From 0858036401dc920b2ada54b91cb68091d3d0d395 Mon Sep 17 00:00:00 2001 From: Antonio De Lucreziis Date: Sat, 21 Dec 2024 20:14:12 +0100 Subject: [PATCH] minimal working spack+cmake+petsc+lapack+clangd setup --- .clang-format | 2 + .gitignore | 2 + .vscode/settings.json | 3 + CMakeLists.txt | 23 ++++ README.md | 14 +++ main.c | 273 ++++++++++++++++++++++++++++++++++++++++++ spack-env/loads | 64 ++++++++++ spack-env/spack.lock | 1 + spack-env/spack.yaml | 18 +++ 9 files changed, 400 insertions(+) create mode 100644 .clang-format create mode 100644 .gitignore create mode 100644 .vscode/settings.json create mode 100644 CMakeLists.txt create mode 100644 README.md create mode 100644 main.c create mode 100644 spack-env/loads create mode 100644 spack-env/spack.lock create mode 100644 spack-env/spack.yaml diff --git a/.clang-format b/.clang-format new file mode 100644 index 0000000..321c6de --- /dev/null +++ b/.clang-format @@ -0,0 +1,2 @@ +# .clang-format +IndentWidth: 4 diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..f81675c --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +build/ +.spack-env/ \ No newline at end of file diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..0e401cb --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,3 @@ +{ + "clangd.arguments": ["-background-index", "-compile-commands-dir=build/"] +} diff --git a/CMakeLists.txt b/CMakeLists.txt new file mode 100644 index 0000000..1d14f4c --- /dev/null +++ b/CMakeLists.txt @@ -0,0 +1,23 @@ +cmake_minimum_required(VERSION 3.31.1) + +# Enable compile_commands.json generation for IDE support +set(CMAKE_EXPORT_COMPILE_COMMANDS ON) + +set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) + +set(CMAKE_C_COMPILER gcc) +set(CMAKE_CXX_COMPILER g++) +set(CMAKE_Fortran_COMPILER gfortran) + +project(main) + +add_executable(main main.c) + +find_package(PkgConfig REQUIRED) + +pkg_search_module(OpenBLAS REQUIRED IMPORTED_TARGET openblas) +pkg_search_module(PETSc REQUIRED IMPORTED_TARGET petsc) +pkg_search_module(OpenMPI REQUIRED IMPORTED_TARGET ompi) + +target_include_directories(main PUBLIC ${PETSc_INCLUDE_DIRS} ${OpenBLAS_INCLUDE_DIRS} ${OpenMPI_INCLUDE_DIRS}) +target_link_libraries(main PUBLIC m PkgConfig::PETSc PkgConfig::OpenBLAS PkgConfig::OpenMPI) \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..497db0e --- /dev/null +++ b/README.md @@ -0,0 +1,14 @@ +# Arnoldi Iteration + +## Usage + +To build main from main.c + +```bash shell +$ rm -rf build +$ mkdir build +$ cd build +$ cmake .. +$ make +$ mpirun -n 2 ./main +``` diff --git a/main.c b/main.c new file mode 100644 index 0000000..2bdcc16 --- /dev/null +++ b/main.c @@ -0,0 +1,273 @@ +static char help[] = "Basic vector routines.\n\n"; + +/* + Include "petscvec.h" so that we can use vectors. Note that this file + automatically includes: + petscsys.h - base PETSc routines petscis.h - index sets + petscviewer.h - viewers +*/ + +#include +#include +#include + +#include + +int example_lapack() { + int n = 2; // Dimension of the matrix A + int nrhs = 1; // Number of right-hand sides + int lda = 2; // Leading dimension of A + int ldb = 2; // Leading dimension of B + int info; // Status output + int ipiv[2]; // Pivot indices for the LU decomposition + + // Define matrix A (row-major order) + double A[4] = {3, 1, 1, 2}; + + // Define right-hand side vector b + double b[2] = {9, 8}; + + // Call LAPACK dgesv to solve Ax = b + info = LAPACKE_dgesv(LAPACK_ROW_MAJOR, n, nrhs, A, lda, ipiv, b, ldb); + + // Check for success + if (info == 0) { + printf("Solution:\n"); + for (int i = 0; i < n; i++) { + printf("x[%d] = %f\n", i, b[i]); + } + } else if (info < 0) { + printf("Argument %d had an illegal value.\n", -info); + } else { + printf("Matrix is singular. Solution could not be computed.\n"); + } +} + +int main(int argc, char **argv) { + printf("LAPACKE Example:\n"); + example_lapack(); + + printf("PETSC Example:\n"); + Vec x, y, w; /* vectors */ + Vec *z; /* array of vectors */ + PetscReal norm, v, v1, v2, maxval; + PetscInt n = 20, maxind; + PetscScalar one = 1.0, two = 2.0, three = 3.0, dots[3], dot; + + PetscFunctionBeginUser; + PetscCall(PetscInitialize(&argc, &argv, NULL, help)); + PetscCall(PetscOptionsGetInt(NULL, NULL, "-n", &n, NULL)); + + /* + Create a vector, specifying only its global dimension. + When using VecCreate(), VecSetSizes() and VecSetFromOptions(), the vector + format (currently parallel, shared, or sequential) is determined at + runtime. Also, the parallel partitioning of the vector is determined by + PETSc at runtime. + */ + PetscCall(VecCreate(PETSC_COMM_WORLD, &x)); + PetscCall(VecSetSizes(x, PETSC_DECIDE, n)); + PetscCall(VecSetFromOptions(x)); + + /* + Duplicate some work vectors (of the same format and + partitioning as the initial vector). + */ + PetscCall(VecDuplicate(x, &y)); + PetscCall(VecDuplicate(x, &w)); + + /* + Duplicate more work vectors (of the same format and + partitioning as the initial vector). Here we duplicate + an array of vectors, which is often more convenient than + duplicating individual ones. + */ + PetscCall(VecDuplicateVecs(x, 3, &z)); + /* + Set the vectors to entries to a constant value. + */ + PetscCall(VecSet(x, one)); + PetscCall(VecSet(y, two)); + PetscCall(VecSet(z[0], one)); + PetscCall(VecSet(z[1], two)); + PetscCall(VecSet(z[2], three)); + /* + Demonstrate various basic vector routines. + */ + PetscCall(VecDot(x, y, &dot)); + PetscCall(VecMDot(x, 3, z, dots)); + + /* + Note: If using a complex numbers version of PETSc, then + PETSC_USE_COMPLEX is defined in the makefiles; otherwise, + (when using real numbers) it is undefined. + */ + + PetscCall( + PetscPrintf(PETSC_COMM_WORLD, "Vector length %" PetscInt_FMT "\n", n)); + PetscCall(VecMax(x, &maxind, &maxval)); + PetscCall(PetscPrintf(PETSC_COMM_WORLD, + "VecMax %g, VecInd %" PetscInt_FMT "\n", + (double)maxval, maxind)); + + PetscCall(VecMin(x, &maxind, &maxval)); + PetscCall(PetscPrintf(PETSC_COMM_WORLD, + "VecMin %g, VecInd %" PetscInt_FMT "\n", + (double)maxval, maxind)); + PetscCall(PetscPrintf(PETSC_COMM_WORLD, + "All other values should be near zero\n")); + + PetscCall(VecScale(x, two)); + PetscCall(VecNorm(x, NORM_2, &norm)); + v = norm - 2.0 * PetscSqrtReal((PetscReal)n); + if (v > -PETSC_SMALL && v < PETSC_SMALL) + v = 0.0; + PetscCall(PetscPrintf(PETSC_COMM_WORLD, "VecScale %g\n", (double)v)); + + PetscCall(VecCopy(x, w)); + PetscCall(VecNorm(w, NORM_2, &norm)); + v = norm - 2.0 * PetscSqrtReal((PetscReal)n); + if (v > -PETSC_SMALL && v < PETSC_SMALL) + v = 0.0; + PetscCall(PetscPrintf(PETSC_COMM_WORLD, "VecCopy %g\n", (double)v)); + + PetscCall(VecAXPY(y, three, x)); + PetscCall(VecNorm(y, NORM_2, &norm)); + v = norm - 8.0 * PetscSqrtReal((PetscReal)n); + if (v > -PETSC_SMALL && v < PETSC_SMALL) + v = 0.0; + PetscCall(PetscPrintf(PETSC_COMM_WORLD, "VecAXPY %g\n", (double)v)); + + PetscCall(VecAYPX(y, two, x)); + PetscCall(VecNorm(y, NORM_2, &norm)); + v = norm - 18.0 * PetscSqrtReal((PetscReal)n); + if (v > -PETSC_SMALL && v < PETSC_SMALL) + v = 0.0; + PetscCall(PetscPrintf(PETSC_COMM_WORLD, "VecAYPX %g\n", (double)v)); + + PetscCall(VecSwap(x, y)); + PetscCall(VecNorm(y, NORM_2, &norm)); + v = norm - 2.0 * PetscSqrtReal((PetscReal)n); + if (v > -PETSC_SMALL && v < PETSC_SMALL) + v = 0.0; + PetscCall(PetscPrintf(PETSC_COMM_WORLD, "VecSwap %g\n", (double)v)); + PetscCall(VecNorm(x, NORM_2, &norm)); + v = norm - 18.0 * PetscSqrtReal((PetscReal)n); + if (v > -PETSC_SMALL && v < PETSC_SMALL) + v = 0.0; + PetscCall(PetscPrintf(PETSC_COMM_WORLD, "VecSwap %g\n", (double)v)); + + PetscCall(VecWAXPY(w, two, x, y)); + PetscCall(VecNorm(w, NORM_2, &norm)); + v = norm - 38.0 * PetscSqrtReal((PetscReal)n); + if (v > -PETSC_SMALL && v < PETSC_SMALL) + v = 0.0; + PetscCall(PetscPrintf(PETSC_COMM_WORLD, "VecWAXPY %g\n", (double)v)); + + PetscCall(VecPointwiseMult(w, y, x)); + PetscCall(VecNorm(w, NORM_2, &norm)); + v = norm - 36.0 * PetscSqrtReal((PetscReal)n); + if (v > -PETSC_SMALL && v < PETSC_SMALL) + v = 0.0; + PetscCall( + PetscPrintf(PETSC_COMM_WORLD, "VecPointwiseMult %g\n", (double)v)); + + PetscCall(VecPointwiseDivide(w, x, y)); + PetscCall(VecNorm(w, NORM_2, &norm)); + v = norm - 9.0 * PetscSqrtReal((PetscReal)n); + if (v > -PETSC_SMALL && v < PETSC_SMALL) + v = 0.0; + PetscCall( + PetscPrintf(PETSC_COMM_WORLD, "VecPointwiseDivide %g\n", (double)v)); + + PetscCall(VecSetValue(y, 0, 0.0, INSERT_VALUES)); + PetscCall(VecAssemblyBegin(y)); + PetscCall(VecAssemblyEnd(y)); + PetscCall(VecPointwiseDivide(w, x, y)); + PetscCall(VecNorm(w, NORM_2, &norm)); + v = norm - 9.0 * PetscSqrtReal((PetscReal)n); + if (v > -PETSC_SMALL && v < PETSC_SMALL) + v = 0.0; + PetscCall( + PetscPrintf(PETSC_COMM_WORLD, "VecPointwiseDivide %g\n", (double)v)); + + dots[0] = one; + dots[1] = three; + dots[2] = two; + + PetscCall(VecSet(x, one)); + PetscCall(VecMAXPY(x, 3, dots, z)); + PetscCall(VecNorm(z[0], NORM_2, &norm)); + v = norm - PetscSqrtReal((PetscReal)n); + if (v > -PETSC_SMALL && v < PETSC_SMALL) + v = 0.0; + PetscCall(VecNorm(z[1], NORM_2, &norm)); + v1 = norm - 2.0 * PetscSqrtReal((PetscReal)n); + if (v1 > -PETSC_SMALL && v1 < PETSC_SMALL) + v1 = 0.0; + PetscCall(VecNorm(z[2], NORM_2, &norm)); + v2 = norm - 3.0 * PetscSqrtReal((PetscReal)n); + if (v2 > -PETSC_SMALL && v2 < PETSC_SMALL) + v2 = 0.0; + PetscCall(PetscPrintf(PETSC_COMM_WORLD, "VecMAXPY %g %g %g \n", (double)v, + (double)v1, (double)v2)); + + /* + Free work space. All PETSc objects should be destroyed when they + are no longer needed. + */ + PetscCall(VecDestroy(&x)); + PetscCall(VecDestroy(&y)); + PetscCall(VecDestroy(&w)); + PetscCall(VecDestroyVecs(3, &z)); + PetscCall(PetscFinalize()); + return 0; +} + +/*TEST + + testset: + output_file: output/ex1_1.out + # This is a test where the exact numbers are critical + diff_args: -j + + test: + + test: + suffix: cuda + args: -vec_type cuda + requires: cuda + + test: + suffix: kokkos + args: -vec_type kokkos + requires: kokkos_kernels + + test: + suffix: hip + args: -vec_type hip + requires: hip + + test: + suffix: 2 + nsize: 2 + + test: + suffix: 2_cuda + nsize: 2 + args: -vec_type cuda + requires: cuda + + test: + suffix: 2_kokkos + nsize: 2 + args: -vec_type kokkos + requires: kokkos_kernels + + test: + suffix: 2_hip + nsize: 2 + args: -vec_type hip + requires: hip + +TEST*/ diff --git a/spack-env/loads b/spack-env/loads new file mode 100644 index 0000000..79fe079 --- /dev/null +++ b/spack-env/loads @@ -0,0 +1,64 @@ +# petsc@=3.22.2%gcc@=14.2.1~X~batch~cgns~complex~cuda~debug+double~exodusii~fftw+fortran~giflib+hdf5~hpddm~hwloc+hypre~int64~jpeg~knl~kokkos~libpng~libyaml~memkind+metis~mkl-pardiso~mmg~moab~mpfr+mpi~mumps~openmp~p4est~parmmg~ptscotch~random123~rocm~saws~scalapack+shared~strumpack~suite-sparse+superlu-dist~sycl~tetgen~trilinos~valgrind~zoltan build_system=generic clanguage=C memalign=none arch=linux-arch-skylake +module load petsc/3.22.2-gcc-14.2.1-gihwmbe +# openblas@=0.3.28%gcc@=14.2.1~bignuma~consistent_fpcsr+dynamic_dispatch+fortran~ilp64+locking+pic+shared build_system=makefile patches=d0b9276 symbol_suffix=none threads=none arch=linux-arch-skylake +module load openblas/0.3.28-gcc-14.2.1-qkz6rin +# gcc-runtime@=14.2.1%gcc@=14.2.1 build_system=generic arch=linux-arch-skylake +module load gcc-runtime/14.2.1-gcc-14.2.1-iznjxul +# glibc@=2.40%gcc@=14.2.1 build_system=autotools arch=linux-arch-skylake +module load glibc/2.40-gcc-14.2.1-hr3l3g3 +# gmake@=4.4.1%gcc@=14.2.1~guile build_system=generic arch=linux-arch-skylake +module load gmake/4.4.1-gcc-14.2.1-hkretjr +# hdf5@=1.14.5%gcc@=14.2.1~cxx~fortran~hl~ipo~java~map+mpi+shared~subfiling~szip~threadsafe+tools api=default build_system=cmake build_type=Release generator=make arch=linux-arch-skylake +module load hdf5/1.14.5-gcc-14.2.1-6ll3mut +# openmpi@=5.0.5%gcc@=14.2.1+atomics~cuda~debug~gpfs~internal-hwloc~internal-libevent~internal-pmix~java~lustre~memchecker~openshmem~romio+rsh~static~two_level_namespace+vt+wrapper-rpath build_system=autotools fabrics=none romio-filesystem=none schedulers=none arch=linux-arch-skylake +module load openmpi/5.0.5-gcc-14.2.1-6xhzsjq +# hwloc@=2.11.1%gcc@=14.2.1~cairo~cuda~gl~level_zero~libudev+libxml2~nvml~opencl+pci~rocm build_system=autotools libs=shared,static arch=linux-arch-skylake +module load hwloc/2.11.1-gcc-14.2.1-2lq5p2l +# libpciaccess@=0.17%gcc@=14.2.1 build_system=autotools arch=linux-arch-skylake +module load libpciaccess/0.17-gcc-14.2.1-yy6pv2y +# libxml2@=2.13.4%gcc@=14.2.1+pic~python+shared build_system=autotools arch=linux-arch-skylake +module load libxml2/2.13.4-gcc-14.2.1-dcszipz +# xz@=5.4.6%gcc@=14.2.1~pic build_system=autotools libs=shared,static arch=linux-arch-skylake +module load xz/5.4.6-gcc-14.2.1-5zfe3p6 +# zlib-ng@=2.2.1%gcc@=14.2.1+compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-arch-skylake +module load zlib-ng/2.2.1-gcc-14.2.1-i6qthch +# ncurses@=6.5%gcc@=14.2.1~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=linux-arch-skylake +module load ncurses/6.5-gcc-14.2.1-z7vtx7m +# libevent@=2.1.12%gcc@=14.2.1+openssl build_system=autotools arch=linux-arch-skylake +module load libevent/2.1.12-gcc-14.2.1-yovxoxy +# openssl@=3.4.0%gcc@=14.2.1~docs+shared build_system=generic certs=mozilla arch=linux-arch-skylake +module load openssl/3.4.0-gcc-14.2.1-zrlz2dj +# numactl@=2.0.18%gcc@=14.2.1 build_system=autotools arch=linux-arch-skylake +module load numactl/2.0.18-gcc-14.2.1-jb2iuoi +# openssh@=9.9p1%gcc@=14.2.1+gssapi build_system=autotools arch=linux-arch-skylake +module load openssh/9.9p1-gcc-14.2.1-5gqzmmn +# krb5@=1.21.3%gcc@=14.2.1+shared build_system=autotools arch=linux-arch-skylake +module load krb5/1.21.3-gcc-14.2.1-jq6txro +# gettext@=0.22.5%gcc@=14.2.1+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-arch-skylake +module load gettext/0.22.5-gcc-14.2.1-n2v3h2a +# bzip2@=1.0.8%gcc@=14.2.1~debug~pic+shared build_system=generic arch=linux-arch-skylake +module load bzip2/1.0.8-gcc-14.2.1-6n7jklp +# tar@=1.35%gcc@=14.2.1 build_system=autotools zip=pigz arch=linux-arch-skylake +module load tar/1.35-gcc-14.2.1-r7qqd7q +# pigz@=2.8%gcc@=14.2.1 build_system=makefile arch=linux-arch-skylake +module load pigz/2.8-gcc-14.2.1-xlmu6ri +# zstd@=1.5.6%gcc@=14.2.1+programs build_system=makefile compression=none libs=shared,static arch=linux-arch-skylake +module load zstd/1.5.6-gcc-14.2.1-mtfh4kv +# libedit@=3.1-20240808%gcc@=14.2.1 build_system=autotools arch=linux-arch-skylake +module load libedit/3.1-20240808-gcc-14.2.1-mopvlvk +# libxcrypt@=4.4.35%gcc@=14.2.1~obsolete_api build_system=autotools patches=4885da3 arch=linux-arch-skylake +module load libxcrypt/4.4.35-gcc-14.2.1-jgg5ryn +# pmix@=5.0.3%gcc@=14.2.1~munge~python~restful build_system=autotools arch=linux-arch-skylake +module load pmix/5.0.3-gcc-14.2.1-5oppajs +# pkgconf@=2.2.0%gcc@=14.2.1 build_system=autotools arch=linux-arch-skylake +module load pkgconf/2.2.0-gcc-14.2.1-odevpf2 +# hypre@=2.32.0%gcc@=14.2.1~caliper~complex~cublas~cuda~debug+fortran~gptune~gpu-aware-mpi~int64~internal-superlu+lapack~magma~mixedint+mpi~openmp~rocblas~rocm+shared~superlu-dist~sycl~umpire~unified-memory build_system=autotools precision=double arch=linux-arch-skylake +module load hypre/2.32.0-gcc-14.2.1-otntewq +# openblas@=0.3.28%gcc@=14.2.1~bignuma~consistent_fpcsr+dynamic_dispatch+fortran~ilp64+locking+pic+shared build_system=makefile patches=d0b9276 symbol_suffix=none threads=none arch=linux-arch-skylake +module load openblas/0.3.28-gcc-14.2.1-qkz6rin +# metis@=5.1.0%gcc@=14.2.1~gdb~int64~ipo~no_warning~real64+shared build_system=cmake build_type=Release generator=make patches=4991da9,93a7903,b1225da arch=linux-arch-skylake +module load metis/5.1.0-gcc-14.2.1-qug2wej +# parmetis@=4.0.3%gcc@=14.2.1~gdb~int64~ipo+shared build_system=cmake build_type=Release generator=make patches=4f89253,50ed208,704b84f arch=linux-arch-skylake +module load parmetis/4.0.3-gcc-14.2.1-nuynu5c +# superlu-dist@=9.1.0%gcc@=14.2.1~cuda~int64~ipo~openmp+parmetis~rocm+shared build_system=cmake build_type=Release generator=make arch=linux-arch-skylake +module load superlu-dist/9.1.0-gcc-14.2.1-a2ygwev diff --git a/spack-env/spack.lock b/spack-env/spack.lock new file mode 100644 index 0000000..0f1bbf4 --- /dev/null +++ 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