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 <ajstewart426@gmail.com>

* 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 <ajstewart426@gmail.com>

* 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 <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

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))

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},

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):

var/spack/repos/builtin/packages/kokkos-nvcc-wrapper/package.py

@@ -42,7 +42,7 @@ def setup_dependent_build_environment(self, env, dependent_spec):
         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")

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

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

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')

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')

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')

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')
 

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"

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', sha256='6a39dadbd2a83b6fd5ab7f5402f8a4befd467b5c0404b8610a8797f748b72a38')
+    version('4.58', sha256='2c6d133bcec6039a681475bc878ec98c598ccd33105c1994c7b5217932ee2c0c')
+    version('4.57', sha256='fb3bf07951c2942b5f955770d50c0152565f0da79a2c1a359cfe2062fe0a82b2')
+    version('4.56', sha256='a80c27e1debbd8d8725ee4a8f0d30cf831dde5e80b04bfa9c912932c4c13d6aa')
+    version('4.55', sha256='49a7a142542d87dde1cecc8d3ee048ec9481ba861d61234d219fadd06e6ced96')
+    version('4.54', sha256='aede879916c0f6e84e560b38af421c24cb5089b66c8f632aa5ac48b20ecde93a')
+    version('4.53', sha256='c6ca6461472a74a7608a2247413b66e951889351fcf8e9eed5d7232ae844b702')
+    version('4.52', sha256='449f4bdf8dcbaca90e6436eb40c4e860b0de47346e2c7735d0584496d28451e5')
+    version('4.51', sha256='d6508b8c70d612356a8ddbe486890b03d840c37b5f7cd8e9366bc4c0dd44d3e6')
+    version('4.50', sha256='cb199540c2ceae9d67d5f2b20dc002d93f909d5072c3da4381c119d7a4b6d1cf')
+    version('4.49', sha256='6ae7fb0ce9ae5ca6f1d32487d8606219e7296ae7d22e650e7f9db63399608b76')
+    version('4.48', sha256='3115def913cf6035000047bb270efefb55a25449a17ed392afde6fd531c82fd2')
+    version('4.47', sha256='9354b722f9f5965ade5839241c8d7ff06ec2fac678a2c9e197a63966da241c89')
+    version('4.46', sha256='165ed717275217448d786f9c15777eca889f5344d54eef9482996dfee01b668b')
+    version('4.45', sha256='e32d3f32e52d84e3456c0d389a115b5430a8bb14dd01336c627355a2f34dba78')
+    version('4.43', sha256='b6f924fa74f21d14c851450e157711914a402bfc2f3a880c1b2c275fd4cda6d6')
+    version('4.42', sha256='03951643015a1537ad82fbf99fba6e208007447404aab1a020dce7216120d32a')
+    version('4.41', sha256='3af4749140e9d4032632277ac19e7fd4761856d2df0f0643c574d1e7174a9703')
+    version('4.40', sha256='00423d3710f60b2da146075a59e17bfa837f556ed2c8acafe05bc209dcaac3e9')
+    version('4.39', sha256='39c6ca7f86b0f0bebfeada687a5a8b99f66470a52b0f815195ae63c683266f24')
+    version('4.38', 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'))

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')

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
+ 

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'))

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'))

var/spack/repos/builtin/packages/py-ytopt-autotune/package.py

@@ -9,12 +9,16 @@
 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')

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__
+ 

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

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 @@ def cmake_args(self):
             '-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 @@ def cmake_args(self):
                 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: