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14 files changed, 958 insertions, 35 deletions
diff --git a/lib/spack/docs/tutorial_advanced_packaging.rst b/lib/spack/docs/tutorial_advanced_packaging.rst index f72f483fcb..9b41980a69 100644 --- a/lib/spack/docs/tutorial_advanced_packaging.rst +++ b/lib/spack/docs/tutorial_advanced_packaging.rst @@ -25,46 +25,22 @@ dependents in your package. Setup for the tutorial ---------------------- -The simplest way to follow along with this tutorial is to use our Docker image, -which comes with Spack and various packages pre-installed: +.. note:: -.. code-block:: console - - $ docker pull alalazo/spack:advanced_packaging_tutorial - $ docker run --rm -h advanced-packaging-tutorial -it alalazo/spack:advanced_packaging_tutorial - root@advanced-packaging-tutorial:/# - root@advanced-packaging-tutorial:/# spack find - ==> 20 installed packages. - -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 ------------------------- - arpack-ng@3.5.0 hdf5@1.10.1 libpciaccess@0.13.5 libtool@2.4.6 m4@1.4.18 ncurses@6.0 openblas@0.2.20 openssl@1.0.2k superlu@5.2.1 xz@5.2.3 - cmake@3.9.4 hwloc@1.11.8 libsigsegv@2.11 libxml2@2.9.4 mpich@3.2 netlib-lapack@3.6.1 openmpi@3.0.0 pkg-config@0.29.2 util-macros@1.19.1 zlib@1.2.11 + If you are not using the tutorial docker image, it is recommended that you + do this section of the tutorial in a fresh clone of Spack -If you already started the image, you can set the ``EDITOR`` environment -variable to your preferred editor (``vi``, ``emacs``, and ``nano`` are included in the image) -and move directly to :ref:`adv_pkg_tutorial_start`. - -If you choose not to use the Docker image, you can clone the Spack repository -and build the necessary bits yourself: +The tutorial uses custom package definitions with missing sections that +will be filled in during the tutorial. These package definitions are stored +in a separate package repository, which can be enabled with: .. code-block:: console - $ git clone https://github.com/spack/spack.git - Cloning into 'spack'... - remote: Counting objects: 92731, done. - remote: Compressing objects: 100% (1108/1108), done. - remote: Total 92731 (delta 1964), reused 4186 (delta 1637), pack-reused 87932 - Receiving objects: 100% (92731/92731), 33.31 MiB | 64.00 KiB/s, done. - Resolving deltas: 100% (43557/43557), done. - Checking connectivity... done. - - $ cd spack - $ git checkout tutorials/advanced_packaging - Branch tutorials/advanced_packaging set up to track remote branch tutorials/advanced_packaging from origin. - Switched to a new branch 'tutorials/advanced_packaging' - -At this point you can install the software that will be used -during the rest of the tutorial (the output of the commands is omitted -for the sake of brevity): + $ spack repo add --scope=site var/spack/repos/tutorial + +If you are using the tutorial docker image, all dependency packages +will have been installed. Otherwise, to install these packages you can use +the following commands: .. code-block:: console diff --git a/var/spack/repos/tutorial/packages/armadillo/package.py b/var/spack/repos/tutorial/packages/armadillo/package.py new file mode 100644 index 0000000000..d95a61f67d --- /dev/null +++ b/var/spack/repos/tutorial/packages/armadillo/package.py @@ -0,0 +1,62 @@ +# Copyright 2013-2018 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 Armadillo(CMakePackage): + """Armadillo is a high quality linear algebra library (matrix maths) + for the C++ language, aiming towards a good balance between speed and + ease of use. + """ + + homepage = "http://arma.sourceforge.net/" + url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz" + + version('8.100.1', 'd9762d6f097e0451d0cfadfbda295e7c') + version('7.950.1', 'c06eb38b12cae49cab0ce05f96147147') + version('7.900.1', '5ef71763bd429a3d481499878351f3be') + version('7.500.0', '7d316fdf3c3c7ea92b64704180ae315d') + version('7.200.2', 'b21585372d67a8876117fd515d8cf0a2') + version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e') + + variant('hdf5', default=False, description='Include HDF5 support') + + depends_on('cmake@2.8.12:', type='build') + depends_on('arpack-ng') # old arpack causes undefined symbols + depends_on('blas') + depends_on('lapack') + depends_on('superlu@5.2:') + depends_on('hdf5', when='+hdf5') + + patch('undef_linux.patch', when='platform=linux') + + def cmake_args(self): + spec = self.spec + + # TUTORIAL: fix the lines below by adding the appropriate query to + # the right dependency. To ask a dependency, e.g. `blas`, for the + # list of libraries it provides it suffices to access its `libs` + # attribute: + # + # blas_libs = spec['blas'].libs + # + # The CMake variables below require a semicolon separated list: + # + # blas_libs.joined(';') + + return [ + # ARPACK support + '-DARPACK_LIBRARY={0}'.format('FIXME: arpack-ng'), + # BLAS support + '-DBLAS_LIBRARY={0}'.format('FIXME: blas'), + # LAPACK support + '-DLAPACK_LIBRARY={0}'.format('FIXME: lapack'), + # SuperLU support + '-DSuperLU_INCLUDE_DIR={0}'.format(spec['superlu'].prefix.include), + '-DSuperLU_LIBRARY={0}'.format('FIXME: superlu'), + # HDF5 support + '-DDETECT_HDF5={0}'.format('ON' if '+hdf5' in spec else 'OFF') + ] diff --git a/var/spack/repos/tutorial/packages/armadillo/undef_linux.patch b/var/spack/repos/tutorial/packages/armadillo/undef_linux.patch new file mode 100644 index 0000000000..68b434dca8 --- /dev/null +++ b/var/spack/repos/tutorial/packages/armadillo/undef_linux.patch @@ -0,0 +1,4 @@ +--- a/include/armadillo_bits/compiler_setup.hpp ++++ b/include/armadillo_bits/compiler_setup.hpp +@@ -0,0 +1 @@ ++#undef linux diff --git a/var/spack/repos/tutorial/packages/elpa/package.py b/var/spack/repos/tutorial/packages/elpa/package.py new file mode 100644 index 0000000000..386295eea9 --- /dev/null +++ b/var/spack/repos/tutorial/packages/elpa/package.py @@ -0,0 +1,78 @@ +# Copyright 2013-2018 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 Elpa(AutotoolsPackage): + """Eigenvalue solvers for Petaflop-Applications (ELPA)""" + + homepage = 'http://elpa.mpcdf.mpg.de/' + url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz' + + version('2018.05.001.rc1', 'ccd77bd8036988ee624f43c04992bcdd') + version('2017.11.001', '4a437be40cc966efb07aaab84c20cd6e', preferred=True) + version('2017.05.003', '7c8e5e58cafab212badaf4216695700f') + version('2017.05.002', 'd0abc1ac1f493f93bf5e30ec8ab155dc') + version('2016.11.001.pre', '5656fd066cf0dcd071dbcaf20a639b37') + version('2016.05.004', 'c0dd3a53055536fc3a2a221e78d8b376') + version('2016.05.003', '88a9f3f3bfb63e16509dd1be089dcf2c') + version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6') + + variant('openmp', default=False, description='Activates OpenMP support') + variant('optflags', default=True, description='Build with optimization flags') + + depends_on('mpi') + depends_on('blas') + depends_on('lapack') + depends_on('scalapack') + + def url_for_version(self, version): + t = 'http://elpa.mpcdf.mpg.de/html/Releases/{0}/elpa-{0}.tar.gz' + if version < Version('2016.05.003'): + t = 'http://elpa.mpcdf.mpg.de/elpa-{0}.tar.gz' + return t.format(str(version)) + + @property + def libs(self): + libname = 'libelpa_openmp' if '+openmp' in self.spec else 'libelpa' + return find_libraries( + libname, root=self.prefix, shared=True, recursive=True + ) + + build_directory = 'spack-build' + + def setup_environment(self, spack_env, run_env): + # TUTORIAL: set the following environment variables: + # + # CC=spec['mpi'].mpicc + # FC=spec['mpi'].mpifc + # CXX=spec['mpi'].mpicxx + # SCALAPACK_LDFLAGS=spec['scalapack'].libs.joined() + # + # and append the following flags: + # + # LDFLAGS -> spec['lapack'].libs.search_flags + # LIBS -> spec['lapack'].libs.link_flags + pass + + def configure_args(self): + # TODO: set optimum flags for platform+compiler combo, see + # https://github.com/hfp/xconfigure/tree/master/elpa + # also see: + # https://src.fedoraproject.org/cgit/rpms/elpa.git/ + # https://packages.qa.debian.org/e/elpa.html + options = [] + # without -march=native there is configure error for 2017.05.02 + # Could not compile test program, try with --disable-sse, or + # adjust the C compiler or CFLAGS + if '+optflags' in self.spec: + options.extend([ + 'FCFLAGS=-O2 -march=native -ffree-line-length-none', + 'CFLAGS=-O2 -march=native' + ]) + if '+openmp' in self.spec: + options.append('--enable-openmp') + return options diff --git a/var/spack/repos/tutorial/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch b/var/spack/repos/tutorial/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch new file mode 100644 index 0000000000..8bf5c142e9 --- /dev/null +++ b/var/spack/repos/tutorial/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch @@ -0,0 +1,16 @@ +diff --git a/fortran/src/H5f90global.F90 b/fortran/src/H5f90global.F90 +index dd2b171..629418a 100644 +--- a/fortran/src/H5f90global.F90 ++++ b/fortran/src/H5f90global.F90 +@@ -142,10 +142,7 @@ MODULE H5GLOBAL + + INTEGER(HID_T), DIMENSION(PREDEF_TYPES_LEN) :: predef_types + EQUIVALENCE (predef_types(1), H5T_NATIVE_INTEGER_KIND(1)) +- EQUIVALENCE (predef_types(2), H5T_NATIVE_INTEGER_KIND(2)) +- EQUIVALENCE (predef_types(3), H5T_NATIVE_INTEGER_KIND(3)) +- EQUIVALENCE (predef_types(4), H5T_NATIVE_INTEGER_KIND(4)) +- EQUIVALENCE (predef_types(5), H5T_NATIVE_INTEGER_KIND(5)) ++ ! EQUIVALENCE predef_types(2:5) are unnecessary and violate the standard + EQUIVALENCE (predef_types(6), H5T_NATIVE_INTEGER) + EQUIVALENCE (predef_types(7), H5T_NATIVE_REAL) + EQUIVALENCE (predef_types(8), H5T_NATIVE_DOUBLE) diff --git a/var/spack/repos/tutorial/packages/hdf5/package.py b/var/spack/repos/tutorial/packages/hdf5/package.py new file mode 100644 index 0000000000..b879d81f1c --- /dev/null +++ b/var/spack/repos/tutorial/packages/hdf5/package.py @@ -0,0 +1,307 @@ +# Copyright 2013-2018 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) + +import shutil +import sys + +from spack import * + + +class Hdf5(AutotoolsPackage): + """HDF5 is a data model, library, and file format for storing and managing + data. It supports an unlimited variety of datatypes, and is designed for + flexible and efficient I/O and for high volume and complex data. + """ + + homepage = "https://support.hdfgroup.org/HDF5/" + url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz" + list_url = "https://support.hdfgroup.org/ftp/HDF5/releases" + list_depth = 3 + + version('1.10.4', '8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2') + version('1.10.3', 'b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39') + version('1.10.2', '8d4eae84e533efa57496638fd0dca8c3') + version('1.10.1', '43a2f9466702fb1db31df98ae6677f15') + version('1.10.0-patch1', '9180ff0ef8dc2ef3f61bd37a7404f295') + version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199') + version('1.8.19', '7f568e2464d4ab0a74d16b23956d900b') + version('1.8.18', 'dd2148b740713ca0295442ec683d7b1c') + version('1.8.17', '7d572f8f3b798a628b8245af0391a0ca') + version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618') + version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24') + version('1.8.14', 'a482686e733514a51cde12d6fe5c5d95') + version('1.8.13', 'c03426e9e77d7766944654280b467289') + version('1.8.12', 'd804802feb99b87fc668a90e6fa34411') + version('1.8.10', '710aa9fb61a51d61a7e2c09bf0052157') + + variant('debug', default=False, + description='Builds a debug version of the library') + variant('shared', default=True, + description='Builds a shared version of the library') + + variant('hl', default=False, description='Enable the high-level library') + variant('cxx', default=False, description='Enable C++ support') + variant('fortran', default=False, description='Enable Fortran support') + variant('threadsafe', default=False, + description='Enable thread-safe capabilities') + + variant('mpi', default=True, description='Enable MPI support') + variant('szip', default=False, description='Enable szip support') + variant('pic', default=True, + description='Produce position-independent code (for shared libs)') + + depends_on('mpi', when='+mpi') + # numactl does not currently build on darwin + if sys.platform != 'darwin': + depends_on('numactl', when='+mpi+fortran') + depends_on('szip', when='+szip') + depends_on('zlib@1.1.2:') + + # There are several officially unsupported combinations of the features: + # 1. Thread safety is not guaranteed via high-level C-API but in some cases + # it works. + # conflicts('+threadsafe+hl') + + # 2. Thread safety is not guaranteed via Fortran (CXX) API, but it's + # possible for a dependency tree to contain a package that uses Fortran + # (CXX) API in a single thread and another one that uses low-level C-API + # in multiple threads. To allow for such scenarios, we don't specify the + # following conflicts. + # conflicts('+threadsafe+cxx') + # conflicts('+threadsafe+fortran') + + # 3. Parallel features are not supported via CXX API, but for the reasons + # described in #2 we allow for such combination. + # conflicts('+mpi+cxx') + + # There are known build failures with intel@18.0.1. This issue is + # discussed and patch is provided at + # https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951. + patch('h5f90global-mult-obj-same-equivalence-same-common-block.patch', + when='@1.10.1%intel@18') + + # Turn line comments into block comments to conform with pre-C99 language + # standards. Versions of hdf5 after 1.8.10 don't require this patch, + # either because they conform to pre-C99 or neglect to ask for pre-C99 + # language standards from their compiler. The hdf5 build system adds + # the -ansi cflag (run 'man gcc' for info on -ansi) for some versions + # of some compilers (see hdf5-1.8.10/config/gnu-flags). The hdf5 build + # system does not provide an option to disable -ansi, but since the + # pre-C99 code is restricted to just five lines of line comments in + # three src files, this patch accomplishes the simple task of patching the + # three src files and leaves the hdf5 build system alone. + patch('pre-c99-comments.patch', when='@1.8.10') + + # There are build errors with GCC 8, see + # https://forum.hdfgroup.org/t/1-10-2-h5detect-compile-error-gcc-8-1-0-on-centos-7-2-solved/4441 + patch('https://salsa.debian.org/debian-gis-team/hdf5/raw/bf94804af5f80f662cad80a5527535b3c6537df6/debian/patches/gcc-8.patch', sha256='57cee5ff1992b4098eda079815c36fc2da9b10e00a9056df054f2384c4fc7523', when='@1.10.2%gcc@8:') + + filter_compiler_wrappers('h5cc', 'h5c++', 'h5fc', relative_root='bin') + + def url_for_version(self, version): + url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-{0}/hdf5-{1}/src/hdf5-{1}.tar.gz" + return url.format(version.up_to(2), version) + + @property + def libs(self): + """HDF5 can be queried for the following parameters: + + - "hl": high-level interface + - "cxx": C++ APIs + - "fortran": Fortran APIs + + :return: list of matching libraries + """ + # This map contains a translation from query_parameters + # to the libraries needed + query2libraries = { # noqa: F841 + tuple(): ['libhdf5'], + ('cxx', 'fortran', 'hl'): [ + 'libhdf5hl_fortran', + 'libhdf5_hl_cpp', + 'libhdf5_hl', + 'libhdf5_fortran', + 'libhdf5', + ], + ('cxx', 'hl'): [ + 'libhdf5_hl_cpp', + 'libhdf5_hl', + 'libhdf5', + ], + ('fortran', 'hl'): [ + 'libhdf5hl_fortran', + 'libhdf5_hl', + 'libhdf5_fortran', + 'libhdf5', + ], + ('hl',): [ + 'libhdf5_hl', + 'libhdf5', + ], + ('cxx', 'fortran'): [ + 'libhdf5_fortran', + 'libhdf5_cpp', + 'libhdf5', + ], + ('cxx',): [ + 'libhdf5_cpp', + 'libhdf5', + ], + ('fortran',): [ + 'libhdf5_fortran', + 'libhdf5', + ] + } + + # TUTORIAL: you need to fix the implementation below, and + # return the correct list of libraries according to the + # query parameters your dependency has used. + # + # You can retrieve the query parameters by doing + # + # query_parameters = self.spec.last_query.extra_parameters + # + # and use the map above to query the list of libraries you need + # to search. + # + # Finally uncomment the lines below to return a LibraryList + # + # shared = '+shared' in self.spec + # return find_libraries( + # libraries, root=self.prefix, shared=shared, recursive=True + # ) + return [] + + @run_before('configure') + def fortran_check(self): + if '+fortran' in self.spec and not self.compiler.fc: + msg = 'cannot build a Fortran variant without a Fortran compiler' + raise RuntimeError(msg) + + def configure_args(self): + # Always enable this option. This does not actually enable any + # features: it only *allows* the user to specify certain + # combinations of other arguments. Enabling it just skips a + # sanity check in configure, so this doesn't merit a variant. + extra_args = ['--enable-unsupported'] + extra_args += self.enable_or_disable('threadsafe') + extra_args += self.enable_or_disable('cxx') + extra_args += self.enable_or_disable('hl') + extra_args += self.enable_or_disable('fortran') + + if '+szip' in self.spec: + extra_args.append('--with-szlib=%s' % self.spec['szip'].prefix) + else: + extra_args.append('--without-szlib') + + if self.spec.satisfies('@1.10:'): + if '+debug' in self.spec: + extra_args.append('--enable-build-mode=debug') + else: + extra_args.append('--enable-build-mode=production') + else: + if '+debug' in self.spec: + extra_args.append('--enable-debug=all') + else: + extra_args.append('--enable-production') + + # '--enable-fortran2003' no longer exists as of version 1.10.0 + if '+fortran' in self.spec: + extra_args.append('--enable-fortran2003') + else: + extra_args.append('--disable-fortran2003') + + if '+shared' in self.spec: + extra_args.append('--enable-shared') + else: + extra_args.append('--disable-shared') + extra_args.append('--enable-static-exec') + + if '+pic' in self.spec: + extra_args += ['%s=%s' % (f, self.compiler.pic_flag) + for f in ['CFLAGS', 'CXXFLAGS', 'FCFLAGS']] + + if '+mpi' in self.spec: + # The HDF5 configure script warns if cxx and mpi are enabled + # together. There doesn't seem to be a real reason for this, except + # that parts of the MPI interface are not accessible via the C++ + # interface. Since they are still accessible via the C interface, + # this is not actually a problem. + extra_args += ['--enable-parallel', + 'CC=%s' % self.spec['mpi'].mpicc] + + if '+cxx' in self.spec: + extra_args.append('CXX=%s' % self.spec['mpi'].mpicxx) + + if '+fortran' in self.spec: + extra_args.append('FC=%s' % self.spec['mpi'].mpifc) + + extra_args.append('--with-zlib=%s' % self.spec['zlib'].prefix) + + return extra_args + + @run_after('configure') + def patch_postdeps(self): + if '@:1.8.14' in self.spec: + # On Ubuntu14, HDF5 1.8.12 (and maybe other versions) + # mysteriously end up with "-l -l" in the postdeps in the + # libtool script. Patch this by removing the spurious -l's. + filter_file( + r'postdeps="([^"]*)"', + lambda m: 'postdeps="%s"' % ' '.join( + arg for arg in m.group(1).split(' ') if arg != '-l'), + 'libtool') + + @run_after('install') + @on_package_attributes(run_tests=True) + def check_install(self): + # Build and run a small program to test the installed HDF5 library + spec = self.spec + print("Checking HDF5 installation...") + checkdir = "spack-check" + with working_dir(checkdir, create=True): + source = r""" +#include <hdf5.h> +#include <assert.h> +#include <stdio.h> +int main(int argc, char **argv) { + unsigned majnum, minnum, relnum; + herr_t herr = H5get_libversion(&majnum, &minnum, &relnum); + assert(!herr); + printf("HDF5 version %d.%d.%d %u.%u.%u\n", H5_VERS_MAJOR, H5_VERS_MINOR, + H5_VERS_RELEASE, majnum, minnum, relnum); + return 0; +} +""" + expected = """\ +HDF5 version {version} {version} +""".format(version=str(spec.version.up_to(3))) + with open("check.c", 'w') as f: + f.write(source) + if '+mpi' in spec: + cc = Executable(spec['mpi'].mpicc) + else: + cc = Executable(self.compiler.cc) + cc(*(['-c', "check.c"] + spec['hdf5'].headers.cpp_flags.split())) + cc(*(['-o', "check", + "check.o"] + spec['hdf5'].libs.ld_flags.split())) + try: + check = Executable('./check') + output = check(output=str) + except ProcessError: + output = "" + success = output == expected + if not success: + print("Produced output does not match expected output.") + print("Expected output:") + print('-' * 80) + print(expected) + print('-' * 80) + print("Produced output:") + print('-' * 80) + print(output) + print('-' * 80) + raise RuntimeError("HDF5 install check failed") + shutil.rmtree(checkdir) diff --git a/var/spack/repos/tutorial/packages/hdf5/pre-c99-comments.patch b/var/spack/repos/tutorial/packages/hdf5/pre-c99-comments.patch new file mode 100644 index 0000000000..97743e8fa5 --- /dev/null +++ b/var/spack/repos/tutorial/packages/hdf5/pre-c99-comments.patch @@ -0,0 +1,43 @@ +diff --git a/test/th5s.c b/test/th5s.c +index 462bc36..8e18fad 100644 +--- a/test/th5s.c ++++ b/test/th5s.c +@@ -730,8 +730,8 @@ test_h5s_zero_dim(void) + ret = H5Pset_chunk(plist_id, SPACE1_RANK, chunk_dims); + CHECK(ret, FAIL, "H5Pset_chunk"); + +- // ret = H5Pset_alloc_time(plist_id, alloc_time); +- // CHECK(ret, FAIL, "H5Pset_alloc_time"); ++ /* ret = H5Pset_alloc_time(plist_id, alloc_time); */ ++ /* CHECK(ret, FAIL, "H5Pset_alloc_time"); */ + + dset1 = H5Dcreate2(fid1, BASICDATASET1, H5T_NATIVE_INT, sid_chunk, H5P_DEFAULT, plist_id, H5P_DEFAULT); + CHECK(dset1, FAIL, "H5Dcreate2"); +diff --git a/tools/h5dump/h5dump_ddl.c b/tools/h5dump/h5dump_ddl.c +index ee6de5e..3ed6045 100644 +--- a/tools/h5dump/h5dump_ddl.c ++++ b/tools/h5dump/h5dump_ddl.c +@@ -1341,8 +1341,8 @@ handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int UNUSED pe + string_dataformat.do_escape = display_escape; + outputformat = &string_dataformat; + +- //attr_name = attr + j + 1; +- // need to replace escape characters ++ /* attr_name = attr + j + 1; */ ++ /* need to replace escape characters */ + attr_name = h5tools_str_replace(attr + j + 1, "\\/", "/"); + + +diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c +index 9ce3524..3b4e5e7 100644 +--- a/tools/lib/h5tools_str.c ++++ b/tools/lib/h5tools_str.c +@@ -632,7 +632,7 @@ h5tools_str_indent(h5tools_str_t *str, const h5tool_format_t *info, + h5tools_str_append(str, "%s", OPT(info->line_indent, "")); + } + +-// ctx->need_prefix = 0; ++/* ctx->need_prefix = 0; */ + } + + /*------------------------------------------------------------------------- diff --git a/var/spack/repos/tutorial/packages/mpich/mpich32_clang.patch b/var/spack/repos/tutorial/packages/mpich/mpich32_clang.patch new file mode 100644 index 0000000000..01243072f7 --- /dev/null +++ b/var/spack/repos/tutorial/packages/mpich/mpich32_clang.patch @@ -0,0 +1,13 @@ +diff --git a/src/include/mpiimpl.h b/src/include/mpiimpl.h +index e705e5d..3bfcbee 100644 +--- a/src/include/mpiimpl.h ++++ b/src/include/mpiimpl.h +@@ -1528,7 +1528,7 @@ typedef struct MPID_Request { + #ifdef MPID_DEV_REQUEST_DECL + MPID_DEV_REQUEST_DECL + #endif +-} MPID_Request ATTRIBUTE((__aligned__(32))); ++} ATTRIBUTE((__aligned__(32))) MPID_Request; + + extern MPIU_Object_alloc_t MPID_Request_mem; + /* Preallocated request objects */ diff --git a/var/spack/repos/tutorial/packages/mpich/package.py b/var/spack/repos/tutorial/packages/mpich/package.py new file mode 100644 index 0000000000..c3e0b8a54b --- /dev/null +++ b/var/spack/repos/tutorial/packages/mpich/package.py @@ -0,0 +1,155 @@ +# Copyright 2013-2018 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 * +import os + + +class Mpich(AutotoolsPackage): + """MPICH is a high performance and widely portable implementation of + the Message Passing Interface (MPI) standard.""" + + homepage = "http://www.mpich.org" + url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz" + git = "https://github.com/pmodels/mpich.git" + list_url = "http://www.mpich.org/static/downloads/" + list_depth = 1 + + version('develop', submodules=True) + version('3.2.1', 'e175452f4d61646a52c73031683fc375') + version('3.2', 'f414cfa77099cd1fa1a5ae4e22db508a') + version('3.1.4', '2ab544607986486562e076b83937bba2') + version('3.1.3', '93cb17f91ac758cbf9174ecb03563778') + version('3.1.2', '7fbf4b81dcb74b07ae85939d1ceee7f1') + version('3.1.1', '40dc408b1e03cc36d80209baaa2d32b7') + version('3.1', '5643dd176499bfb7d25079aaff25f2ec') + version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0') + + variant('hydra', default=True, description='Build the hydra process manager') + variant('pmi', default=True, description='Build with PMI support') + variant('romio', default=True, description='Enable ROMIO MPI I/O implementation') + variant('verbs', default=False, description='Build support for OpenFabrics verbs.') + variant( + 'device', + default='ch3', + description='''Abstract Device Interface (ADI) +implementation. The ch4 device is currently in experimental state''', + values=('ch3', 'ch4'), + multi=False + ) + variant( + 'netmod', + default='tcp', + description='''Network module. Only single netmod builds are +supported. For ch3 device configurations, this presumes the +ch3:nemesis communication channel. ch3:sock is not supported by this +spack package at this time.''', + values=('tcp', 'mxm', 'ofi', 'ucx'), + multi=False + ) + + provides('mpi') + provides('mpi@:3.0', when='@3:') + provides('mpi@:1.3', when='@1:') + + filter_compiler_wrappers( + 'mpicc', 'mpicxx', 'mpif77', 'mpif90', 'mpifort', relative_root='bin' + ) + + # fix MPI_Barrier segmentation fault + # see https://lists.mpich.org/pipermail/discuss/2016-May/004764.html + # and https://lists.mpich.org/pipermail/discuss/2016-June/004768.html + patch('mpich32_clang.patch', when='@3.2:3.2.0%clang') + + depends_on('findutils', type='build') + + depends_on('libfabric', when='netmod=ofi') + + conflicts('device=ch4', when='@:3.2') + conflicts('netmod=ofi', when='@:3.1.4') + conflicts('netmod=ucx', when='device=ch3') + conflicts('netmod=mxm', when='device=ch4') + conflicts('netmod=mxm', when='@:3.1.3') + conflicts('netmod=tcp', when='device=ch4') + + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + # TUTORIAL: set the following variables for dependents: + # + # MPICC=join_path(self.prefix.bin, 'mpicc') + # MPICXX=join_path(self.prefix.bin, 'mpic++') + # MPIF77=join_path(self.prefix.bin, 'mpif77') + # MPIF90=join_path(self.prefix.bin, 'mpif90') + # MPICH_CC=spack_cc + # MPICH_CXX=spack_cxx + # MPICH_F77=spack_f77 + # MPICH_F90=spack_fc + # MPICH_FC=spack_fc + pass + + def setup_dependent_package(self, module, dependent_spec): + if 'platform=cray' in self.spec: + self.spec.mpicc = spack_cc + self.spec.mpicxx = spack_cxx + self.spec.mpifc = spack_fc + self.spec.mpif77 = spack_f77 + else: + self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') + self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++') + self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') + self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') + + self.spec.mpicxx_shared_libs = [ + join_path(self.prefix.lib, 'libmpicxx.{0}'.format(dso_suffix)), + join_path(self.prefix.lib, 'libmpi.{0}'.format(dso_suffix)) + ] + + def autoreconf(self, spec, prefix): + """Not needed usually, configure should be already there""" + # If configure exists nothing needs to be done + if os.path.exists(self.configure_abs_path): + return + # Else bootstrap with autotools + bash = which('bash') + bash('./autogen.sh') + + @run_before('autoreconf') + def die_without_fortran(self): + # Until we can pass variants such as +fortran through virtual + # dependencies depends_on('mpi'), require Fortran compiler to + # avoid delayed build errors in dependents. + if (self.compiler.f77 is None) or (self.compiler.fc is None): + raise InstallError( + 'Mpich requires both C and Fortran compilers!' + ) + + def configure_args(self): + spec = self.spec + config_args = [ + '--enable-shared', + '--with-pm={0}'.format('hydra' if '+hydra' in spec else 'no'), + '--with-pmi={0}'.format('yes' if '+pmi' in spec else 'no'), + '--{0}-romio'.format('enable' if '+romio' in spec else 'disable'), + '--{0}-ibverbs'.format('with' if '+verbs' in spec else 'without') + ] + + # setup device configuration + device_config = '' + if 'device=ch4' in spec: + device_config = '--with-device=ch4:' + elif 'device=ch3' in spec: + device_config = '--with-device=ch3:nemesis:' + + if 'netmod=ucx' in spec: + device_config += 'ucx' + elif 'netmod=ofi' in spec: + device_config += 'ofi' + elif 'netmod=mxm' in spec: + device_config += 'mxm' + elif 'netmod=tcp' in spec: + device_config += 'tcp' + + config_args.append(device_config) + + return config_args diff --git a/var/spack/repos/tutorial/packages/netlib-lapack/ibm-xl.patch b/var/spack/repos/tutorial/packages/netlib-lapack/ibm-xl.patch new file mode 100644 index 0000000000..c6fba2a028 --- /dev/null +++ b/var/spack/repos/tutorial/packages/netlib-lapack/ibm-xl.patch @@ -0,0 +1,42 @@ +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -62,7 +62,7 @@ + set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fp-model strict") + endif() + if("${CMAKE_Fortran_COMPILER}" MATCHES "xlf") +- set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qnosave -qstrict=none") ++ set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qnosave -qstrict") + endif() + # Delete libmtsk in linking sequence for Sun/Oracle Fortran Compiler. + # This library is not present in the Sun package SolarisStudio12.3-linux-x86-bin + +--- a/CMAKE/CheckLAPACKCompilerFlags.cmake ++++ b/CMAKE/CheckLAPACKCompilerFlags.cmake +@@ -43,12 +43,6 @@ + if( "${CMAKE_Fortran_FLAGS}" MATCHES "-qflttrap=[a-zA-Z:]:enable" ) + set( FPE_EXIT TRUE ) + endif() +- +- if( NOT ("${CMAKE_Fortran_FLAGS}" MATCHES "-qfixed") ) +- message( STATUS "Enabling fixed format F90/F95 with -qfixed" ) +- set( CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qfixed" +- CACHE STRING "Flags for Fortran compiler." FORCE ) +- endif() + + # HP Fortran + elseif( CMAKE_Fortran_COMPILER_ID STREQUAL "HP" ) + +--- a/CBLAS/CMakeLists.txt ++++ b/CBLAS/CMakeLists.txt +@@ -12,8 +12,8 @@ + SYMBOL_NAMESPACE "F77_") + if(NOT FortranCInterface_GLOBAL_FOUND OR NOT FortranCInterface_MODULE_FOUND) + message(WARNING "Reverting to pre-defined include/lapacke_mangling.h") +- configure_file(include/lapacke_mangling_with_flags.h.in +- ${LAPACK_BINARY_DIR}/include/lapacke_mangling.h) ++ configure_file(include/cblas_mangling_with_flags.h.in ++ ${LAPACK_BINARY_DIR}/include/cblas_mangling.h) + endif() + + include_directories(include ${LAPACK_BINARY_DIR}/include) + diff --git a/var/spack/repos/tutorial/packages/netlib-lapack/package.py b/var/spack/repos/tutorial/packages/netlib-lapack/package.py new file mode 100644 index 0000000000..ef43b8a2e0 --- /dev/null +++ b/var/spack/repos/tutorial/packages/netlib-lapack/package.py @@ -0,0 +1,186 @@ +# Copyright 2013-2018 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 NetlibLapack(CMakePackage): + """LAPACK version 3.X is a comprehensive FORTRAN library that does + linear algebra operations including matrix inversions, least squared + solutions to linear sets of equations, eigenvector analysis, singular + value decomposition, etc. It is a very comprehensive and reputable + package that has found extensive use in the scientific community. + + """ + homepage = "http://www.netlib.org/lapack/" + url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz" + + version('3.8.0', '96591affdbf58c450d45c1daa540dbd2', + url='http://www.netlib.org/lapack/lapack-3.8.0.tar.gz') + version('3.7.1', 'dcdeeed73de152c4643ccc5b1aeb453c') + version('3.7.0', '697bb8d67c7d336a0f339cc9dd0fa72f') + version('3.6.1', '421b2cb72e15f237e144428f9c460ee0') + version('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101') + version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf') + version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478') + version('3.4.1', '44c3869c38c8335c2b9c2a8bb276eb55') + version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70') + version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4') + + variant('shared', default=True, description="Build shared library version") + variant('external-blas', default=False, + description='Build lapack with an external blas') + + variant('lapacke', default=True, + description='Activates the build of the LAPACKE C interface') + variant('xblas', default=False, + description='Builds extended precision routines using XBLAS') + + patch('ibm-xl.patch', when='@3.7: %xl') + patch('ibm-xl.patch', when='@3.7: %xl_r') + + # https://github.com/Reference-LAPACK/lapack/issues/228 + # TODO: update 'when' once the version of lapack + # containing the fix is released and added to Spack. + patch('undefined_declarations.patch', when='@3.8.0:') + + # https://github.com/Reference-LAPACK/lapack/pull/268 + # TODO: update 'when' once the version of lapack + # containing the fix is released and added to Spack. + patch('testing.patch', when='@3.7.0:') + + # virtual dependency + provides('blas', when='~external-blas') + provides('lapack') + + depends_on('blas', when='+external-blas') + depends_on('netlib-xblas+fortran+plain_blas', when='+xblas') + depends_on('python@2.7:', type='test') + + # We need to run every phase twice in order to get static and shared + # versions of the libraries. When ~shared, we run the default + # implementations of the CMakePackage's phases and get only one building + # directory 'spack-build-static' with -DBUILD_SHARED_LIBS:BOOL=OFF (see + # implementations of self.build_directory and self.cmake_args() below). + # When +shared, we run the overridden methods for the phases, each + # running the default implementation twice with different values for + # self._building_shared. As a result, we get two building directories: + # 'spack-build-static' with -DBUILD_SHARED_LIBS:BOOL=OFF and + # 'spack-build-shared' with -DBUILD_SHARED_LIBS:BOOL=ON. + _building_shared = False + + def patch(self): + # Fix cblas CMakeLists.txt -- has wrong case for subdirectory name. + if self.spec.satisfies('@3.6.0:'): + filter_file( + '${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/', + '${CMAKE_CURRENT_SOURCE_DIR}/cmake/', + 'CBLAS/CMakeLists.txt', string=True) + + @property + def blas_libs(self): + shared = True if '+shared' in self.spec else False + query_parameters = self.spec.last_query.extra_parameters + query2libraries = { + tuple(): ['libblas'], + ('c', 'fortran'): [ + 'libcblas', + 'libblas', + ], + ('c',): [ + 'libcblas', + ], + ('fortran',): [ + 'libblas', + ] + } + key = tuple(sorted(query_parameters)) + libraries = query2libraries[key] + return find_libraries( + libraries, root=self.prefix, shared=shared, recursive=True + ) + + # TUTORIAL: add a proper `lapack_lib` property, along the lines + # of the `blas_lib` property above. The library that provides + # the lapack API is called `liblapack`. + + @property + def headers(self): + include_dir = self.spec.prefix.include + cblas_h = join_path(include_dir, 'cblas.h') + lapacke_h = join_path(include_dir, 'lapacke.h') + return HeaderList([cblas_h, lapacke_h]) + + @property + def build_directory(self): + return join_path(self.stage.source_path, + 'spack-build-shared' if self._building_shared + else 'spack-build-static') + + def cmake_args(self): + args = ['-DBUILD_SHARED_LIBS:BOOL=' + + ('ON' if self._building_shared else 'OFF')] + + if self.spec.satisfies('+lapacke'): + args.extend(['-DLAPACKE:BOOL=ON', '-DLAPACKE_WITH_TMG:BOOL=ON']) + else: + args.extend(['-DLAPACKE:BOOL=OFF', '-DLAPACKE_WITH_TMG:BOOL=OFF']) + + if self.spec.satisfies('@3.6.0:'): + args.append('-DCBLAS=ON') # always build CBLAS + + if self.spec.satisfies('%intel'): + # Intel compiler finds serious syntax issues when trying to + # build CBLAS and LapackE + args.extend(['-DCBLAS=OFF', '-DLAPACKE:BOOL=OFF']) + + if self.spec.satisfies('%xl') or self.spec.satisfies('%xl_r'): + # use F77 compiler if IBM XL + args.extend(['-DCMAKE_Fortran_COMPILER=' + self.compiler.f77, + '-DCMAKE_Fortran_FLAGS=' + + (' '.join(self.spec.compiler_flags['fflags'])) + + " -O3 -qnohot"]) + + # deprecated routines are commonly needed by, for example, suitesparse + # Note that OpenBLAS spack is built with deprecated routines + args.append('-DBUILD_DEPRECATED:BOOL=ON') + + if self.spec.satisfies('+external-blas'): + args.extend(['-DUSE_OPTIMIZED_BLAS:BOOL=ON', + '-DBLAS_LIBRARIES:PATH=' + + self.spec['blas'].libs.joined(';')]) + + if self.spec.satisfies('+xblas'): + args.extend(['-DXBLAS_INCLUDE_DIR=' + + self.spec['netlib-xblas'].prefix.include, + '-DXBLAS_LIBRARY=' + + self.spec['netlib-xblas'].libs.joined(';')]) + + args.append('-DBUILD_TESTING:BOOL=' + + ('ON' if self.run_tests else 'OFF')) + + return args + + # Build, install, and check both static and shared versions of the + # libraries when +shared + @when('+shared') + def cmake(self, spec, prefix): + for self._building_shared in (False, True): + super(NetlibLapack, self).cmake(spec, prefix) + + @when('+shared') + def build(self, spec, prefix): + for self._building_shared in (False, True): + super(NetlibLapack, self).build(spec, prefix) + + @when('+shared') + def install(self, spec, prefix): + for self._building_shared in (False, True): + super(NetlibLapack, self).install(spec, prefix) + + @when('+shared') + def check(self): + for self._building_shared in (False, True): + super(NetlibLapack, self).check() diff --git a/var/spack/repos/tutorial/packages/netlib-lapack/testing.patch b/var/spack/repos/tutorial/packages/netlib-lapack/testing.patch new file mode 100644 index 0000000000..fce18548c4 --- /dev/null +++ b/var/spack/repos/tutorial/packages/netlib-lapack/testing.patch @@ -0,0 +1,13 @@ +diff --git a/TESTING/LIN/alahd.f b/TESTING/LIN/alahd.f +index 8f4cd58d..6a4946e0 100644 +--- a/TESTING/LIN/alahd.f ++++ b/TESTING/LIN/alahd.f +@@ -1036,7 +1036,7 @@ + 9929 FORMAT( ' Test ratios (1-3: ', A1, 'TZRZF):' ) + 9920 FORMAT( 3X, ' 7-10: same as 3-6', 3X, ' 11-14: same as 3-6' ) + 9921 FORMAT( ' Test ratios:', / ' (1-2: ', A1, 'GELS, 3-6: ', A1, +- $ 'GELSY, 7-10: ', A1, 'GELSS, 11-14: ', A1, 'GELSD, 15-16: ' ++ $ 'GELSY, 7-10: ', A1, 'GELSS, 11-14: ', A1, 'GELSD, 15-16: ', + $ A1, 'GETSLS)') + 9928 FORMAT( 7X, 'where ALPHA = ( 1 + SQRT( 17 ) ) / 8' ) + 9927 FORMAT( 3X, I2, ': ABS( Largest element in L )', / 12X, diff --git a/var/spack/repos/tutorial/packages/netlib-lapack/undefined_declarations.patch b/var/spack/repos/tutorial/packages/netlib-lapack/undefined_declarations.patch new file mode 100644 index 0000000000..9dac2562f7 --- /dev/null +++ b/var/spack/repos/tutorial/packages/netlib-lapack/undefined_declarations.patch @@ -0,0 +1,26 @@ +diff --git a/SRC/dsytrf_aa_2stage.f b/SRC/dsytrf_aa_2stage.f +index 2991305..f5f06cc 100644 +--- a/SRC/dsytrf_aa_2stage.f ++++ b/SRC/dsytrf_aa_2stage.f +@@ -191,7 +191,7 @@ + EXTERNAL LSAME, ILAENV + * .. + * .. External Subroutines .. +- EXTERNAL XERBLA, DCOPY, DLACGV, DLACPY, ++ EXTERNAL XERBLA, DCOPY, DLACPY, + $ DLASET, DGBTRF, DGEMM, DGETRF, + $ DSYGST, DSWAP, DTRSM + * .. +diff --git a/SRC/ssytrf_aa_2stage.f b/SRC/ssytrf_aa_2stage.f +index be6809d..a929749 100644 +--- a/SRC/ssytrf_aa_2stage.f ++++ b/SRC/ssytrf_aa_2stage.f +@@ -191,7 +191,7 @@ + EXTERNAL LSAME, ILAENV + * .. + * .. External Subroutines .. +- EXTERNAL XERBLA, SCOPY, SLACGV, SLACPY, ++ EXTERNAL XERBLA, SCOPY, SLACPY, + $ SLASET, SGBTRF, SGEMM, SGETRF, + $ SSYGST, SSWAP, STRSM + * .. diff --git a/var/spack/repos/tutorial/repo.yaml b/var/spack/repos/tutorial/repo.yaml new file mode 100644 index 0000000000..b43f511136 --- /dev/null +++ b/var/spack/repos/tutorial/repo.yaml @@ -0,0 +1,2 @@ +repo: + namespace: tutorial |