[petsc-dev] First call to cudaMalloc or cudaFree is very slow on summit
Junchao Zhang
jczhang at mcs.anl.gov
Mon Feb 10 10:44:54 CST 2020
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/
> <http://www.cse.buffalo.edu/~knepley/>
>
>
>
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