I did have -DMPI_CXX_COMPILER set, so I added -DCMAKE_C_COMPILER and now get these errors:
[ 25%] Linking CXX shared library librichdem.so /lib/../lib64/crt1.o: In function `_start': (.text+0x24): undefined reference to `main' CMakeFiles/richdem.dir/src/random.cpp.o: In function `richdem::rand_engine()': random.cpp:(.text+0x45): undefined reference to `omp_get_thread_num' CMakeFiles/richdem.dir/src/random.cpp.o: In function `richdem::seed_rand(unsigned long)': random.cpp:(.text+0xb6): undefined reference to `GOMP_parallel' CMakeFiles/richdem.dir/src/random.cpp.o: In function `richdem::uniform_rand_int(int, int)': random.cpp:(.text+0x10c): undefined reference to `omp_get_thread_num' CMakeFiles/richdem.dir/src/random.cpp.o: In function `richdem::uniform_rand_real(double, double)': random.cpp:(.text+0x1cb): undefined reference to `omp_get_thread_num' CMakeFiles/richdem.dir/src/random.cpp.o: In function `richdem::normal_rand(double, double)': random.cpp:(.text+0x29e): undefined reference to `omp_get_thread_num' CMakeFiles/richdem.dir/src/random.cpp.o: In function `richdem::seed_rand(unsigned long) [clone ._omp_fn.0]': random.cpp:(.text+0x4a3): undefined reference to `GOMP_critical_start' random.cpp:(.text+0x4b1): undefined reference to `GOMP_critical_end' random.cpp:(.text+0x4c3): undefined reference to `omp_get_thread_num' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Comm_rank' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Get_address' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Comm_get_name' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Add_error_string' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Type_get_name' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Abort' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Alloc_mem' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Isend' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Barrier' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Allgather' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Reduce' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Send' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Init' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Type_size' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Accumulate' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Add_error_class' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Finalize' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Allgatherv' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Bcast' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Recv' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Request_free' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Allreduce' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `ompi_mpi_comm_world' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Sendrecv' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Add_error_code' /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0: undefined reference to `PMPI_Win_get_name' collect2: error: ld returned 1 exit status make[2]: *** [common/richdem/CMakeFiles/richdem.dir/build.make:163: common/richdem/librichdem.so] Error 1 make[1]: *** [CMakeFiles/Makefile2:306: common/richdem/CMakeFiles/richdem.dir/all] Error 2 make: *** [Makefile:136: all] Error 2 I took a guess at using -DOpenMP_libomp_LIBRARY="/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0" as as otherwise I'd get: CMake Error at /path/to/cmake/cmake-3.22.1-linux-x86_64/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:230 (message): Could NOT find OpenMP_CXX (missing: OpenMP_libomp_LIBRARY OpenMP_libomp_LIBRARY) (found version "4.5") So perhaps that's the real problem? On Sun, Oct 9, 2022 at 9:31 PM Junchao Zhang <junchao.zh...@gmail.com> wrote: > In the last link step to generate the executable > /cm/local/apps/gcc/10.2.0/bin/c++ -isystem -O3 -g -Wall -Wextra -pedantic > -Wshadow CMakeFiles/wtm.x.dir/src/WTM.cpp.o -o wtm.x > -Wl,-rpath,/path/to/WTM/build/common/richdem:/path/to/ > gdal-3.3.0/lib:/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_ > support/lib:/path/to/petsc/arch-linux-cxx-debug/lib libwtm.a > common/richdem/librichdem.so /path/to/gdal-3.3.0/lib/libgdal.so > /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0 > common/fmt/libfmt.a /path/to/petsc/arch-linux-cxx-debug/lib/libpetsc.so > > I did not find -lmpi to link in the mpi library. You can try to use cmake > -DCMAKE_C_COMPILER=/path/to/mpicc -DCMAKE_CXX_COMPILER=/path/to/mpicxx to > build your code > > On Sat, Oct 8, 2022 at 9:32 PM Rob Kudyba <rk3...@columbia.edu> wrote: > >> Perhaps we can back one step: >>> Use your mpicc to build a "hello world" mpi test, then run it on a >>> compute node (with GPU) to see if it works. >>> If no, then your MPI environment has problems; >>> If yes, then use it to build petsc (turn on petsc's gpu support, >>> --with-cuda --with-cudac=nvcc), and then your code. >>> --Junchao Zhang >> >> OK tried this just to eliminate that the CUDA-capable OpenMPI is a factor: >> ./configure --with-debugging=0 --with-cmake=true --with-mpi=true >> --with-mpi-dir=/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support --with-fc=0 >> --with-cuda=1 >> [..] >> cuda: >> Version: 11.7 >> Includes: -I/path/to/cuda11.7/toolkit/11.7.1/include >> Libraries: -Wl,-rpath,/path/to/cuda11.7/toolkit/11.7.1/lib64 >> -L/cm/shared/apps/cuda11.7/toolkit/11.7.1/lib64 >> -L/path/to/cuda11.7/toolkit/11.7.1/lib64/stubs -lcudart -lnvToolsExt >> -lcufft -lcublas -lcusparse -lcusolver -lcurand -lcuda >> CUDA SM 75 >> CUDA underlying compiler: >> CUDA_CXX="/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/bin"/mpicxx >> CUDA underlying compiler flags: CUDA_CXXFLAGS= >> CUDA underlying linker libraries: CUDA_CXXLIBS= >> [...] >> Configure stage complete. Now build PETSc libraries with: >> make PETSC_DIR=/path/to/petsc PETSC_ARCH=arch-linux-c-opt all >> >> C++ compiler version: g++ (GCC) 10.2.0 >> Using C++ compiler to compile PETSc >> ----------------------------------------- >> Using C/C++ linker: >> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/bin/mpicxx >> Using C/C++ flags: -Wall -Wwrite-strings -Wno-strict-aliasing >> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >> -fvisibility=hidden -g -O0 >> ----------------------------------------- >> Using system modules: >> shared:slurm/20.02.6:DefaultModules:openmpi/gcc/64/4.1.1_cuda_11.0.3_aware:gdal/3.3.0:cmake/3.22.1:cuda11.7/toolkit/11.7.1:openblas/dynamic/0.3.7:gcc/10.2.0 >> Using mpi.h: # 1 >> "/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/include/mpi.h" 1 >> ----------------------------------------- >> Using libraries: -Wl,-rpath,/path/to/petsc/arch-linux-cxx-debug/lib >> -L/path/to/petsc/arch-linux-cxx-debug/lib -lpetsc -lopenblas -lm -lX11 >> -lquadmath -lstdc++ -ldl >> ------------------------------------------ >> Using mpiexec: mpiexec -mca orte_base_help_aggregate 0 -mca pml ucx >> --mca btl '^openib' >> ------------------------------------------ >> Using MAKE: /path/to/petsc/arch-linux-cxx-debug/bin/make >> Using MAKEFLAGS: -j24 -l48.0 --no-print-directory -- MPIEXEC=mpiexec\ >> -mca\ orte_base_help_aggregate\ 0\ \ -mca\ pml\ ucx\ --mca\ btl\ '^openib' >> PETSC_ARCH=arch-linux-cxx-debug PETSC_DIR=/path/to/petsc >> ========================================== >> make[3]: Nothing to be done for 'libs'. >> ========================================= >> Now to check if the libraries are working do: >> make PETSC_DIR=/path/to/petsc PETSC_ARCH=arch-linux-cxx-debug check >> ========================================= >> [me@xxx petsc]$ make PETSC_DIR=/path/to/petsc >> PETSC_ARCH=arch-linux-cxx-debug MPIEXEC="mpiexec -mca >> orte_base_help_aggregate 0 -mca pml ucx --mca btl '^openib'" check >> Running check examples to verify correct installation >> Using PETSC_DIR=/path/to/petsc and PETSC_ARCH=arch-linux-cxx-debug >> C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process >> C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI >> processes >> >> ./bandwidthTest >> [CUDA Bandwidth Test] - Starting... >> Running on... >> >> Device 0: Quadro RTX 8000 >> Quick Mode >> >> Host to Device Bandwidth, 1 Device(s) >> PINNED Memory Transfers >> Transfer Size (Bytes) Bandwidth(GB/s) >> 32000000 12.3 >> >> Device to Host Bandwidth, 1 Device(s) >> PINNED Memory Transfers >> Transfer Size (Bytes) Bandwidth(GB/s) >> 32000000 13.2 >> >> Device to Device Bandwidth, 1 Device(s) >> PINNED Memory Transfers >> Transfer Size (Bytes) Bandwidth(GB/s) >> 32000000 466.2 >> >> Result = PASS >> >> On Sat, Oct 8, 2022 at 7:56 PM Barry Smith <bsm...@petsc.dev> wrote: >> >>> >>> True, but when users send reports back to us they will never have used >>> the VERBOSE=1 option, so it requires one more round trip of email to get >>> this additional information. >>> >>> > On Oct 8, 2022, at 6:48 PM, Jed Brown <j...@jedbrown.org> wrote: >>> > >>> > Barry Smith <bsm...@petsc.dev> writes: >>> > >>> >> I hate these kinds of make rules that hide what the compiler is >>> doing (in the name of having less output, I guess) it makes it difficult to >>> figure out what is going wrong. >>> > >>> > You can make VERBOSE=1 with CMake-generated makefiles. >>> >> >> >>> Anyways, either some of the MPI libraries are missing from the link line >>> or they are in the wrong order and thus it is not able to search them >>> properly. Here is a bunch of discussions on why that error message can >>> appear >>> https://stackoverflow.com/questions/19901934/libpthread-so-0-error-adding-symbols-dso-missing-from-command-line >>> >> >> >> Still same but more noise and I have been using the suggestion of >> LDFLAGS="-Wl,--copy-dt-needed-entries" along with make: >> make[2]: Entering directory '/path/to/WTM/build' >> cd /path/to/WTM/build && >> /path/to/cmake/cmake-3.22.1-linux-x86_64/bin/cmake -E cmake_depends "Unix >> Makefiles" /path/to/WTM /path/to/WTM /path/to/WTM/build /path/to/WTM/build >> /path/to/WTM/build/CMakeFiles/wtm.x.dir/DependInfo.cmake --color= >> make[2]: Leaving directory '/path/to/WTM/build' >> make -f CMakeFiles/wtm.x.dir/build.make CMakeFiles/wtm.x.dir/build >> make[2]: Entering directory '/path/to/WTM/build' >> [ 66%] Building CXX object CMakeFiles/wtm.x.dir/src/WTM.cpp.o >> /cm/local/apps/gcc/10.2.0/bin/c++ -I/path/to/WTM/common/richdem/include >> -I/path/to/gdal-3.3.0/include -I/path/to/WTM/common/fmt/include -isystem >> /path/to/petsc/arch-linux-cxx-debug/include -isystem /path/to/petsc/include >> -isystem -O3 -g -Wall -Wextra -pedantic -Wshadow -Wfloat-conversion -Wall >> -Wextra -pedantic -Wshadow -DRICHDEM_GIT_HASH=\"xxx\" >> -DRICHDEM_COMPILE_TIME=\"2022-10-09T02:21:11Z\" -DUSEGDAL -Xpreprocessor >> -fopenmp >> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40.30.1 >> -I/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/include -std=gnu++2a -MD >> -MT CMakeFiles/wtm.x.dir/src/WTM.cpp.o -MF >> CMakeFiles/wtm.x.dir/src/WTM.cpp.o.d -o CMakeFiles/wtm.x.dir/src/WTM.cpp.o >> -c /path/to/WTM/src/WTM.cpp >> c++: warning: >> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40.30.1: >> linker input file unused because linking not done >> [ 70%] Linking CXX executable wtm.x >> /path/to/cmake/cmake-3.22.1-linux-x86_64/bin/cmake -E cmake_link_script >> CMakeFiles/wtm.x.dir/link.txt --verbose=1 >> /cm/local/apps/gcc/10.2.0/bin/c++ -isystem -O3 -g -Wall -Wextra -pedantic >> -Wshadow CMakeFiles/wtm.x.dir/src/WTM.cpp.o -o wtm.x >> >> -Wl,-rpath,/path/to/WTM/build/common/richdem:/path/to/gdal-3.3.0/lib:/path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib:/path/to/petsc/arch-linux-cxx-debug/lib >> libwtm.a common/richdem/librichdem.so /path/to/gdal-3.3.0/lib/libgdal.so >> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libompitrace.so.40.30.0 >> common/fmt/libfmt.a /path/to/petsc/arch-linux-cxx-debug/lib/libpetsc.so >> /usr/bin/ld: CMakeFiles/wtm.x.dir/src/WTM.cpp.o: undefined reference to >> symbol 'ompi_mpi_comm_self' >> /path/to/openmpi-4.1.1_ucx_cuda_11.0.3_support/lib/libmpi.so.40: error >> adding symbols: DSO missing from command line >> collect2: error: ld returned 1 exit status >> make[2]: *** [CMakeFiles/wtm.x.dir/build.make:103: wtm.x] Error 1 >> make[2]: Leaving directory '/path/to/WTM/build' >> make[1]: *** [CMakeFiles/Makefile2:225: CMakeFiles/wtm.x.dir/all] Error 2 >> make[1]: Leaving directory '/path/to/WTM/build' >> make: *** [Makefile:136: all] Error 2 >> >> Anything stick out? >> >
