[petsc-dev] First call to cudaMalloc or cudaFree is very slow on summit
Matthew Knepley
knepley at gmail.com
Wed Feb 12 13:09:58 CST 2020
On Wed, Feb 12, 2020 at 11:06 AM Zhang, Hong via petsc-dev <
petsc-dev at mcs.anl.gov> wrote:
> Sorry for the long post. Here are replies I have got from OLCF so far. We
> still don’t know how to solve the problem.
>
> One interesting thing that Tom noticed is PetscInitialize() may have
> called cudaFree(0) 32 times as NVPROF shows, and they all run very fast.
> These calls may be triggered by some other libraries like cublas. But if
> PETSc calls cudaFree() explicitly, it is always very slow.
>
It sounds really painful, but I would start removing lines from
PetscInitialize() until it runs fast.
Thanks,
Matt
> Hong
>
>
> On Wed Feb 12 09:51:33 2020, tpapathe wrote:
>
> Something else I noticed from the nvprof output (see my previous post) is
> that the runs with PETSc initialized have 33 calls to cudaFree, whereas
> the
> non-PETSc versions only have the 1 call to cudaFree. I'm not sure what is
> happening in the PETSc initialize/finalize, but it appears to be doing a
> lot under the hood. You can also see there are many additional CUDA calls
> that are not shown in the profiler output from the non-PETSc runs (e.g.,
> additional cudaMalloc and cudaMemcpy calls, cudaDeviceSychronize, etc.).
> Which other systems have you tested this on? Which CUDA Toolkits and CUDA
> drivers were installed on those systems? Please let me know if there is
> any
> additional information you can share with me about this.
>
> -Tom
> On Wed Feb 12 09:25:23 2020, tpapathe wrote:
>
> Ok. Thanks for the additional info, Hong. I'll ask around to see if any
> local (PETSc or CUDA) experts have experienced this behavior. In the
> meantime, is this impacting your work or something you're just curious
> about? A 5-7 second initialization time is indeed unusual, but is it
> negligible relative to the overall walltime of your jobs, or is it
> somehow affecting your productivity?
>
> -Tom
> On Tue Feb 11 17:04:25 2020, hongzhang at anl.gov wrote:
>
> We know it happens with PETSc. But note that the slow down occurs on
> the first CUDA function call. In the example I sent to you, if we simply
> link it to the PETSc shared library and don’t call any PETSc function, the
> slow down still happens on cudaFree(0). We have never seen this behavior on
> other GPU systems.
>
> On Feb 11, 2020, at 3:31 PM, Thomas Papatheodore via RT <help at nccs.gov>
> wrote:
>
> Thanks for the update. I have now reproduced the behavior you described
> with
> PETSc + CUDA using your example code:
>
> [tpapathe at batch2: /gpfs/alpine/scratch/tpapathe/stf007/petsc/src]$ jsrun
> -n1
> -a1 -c1 -g1 -r1 -l cpu-cpu -dpacked -bpacked:1 nvprof
> /gpfs/alpine/scratch/tpapathe/stf007/petsc/src/ex_simple_petsc
>
> ==16991== NVPROF is profiling process 16991, command:
> /gpfs/alpine/scratch/tpapathe/stf007/petsc/src/ex_simple_petsc
>
> ==16991== Profiling application:
> /gpfs/alpine/scratch/tpapathe/stf007/petsc/src/ex_simple_petsc
>
> free time =4.730000 malloc time =0.000000 copy time =0.000000
>
> ==16991== Profiling result:
>
> Type Time(%) Time Calls Avg Min Max Name
>
> GPU activities: 100.00% 9.3760us 6 1.5620us 1.3440us 1.7920us [CUDA memcpy
> HtoD]
>
> API calls: 99.78% 5.99333s 33 181.62ms 883ns 4.71976s cudaFree
>
> 0.11% 6.3603ms 379 16.781us 233ns 693.40us cuDeviceGetAttribute
>
> 0.07% 4.1453ms 4 1.0363ms 1.0186ms 1.0623ms cuDeviceTotalMem
>
> 0.02% 1.0046ms 4 251.15us 131.45us 449.32us cuDeviceGetName
>
> 0.01% 808.21us 16 50.513us 6.7080us 621.54us cudaMalloc
>
> 0.01% 452.06us 450 1.0040us 830ns 6.4430us cudaFuncSetAttribute
>
> 0.00% 104.89us 6 17.481us 13.419us 21.338us cudaMemcpy
>
> 0.00% 102.26us 15 6.8170us 6.1900us 10.072us cudaDeviceSynchronize
>
> 0.00% 93.635us 80 1.1700us 1.0190us 2.1990us cudaEventCreateWithFlags
>
> 0.00% 92.168us 83 1.1100us 951ns 2.3550us cudaEventDestroy
>
> 0.00% 52.277us 74 706ns 592ns 1.5640us cudaDeviceGetAttribute
>
> 0.00% 34.558us 3 11.519us 9.5410us 15.129us cudaStreamDestroy
>
> 0.00% 27.778us 3 9.2590us 4.9120us 17.632us cudaStreamCreateWithFlags
>
> 0.00% 11.955us 1 11.955us 11.955us 11.955us cudaSetDevice
>
> 0.00% 10.361us 7 1.4800us 809ns 3.6580us cudaGetDevice
>
> 0.00% 5.4310us 3 1.8100us 1.6420us 1.9980us cudaEventCreate
>
> 0.00% 3.8040us 6 634ns 391ns 1.5350us cuDeviceGetCount
>
> 0.00% 3.5350us 1 3.5350us 3.5350us 3.5350us cuDeviceGetPCIBusId
>
> 0.00% 3.2210us 3 1.0730us 949ns 1.1640us cuInit
>
> 0.00% 2.6780us 5 535ns 369ns 1.0210us cuDeviceGet
>
> 0.00% 2.5080us 1 2.5080us 2.5080us 2.5080us cudaSetDeviceFlags
>
> 0.00% 1.6800us 4 420ns 392ns 488ns cuDeviceGetUuid
>
> 0.00% 1.5720us 3 524ns 398ns 590ns cuDriverGetVersion
>
>
>
> If I remove all mention of PETSc from the code, compile manually and run,
> I get
> the expected behavior:
>
> [tpapathe at batch2: /gpfs/alpine/scratch/tpapathe/stf007/petsc/src]$ pgc++
> -L$OLCF_CUDA_ROOT/lib64 -lcudart ex_simple.c -o ex_simple
>
>
> [tpapathe at batch2: /gpfs/alpine/scratch/tpapathe/stf007/petsc/src]$ jsrun
> -n1
> -a1 -c1 -g1 -r1 -l cpu-cpu -dpacked -bpacked:1 nvprof
> /gpfs/alpine/scratch/tpapathe/stf007/petsc/src/ex_simple
>
> ==17248== NVPROF is profiling process 17248, command:
> /gpfs/alpine/scratch/tpapathe/stf007/petsc/src/ex_simple
>
> ==17248== Profiling application:
> /gpfs/alpine/scratch/tpapathe/stf007/petsc/src/ex_simple
>
> free time =0.340000 malloc time =0.000000 copy time =0.000000
>
> ==17248== Profiling result:
>
> Type Time(%) Time Calls Avg Min Max Name
>
> GPU activities: 100.00% 1.7600us 1 1.7600us 1.7600us 1.7600us [CUDA memcpy
> HtoD]
>
> API calls: 98.56% 231.76ms 1 231.76ms 231.76ms 231.76ms cudaFree
>
> 0.67% 1.5764ms 97 16.251us 234ns 652.65us cuDeviceGetAttribute
>
> 0.46% 1.0727ms 1 1.0727ms 1.0727ms 1.0727ms cuDeviceTotalMem
>
> 0.23% 537.38us 1 537.38us 537.38us 537.38us cudaMalloc
>
> 0.07% 172.80us 1 172.80us 172.80us 172.80us cuDeviceGetName
>
> 0.01% 21.648us 1 21.648us 21.648us 21.648us cudaMemcpy
>
> 0.00% 3.3470us 1 3.3470us 3.3470us 3.3470us cuDeviceGetPCIBusId
>
> 0.00% 2.5310us 3 843ns 464ns 1.3700us cuDeviceGetCount
>
> 0.00% 1.7260us 2 863ns 490ns 1.2360us cuDeviceGet
>
> 0.00% 377ns 1 377ns 377ns 377ns cuDeviceGetUuid
>
>
>
> I also get the expected behavior if I add an MPI_Init and MPI_Finalize to
> the
> code instead of PETSc initialization:
>
> [tpapathe at login1: /gpfs/alpine/scratch/tpapathe/stf007/petsc/src]$ mpicc
> -L$OLCF_CUDA_ROOT/lib64 -lcudart ex_simple_mpi.c -o ex_simple_mpi
>
>
> [tpapathe at batch1: /gpfs/alpine/scratch/tpapathe/stf007/petsc/src]$ jsrun
> -n1
> -a1 -c1 -g1 -r1 -l cpu-cpu -dpacked -bpacked:1 nvprof
> /gpfs/alpine/scratch/tpapathe/stf007/petsc/src/ex_simple_mpi
>
> ==35166== NVPROF is profiling process 35166, command:
> /gpfs/alpine/scratch/tpapathe/stf007/petsc/src/ex_simple_mpi
>
> ==35166== Profiling application:
> /gpfs/alpine/scratch/tpapathe/stf007/petsc/src/ex_simple_mpi
>
> free time =0.340000 malloc time =0.000000 copy time =0.000000
>
> ==35166== Profiling result:
>
> Type Time(%) Time Calls Avg Min Max Name
>
> GPU activities: 100.00% 1.7600us 1 1.7600us 1.7600us 1.7600us [CUDA memcpy
> HtoD]
>
> API calls: 98.57% 235.61ms 1 235.61ms 235.61ms 235.61ms cudaFree
>
> 0.66% 1.5802ms 97 16.290us 239ns 650.72us cuDeviceGetAttribute
>
> 0.45% 1.0825ms 1 1.0825ms 1.0825ms 1.0825ms cuDeviceTotalMem
>
> 0.23% 542.73us 1 542.73us 542.73us 542.73us cudaMalloc
>
> 0.07% 174.77us 1 174.77us 174.77us 174.77us cuDeviceGetName
>
> 0.01% 26.431us 1 26.431us 26.431us 26.431us cudaMemcpy
>
> 0.00% 4.0330us 1 4.0330us 4.0330us 4.0330us cuDeviceGetPCIBusId
>
> 0.00% 2.8560us 3 952ns 528ns 1.6150us cuDeviceGetCount
>
> 0.00% 1.6190us 2 809ns 576ns 1.0430us cuDeviceGet
>
> 0.00% 341ns 1 341ns 341ns 341ns cuDeviceGetUuid
>
>
> So this appears to be something specific happening within PETSc itself -
> not
> necessarily an OLCF issue. I would suggest asking this question within the
> PETSc community to understand what's happening. Please let me know if you
> have
> any additional questions.
>
> -Tom
>
> On Feb 10, 2020, at 11:14 AM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
>
>
> gprof or some similar tool?
>
>
> On Feb 10, 2020, at 11:18 AM, Zhang, Hong via petsc-dev <
> petsc-dev at mcs.anl.gov> wrote:
>
> -cuda_initialize 0 does not make any difference. Actually this issue has
> nothing to do with PetscInitialize(). I tried to call cudaFree(0) before
> PetscInitialize(), and it still took 7.5 seconds.
>
> Hong
>
> On Feb 10, 2020, at 10:44 AM, Zhang, Junchao <jczhang at mcs.anl.gov> wrote:
>
> As I mentioned, have you tried -cuda_initialize 0? Also,
> PetscCUDAInitialize contains
> ierr = PetscCUBLASInitializeHandle();CHKERRQ(ierr);
> ierr = PetscCUSOLVERDnInitializeHandle();CHKERRQ(ierr);
> Have you tried to comment out them and test again?
> --Junchao Zhang
>
>
> On Sat, Feb 8, 2020 at 5:22 PM Zhang, Hong via petsc-dev <
> petsc-dev at mcs.anl.gov> wrote:
>
>
> On Feb 8, 2020, at 5:03 PM, Matthew Knepley <knepley at gmail.com> wrote:
>
> On Sat, Feb 8, 2020 at 4:34 PM Zhang, Hong via petsc-dev <
> petsc-dev at mcs.anl.gov> wrote:
> I did some further investigation. The overhead persists for both the PETSc
> shared library and the static library. In the previous example, it does not
> call any PETSc function, the first CUDA function becomes very slow when it
> is linked to the petsc so. This indicates that the slowdown occurs if the
> symbol (cudafree)is searched through the petsc so, but does not occur if
> the symbol is found directly in the cuda runtime lib.
>
> So the issue has nothing to do with the dynamic linker. The following
> example can be used to easily reproduce the problem (cudaFree(0) always
> takes ~7.5 seconds).
>
> 1) This should go to OLCF admin as Jeff suggests
>
>
> I had sent this to OLCF admin before the discussion was started here.
> Thomas Papatheodore has followed up. I am trying to help him reproduce the
> problem on summit.
>
>
> 2) Just to make sure I understand, a static executable with this code is
> still slow on the cudaFree(), since CUDA is a shared library by default.
>
>
> I prepared the code as a minimal example to reproduce the problem. It
> would be fair to say any code using PETSc (with CUDA enabled, built
> statically or dynamically) on summit suffers a 7.5-second overhead on the
> first CUDA function call (either in the user code or inside PETSc).
>
> Thanks,
> Hong
>
>
> I think we should try:
>
> a) Forcing a full static link, if possible
>
> b) Asking OLCF about link resolution order
>
> It sounds like a similar thing I have seen in the past where link
> resolution order can exponentially increase load time.
>
> Thanks,
>
> Matt
>
> bash-4.2$ cat ex_simple_petsc.c
> #include <time.h>
> #include <cuda_runtime.h>
> #include <stdio.h>
> #include <petscmat.h>
>
> int main(int argc,char **args)
> {
> clock_t start,s1,s2,s3;
> double cputime;
> double *init,tmp[100] = {0};
> PetscErrorCode ierr=0;
>
> ierr = PetscInitialize(&argc,&args,(char*)0,NULL);if (ierr) return ierr;
> start = clock();
> cudaFree(0);
> s1 = clock();
> cudaMalloc((void **)&init,100*sizeof(double));
> s2 = clock();
> cudaMemcpy(init,tmp,100*sizeof(double),cudaMemcpyHostToDevice);
> s3 = clock();
> printf("free time =%lf malloc time =%lf copy time =%lf\n",((double) (s1 -
> start)) / CLOCKS_PER_SEC,((double) (s2 - s1)) / CLOCKS_PER_SEC,((double)
> (s3 - s2)) / CLOCKS_PER_SEC);
> ierr = PetscFinalize();
> return ierr;
> }
>
> Hong
>
> On Feb 7, 2020, at 3:09 PM, Zhang, Hong <hongzhang at anl.gov> wrote:
>
> Note that the overhead was triggered by the first call to a CUDA function.
> So it seems that the first CUDA function triggered loading petsc so (if
> petsc so is linked), which is slow on the summit file system.
>
> Hong
>
> On Feb 7, 2020, at 2:54 PM, Zhang, Hong via petsc-dev <
> petsc-dev at mcs.anl.gov> wrote:
>
> Linking any other shared library does not slow down the execution. The
> PETSc shared library is the only one causing trouble.
>
> Here are the ldd output for two different versions. For the first version,
> I removed -lpetsc and it ran very fast. The second (slow) version was
> linked to petsc so.
>
> bash-4.2$ ldd ex_simple
> linux-vdso64.so.1 => (0x0000200000050000)
> liblapack.so.0 =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/liblapack.so.0
> (0x0000200000070000)
> libblas.so.0 =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libblas.so.0
> (0x00002000009b0000)
> libhdf5hl_fortran.so.100 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/hdf5-1.10.3-pgiul2yf4auv7krecd72t6vupd7e3qgn/lib/libhdf5hl_fortran.so.100
> (0x0000200000e80000)
> libhdf5_fortran.so.100 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/hdf5-1.10.3-pgiul2yf4auv7krecd72t6vupd7e3qgn/lib/libhdf5_fortran.so.100
> (0x0000200000ed0000)
> libhdf5_hl.so.100 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/hdf5-1.10.3-pgiul2yf4auv7krecd72t6vupd7e3qgn/lib/libhdf5_hl.so.100
> (0x0000200000f50000)
> libhdf5.so.103 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/hdf5-1.10.3-pgiul2yf4auv7krecd72t6vupd7e3qgn/lib/libhdf5.so.103
> (0x0000200000fb0000)
> libX11.so.6 => /usr/lib64/libX11.so.6 (0x00002000015e0000)
> libcufft.so.10 => /sw/summit/cuda/10.1.168/lib64/libcufft.so.10
> (0x0000200001770000)
> libcublas.so.10 => /sw/summit/cuda/10.1.168/lib64/libcublas.so.10
> (0x0000200009b00000)
> libcudart.so.10.1 =>
> /sw/summit/cuda/10.1.168/lib64/libcudart.so.10.1 (0x000020000d950000)
> libcusparse.so.10 =>
> /sw/summit/cuda/10.1.168/lib64/libcusparse.so.10 (0x000020000d9f0000)
> libcusolver.so.10 =>
> /sw/summit/cuda/10.1.168/lib64/libcusolver.so.10 (0x0000200012f50000)
> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x000020001dc40000)
> libdl.so.2 => /usr/lib64/libdl.so.2 (0x000020001ddd0000)
> libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x000020001de00000)
> libmpiprofilesupport.so.3 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libmpiprofilesupport.so.3
> (0x000020001de40000)
> libmpi_ibm_usempi.so =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libmpi_ibm_usempi.so
> (0x000020001de70000)
> libmpi_ibm_mpifh.so.3 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libmpi_ibm_mpifh.so.3
> (0x000020001dea0000)
> libmpi_ibm.so.3 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libmpi_ibm.so.3
> (0x000020001df40000)
> libpgf90rtl.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgf90rtl.so
> (0x000020001e0b0000)
> libpgf90.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgf90.so
> (0x000020001e0f0000)
> libpgf90_rpm1.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgf90_rpm1.so
> (0x000020001e6a0000)
> libpgf902.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgf902.so
> (0x000020001e6d0000)
> libpgftnrtl.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgftnrtl.so
> (0x000020001e700000)
> libatomic.so.1 => /usr/lib64/libatomic.so.1 (0x000020001e730000)
> libpgkomp.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgkomp.so
> (0x000020001e760000)
> libomp.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libomp.so
> (0x000020001e790000)
> libomptarget.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libomptarget.so
> (0x000020001e880000)
> libpgmath.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgmath.so
> (0x000020001e8b0000)
> libpgc.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgc.so
> (0x000020001e9d0000)
> librt.so.1 => /usr/lib64/librt.so.1 (0x000020001eb40000)
> libm.so.6 => /usr/lib64/libm.so.6 (0x000020001eb70000)
> libgcc_s.so.1 => /usr/lib64/libgcc_s.so.1 (0x000020001ec60000)
> libc.so.6 => /usr/lib64/libc.so.6 (0x000020001eca0000)
> libz.so.1 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/zlib-1.2.11-2htm7ws4hgrthi5tyjnqxtjxgpfklxsc/lib/libz.so.1
> (0x000020001ee90000)
> libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x000020001eef0000)
> /lib64/ld64.so.2 (0x0000200000000000)
> libcublasLt.so.10 =>
> /sw/summit/cuda/10.1.168/lib64/libcublasLt.so.10 (0x000020001ef40000)
> libutil.so.1 => /usr/lib64/libutil.so.1 (0x0000200020e50000)
> libhwloc_ompi.so.15 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libhwloc_ompi.so.15
> (0x0000200020e80000)
> libevent-2.1.so.6 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libevent-2.1.so.6
> (0x0000200020ef0000)
> libevent_pthreads-2.1.so.6 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libevent_pthreads-2.1.so.6
> (0x0000200020f70000)
> libopen-rte.so.3 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libopen-rte.so.3
> (0x0000200020fa0000)
> libopen-pal.so.3 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libopen-pal.so.3
> (0x00002000210b0000)
> libXau.so.6 => /usr/lib64/libXau.so.6 (0x00002000211a0000)
>
>
> bash-4.2$ ldd ex_simple_slow
> linux-vdso64.so.1 => (0x0000200000050000)
> libpetsc.so.3.012 =>
> /autofs/nccs-svm1_home1/hongzh/Projects/petsc/arch-olcf-summit-sell-opt/lib/libpetsc.so.3.012
> (0x0000200000070000)
> liblapack.so.0 =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/liblapack.so.0
> (0x0000200002be0000)
> libblas.so.0 =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libblas.so.0
> (0x0000200003520000)
> libhdf5hl_fortran.so.100 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/hdf5-1.10.3-pgiul2yf4auv7krecd72t6vupd7e3qgn/lib/libhdf5hl_fortran.so.100
> (0x00002000039f0000)
> libhdf5_fortran.so.100 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/hdf5-1.10.3-pgiul2yf4auv7krecd72t6vupd7e3qgn/lib/libhdf5_fortran.so.100
> (0x0000200003a40000)
> libhdf5_hl.so.100 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/hdf5-1.10.3-pgiul2yf4auv7krecd72t6vupd7e3qgn/lib/libhdf5_hl.so.100
> (0x0000200003ac0000)
> libhdf5.so.103 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/hdf5-1.10.3-pgiul2yf4auv7krecd72t6vupd7e3qgn/lib/libhdf5.so.103
> (0x0000200003b20000)
> libX11.so.6 => /usr/lib64/libX11.so.6 (0x0000200004150000)
> libcufft.so.10 => /sw/summit/cuda/10.1.168/lib64/libcufft.so.10
> (0x00002000042e0000)
> libcublas.so.10 => /sw/summit/cuda/10.1.168/lib64/libcublas.so.10
> (0x000020000c670000)
> libcudart.so.10.1 =>
> /sw/summit/cuda/10.1.168/lib64/libcudart.so.10.1 (0x00002000104c0000)
> libcusparse.so.10 =>
> /sw/summit/cuda/10.1.168/lib64/libcusparse.so.10 (0x0000200010560000)
> libcusolver.so.10 =>
> /sw/summit/cuda/10.1.168/lib64/libcusolver.so.10 (0x0000200015ac0000)
> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002000207b0000)
> libdl.so.2 => /usr/lib64/libdl.so.2 (0x0000200020940000)
> libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x0000200020970000)
> libmpiprofilesupport.so.3 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libmpiprofilesupport.so.3
> (0x00002000209b0000)
> libmpi_ibm_usempi.so =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libmpi_ibm_usempi.so
> (0x00002000209e0000)
> libmpi_ibm_mpifh.so.3 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libmpi_ibm_mpifh.so.3
> (0x0000200020a10000)
> libmpi_ibm.so.3 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libmpi_ibm.so.3
> (0x0000200020ab0000)
> libpgf90rtl.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgf90rtl.so
> (0x0000200020c20000)
> libpgf90.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgf90.so
> (0x0000200020c60000)
> libpgf90_rpm1.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgf90_rpm1.so
> (0x0000200021210000)
> libpgf902.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgf902.so
> (0x0000200021240000)
> libpgftnrtl.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgftnrtl.so
> (0x0000200021270000)
> libatomic.so.1 => /usr/lib64/libatomic.so.1 (0x00002000212a0000)
> libpgkomp.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgkomp.so
> (0x00002000212d0000)
> libomp.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libomp.so
> (0x0000200021300000)
> libomptarget.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libomptarget.so
> (0x00002000213f0000)
> libpgmath.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgmath.so
> (0x0000200021420000)
> libpgc.so =>
> /autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/pgi-19.4-6acz4xyqjlpoaonjiiqjme2aknrfnzoy/linuxpower/19.4/lib/libpgc.so
> (0x0000200021540000)
> librt.so.1 => /usr/lib64/librt.so.1 (0x00002000216b0000)
> libm.so.6 => /usr/lib64/libm.so.6 (0x00002000216e0000)
> libgcc_s.so.1 => /usr/lib64/libgcc_s.so.1 (0x00002000217d0000)
> libc.so.6 => /usr/lib64/libc.so.6 (0x0000200021810000)
> libz.so.1 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/zlib-1.2.11-2htm7ws4hgrthi5tyjnqxtjxgpfklxsc/lib/libz.so.1
> (0x0000200021a10000)
> libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x0000200021a60000)
> /lib64/ld64.so.2 (0x0000200000000000)
> libcublasLt.so.10 =>
> /sw/summit/cuda/10.1.168/lib64/libcublasLt.so.10 (0x0000200021ab0000)
> libutil.so.1 => /usr/lib64/libutil.so.1 (0x00002000239c0000)
> libhwloc_ompi.so.15 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libhwloc_ompi.so.15
> (0x00002000239f0000)
> libevent-2.1.so.6 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libevent-2.1.so.6
> (0x0000200023a60000)
> libevent_pthreads-2.1.so.6 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libevent_pthreads-2.1.so.6
> (0x0000200023ae0000)
> libopen-rte.so.3 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libopen-rte.so.3
> (0x0000200023b10000)
> libopen-pal.so.3 =>
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/pgi-19.4/spectrum-mpi-10.3.0.1-20190611-4ymaahbai7ehhw4rves5jjiwon2laz3a/lib/libopen-pal.so.3
> (0x0000200023c20000)
> libXau.so.6 => /usr/lib64/libXau.so.6 (0x0000200023d10000)
>
>
> On Feb 7, 2020, at 2:31 PM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
>
>
> ldd -o on the executable of both linkings of your code.
>
> My guess is that without PETSc it is linking the static version of the
> needed libraries and with PETSc the shared. And, in typical fashion, the
> shared libraries are off on some super slow file system so take a long time
> to be loaded and linked in on demand.
>
> Still a performance bug in Summit.
>
> Barry
>
>
> On Feb 7, 2020, at 12:23 PM, Zhang, Hong via petsc-dev <
> petsc-dev at mcs.anl.gov> wrote:
>
> Hi all,
>
> Previously I have noticed that the first call to a CUDA function such as
> cudaMalloc and cudaFree in PETSc takes a long time (7.5 seconds) on summit.
> Then I prepared a simple example as attached to help OCLF reproduce the
> problem. It turned out that the problem was caused by PETSc. The
> 7.5-second overhead can be observed only when the PETSc lib is linked. If I
> do not link PETSc, it runs normally. Does anyone have any idea why this
> happens and how to fix it?
>
> Hong (Mr.)
>
> bash-4.2$ cat ex_simple.c
> #include <time.h>
> #include <cuda_runtime.h>
> #include <stdio.h>
>
> int main(int argc,char **args)
> {
> clock_t start,s1,s2,s3;
> double cputime;
> double *init,tmp[100] = {0};
>
> start = clock();
> cudaFree(0);
> s1 = clock();
> cudaMalloc((void **)&init,100*sizeof(double));
> s2 = clock();
> cudaMemcpy(init,tmp,100*sizeof(double),cudaMemcpyHostToDevice);
> s3 = clock();
> printf("free time =%lf malloc time =%lf copy time =%lf\n",((double) (s1 -
> start)) / CLOCKS_PER_SEC,((double) (s2 - s1)) / CLOCKS_PER_SEC,((double)
> (s3 - s2)) / CLOCKS_PER_SEC);
>
> return 0;
> }
>
>
>
>
>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/
>
>
>
>
>
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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