From 83f97e8ebab21b3c383572874b1135384c185227 Mon Sep 17 00:00:00 2001 From: liuyangzhuan Date: Wed, 24 Nov 2021 14:06:43 -0800 Subject: Adding packages for gptune and its dependencies (#26936) * added package gptune with all its dependencies: adding py-autotune, pygmo, py-pyaml, py-autotune, py-gpy, py-lhsmdu, py-hpbandster, pagmo2, py-opentuner; modifying superlu-dist, py-scikit-optimize * adding gptune package * minor fix for macos spack test * update patch for py-scikit-optimize; update test files for gptune * fixing gptune package style error * fixing unit tests * a few changes reviewed in the PR * improved gptune package.py with a few newly added/improved dependencies * fixed a few style errors * minor fix on package name py-pyro4 * fixing more style errors * Update var/spack/repos/builtin/packages/py-scikit-optimize/package.py Co-authored-by: Adam J. Stewart * resolved a few issues in the PR * fixing file permissions * a few minor changes * style correction * minor correction to jq package file * Update var/spack/repos/builtin/packages/py-pyro4/package.py Co-authored-by: Adam J. Stewart * fixing a few issues in the PR * adding py-selectors34 required by py-pyro4 * improved the superlu-dist package * improved the superlu-dist package * moree changes to gptune and py-selectors34 based on the PR * Update var/spack/repos/builtin/packages/py-selectors34/package.py Co-authored-by: Adam J. Stewart Co-authored-by: Adam J. 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--git a/var/spack/repos/builtin/packages/exaworks/package.py b/var/spack/repos/builtin/packages/exaworks/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/ffr/gfortran_format_30.patch b/var/spack/repos/builtin/packages/ffr/gfortran_format_30.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/ffr/gfortran_format_31.patch b/var/spack/repos/builtin/packages/ffr/gfortran_format_31.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/gptune/package.py b/var/spack/repos/builtin/packages/gptune/package.py new file mode 100644 index 0000000000..e7d952efad --- /dev/null +++ b/var/spack/repos/builtin/packages/gptune/package.py @@ -0,0 +1,173 @@ +# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class Gptune(CMakePackage): + """GPTune is an autotuning framework that relies on multitask and transfer + learnings to help solve the underlying black-box optimization problem using + Bayesian optimization methodologies.""" + + homepage = "https://gptune.lbl.gov/" + git = "https://github.com/gptune/GPTune.git" + maintainers = ['liuyangzhuan'] + + version('master', branch='master') + + variant('app', default=False, description='Build all HPC application examples') + + depends_on('mpi', type=('build', 'link', 'run')) + depends_on('cmake@3.3:', type='build') + depends_on('jq', type='run') + depends_on('blas', type='link') + depends_on('lapack', type='link') + depends_on('scalapack', type='link') + depends_on('py-setuptools', type='build') + depends_on('py-ipyparallel', type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-pandas', type=('build', 'run')) + depends_on('py-joblib', type=('build', 'run')) + depends_on('py-scikit-learn', type=('build', 'run')) + depends_on('py-matplotlib', type=('build', 'run')) + depends_on('py-pyyaml', type=('build', 'run')) + depends_on('py-scikit-optimize@master+gptune', type=('build', 'run')) + depends_on('py-gpy', type=('build', 'run')) + depends_on('py-lhsmdu', type=('build', 'run')) + depends_on('py-hpbandster', type=('build', 'run')) + depends_on('py-opentuner', type=('build', 'run')) + depends_on('py-ytopt-autotune@1.1.0', type=('build', 'run')) + depends_on('py-filelock', type=('build', 'run')) + depends_on('py-requests', type=('build', 'run')) + depends_on('py-cython', type=('build', 'run')) + depends_on('py-pyaml', type=('build', 'run')) + depends_on('py-mpi4py@3.0.3:', type=('build', 'run')) + depends_on('pygmo', type=('build', 'run')) + depends_on('openturns', type=('build', 'run')) + + depends_on('superlu-dist@develop', when='+app', type=('build', 'run')) + + conflicts('openmpi@:3') + + def cmake_args(self): + spec = self.spec + fc_flags = [] + if '%gcc@10:' in spec or self.spec.satisfies('%apple-clang@11:'): + fc_flags.append('-fallow-argument-mismatch') + + args = [ + '-DTPL_BLAS_LIBRARIES=%s' % spec['blas'].libs.joined(";"), + '-DTPL_LAPACK_LIBRARIES=%s' % spec['lapack'].libs.joined(";"), + '-DTPL_SCALAPACK_LIBRARIES=%s' % spec['scalapack']. + libs.joined(";"), + '-DCMAKE_Fortran_FLAGS=' + ''.join(fc_flags), + '-DBUILD_SHARED_LIBS=ON', + ] + + return args + + examples_src_dir = 'examples' + src_dir = 'GPTune' + nodes = 1 + cores = 4 + + @run_after('install') + def cache_test_sources(self): + """Copy the example source files after the package is installed to an + install test subdirectory for use during `spack test run`.""" + self.cache_extra_test_sources([self.examples_src_dir, self.src_dir]) + + def test(self): + spec = self.spec + comp_name = self.compiler.name + comp_version = str(self.compiler.version).replace('.', ',') + test_dir = join_path(self.install_test_root, self.examples_src_dir) + + if '+app' in spec: + superludriver = join_path(spec['superlu-dist'].prefix.bin, 'pddrive_spawn') + op = ['-r', superludriver, '.'] + # copy superlu-dist executables to the correct place + with working_dir(join_path(test_dir, 'SuperLU_DIST'), create=False): + self.run_test('rm', options=['-rf', 'superlu_dist'], work_dir='.') + self.run_test('git', options=['clone', 'https://github.com/xiaoyeli/superlu_dist.git'], work_dir='.') + self.run_test('mkdir', options=['-p', + 'build'], work_dir='./superlu_dist') + self.run_test('mkdir', options=['-p', 'EXAMPLE'], + work_dir='./superlu_dist/build') + self.run_test('cp', options=op, work_dir='./superlu_dist/build/EXAMPLE') + + with working_dir(self.install_test_root, create=False): + cdir = join_path(self.prefix, 'gptuneclcm') + self.run_test('cp', options=['-r', cdir, '.'], work_dir='.') + self.run_test('rm', options=['-rf', 'build'], work_dir='.') + self.run_test('mv', options=['gptuneclcm', 'build'], work_dir='.') + + with open('{0}/run_env.sh'.format(self.install_test_root), 'w') as envfile: + envfile.write('if [[ $NERSC_HOST = "cori" ]]; then\n') + envfile.write(' export machine=cori\n') + envfile.write('elif [[ $(uname -s) = "Darwin" ]]; then\n') + envfile.write(' export machine=mac\n') + envfile.write('elif [[ $(dnsdomainname) = ' + + '"summit.olcf.ornl.gov" ]]; then\n') + envfile.write(' export machine=summit\n') + envfile.write('elif [[ $(cat /etc/os-release | grep "PRETTY_NAME") ==' + + ' *"Ubuntu"* || $(cat /etc/os-release | grep' + + ' "PRETTY_NAME") == *"Debian"* ]]; then\n') + envfile.write(' export machine=unknownlinux\n') + envfile.write('fi\n') + envfile.write('export GPTUNEROOT=$PWD\n') + envfile.write('export MPIRUN={0}\n'.format + (which(spec['mpi'].prefix.bin + '/mpirun'))) + envfile.write('export proc=$(spack arch)\n') + envfile.write('export mpi={0}\n'.format(spec['mpi'].name)) + envfile.write('export compiler={0}\n'.format(comp_name)) + envfile.write('export nodes={0} \n'.format(self.nodes)) + envfile.write('export cores={0} \n'.format(self.cores)) + envfile.write('export ModuleEnv=$machine-$proc-$mpi-$compiler \n') + envfile.write('software_json=$(echo ",\\\"software_configuration\\\":' + + '{\\\"' + spec['blas'].name + + '\\\":{\\\"version_split\\\":' + + ' [' + str(spec['blas'].versions).replace('.', ',') + + ']},\\\"' + spec['mpi'].name + + '\\\":{\\\"version_split\\\": [' + + str(spec['mpi'].versions).replace('.', ',') + ']},\\\"' + + spec['scalapack'].name + + '\\\":{\\\"version_split\\\": [' + + str(spec['scalapack'].versions).replace('.', ',') + + ']},\\\"' + + str(comp_name) + '\\\":{\\\"version_split\\\": [' + + str(comp_version) + ']}}") \n') + envfile.write('loadable_software_json=$(echo ",\\\"loadable_software_' + + 'configurations\\\":{\\\"' + spec['blas'].name + + '\\\":{\\\"version_split\\\": [' + + str(spec['blas'].versions).replace('.', ',') + + ']},\\\"' + spec['mpi'].name + + '\\\":{\\\"version_split\\\": [' + + str(spec['mpi'].versions).replace('.', ',') + ']},\\\"' + + spec['scalapack'].name + + '\\\":{\\\"version_split\\\": [' + + str(spec['scalapack'].versions).replace('.', ',') + + ']},\\\"' + str(comp_name) + + '\\\":{\\\"version_split\\\": [' + + str(comp_version) + ']}}") \n') + envfile.write('machine_json=$(echo ",\\\"machine_configuration\\\":' + + '{\\\"machine_name\\\":\\\"$machine\\\",\\\"$proc\\\":' + + '{\\\"nodes\\\":$nodes,\\\"cores\\\":$cores}}") \n') + envfile.write('loadable_machine_json=$(echo ",\\\"loadable_machine_' + + 'configurations\\\":{\\\"$machine\\\":{\\\"$proc\\\":' + + '{\\\"nodes\\\":$nodes,\\\"cores\\\":$cores}}}") \n') + + if '+app' in spec: + apps = ['GPTune-Demo', 'SuperLU_DIST', 'SuperLU_DIST_RCI', + 'Scalapack-PDGEQRF', 'Scalapack-PDGEQRF_RCI'] + else: + apps = ['GPTune-Demo', 'Scalapack-PDGEQRF', 'Scalapack-PDGEQRF_RCI'] + + for app in apps: + with working_dir(join_path(test_dir, app), create=False): + # PDGEQRF with GPTune + self.run_test('bash', options=['run_examples.sh'], work_dir='.', + purpose='gptune smoke test for {0}'.format(app)) diff --git a/var/spack/repos/builtin/packages/isaac-server/arm.patch b/var/spack/repos/builtin/packages/isaac-server/arm.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/jq/builtinc.patch b/var/spack/repos/builtin/packages/jq/builtinc.patch new file mode 100644 index 0000000000..943edbc9d2 --- /dev/null +++ b/var/spack/repos/builtin/packages/jq/builtinc.patch @@ -0,0 +1,48 @@ +diff --git a/src/builtin.c b/src/builtin.c +old mode 100644 +new mode 100755 +index c6c8c2e..e336472 +--- a/src/builtin.c ++++ b/src/builtin.c +@@ -185,7 +185,7 @@ static jv f_modf(jq_state *jq, jv input) { + return jv_array_append(ret, jv_number(i)); + } + #endif +-#ifdef HAVE_LGAMMA_R ++#if defined(HAVE_LGAMMA_R) && !(defined(__APPLE__) && defined(__GNUC__) && !defined(_REENTRANT)) + static jv f_lgamma_r(jq_state *jq, jv input) { + if (jv_get_kind(input) != JV_KIND_NUMBER) { + return type_error(input, "number required"); +@@ -1581,7 +1581,7 @@ static const struct cfunction function_list[] = { + #ifdef HAVE_MODF + {(cfunction_ptr)f_modf,"modf", 1}, + #endif +-#ifdef HAVE_LGAMMA_R ++#if defined(HAVE_LGAMMA_R) && !(defined(__APPLE__) && defined(__GNUC__) && !defined(_REENTRANT)) + {(cfunction_ptr)f_lgamma_r,"lgamma_r", 1}, + #endif + {(cfunction_ptr)f_plus, "_plus", 3}, +diff --git a/src/builtin.c b/src/builtin.c +old mode 100644 +new mode 100755 +index c6c8c2e..e336472 +--- a/src/builtin.c ++++ b/src/builtin.c +@@ -185,7 +185,7 @@ static jv f_modf(jq_state *jq, jv input) { + return jv_array_append(ret, jv_number(i)); + } + #endif +-#ifdef HAVE_LGAMMA_R ++#if defined(HAVE_LGAMMA_R) && !(defined(__APPLE__) && defined(__GNUC__) && !defined(_REENTRANT)) + static jv f_lgamma_r(jq_state *jq, jv input) { + if (jv_get_kind(input) != JV_KIND_NUMBER) { + return type_error(input, "number required"); +@@ -1581,7 +1581,7 @@ static const struct cfunction function_list[] = { + #ifdef HAVE_MODF + {(cfunction_ptr)f_modf,"modf", 1}, + #endif +-#ifdef HAVE_LGAMMA_R ++#if defined(HAVE_LGAMMA_R) && !(defined(__APPLE__) && defined(__GNUC__) && !defined(_REENTRANT)) + {(cfunction_ptr)f_lgamma_r,"lgamma_r", 1}, + #endif + {(cfunction_ptr)f_plus, "_plus", 3}, diff --git a/var/spack/repos/builtin/packages/jq/package.py b/var/spack/repos/builtin/packages/jq/package.py index 613ed97c20..88061fe266 100644 --- a/var/spack/repos/builtin/packages/jq/package.py +++ b/var/spack/repos/builtin/packages/jq/package.py @@ -4,8 +4,10 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) import os.path +import sys from spack import * +from spack.operating_systems.mac_os import macos_version class Jq(AutotoolsPackage): @@ -20,6 +22,9 @@ class Jq(AutotoolsPackage): depends_on('oniguruma') depends_on('bison@3.0:', type='build') + if sys.platform == 'darwin' and macos_version() >= Version('10.15'): + patch('builtinc.patch', when='@1.5:') + @run_after('install') @on_package_attributes(run_tests=True) def install_test(self): diff --git a/var/spack/repos/builtin/packages/julia/armgcc.patch b/var/spack/repos/builtin/packages/julia/armgcc.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/kokkos-nvcc-wrapper/package.py b/var/spack/repos/builtin/packages/kokkos-nvcc-wrapper/package.py index bdba998849..c26522bea7 100644 --- a/var/spack/repos/builtin/packages/kokkos-nvcc-wrapper/package.py +++ b/var/spack/repos/builtin/packages/kokkos-nvcc-wrapper/package.py @@ -42,7 +42,7 @@ class KokkosNvccWrapper(Package): env.set('KOKKOS_CXX', self.compiler.cxx) env.set('MPICH_CXX', wrapper) env.set('OMPI_CXX', wrapper) - env.set('MPICXX_CXX', wrapper) # HPE MPT + env.set('MPICXX_CXX', wrapper) # HPE MPT def setup_dependent_package(self, module, dependent_spec): wrapper = join_path(self.prefix.bin, "nvcc_wrapper") diff --git a/var/spack/repos/builtin/packages/libsharp/1.0.0-arm.patch b/var/spack/repos/builtin/packages/libsharp/1.0.0-arm.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/libsharp/arm.patch b/var/spack/repos/builtin/packages/libsharp/arm.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/llvm-openmp/package.py b/var/spack/repos/builtin/packages/llvm-openmp/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/megahit/amd.patch b/var/spack/repos/builtin/packages/megahit/amd.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/modylas/gcc_format.patch b/var/spack/repos/builtin/packages/modylas/gcc_format.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/modylas/makefile.patch b/var/spack/repos/builtin/packages/modylas/makefile.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/mt-metis/non_x8664.patch b/var/spack/repos/builtin/packages/mt-metis/non_x8664.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/mvapich2-gdr/package.py b/var/spack/repos/builtin/packages/mvapich2-gdr/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/mvapich2x/package.py b/var/spack/repos/builtin/packages/mvapich2x/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/nnvm/cmake2.patch b/var/spack/repos/builtin/packages/nnvm/cmake2.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/ocaml/fix-duplicate-defs.patch b/var/spack/repos/builtin/packages/ocaml/fix-duplicate-defs.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/opencv/opencv3.2_cmake.patch b/var/spack/repos/builtin/packages/opencv/opencv3.2_cmake.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/opencv/opencv3.2_ffmpeg.patch b/var/spack/repos/builtin/packages/opencv/opencv3.2_ffmpeg.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/opencv/opencv3.2_python3.7.patch b/var/spack/repos/builtin/packages/opencv/opencv3.2_python3.7.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/opencv/opencv3.2_regacyvtk.patch b/var/spack/repos/builtin/packages/opencv/opencv3.2_regacyvtk.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/opencv/opencv3.2_vtk.patch b/var/spack/repos/builtin/packages/opencv/opencv3.2_vtk.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/openturns/package.py b/var/spack/repos/builtin/packages/openturns/package.py new file mode 100644 index 0000000000..7ab5405052 --- /dev/null +++ b/var/spack/repos/builtin/packages/openturns/package.py @@ -0,0 +1,59 @@ +# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Openturns(CMakePackage): + """OpenTURNS is a scientific C++ and Python library featuring an + internal data model and algorithms dedicated to the treatment of + uncertainties. The main goal of this library is to provide all + functionalities needed to treat uncertainties in studies with + industrial applications. Targeted users are all engineers who want + to introduce the probabilistic dimension in their so far + deterministic studies.""" + + homepage = "https://openturns.github.io/www/" + git = "https://github.com/openturns/openturns.git" + maintainers = ['liuyangzhuan'] + + version('master', branch='master') + + variant('python', default=True, description='Build Python bindings') + + extends('python', when='+python') + + depends_on('mpi', type=('build', 'run')) + depends_on('lapack', type=('build', 'run')) + depends_on('cmake@2.8:', type='build') + depends_on('swig', type=('build', 'run')) + depends_on('py-numpy@1.7:', type=('build', 'run')) + depends_on('py-pandas', type=('build', 'run')) + depends_on('py-matplotlib', type=('build', 'run')) + depends_on('boost+system+serialization+thread', type=('build', 'run')) + depends_on('intel-tbb', type=('build', 'run')) + depends_on('py-cloudpickle', type=('build', 'run')) + depends_on('py-urllib3', type=('build', 'run')) + + def cmake_args(self): + spec = self.spec + + args = [ + '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc, + '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx, + '-DCMAKE_INSTALL_LIBDIR:STRING=%s' % self.prefix.lib, + '-DCMAKE_INSTALL_BINDIR:STRING=%s' % self.prefix.bin, + '-DLAPACK_LIBRARIES=%s' % spec['lapack'].libs.joined(";"), + ] + + if '+python' in spec: + args.extend([ + # By default picks up the system python not the Spack build + '-DPYTHON_EXECUTABLE={0}'.format(spec['python'].command.path), + # By default installs to the python prefix + '-DPYTHON_SITE_PACKAGES={0}'.format(site_packages_dir), + ]) + + return args diff --git a/var/spack/repos/builtin/packages/pagmo2/package.py b/var/spack/repos/builtin/packages/pagmo2/package.py new file mode 100644 index 0000000000..29f71963da --- /dev/null +++ b/var/spack/repos/builtin/packages/pagmo2/package.py @@ -0,0 +1,39 @@ +# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Pagmo2(CMakePackage): + """Parallel Global Multiobjective Optimizer (and its Python alter ego + PyGMO) is a C++ / Python platform to perform parallel computations of + optimisation tasks (global and local) via the asynchronous generalized + island model.""" + + homepage = "https://esa.github.io/pagmo2/" + url = "https://github.com/esa/pagmo2/archive/v2.18.0.tar.gz" + git = "https://github.com/esa/pagmo2.git" + maintainers = ['liuyangzhuan'] + + version('master', branch='master') + version('2.18.0', sha256='5ad40bf3aa91857a808d6b632d9e1020341a33f1a4115d7a2b78b78fd063ae31') + + depends_on('boost+system+serialization+thread') + depends_on('intel-tbb') + depends_on('mpi') + depends_on('cmake@3.1:', type='build') + + variant('shared', default=True, description='Build shared libraries') + + def cmake_args(self): + spec = self.spec + + args = [ + '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc, + '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx, + self.define_from_variant('BUILD_SHARED_LIBS', 'shared'), + ] + + return args diff --git a/var/spack/repos/builtin/packages/parsimonator/nox86.patch b/var/spack/repos/builtin/packages/parsimonator/nox86.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/php/sbang.patch b/var/spack/repos/builtin/packages/php/sbang.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/poppler/poppler_page_splash.0.90.1.patch b/var/spack/repos/builtin/packages/poppler/poppler_page_splash.0.90.1.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/poppler/poppler_page_splash.patch b/var/spack/repos/builtin/packages/poppler/poppler_page_splash.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/ppopen-appl-amr-fdm/package.py b/var/spack/repos/builtin/packages/ppopen-appl-amr-fdm/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/ppopen-appl-bem-at/duplicate_defs.patch b/var/spack/repos/builtin/packages/ppopen-appl-bem-at/duplicate_defs.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/ppopen-appl-dem-util/package.py b/var/spack/repos/builtin/packages/ppopen-appl-dem-util/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/ppopen-appl-fdm-at/package.py b/var/spack/repos/builtin/packages/ppopen-appl-fdm-at/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/ppopen-appl-fdm/gfortran_iargc.patch b/var/spack/repos/builtin/packages/ppopen-appl-fdm/gfortran_iargc.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/ppopen-appl-fdm/package.py b/var/spack/repos/builtin/packages/ppopen-appl-fdm/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/ppopen-appl-fdm/unused.patch b/var/spack/repos/builtin/packages/ppopen-appl-fdm/unused.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/ppopen-appl-fem/gcc_struct_atomic.patch b/var/spack/repos/builtin/packages/ppopen-appl-fem/gcc_struct_atomic.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/py-gpy/package.py b/var/spack/repos/builtin/packages/py-gpy/package.py index 920cd39755..c45c1674af 100644 --- a/var/spack/repos/builtin/packages/py-gpy/package.py +++ b/var/spack/repos/builtin/packages/py-gpy/package.py @@ -11,6 +11,7 @@ class PyGpy(PythonPackage): homepage = "https://sheffieldml.github.io/GPy/" pypi = "gpy/GPy-1.9.9.tar.gz" + maintainers = ['liuyangzhuan'] version('1.9.9', sha256='04faf0c24eacc4dea60727c50a48a07ddf9b5751a3b73c382105e2a31657c7ed') version('0.8.8', sha256='e135d928cf170e2ec7fb058a035b5a7e334dc6b84d0bfb981556782528341988') diff --git a/var/spack/repos/builtin/packages/py-hpbandster/package.py b/var/spack/repos/builtin/packages/py-hpbandster/package.py new file mode 100644 index 0000000000..08703b0c6d --- /dev/null +++ b/var/spack/repos/builtin/packages/py-hpbandster/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +# Package automatically generated using 'pip2spack' converter + + +class PyHpbandster(PythonPackage): + """ + A distributed Hyperband implementation with lots of room for improvement + """ + + homepage = "https://github.com/automl/HpBandSter" + pypi = 'hpbandster/hpbandster-0.7.4.tar.gz' + maintainers = ['liuyangzhuan'] + + version('0.7.4', sha256='49ffc32688155b509e62f3617b52ae15a96c9bff2c996a23df83f279106c5921') + version('0.7.3', sha256='dd6c255f5dfe773a7f0c5ecf580b46a406d9f691303e2f849a14f7ae08ff9f13') + version('0.7.2', sha256='24dd3311b14fa76ab8111062ced670ff888e7e99cad07dcc3398361689c09f90') + version('0.7.1', sha256='41a55c95787eccd23def00f73013fbc9efad3cdc20d9e03270c7c959643dc5ff') + version('0.7.0', sha256='b6a46c73cb6a62e2f2d20984087a3458cea056aef5aa0fc0cd606bdd116eed94') + version('0.6.1', sha256='8812743b43b228dbf38fe2d5c5ecf238c6a742d02d8bdd264a2f193b96ca3b92') + version('0.6.0', sha256='26e69a2f84c8d41bea2fd703f489453a3e9301dcb62f15271b16a3db4ccf225d') + version('0.5.6', sha256='bc8a93638adda5cc0838c836402f18b456631363aefbfdf52942e9f8c7251893') + + depends_on('python@3:', type=('build', 'run')) + depends_on('py-configspace', type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-statsmodels', type=('build', 'run')) + depends_on('py-netifaces', type=('build', 'run')) + depends_on('py-scipy', type=('build', 'run')) + depends_on('py-serpent', type=('build', 'run')) + depends_on('py-pyro4', type=('build', 'run')) + depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-lhsmdu/package.py b/var/spack/repos/builtin/packages/py-lhsmdu/package.py new file mode 100644 index 0000000000..2a8b61b4b8 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-lhsmdu/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +# Package automatically generated using 'pip2spack' converter + + +class PyLhsmdu(PythonPackage): + """Latin Hypercube Sampling with Multi-Dimensional Uniformity (LHS-MDU) + from Deutsch and Deutsch, Latin hypercube sampling with multidimensional + uniformity.""" + + homepage = "http://github.com/sahilm89/lhsmdu" + pypi = 'lhsmdu/lhsmdu-1.1.tar.gz' + maintainers = ['liuyangzhuan'] + + version('1.1', sha256='4bc1df6b9cdd27bae0bff75cf1693f455ba32e4fa87ca9a932f60696607fe712') + version('0.1', sha256='ef462054b354cd20b10c6d80876c8fdb552a8d2e23eaf74179dc91956d68d32a') + + depends_on('py-setuptools', type='build') + depends_on('py-numpy', type='build') + depends_on('py-scipy', type='build') diff --git a/var/spack/repos/builtin/packages/py-ntplib/package.py b/var/spack/repos/builtin/packages/py-ntplib/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/py-opentuner/package.py b/var/spack/repos/builtin/packages/py-opentuner/package.py index 0e367bf55d..f4f054e8ec 100644 --- a/var/spack/repos/builtin/packages/py-opentuner/package.py +++ b/var/spack/repos/builtin/packages/py-opentuner/package.py @@ -14,6 +14,7 @@ class PyOpentuner(PythonPackage): maintainers = ['matthiasdiener'] + version('0.8.7', commit='070c5ce') version('0.8.2', commit='8e720a2') version('0.8.0', commit='4cb9135') diff --git a/var/spack/repos/builtin/packages/py-pika/package.py b/var/spack/repos/builtin/packages/py-pika/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/py-pyaml/package.py b/var/spack/repos/builtin/packages/py-pyaml/package.py index 51b74a471e..148c42f1f2 100644 --- a/var/spack/repos/builtin/packages/py-pyaml/package.py +++ b/var/spack/repos/builtin/packages/py-pyaml/package.py @@ -10,7 +10,7 @@ class PyPyaml(PythonPackage): """PyYAML-based python module to produce pretty and readable YAML-serialized data.""" - maintainers = ['Kerilk'] + maintainers = ['Kerilk', 'liuyangzhuan'] homepage = "https://github.com/mk-fg/pretty-yaml" pypi = "pyaml/pyaml-21.8.3.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-pyro4/package.py b/var/spack/repos/builtin/packages/py-pyro4/package.py new file mode 100644 index 0000000000..fa58bb13a7 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pyro4/package.py @@ -0,0 +1,85 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +# Package automatically generated using 'pip2spack' converter + + +class PyPyro4(PythonPackage): + """ + distributed object middleware for Python (RPC) + """ + + homepage = "http://pyro4.readthedocs.io" + pypi = 'Pyro4/Pyro4-4.81.tar.gz' + maintainers = ['liuyangzhuan'] + + version('4.81', sha256='e130da06478b813173b959f7013d134865e07fbf58cc5f1a2598f99479cdac5f') + version('4.80', sha256='46847ca703de3f483fbd0b2d22622f36eff03e6ef7ec7704d4ecaa3964cb2220') + version('4.79', sha256='b1eb34c9a1e63f731ca480f3e2c48169341a25a7504397badbaaab07e0f3241e') + version('4.78', sha256='b69200747c4c69bfa6fa8b917806b0a9ee7939daaf67ab9bb5ccac7e5179feee') + version('4.77', sha256='2bfe12a22f396474b0e57c898c7e2c561a8f850bf2055d8cf0f7119f0c7a523f') + version('4.76', sha256='ac1fda8d3fd9b5ff2cb8e7e400f95a1b1ae28c5df1aa82d1833a5a898e476334') + version('4.75', sha256='3897c0254046d4cb412a4d1a8f2f9c2c1c1ae643a24db07d0abdb51acdb8d7b5') + version('4.74', sha256='89ed7b12c162e5124f322f992f9506c44f5e1a379926cf01ee73ef810d3bf75f') + version('4.73', sha256='536b07a097d0619e7ab1effa3747fda177a24168d17a07a93ca9ac30977608f7') + version('4.72', sha256='2766b53db49f70b0d047fa6871aeb47484ba7e50cf53cfa37d26f87742c0b6a8') + version('4.71', sha256='78b686b584c180061fe3cfc3adcad4da46b3a7f42be1f9f0d7491cd006541cf3') + version('4.70', sha256='614dc4a7a79a861ee15215a6e60081950b2790b7b5cc91555ebeec75d8444aa5') + version('4.63', sha256='67d2b34156619ba37e92100af95aade8129dd2b7327eb05821d43887451f7d7b') + version('4.62', sha256='e301edfb2bc47768b7222a68cae8de8be796d1d9f61cdbd1af9039985ed5009c') + version('4.61', sha256='c465cb2ea2a90b887988d4249de8c0566bdfb16101fdc570e07e598a92e94d1e') + version('4.60', sha256='52fa5fe8173d234f57b6ca3214df3f34e88356c94081685db6249bff8f0b4f7f') + version('4.59', 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sha256='837fb552f54e46e54a13fa03c321073ba8373715346c4bc7e522b2c82a2c75c9') + version('4.37', sha256='2c4c9e7c3dbace3c75524324b6a686381be37bebab89b5001c0670418cec89c7') + version('4.36', sha256='fcbfbe22b044440fab3d6cbee11d18532b63accefe9cc30b2c41994cdeb08829') + version('4.35', sha256='97ef658b96fa10bac3e01097b1e2b6630fea2b307081ec6f2ac00f85e6020178') + version('4.34', sha256='36886e660290aa5afd06f735f587717f7f366b3535b7b0d3082b4e99ded9dc37') + version('4.33', sha256='9c01202190b7cdebe629e13abb70f050f421139f8115d1626321f442a9f54df8') + version('4.32', sha256='736eb96801881a61b9da72dced2d49574067443545892355af94411392526902') + version('4.31', sha256='0fd9342a216299ff24761e641714c7bd3e42c364f277eb3600d40085f4ace6c3') + version('4.30', sha256='1b38a52dd89cc6aee145d23bd74f586c73268938c6f346b20583ee0242d7d170') + version('4.29', sha256='3a17eaea8055962ff35bb9117f0860243d7977c34cbfcafc76e8e26309e339cf') + version('4.28', sha256='a094cb12e4e328e8b3b06bb313212f1826208c107fa6b48cf02f0ccdc32b562b') + version('4.27', sha256='ee32544fb04e7f4a2d223b442b306bd67cc900b7e9b5917f0b33d1979e6db34f') + version('4.26', sha256='213145815f00b6855b1ba71c20e78fd1d3c41595fae270308483cdba8d3fcec6') + version('4.25', sha256='ac2b0123badcb76c63eb716fcd95e0ee4021d345b5db05fda19253c59e39b384') + version('4.24', sha256='24d2ceaabbd886981d0df56f8f7e5f7f1a9db173778baa4965605f6880c90eb8') + version('4.23', sha256='57d6feee20a565f9de3302376a2531cfda50755088442102963b16e6f70b2e3b') + version('4.22', sha256='d8f611f384edbd240006d8c0f56135e74199ab88e9416cfc78cf5472f1ff337d') + version('4.21', sha256='96bc4bdccab27d935a44f1d9a8df94986d4b3361f5ff9382e86300ed5b9fdfa2') + version('4.20', sha256='72d3fb6dc653e6ae36bd47f2667fbff3c587c72f8bfb3f0dcb1763ee86c906f8') + version('4.18', sha256='52d7f6e10c44475052ac8b6828ed6f8b728a1c5d7e674b441eb0e930029ea4cd') + version('4.17', sha256='1d0cecdd3340dca695d6f833830e7a59f937d4bedbcff53109abe66e5a65d22c') + version('4.16', sha256='6a996700b877d268b48f91f91e356d2a4b20cb12207c05943d04504f6a0de0c7') + version('4.15', sha256='7b9dc43d6be79e4e542b8520715cb3ab7f9095afccc93bce9cacc271c665bf7d') + version('4.14', sha256='90c4f84ae9932d66825c61af9cd67b0b2877b477c967812a5d6953d67f3b003d') + version('4.13', sha256='afbc6964e593e7efed3fa5c91af45c4491cfdb994e7fdbe285cbb3719162cb90') + version('4.12', sha256='69f1beeafbe8f27bdac18e29ce97dd63cc1bdf847ff221ed0a6f0042047fa237') + version('4.11', sha256='d84ccfe85b14b3cb086f98d70dbf05671d6cb8498bd6f20f0041d6010dd320da') + version('4.10', sha256='de74e5e020a8a26cd357f5917afb48f7e14e161ca58574a1c653441bdbe9711c') + + depends_on('py-setuptools', type='build') + depends_on('py-serpent@1.27:', type=('build', 'run')) + depends_on('py-selectors34', when='^python@:3.3', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-radical-entk/package.py b/var/spack/repos/builtin/packages/py-radical-entk/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/py-radical-gtod/package.py b/var/spack/repos/builtin/packages/py-radical-gtod/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/py-radical-pilot/package.py b/var/spack/repos/builtin/packages/py-radical-pilot/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/py-radical-saga/package.py b/var/spack/repos/builtin/packages/py-radical-saga/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/py-radical-utils/package.py b/var/spack/repos/builtin/packages/py-radical-utils/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/py-scikit-optimize/package.py b/var/spack/repos/builtin/packages/py-scikit-optimize/package.py index b3d62fc1d3..fdf8db4756 100644 --- a/var/spack/repos/builtin/packages/py-scikit-optimize/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-optimize/package.py @@ -16,15 +16,24 @@ class PyScikitOptimize(PythonPackage): homepage = "https://scikit-optimize.github.io" pypi = "scikit-optimize/scikit-optimize-0.5.2.tar.gz" + git = "https://github.com/scikit-optimize/scikit-optimize.git" + maintainers = ['liuyangzhuan'] + + version('master', branch='master') version('0.5.2', sha256='1d7657a4b8ef9aa6d81e49b369c677c584e83269f11710557741d3b3f8fa0a75') variant('plots', default=True, description='Build with plot support from py-matplotlib') + variant('gptune', default=False, + description='Build with patches for GPTune') depends_on('py-setuptools', type='build') depends_on('py-numpy', type=('build', 'run')) depends_on('py-scipy@0.14.0:', type=('build', 'run')) depends_on('py-scikit-learn@0.19.1:', type=('build', 'run')) + depends_on('py-pyyaml', when='+gptune', type=('build', 'run')) depends_on('py-matplotlib', when='+plots') + + patch('space.patch', when='+gptune') diff --git a/var/spack/repos/builtin/packages/py-scikit-optimize/space.patch b/var/spack/repos/builtin/packages/py-scikit-optimize/space.patch new file mode 100644 index 0000000000..c608bbb78a --- /dev/null +++ b/var/spack/repos/builtin/packages/py-scikit-optimize/space.patch @@ -0,0 +1,57 @@ +diff --git a/skopt/space/space.py b/skopt/space/space.py +old mode 100644 +new mode 100755 +index 329b0c1..bed1e05 +--- a/skopt/space/space.py ++++ b/skopt/space/space.py +@@ -244,13 +244,13 @@ class Real(Dimension): + name : str or None + Name associated with the dimension, e.g., "learning rate". + +- dtype : str or dtype, default=float ++ dtype : str or dtype, default=np.float + float type which will be used in inverse_transform, + can be float. + + """ + def __init__(self, low, high, prior="uniform", base=10, transform=None, +- name=None, dtype=float): ++ name=None, dtype=np.float, optimize=True): + if high <= low: + raise ValueError("the lower bound {} has to be less than the" + " upper bound {}".format(low, high)) +@@ -267,6 +267,7 @@ class Real(Dimension): + self._rvs = None + self.transformer = None + self.transform_ = transform ++ self.optimize = optimize + if isinstance(self.dtype, str) and self.dtype\ + not in ['float', 'float16', 'float32', 'float64']: + raise ValueError("dtype must be 'float', 'float16', 'float32'" +@@ -346,7 +347,8 @@ class Real(Dimension): + self.low, self.high).astype(self.dtype) + if self.dtype == float or self.dtype == 'float': + # necessary, otherwise the type is converted to a numpy type +- return getattr(inv_transform, "tolist", lambda: value)() ++ inv_transform = getattr(inv_transform, "tolist", lambda: value)() ++ return [round(val, 6) for val in inv_transform] + else: + return inv_transform + +@@ -435,7 +437,7 @@ class Integer(Dimension): + + """ + def __init__(self, low, high, prior="uniform", base=10, transform=None, +- name=None, dtype=np.int64): ++ name=None, dtype=np.int64, optimize=True): + if high <= low: + raise ValueError("the lower bound {} has to be less than the" + " upper bound {}".format(low, high)) +@@ -450,6 +452,7 @@ class Integer(Dimension): + self.name = name + self.dtype = dtype + self.transform_ = transform ++ self.optimize = optimize + self._rvs = None + self.transformer = None + diff --git a/var/spack/repos/builtin/packages/py-selectors34/package.py b/var/spack/repos/builtin/packages/py-selectors34/package.py new file mode 100644 index 0000000000..55f86bc604 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-selectors34/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +# Package automatically generated using 'pip2spack' converter + + +class PySelectors34(PythonPackage): + """ + Backport of the selectors module from Python 3.4. + """ + + homepage = "https://github.com/berkerpeksag/selectors34" + pypi = 'selectors34/selectors34-1.2.tar.gz' + maintainers = ['liuyangzhuan'] + + version('1.2', sha256='09f5066337f8a76fb5233f267873f89a27a17c10bf79575954894bb71686451c') + + depends_on('py-setuptools', type='build') + depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-serpent/package.py b/var/spack/repos/builtin/packages/py-serpent/package.py new file mode 100644 index 0000000000..b2113cfbf4 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-serpent/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +# Package automatically generated using 'pip2spack' converter + + +class PySerpent(PythonPackage): + """ + Serialization based on ast.literal_eval + """ + + homepage = "https://github.com/irmen/Serpent" + pypi = 'serpent/serpent-1.40.tar.gz' + maintainers = ['liuyangzhuan'] + + version('1.40', sha256='10b34e7f8e3207ee6fb70dcdc9bce473851ee3daf0b47c58aec1b48032ac11ce') + + depends_on('py-setuptools', type='build') + depends_on('python@3.2:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-ytopt-autotune/package.py b/var/spack/repos/builtin/packages/py-ytopt-autotune/package.py index 979c6562d1..19f90a2aa8 100644 --- a/var/spack/repos/builtin/packages/py-ytopt-autotune/package.py +++ b/var/spack/repos/builtin/packages/py-ytopt-autotune/package.py @@ -9,12 +9,16 @@ from spack import * class PyYtoptAutotune(PythonPackage): """Common interface for autotuning search space and method definition.""" - maintainers = ['Kerilk'] + maintainers = ['Kerilk', 'liuyangzhuan'] homepage = "https://github.com/ytopt-team/autotune" url = "https://github.com/ytopt-team/autotune/archive/refs/tags/v1.1.0.tar.gz" + git = "https://github.com/ytopt-team/autotune.git" + version('master', branch='master') version('1.1.0', sha256='5ee7fa6a1c83131c5ceba1537b25f00de84182e4d0e6ebd0fd6efa4e8aee1bc4') + patch('version.patch', when='@1.1.0') + depends_on('python@3:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-ytopt-autotune/version.patch b/var/spack/repos/builtin/packages/py-ytopt-autotune/version.patch new file mode 100644 index 0000000000..2e00b9b245 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-ytopt-autotune/version.patch @@ -0,0 +1,10 @@ +diff --git a/autotune/__init__.py b/autotune/__init__.py +index 5636cf1..6c9488d 100644 +--- a/autotune/__init__.py ++++ b/autotune/__init__.py +@@ -1,4 +1,4 @@ +-from autotune.__version__ import __version__, __version_suffix__ ++from autotune.__version__ import __version__ + name = 'autotune' + version = __version__ + diff --git a/var/spack/repos/builtin/packages/pygmo/package.py b/var/spack/repos/builtin/packages/pygmo/package.py new file mode 100644 index 0000000000..80c5abe893 --- /dev/null +++ b/var/spack/repos/builtin/packages/pygmo/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Pygmo(CMakePackage): + """Parallel Global Multiobjective Optimizer (and its Python alter ego + PyGMO) is a C++ / Python platform to perform parallel computations of + optimisation tasks (global and local) via the asynchronous generalized + island model.""" + + homepage = "https://esa.github.io/pygmo2/" + url = "https://github.com/esa/pygmo2/archive/v2.18.0.tar.gz" + git = "https://github.com/esa/pygmo2.git" + + version('master', branch='master') + version('2.18.0', sha256='9f081cc973297894af09f713f889870ac452bfb32b471f9f7ba08a5e0bb9a125') + + depends_on('pagmo2', type=('build', 'link')) + depends_on('mpi', type='build') + depends_on('py-pybind11@2.6.0:2.6.2', type='build') + depends_on('cmake@3.1:', type='build') + + variant('shared', default=True, description='Build shared libraries') + + def cmake_args(self): + + args = [ + self.define_from_variant('BUILD_SHARED_LIBS', 'shared'), + ] + + return args diff --git a/var/spack/repos/builtin/packages/rapidjson/arm.patch b/var/spack/repos/builtin/packages/rapidjson/arm.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/raxml/nox86.patch b/var/spack/repos/builtin/packages/raxml/nox86.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/salmon-tddft/cmakefix.patch b/var/spack/repos/builtin/packages/salmon-tddft/cmakefix.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/salmon-tddft/fjmpi.patch b/var/spack/repos/builtin/packages/salmon-tddft/fjmpi.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/salmon-tddft/package.py b/var/spack/repos/builtin/packages/salmon-tddft/package.py old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/salmon-tddft/v2.0.libxc-5.0.patch b/var/spack/repos/builtin/packages/salmon-tddft/v2.0.libxc-5.0.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index 9d5704ac12..943cfb5d8e 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -6,7 +6,7 @@ from spack import * -class SuperluDist(CMakePackage, CudaPackage): +class SuperluDist(CMakePackage, CudaPackage, ROCmPackage): """A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" @@ -16,9 +16,10 @@ class SuperluDist(CMakePackage, CudaPackage): tags = ['e4s'] - maintainers = ['xiaoye', 'gchavez2', 'balay', 'pghysels'] + maintainers = ['xiaoye', 'gchavez2', 'balay', 'pghysels', 'liuyangzhuan'] version('develop', branch='master') + version('amd', branch='amd') version('7.1.1', sha256='558053b3d4a56eb661c4f04d4fcab6604018ce5db97115394c161b56c9c278ff') version('7.1.0', sha256='edbea877562be95fb22c7de1ff484f18685bec4baa8e4f703c414d3c035d4a66') version('6.4.0', sha256='cb9c0b2ba4c28e5ed5817718ba19ae1dd63ccd30bc44c8b8252b54f5f04a44cc') @@ -47,7 +48,10 @@ class SuperluDist(CMakePackage, CudaPackage): depends_on('parmetis') depends_on('metis@5:') depends_on('cmake@3.18.1:', type='build', when='@7.1.0:') + depends_on('hipblas', when='+rocm') + depends_on('rocsolver', when='+rocm') + conflicts('+rocm', when='+cuda') conflicts('+cuda', when='@:6.3') conflicts('^cuda@11.5.0:', when='@7.1.0:') @@ -61,6 +65,7 @@ class SuperluDist(CMakePackage, CudaPackage): '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc, '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx, '-DCMAKE_INSTALL_LIBDIR:STRING=%s' % self.prefix.lib, + '-DCMAKE_INSTALL_BINDIR:STRING=%s' % self.prefix.bin, '-DTPL_BLAS_LIBRARIES=%s' % spec['blas'].libs.joined(";"), '-DTPL_LAPACK_LIBRARIES=%s' % spec['lapack'].libs.joined(";"), '-DUSE_XSDK_DEFAULTS=YES', @@ -95,6 +100,15 @@ class SuperluDist(CMakePackage, CudaPackage): args.append( '-DCMAKE_CUDA_FLAGS=-arch=sm_{0}'.format(cuda_arch[0])) + if '+rocm' in spec and spec.satisfies('@amd'): + args.append('-DTPL_ENABLE_HIPLIB=TRUE') + args.append( + '-DHIP_ROOT_DIR={0}'.format(spec['hip'].prefix)) + rocm_archs = spec.variants['amdgpu_target'].value + if 'none' not in rocm_archs: + args.append('-DHIP_HIPCC_FLAGS=--amdgpu-target={0}'. + format(",".join(rocm_archs))) + if '+shared' in spec: args.append('-DBUILD_SHARED_LIBS:BOOL=ON') else: diff --git a/var/spack/repos/builtin/packages/tiptop/NR_perf_counter_open_aarch64.patch b/var/spack/repos/builtin/packages/tiptop/NR_perf_counter_open_aarch64.patch old mode 100755 new mode 100644 diff --git a/var/spack/repos/builtin/packages/vvtest/package.py b/var/spack/repos/builtin/packages/vvtest/package.py old mode 100755 new mode 100644 -- cgit v1.2.3-60-g2f50