[gmx-users] GMX 2018 regression tests: cufftPlanMany R2C plan failure (error code 5)
Alex
nedomacho at gmail.com
Thu Feb 8 18:54:13 CET 2018
Got it. Given all the messing around, I am rebuilding GMX and if make check
results are the same, will install. We have an angry postdoc here demanding
tools.
Thank you gentlemen.
Alex
On Thu, Feb 8, 2018 at 10:50 AM, Szilárd Páll <pall.szilard at gmail.com>
wrote:
> On Thu, Feb 8, 2018 at 6:46 PM, Alex <nedomacho at gmail.com> wrote:
>
> > Are you suggesting that i should accept these results and install the
> 2018
> > version?
> >
>
> Yes, your GROMACS build seems fine.
>
> make check simply runs the test that I suggested you to run manually (and
> which successfully finished). The 30 s timeout on CMake tests interrupts
> this set of unit tests given your unusually long execution time which is
> the reason for the failure.
>
>
> >
> > Thanks,
> >
> > Alex
> >
> > On Thu, Feb 8, 2018 at 10:43 AM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > PATH doesn't matter, only what ldd thinks matters.
> > >
> > > I have opened https://redmine.gromacs.org/issues/2405 to address that
> > the
> > > implementation of these tests are perhaps proving more pain than
> > usefulness
> > > (from this thread and others I have seen).
> > >
> > > Mark
> > >
> > > On Thu, Feb 8, 2018 at 6:41 PM Alex <nedomacho at gmail.com> wrote:
> > >
> > > > That is quite weird. We found that I have PATH values pointing to the
> > old
> > > > gmx installation while running these tests. Do you think that could
> > cause
> > > > issues?
> > > >
> > > > Alex
> > > >
> > > > On Thu, Feb 8, 2018 at 10:36 AM, Mark Abraham <
> > mark.j.abraham at gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > Great. The manual run took 74.5 seconds, failing the 30 second
> > timeout.
> > > > So
> > > > > the code is fine.
> > > > >
> > > > > But you have some crazy large overhead going on - gpu_utils-test
> runs
> > > in
> > > > 7s
> > > > > on my 2013 desktop with CUDA 9.1.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Thu, Feb 8, 2018 at 6:29 PM Alex <nedomacho at gmail.com> wrote:
> > > > >
> > > > > > uh, no sir.
> > > > > >
> > > > > > > 9/39 Test #9: GpuUtilsUnitTests ................***Timeout
> > 30.43
> > > > sec
> > > > > >
> > > > > >
> > > > > > On Thu, Feb 8, 2018 at 10:25 AM, Mark Abraham <
> > > > mark.j.abraham at gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > Those all succeeded. Does make check now also succeed?
> > > > > > >
> > > > > > > Mark
> > > > > > >
> > > > > > > On Thu, Feb 8, 2018 at 6:24 PM Alex <nedomacho at gmail.com>
> wrote:
> > > > > > >
> > > > > > > > Here you are:
> > > > > > > >
> > > > > > > > [==========] Running 35 tests from 7 test cases.
> > > > > > > > [----------] Global test environment set-up.
> > > > > > > > [----------] 7 tests from HostAllocatorTest/0, where
> TypeParam
> > =
> > > > int
> > > > > > > > [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
> > > > > > > > [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
> (5457
> > > ms)
> > > > > > > > [ RUN ] HostAllocatorTest/0.
> > VectorsWithDefaultHostAllocato
> > > > > > > rAlwaysWorks
> > > > > > > > [ OK ] HostAllocatorTest/0.
> > VectorsWithDefaultHostAllocato
> > > > > > > rAlwaysWorks
> > > > > > > > (2861 ms)
> > > > > > > > [ RUN ] HostAllocatorTest/0.TransfersWithoutPinningWork
> > > > > > > > [ OK ] HostAllocatorTest/0.TransfersWithoutPinningWork
> > > (3254
> > > > > ms)
> > > > > > > > [ RUN ] HostAllocatorTest/0.
> > FillInputAlsoWorksAfterCalling
> > > > > Reserve
> > > > > > > > [ OK ] HostAllocatorTest/0.
> > FillInputAlsoWorksAfterCalling
> > > > > Reserve
> > > > > > > > (2221 ms)
> > > > > > > > [ RUN ] HostAllocatorTest/0.
> > TransfersWithPinningWorkWithCu
> > > da
> > > > > > > > [ OK ] HostAllocatorTest/0.
> > TransfersWithPinningWorkWithCu
> > > da
> > > > > (3801
> > > > > > > ms)
> > > > > > > > [ RUN ]
> > > > HostAllocatorTest/0.ManualPinningOperationsWorkWithCuda
> > > > > > > > [ OK ]
> > > > HostAllocatorTest/0.ManualPinningOperationsWorkWithCuda
> > > > > > > (2157
> > > > > > > > ms)
> > > > > > > > [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
> > > > > > > > [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
> > > (2179
> > > > > ms)
> > > > > > > > [----------] 7 tests from HostAllocatorTest/0 (21930 ms
> total)
> > > > > > > >
> > > > > > > > [----------] 7 tests from HostAllocatorTest/1, where
> TypeParam
> > =
> > > > > float
> > > > > > > > [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
> > > > > > > > [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
> (2739
> > > ms)
> > > > > > > > [ RUN ] HostAllocatorTest/1.
> > VectorsWithDefaultHostAllocato
> > > > > > > rAlwaysWorks
> > > > > > > > [ OK ] HostAllocatorTest/1.
> > VectorsWithDefaultHostAllocato
> > > > > > > rAlwaysWorks
> > > > > > > > (2731 ms)
> > > > > > > > [ RUN ] HostAllocatorTest/1.TransfersWithoutPinningWork
> > > > > > > > [ OK ] HostAllocatorTest/1.TransfersWithoutPinningWork
> > > (3281
> > > > > ms)
> > > > > > > > [ RUN ] HostAllocatorTest/1.
> > FillInputAlsoWorksAfterCalling
> > > > > Reserve
> > > > > > > > [ OK ] HostAllocatorTest/1.
> > FillInputAlsoWorksAfterCalling
> > > > > Reserve
> > > > > > > > (2164 ms)
> > > > > > > > [ RUN ] HostAllocatorTest/1.
> > TransfersWithPinningWorkWithCu
> > > da
> > > > > > > > [ OK ] HostAllocatorTest/1.
> > TransfersWithPinningWorkWithCu
> > > da
> > > > > (3908
> > > > > > > ms)
> > > > > > > > [ RUN ]
> > > > HostAllocatorTest/1.ManualPinningOperationsWorkWithCuda
> > > > > > > > [ OK ]
> > > > HostAllocatorTest/1.ManualPinningOperationsWorkWithCuda
> > > > > > > (2202
> > > > > > > > ms)
> > > > > > > > [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
> > > > > > > > [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
> > > (2261
> > > > > ms)
> > > > > > > > [----------] 7 tests from HostAllocatorTest/1 (19287 ms
> total)
> > > > > > > >
> > > > > > > > [----------] 7 tests from HostAllocatorTest/2, where
> TypeParam
> > =
> > > > > > > > gmx::BasicVector<float>
> > > > > > > > [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
> > > > > > > > [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
> (2771
> > > ms)
> > > > > > > > [ RUN ] HostAllocatorTest/2.
> > VectorsWithDefaultHostAllocato
> > > > > > > rAlwaysWorks
> > > > > > > > [ OK ] HostAllocatorTest/2.
> > VectorsWithDefaultHostAllocato
> > > > > > > rAlwaysWorks
> > > > > > > > (2846 ms)
> > > > > > > > [ RUN ] HostAllocatorTest/2.TransfersWithoutPinningWork
> > > > > > > > [ OK ] HostAllocatorTest/2.TransfersWithoutPinningWork
> > > (3283
> > > > > ms)
> > > > > > > > [ RUN ] HostAllocatorTest/2.
> > FillInputAlsoWorksAfterCalling
> > > > > Reserve
> > > > > > > > [ OK ] HostAllocatorTest/2.
> > FillInputAlsoWorksAfterCalling
> > > > > Reserve
> > > > > > > > (2131 ms)
> > > > > > > > [ RUN ] HostAllocatorTest/2.
> > TransfersWithPinningWorkWithCu
> > > da
> > > > > > > > [ OK ] HostAllocatorTest/2.
> > TransfersWithPinningWorkWithCu
> > > da
> > > > > (3833
> > > > > > > ms)
> > > > > > > > [ RUN ]
> > > > HostAllocatorTest/2.ManualPinningOperationsWorkWithCuda
> > > > > > > > [ OK ]
> > > > HostAllocatorTest/2.ManualPinningOperationsWorkWithCuda
> > > > > > > (2232
> > > > > > > > ms)
> > > > > > > > [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
> > > > > > > > [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
> > > (2164
> > > > > ms)
> > > > > > > > [----------] 7 tests from HostAllocatorTest/2 (19261 ms
> total)
> > > > > > > >
> > > > > > > > [----------] 3 tests from AllocatorTest/0, where TypeParam =
> > > > > > > > gmx::Allocator<float, gmx::HostAllocationPolicy>
> > > > > > > > [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAli
> > > gnment
> > > > > > > > [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAli
> > > gnment
> > > > (0
> > > > > > ms)
> > > > > > > > [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithA
> > > lignment
> > > > > > > > [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithA
> > > lignment
> > > > > (0
> > > > > > > ms)
> > > > > > > > [ RUN ]
> > > > AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
> > > > > > > > [ OK ]
> > > > AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
> > > > > (0
> > > > > > > ms)
> > > > > > > > [----------] 3 tests from AllocatorTest/0 (0 ms total)
> > > > > > > >
> > > > > > > > [----------] 3 tests from AllocatorTest/1, where TypeParam =
> > > > > > > > gmx::Allocator<int, gmx::HostAllocationPolicy>
> > > > > > > > [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAli
> > > gnment
> > > > > > > > [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAli
> > > gnment
> > > > (0
> > > > > > ms)
> > > > > > > > [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithA
> > > lignment
> > > > > > > > [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithA
> > > lignment
> > > > > (0
> > > > > > > ms)
> > > > > > > > [ RUN ]
> > > > AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
> > > > > > > > [ OK ]
> > > > AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
> > > > > (0
> > > > > > > ms)
> > > > > > > > [----------] 3 tests from AllocatorTest/1 (0 ms total)
> > > > > > > >
> > > > > > > > [----------] 3 tests from AllocatorTest/2, where TypeParam =
> > > > > > > > gmx::Allocator<gmx::BasicVector<float>,
> > > gmx::HostAllocationPolicy>
> > > > > > > > [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAli
> > > gnment
> > > > > > > > [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAli
> > > gnment
> > > > (0
> > > > > > ms)
> > > > > > > > [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithA
> > > lignment
> > > > > > > > [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithA
> > > lignment
> > > > > (0
> > > > > > > ms)
> > > > > > > > [ RUN ]
> > > > AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
> > > > > > > > [ OK ]
> > > > AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
> > > > > (0
> > > > > > > ms)
> > > > > > > > [----------] 3 tests from AllocatorTest/2 (0 ms total)
> > > > > > > >
> > > > > > > > [----------] 5 tests from PinnedMemoryCheckerTest
> > > > > > > > [ RUN ] PinnedMemoryCheckerTest.
> > > DefaultContainerIsRecognized
> > > > > > > > [ OK ] PinnedMemoryCheckerTest.
> > > DefaultContainerIsRecognized
> > > > > (3248
> > > > > > > ms)
> > > > > > > > [ RUN ] PinnedMemoryCheckerTest.
> > > NonpinnedContainerIsRecognized
> > > > > > > > [ OK ] PinnedMemoryCheckerTest.
> > > NonpinnedContainerIsRecognized
> > > > > > > (2752
> > > > > > > > ms)
> > > > > > > > [ RUN ] PinnedMemoryCheckerTest.
> > PinnedContainerIsRecognized
> > > > > > > > [ OK ] PinnedMemoryCheckerTest.
> > PinnedContainerIsRecognized
> > > > > (2709
> > > > > > > ms)
> > > > > > > > [ RUN ] PinnedMemoryCheckerTest.
> > DefaultCBufferIsRecognized
> > > > > > > > [ OK ] PinnedMemoryCheckerTest.
> > DefaultCBufferIsRecognized
> > > > > (2675
> > > > > > > ms)
> > > > > > > > [ RUN ] PinnedMemoryCheckerTest.
> PinnedCBufferIsRecognized
> > > > > > > > [ OK ] PinnedMemoryCheckerTest.
> PinnedCBufferIsRecognized
> > > > (2686
> > > > > > ms)
> > > > > > > > [----------] 5 tests from PinnedMemoryCheckerTest (14071 ms
> > > total)
> > > > > > > >
> > > > > > > > [----------] Global test environment tear-down
> > > > > > > > [==========] 35 tests from 7 test cases ran. (74549 ms total)
> > > > > > > > [ PASSED ] 35 tests.
> > > > > > > >
> > > > > > > >
> > > > > > > > On Thu, Feb 8, 2018 at 10:00 AM, Szilárd Páll <
> > > > > pall.szilard at gmail.com>
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > > It might help to know which of the unit test(s) in that
> group
> > > > > stall?
> > > > > > > Can
> > > > > > > > > you run it manually (bin/gpu_utils-test) and report back
> the
> > > > > standard
> > > > > > > > > output?
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > --
> > > > > > > > > Szilárd
> > > > > > > > >
> > > > > > > > > On Thu, Feb 8, 2018 at 3:56 PM, Alex <nedomacho at gmail.com>
> > > > wrote:
> > > > > > > > >
> > > > > > > > > > Nope, still persists after reboot and no other jobs
> > running:
> > > > > > > > > > 9/39 Test #9: GpuUtilsUnitTests
> > ................***Timeout
> > > > > 30.59
> > > > > > > sec
> > > > > > > > > >
> > > > > > > > > > Any additional suggestions?
> > > > > > > > > >
> > > > > > > > > > --
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