> On Feb 12, 2020, at 5:11 PM, Smith, Barry F. <[email protected]> wrote: > > > ldd -o on the petsc program (static) and the non petsc program (static), > what are the differences?
There is no difference in the outputs. > > nm -o both executables | grep cudaFree() Non petsc program: [[email protected] tests]$ nm ex_simple | grep cudaFree 0000000010000ae0 t 00000017.plt_call.cudaFree@@libcudart.so.10.1 U cudaFree@@libcudart.so.10.1 Petsc program: [[email protected] tests]$ nm ex_simple_petsc | grep cudaFree 0000000010016550 t 00000017.plt_call.cudaFree@@libcudart.so.10.1 0000000010017010 t 00000017.plt_call.cudaFreeHost@@libcudart.so.10.1 00000000124c3f48 V _ZGVZN6thrust2mr19get_global_resourceINS_26device_ptr_memory_resou rceINS_6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_ 8cuda_cub7pointerIvEEEEEEEEPT_vE8resource 00000000124c3f50 V _ZGVZN6thrust2mr19get_global_resourceINS_6system4cuda6detail20cuda _memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEEEEEPT_vE8r esource 0000000010726788 W _ZN6thrust26device_ptr_memory_resourceINS_6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEEEE11do_allocateEmm 00000000107267e8 W _ZN6thrust26device_ptr_memory_resourceINS_6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEEEE13do_deallocateENS_10device_ptrIvEEmm 0000000010726878 W _ZN6thrust26device_ptr_memory_resourceINS_6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEEEED0Ev 0000000010726848 W _ZN6thrust26device_ptr_memory_resourceINS_6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEEEED1Ev 0000000010729f78 W _ZN6thrust6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEE11do_allocateEmm 000000001072a218 W _ZN6thrust6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEE13do_deallocateES6_mm 000000001072a388 W _ZN6thrust6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEED0Ev 000000001072a358 W _ZN6thrust6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEED1Ev 0000000012122300 V _ZTIN6thrust26device_ptr_memory_resourceINS_6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEEEEE 0000000012122370 V _ZTIN6thrust6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEEE 0000000012122410 V _ZTSN6thrust26device_ptr_memory_resourceINS_6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEEEEE 00000000121225f0 V _ZTSN6thrust6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEEE 0000000012120630 V _ZTVN6thrust26device_ptr_memory_resourceINS_6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEEEEE 00000000121205b0 V _ZTVN6thrust6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEEE 00000000124c3f30 V _ZZN6thrust2mr19get_global_resourceINS_26device_ptr_memory_resourceINS_6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEEEEEEEPT_vE8resource 00000000124c3f20 V _ZZN6thrust2mr19get_global_resourceINS_6system4cuda6detail20cuda_memory_resourceIXadL10cudaMallocEEXadL8cudaFreeEENS_8cuda_cub7pointerIvEEEEEEPT_vE8resource U cudaFree@@libcudart.so.10.1 U cudaFreeHost@@libcudart.so.10.1 Hong > > > > > >> On Feb 12, 2020, at 1:51 PM, Munson, Todd via petsc-dev >> <[email protected]> wrote: >> >> >> There are some side effects when loading shared libraries, such as >> initializations of >> static variables, etc. Is something like that happening? >> >> Another place is the initial runtime library that gets linked (libcrt0 >> maybe?). I >> think some MPI compilers insert their own version. >> >> Todd. >> >>> On Feb 12, 2020, at 11:38 AM, Zhang, Hong via petsc-dev >>> <[email protected]> wrote: >>> >>> >>> >>>> On Feb 12, 2020, at 11:09 AM, Matthew Knepley <[email protected]> wrote: >>>> >>>> On Wed, Feb 12, 2020 at 11:06 AM Zhang, Hong via petsc-dev >>>> <[email protected]> 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. >>> >>> It may be more painful than it sounds. The problem is not really related to >>> PetscInitialize(). In the following simple example, we do not call any >>> PETsc function. But if we link it to the PETSc shared library, cudaFree(0) >>> would be very slow. CUDA is a blackbox. There is not much we can debug with >>> this simple example. >>> >>> 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; >>> } >>> >>> >>>> >>>> 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, [email protected] 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 <[email protected]> >>>> wrote: >>>> >>>> Thanks for the update. I have now reproduced the behavior you described >>>> with >>>> PETSc + CUDA using your example code: >>>> >>>> [tpapathe@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@batch2: /gpfs/alpine/scratch/tpapathe/stf007/petsc/src]$ pgc++ >>>> -L$OLCF_CUDA_ROOT/lib64 -lcudart ex_simple.c -o ex_simple >>>> >>>> >>>> [tpapathe@batch2: /gpfs/alpine/scratch/tpapathe/stf007/petsc/src]$ 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@login1: /gpfs/alpine/scratch/tpapathe/stf007/petsc/src]$ mpicc >>>> -L$OLCF_CUDA_ROOT/lib64 -lcudart ex_simple_mpi.c -o ex_simple_mpi >>>> >>>> >>>> [tpapathe@batch1: /gpfs/alpine/scratch/tpapathe/stf007/petsc/src]$ 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. <[email protected]> wrote: >>>>> >>>>> >>>>> gprof or some similar tool? >>>>> >>>>> >>>>>> On Feb 10, 2020, at 11:18 AM, Zhang, Hong via petsc-dev >>>>>> <[email protected]> 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 <[email protected]> >>>>>>> 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 >>>>>>> <[email protected]> wrote: >>>>>>> >>>>>>> >>>>>>>> On Feb 8, 2020, at 5:03 PM, Matthew Knepley <[email protected]> wrote: >>>>>>>> >>>>>>>> On Sat, Feb 8, 2020 at 4:34 PM Zhang, Hong via petsc-dev >>>>>>>> <[email protected]> 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 <[email protected]> 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 >>>>>>>>>> <[email protected]> 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. <[email protected]> >>>>>>>>>>> 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 >>>>>>>>>>>> <[email protected]> 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/ >>> >> >
