at http://www.gromacs.org/Documentation/Errors
>>> -------------------------------------------------------
>>> ---------------------------------------------------------------------
>>> ----- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>>> with errorcode 1.
>>>
>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>> You may or may not see output from other processes, depending on
>>> exactly when Open MPI kills them.
>>> ---------------------------------------------------------------------
>>> -----
>>>
>>> Start 8: FFTUnitTests
>>> 8/39 Test #8: FFTUnitTests ..................... Passed 0.37 sec
>>> Start 9: GpuUtilsUnitTests
>>> 9/39 Test #9: GpuUtilsUnitTests ................***Failed 0.91 sec
>>> [==========] Running 35 tests from 7 test cases.
>>> [----------] Global test environment set-up.
>>> [----------] 7 tests from HostAllocatorTest/0, where TypeParam = int [
>>> RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
>>>
>>> -------------------------------------------------------
>>> Program: gpu_utils-test, version 2018 Source file:
>>> src/gromacs/gpu_utils/gpu_utils.cu (line 735)
>>> Function: void findGpus(gmx_gpu_info_t*)
>>>
>>> Assertion failed:
>>> Condition: cudaSuccess == cudaPeekAtLastError() Should be cudaSuccess
>>>
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS website at http://www.gromacs.org/Documentation/Errors
>>> -------------------------------------------------------
>>> ---------------------------------------------------------------------
>>> ----- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>>> with errorcode 1.
>>>
>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>> You may or may not see output from other processes, depending on
>>> exactly when Open MPI kills them.
>>> ---------------------------------------------------------------------
>>> -----
>>>
>>> Start 10: HardwareUnitTests
>>> 10/39 Test #10: HardwareUnitTests ................ Passed 0.24 sec
>>> Start 11: MathUnitTests
>>> 11/39 Test #11: MathUnitTests .................... Passed 0.25 sec
>>> Start 12: MdrunUtilityUnitTests
>>> 12/39 Test #12: MdrunUtilityUnitTests ............ Passed 0.22 sec
>>> Start 13: MdrunUtilityMpiUnitTests
>>> 13/39 Test #13: MdrunUtilityMpiUnitTests ......... Passed 0.35 sec
>>> Start 14: OnlineHelpUnitTests
>>> 14/39 Test #14: OnlineHelpUnitTests .............. Passed 0.24 sec
>>> Start 15: OptionsUnitTests
>>> 15/39 Test #15: OptionsUnitTests ................. Passed 0.25 sec
>>> Start 16: RandomUnitTests
>>> 16/39 Test #16: RandomUnitTests .................. Passed 0.26 sec
>>> Start 17: TableUnitTests
>>> 17/39 Test #17: TableUnitTests ................... Passed 0.41 sec
>>> Start 18: TaskAssignmentUnitTests
>>> 18/39 Test #18: TaskAssignmentUnitTests .......... Passed 0.21 sec
>>> Start 19: UtilityUnitTests
>>> 19/39 Test #19: UtilityUnitTests ................. Passed 0.32 sec
>>> Start 20: FileIOTests
>>> 20/39 Test #20: FileIOTests ...................... Passed 0.26 sec
>>> Start 21: PullTest
>>> 21/39 Test #21: PullTest ......................... Passed 0.24 sec
>>> Start 22: AwhTest
>>> 22/39 Test #22: AwhTest .......................... Passed 0.23 sec
>>> Start 23: SimdUnitTests
>>> 23/39 Test #23: SimdUnitTests .................... Passed 0.29 sec
>>> Start 24: GmxAnaTest
>>> 24/39 Test #24: GmxAnaTest ....................... Passed 0.38 sec
>>> Start 25: GmxPreprocessTests
>>> 25/39 Test #25: GmxPreprocessTests ............... Passed 0.58 sec
>>> Start 26: CorrelationsTest
>>> 26/39 Test #26: CorrelationsTest ................. Passed 1.23 sec
>>> Start 27: AnalysisDataUnitTests
>>> 27/39 Test #27: AnalysisDataUnitTests ............ Passed 0.30 sec
>>> Start 28: SelectionUnitTests
>>> 28/39 Test #28: SelectionUnitTests ............... Passed 0.61 sec
>>> Start 29: TrajectoryAnalysisUnitTests
>>> 29/39 Test #29: TrajectoryAnalysisUnitTests ...... Passed 1.19 sec
>>> Start 30: EnergyAnalysisUnitTests
>>> 30/39 Test #30: EnergyAnalysisUnitTests .......... Passed 0.58 sec
>>> Start 31: CompatibilityHelpersTests
>>> 31/39 Test #31: CompatibilityHelpersTests ........ Passed 0.23 sec
>>> Start 32: MdrunTests
>>> 32/39 Test #32: MdrunTests .......................***Failed 0.98 sec
>>> [==========] Running 29 tests from 11 test cases.
>>> [----------] Global test environment set-up.
>>> [----------] 6 tests from BondedInteractionsTest [ RUN ]
>>> BondedInteractionsTest.NormalBondWorks
>>>
>>> NOTE 1 [file
>>> /prd/pkgs/gromacs/gromacs-2018/build/src/programs/mdrun/tests/Testing
>>> /Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp,
>>> line 1]:
>>>
>>> /prd/pkgs/gromacs/gromacs-2018/build/src/programs/mdrun/tests/Testing
>>> /Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp
>>> did not specify a value for the .mdp option "cutoff-scheme". Probably it
>>> was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
>>> scheme was introduced, but the group scheme was still the default. The
>>> default is now the Verlet scheme, so you will observe different
>>> behaviour.
>>>
>>>
>>> NOTE 2 [file
>>> /prd/pkgs/gromacs/gromacs-2018/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
>>> For a correct single-point energy evaluation with nsteps = 0, use
>>> continuation = yes to avoid constraining the input coordinates.
>>>
>>> Setting the LD random seed to 417973934 Generated 3 of the 3
>>> non-bonded parameter combinations Excluding 3 bonded neighbours
>>> molecule type 'butane'
>>> Removing all charge groups because cutoff-scheme=Verlet
>>>
>>> NOTE 3 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
>>> In moleculetype 'butane' 2 atoms are not bound by a potential or
>>> constraint to any other atom in the same moleculetype. Although
>>> technically this might not cause issues in a simulation, this often
>>> means
>>> that the user forgot to add a bond/potential/constraint or put multiple
>>> molecules in the same moleculetype definition by mistake. Run with -v to
>>> get information for each atom.
>>>
>>> Number of degrees of freedom in T-Coupling group rest is 9.00
>>>
>>> NOTE 4 [file
>>> /prd/pkgs/gromacs/gromacs-2018/build/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
>>> NVE simulation with an initial temperature of zero: will use a Verlet
>>> buffer of 10%. Check your energy drift!
>>>
>>>
>>> There were 4 notes
>>>
>>> -------------------------------------------------------
>>> Program: mdrun-test, version 2018
>>> Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 735)
>>> Function: void findGpus(gmx_gpu_info_t*)
>>>
>>> Assertion failed:
>>> Condition: cudaSuccess == cudaPeekAtLastError() Should be cudaSuccess
>>>
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS website at http://www.gromacs.org/Documentation/Errors
>>> -------------------------------------------------------
>>> This run will generate roughly 0 Mb of data
>>> ---------------------------------------------------------------------
>>> ----- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>>> with errorcode 1.
>>>
>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>> You may or may not see output from other processes, depending on
>>> exactly when Open MPI kills them.
>>> ---------------------------------------------------------------------
>>> -----
>>>
>>> Start 33: MdrunMpiTests
>>> 33/39 Test #33: MdrunMpiTests ....................***Failed 2.06 sec
>>> [==========] Running 7 tests from 5 test cases.
>>> [----------] Global test environment set-up.
>>> [----------] 1 test from MultiSimTerminationTest [ RUN ]
>>> MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRe
>>> starts
>>>
>>> NOTE 1 [file
>>> /prd/pkgs/gromacs/gromacs-2018/build/src/programs/mdrun/tests/Testing
>>> /Temporary/MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminati
>>> onAndThenRestarts_input1.mdp,
>>> line 14]:
>>>
>>> /prd/pkgs/gromacs/gromacs-2018/build/src/programs/mdrun/tests/Testing
>>> /Temporary/MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminati
>>> onAndThenRestarts_input1.mdp did not specify a value for the .mdp
>>> option "cutoff-scheme". Probably it
>>> was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
>>> scheme was introduced, but the group scheme was still the default. The
>>> default is now the Verlet scheme, so you will observe different
>>> behaviour.
>>>
>>>
>>> NOTE 1 [file
>>> /prd/pkgs/gromacs/gromacs-2018/build/src/programs/mdrun/tests/Testing
>>> /Temporary/MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminati
>>> onAndThenRestarts_input0.mdp,
>>> line 14]:
>>>
>>> /prd/pkgs/gromacs/gromacs-2018/build/src/programs/mdrun/tests/Testing
>>> /Temporary/MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminati
>>> onAndThenRestarts_input0.mdp did not specify a value for the .mdp
>>> option "cutoff-scheme". Probably it
>>> was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
>>> scheme was introduced, but the group scheme was still the default. The
>>> default is now the Verlet scheme, so you will observe different
>>> behaviour.
>>>
>>> Setting the LD random seed to 73630723 Generated 3 of the 3
>>> non-bonded parameter combinations Generating 1-4
>>> interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter
>>> combinations Excluding 2 bonded neighbours molecule type 'SOL'
>>> Setting gen_seed to -1322183961
>>> Velocities were taken from a Maxwell distribution at 288 K Removing
>>> all charge groups because cutoff-scheme=Verlet Number of degrees of
>>> freedom in T-Coupling group System is 9.00 Determining Verlet buffer
>>> for a tolerance of 0.005 kJ/mol/ps at 298 K Calculated rlist for 1x1
>>> atom pair-list as
>>> 1.026 nm, buffer size 0.026 nm Set rlist, assuming 4x4 atom
>>> pair-list, to
>>> 1.024 nm, buffer size 0.024 nm Note that mdrun will redetermine rlist
>>> based on the actual pair-list setup This run will generate roughly 0
>>> Mb of data
>>>
>>> NOTE 2 [file
>>> /prd/pkgs/gromacs/gromacs-2018/build/src/programs/mdrun/tests/Testing/Temporary/MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input1.mdp]:
>>> You are using a plain Coulomb cut-off, which might produce artifacts.
>>> You might want to consider using PME electrostatics.
>>>
>>>
>>>
>>> There were 2 notes
>>> Setting the LD random seed to 408678750 Generated 3 of the 3
>>> non-bonded parameter combinations Generating 1-4
>>> interactions: fudge = 0.5 Generated 3 of the 3 1-4 parameter
>>> combinations Excluding 2 bonded neighbours molecule type 'SOL'
>>> Setting gen_seed to 1490520586
>>> Velocities were taken from a Maxwell distribution at 298 K Removing
>>> all charge groups because cutoff-scheme=Verlet Number of degrees of
>>> freedom in T-Coupling group System is 9.00 Determining Verlet buffer
>>> for a tolerance of 0.005 kJ/mol/ps at 298 K
>>>
>>> NOTE 2 [file
>>> /prd/pkgs/gromacs/gromacs-2018/build/src/programs/mdrun/tests/Testing/Temporary/MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input0.mdp]:
>>> You are using a plain Coulomb cut-off, which might produce artifacts.
>>> You might want to consider using PME electrostatics.
>>>
>>>
>>>
>>> There were 2 notes
>>> Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size
>>> 0.026 nm Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer
>>> size 0.024 nm Note that mdrun will redetermine rlist based on the
>>> actual pair-list setup This run will generate roughly 0 Mb of data
>>>
>>> -------------------------------------------------------
>>> Program: mdrun-mpi-test, version 2018 Source file:
>>> src/gromacs/gpu_utils/gpu_utils.cu (line 735)
>>> Function: void findGpus(gmx_gpu_info_t*) MPI rank: 0 (out of 2)
>>>
>>> Assertion failed:
>>> Condition: cudaSuccess == cudaPeekAtLastError() Should be cudaSuccess
>>>
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS website at http://www.gromacs.org/Documentation/Errors
>>> -------------------------------------------------------
>>> ---------------------------------------------------------------------
>>> ----- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>>> with errorcode 1.
>>>
>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>> You may or may not see output from other processes, depending on
>>> exactly when Open MPI kills them.
>>> ---------------------------------------------------------------------
>>> -----
>>>
>>> Start 34: regressiontests/simple
>>> 34/39 Test #34: regressiontests/simple ........... Passed 25.95 sec
>>> Start 35: regressiontests/complex
>>> 35/39 Test #35: regressiontests/complex .......... Passed 80.79 sec
>>> Start 36: regressiontests/kernel
>>> 36/39 Test #36: regressiontests/kernel ........... Passed 223.69 sec
>>> Start 37: regressiontests/freeenergy
>>> 37/39 Test #37: regressiontests/freeenergy ....... Passed 16.11 sec
>>> Start 38: regressiontests/pdb2gmx
>>> 38/39 Test #38: regressiontests/pdb2gmx .......... Passed 92.77 sec
>>> Start 39: regressiontests/rotation
>>> 39/39 Test #39: regressiontests/rotation ......... Passed 20.51 sec
>>>
>>> 90% tests passed, 4 tests faile
>>>
>>
> --
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