update tutorial version of hdf5 (#25368)
This commit is contained in:
Chris White
GitHub
parent
b847bb72f0
commit
79ac572f21
@ -0,0 +1,11 @@
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--- a/src/H5public.h 2019-08-28 18:51:39.393781356 -0400
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+++ b/src/H5public.h 2019-08-28 20:59:50.315181711 -0400
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@@ -57,6 +57,8 @@
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# include <stddef.h>
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#endif
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#ifdef H5_HAVE_PARALLEL
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+# define MPICH_SKIP_MPICXX 1
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+# define OMPI_SKIP_MPICXX 1
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# include <mpi.h>
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#ifndef MPI_FILE_NULL /*MPIO may be defined in mpi.h already */
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# include <mpio.h>
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12
var/spack/repos/tutorial/packages/hdf5/hdf5_1.8_gcc10.patch
Normal file
12
var/spack/repos/tutorial/packages/hdf5/hdf5_1.8_gcc10.patch
Normal file
@ -0,0 +1,12 @@
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diff -Naur hdf5.orig/fortran/test/tH5T_F03.f90 hdf5/fortran/test/tH5T_F03.f90
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--- hdf5.orig/fortran/test/tH5T_F03.f90 2021-01-19 13:23:11.298000000 +0100
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+++ hdf5/fortran/test/tH5T_F03.f90 2021-01-19 13:19:17.637000000 +0100
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@@ -1541,7 +1541,7 @@
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INTEGER :: A, B, C, D
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INTEGER :: Aw, Bw, Cw, Dw
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INTEGER :: i, j
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- INTEGER, PARAMETER :: hex = Z'00000003'
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+ INTEGER, PARAMETER :: hex = INT(Z'00000003')
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TYPE(C_PTR) :: f_ptr
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INTEGER :: error ! Error flag
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!
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@ -3,62 +3,109 @@
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import os
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import shutil
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import sys
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from spack import *
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import llnl.util.tty as tty
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class Hdf5(AutotoolsPackage):
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class Hdf5(CMakePackage):
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"""HDF5 is a data model, library, and file format for storing and managing
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data. It supports an unlimited variety of datatypes, and is designed for
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flexible and efficient I/O and for high volume and complex data.
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"""
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homepage = "https://support.hdfgroup.org/HDF5/"
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url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz"
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homepage = "https://portal.hdfgroup.org"
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url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.7/src/hdf5-1.10.7.tar.gz"
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list_url = "https://support.hdfgroup.org/ftp/HDF5/releases"
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list_depth = 3
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git = "https://github.com/HDFGroup/hdf5.git"
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maintainers = ['lrknox', 'brtnfld', 'byrnHDF', 'ChristopherHogan', 'epourmal',
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'gheber', 'hyoklee', 'lkurz', 'soumagne']
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version('1.10.4', '8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2')
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version('1.10.3', 'b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39')
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version('1.10.2', '8d4eae84e533efa57496638fd0dca8c3')
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version('1.10.1', '43a2f9466702fb1db31df98ae6677f15')
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version('1.10.0-patch1', '9180ff0ef8dc2ef3f61bd37a7404f295')
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version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199')
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version('1.8.19', '7f568e2464d4ab0a74d16b23956d900b')
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version('1.8.18', 'dd2148b740713ca0295442ec683d7b1c')
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version('1.8.17', '7d572f8f3b798a628b8245af0391a0ca')
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version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618')
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version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24')
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version('1.8.14', 'a482686e733514a51cde12d6fe5c5d95')
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version('1.8.13', 'c03426e9e77d7766944654280b467289')
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version('1.8.12', 'd804802feb99b87fc668a90e6fa34411')
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version('1.8.10', '710aa9fb61a51d61a7e2c09bf0052157')
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test_requires_compiler = True
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# The 'develop' version is renamed so that we could uninstall (or patch) it
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# without affecting other develop version.
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version('develop-1.13', branch='develop')
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version('develop-1.12', branch='hdf5_1_12')
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version('develop-1.10', branch='hdf5_1_10')
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version('develop-1.8', branch='hdf5_1_8')
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version('1.12.1', sha256='79c66ff67e666665369396e9c90b32e238e501f345afd2234186bfb8331081ca')
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version('1.12.0', sha256='a62dcb276658cb78e6795dd29bf926ed7a9bc4edf6e77025cd2c689a8f97c17a')
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# HDF5 1.12 broke API compatibility, so we currently prefer the latest
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# 1.10 release. packages that want later versions of HDF5 should specify,
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# e.g., depends_on("hdf5@1.12:") to get 1.12 or higher.
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version('1.10.7', sha256='7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15', preferred=True)
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version('1.10.6', sha256='5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa')
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version('1.10.5', sha256='6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8')
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version('1.10.4', sha256='8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2')
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version('1.10.3', sha256='b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39')
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version('1.10.2', sha256='bfec1be8c366965a99812cf02ddc97e4b708c1754fccba5414d4adccdc073866')
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version('1.10.1', sha256='048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172')
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version('1.10.0-patch1', sha256='6e78cfe32a10e6e0629393cdfddf6cfa536571efdaf85f08e35326e1b4e9eff0')
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version('1.10.0', sha256='81f6201aba5c30dced5dcd62f5d5477a2790fd5850e02ac514ca8bf3e2bb375a')
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version('1.8.22', sha256='8406d96d9355ef8961d2739fb8fd5474ad4cdf52f3cfac657733defd9709bfaa')
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version('1.8.21', sha256='87d8c82eba5cf766d97cd06c054f4639c1049c4adeaa3a79f77f8bd374f80f37')
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version('1.8.19', sha256='a4335849f19fae88c264fd0df046bc321a78c536b2548fc508627a790564dc38')
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version('1.8.18', sha256='cdb195ad8d9e6782acf24b2488061289f615628c2ccda8457b0a0c3fb7a8a063')
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version('1.8.17', sha256='d9cda297ee76ade9881c4208987939250d397bae6252d0ccb66fa7d24d67e263')
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version('1.8.16', sha256='ed17178abd9928a7237f30370189ba767b9e39e0db45917c2ac4665eb9cb4771')
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version('1.8.15', sha256='4e963216b7d32469596bc1321a8c3f6e0c278dcbbdb7be6414c63c081b34c275')
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version('1.8.14', sha256='1dbefeeef7f591897c632b2b090db96bb8d35ad035beaa36bc39cb2bc67e0639')
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version('1.8.13', sha256='82f6b38eec103b4fccfbf14892786e0c27a8135d3252d8601cf5bf20066d38c1')
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version('1.8.12', sha256='b5cccea850096962b5fd9e96f22c4f47d2379224bb41130d9bc038bb6c37dfcb')
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version('1.8.10', sha256='4813b79c5fb8701a625b9924b8203bc7154a77f9b826ad4e034144b4056a160a')
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variant('debug', default=False,
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description='Builds a debug version of the library')
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variant('shared', default=True,
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description='Builds a shared version of the library')
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variant('hl', default=False, description='Enable the high-level library')
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variant('cxx', default=False, description='Enable C++ support')
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variant('fortran', default=False, description='Enable Fortran support')
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variant('java', default=False, description='Enable Java support')
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variant('threadsafe', default=False,
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description='Enable thread-safe capabilities')
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variant('tools', default=True, description='Enable building tools')
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variant('mpi', default=True, description='Enable MPI support')
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variant('szip', default=False, description='Enable szip support')
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variant('pic', default=True,
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description='Produce position-independent code (for shared libs)')
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# Build HDF5 with API compatibility.
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variant('api', default='default',
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description='Choose api compatibility for earlier version',
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values=('default', 'v114', 'v112', 'v110', 'v18', 'v16'),
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multi=False)
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depends_on('cmake@3.12:', type='build')
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depends_on('mpi', when='+mpi')
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depends_on('java', type=('build', 'run'), when='+java')
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# numactl does not currently build on darwin
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if sys.platform != 'darwin':
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depends_on('numactl', when='+mpi+fortran')
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depends_on('szip', when='+szip')
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depends_on('zlib@1.1.2:')
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# The compiler wrappers (h5cc, h5fc, etc.) run 'pkg-config'.
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depends_on('pkgconfig', type='run')
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conflicts('api=v114', when='@1.6:1.12.99',
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msg='v114 is not compatible with this release')
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conflicts('api=v112', when='@1.6:1.10.99',
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msg='v112 is not compatible with this release')
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conflicts('api=v110', when='@1.6:1.8.99',
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msg='v110 is not compatible with this release')
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conflicts('api=v18', when='@1.6:1.6.99',
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msg='v18 is not compatible with this release')
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# The Java wrappers and associated libhdf5_java library
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# were first available in 1.10
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conflicts('+java', when='@:1.9')
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# The Java wrappers cannot be built without shared libs.
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conflicts('+java', when='~shared')
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# There are several officially unsupported combinations of the features:
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# 1. Thread safety is not guaranteed via high-level C-API but in some cases
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# it works.
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@ -96,14 +143,74 @@ class Hdf5(AutotoolsPackage):
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# There are build errors with GCC 8, see
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# https://forum.hdfgroup.org/t/1-10-2-h5detect-compile-error-gcc-8-1-0-on-centos-7-2-solved/4441
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patch('https://salsa.debian.org/debian-gis-team/hdf5/raw/bf94804af5f80f662cad80a5527535b3c6537df6/debian/patches/gcc-8.patch', sha256='57cee5ff1992b4098eda079815c36fc2da9b10e00a9056df054f2384c4fc7523', when='@1.10.2%gcc@8:')
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patch('https://salsa.debian.org/debian-gis-team/hdf5/raw/bf94804af5f80f662cad80a5527535b3c6537df6/debian/patches/gcc-8.patch',
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sha256='57cee5ff1992b4098eda079815c36fc2da9b10e00a9056df054f2384c4fc7523',
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when='@1.10.2%gcc@8:')
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filter_compiler_wrappers('h5cc', 'h5c++', 'h5fc', relative_root='bin')
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# Disable MPI C++ interface when C++ is disabled, otherwise downstream
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# libraries fail to link; see https://github.com/spack/spack/issues/12586
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patch('h5public-skip-mpicxx.patch', when='@1.8.10:1.8.21,1.10.0:1.10.5+mpi~cxx',
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sha256='b61e2f058964ad85be6ee5ecea10080bf79e73f83ff88d1fa4b602d00209da9c')
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# Fixes BOZ literal constant error when compiled with GCC 10.
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# The issue is described here: https://github.com/spack/spack/issues/18625
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patch('hdf5_1.8_gcc10.patch', when='@:1.8.21',
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sha256='0e20187cda3980a4fdff410da92358b63de7ebef2df1d7a425371af78e50f666')
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# The argument 'buf_size' of the C function 'h5fget_file_image_c' is
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# declared as intent(in) though it is modified by the invocation. As a
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# result, aggressive compilers such as Fujitsu's may do a wrong
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# optimization to cause an error.
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def patch(self):
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filter_file(
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'INTEGER(SIZE_T), INTENT(IN) :: buf_size',
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'INTEGER(SIZE_T), INTENT(OUT) :: buf_size',
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'fortran/src/H5Fff.F90',
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string=True, ignore_absent=True)
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filter_file(
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'INTEGER(SIZE_T), INTENT(IN) :: buf_size',
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'INTEGER(SIZE_T), INTENT(OUT) :: buf_size',
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'fortran/src/H5Fff_F03.f90',
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string=True, ignore_absent=True)
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# The parallel compiler wrappers (i.e. h5pcc, h5pfc, etc.) reference MPI
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# compiler wrappers and do not need to be changed.
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filter_compiler_wrappers('h5cc', 'h5hlcc',
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'h5fc', 'h5hlfc',
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'h5c++', 'h5hlc++',
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relative_root='bin')
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def url_for_version(self, version):
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url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-{0}/hdf5-{1}/src/hdf5-{1}.tar.gz"
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return url.format(version.up_to(2), version)
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def flag_handler(self, name, flags):
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cmake_flags = []
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if name == "cflags":
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if self.spec.satisfies('%gcc') \
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or self.spec.satisfies('%clang'):
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# Quiet warnings/errors about implicit declaration of functions
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# in C99:
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cmake_flags.append("-Wno-implicit-function-declaration")
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# Note that this flag will cause an error if building %nvhpc.
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if self.spec.satisfies('@:1.8.12~shared'):
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# More recent versions set CMAKE_POSITION_INDEPENDENT_CODE to
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# True and build with PIC flags.
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cmake_flags.append(self.compiler.cc_pic_flag)
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elif name == 'cxxflags':
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if self.spec.satisfies('@:1.8.12+cxx~shared'):
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cmake_flags.append(self.compiler.cxx_pic_flag)
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elif name == "fflags":
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if self.spec.satisfies('@:1.8.12+fortran~shared'):
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cmake_flags.append(self.compiler.fc_pic_flag)
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elif name == "ldlibs":
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if '+fortran %fj' in self.spec:
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cmake_flags.extend(['-lfj90i', '-lfj90f',
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'-lfjsrcinfo', '-lelf'])
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return flags, None, (cmake_flags or None)
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@property
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def libs(self):
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"""HDF5 can be queried for the following parameters:
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@ -111,18 +218,46 @@ def libs(self):
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- "hl": high-level interface
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- "cxx": C++ APIs
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- "fortran": Fortran APIs
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- "java": Java APIs
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:return: list of matching libraries
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"""
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query_parameters = self.spec.last_query.extra_parameters
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shared = '+shared' in self.spec
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# This map contains a translation from query_parameters
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# to the libraries needed
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query2libraries = { # noqa: F841
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query2libraries = {
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tuple(): ['libhdf5'],
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('cxx', 'fortran', 'hl'): [
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'libhdf5hl_fortran',
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('cxx', 'fortran', 'hl', 'java'): [
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# When installed with Autotools, the basename of the real
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# library file implementing the High-level Fortran interface is
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# 'libhdf5hl_fortran'. Starting versions 1.8.22, 1.10.5 and
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# 1.12.0, the Autotools installation also produces a symbolic
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# link 'libhdf5_hl_fortran.<so/a>' to
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# 'libhdf5hl_fortran.<so/a>'. Note that in the case of the
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# dynamic library, the latter is a symlink to the real sonamed
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# file 'libhdf5_fortran.so.<abi-version>'. This means that all
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# dynamically linked executables/libraries of the dependent
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# packages need 'libhdf5_fortran.so.<abi-version>' with the same
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# DT_SONAME entry. However, the CMake installation (at least
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# starting version 1.8.10) does not produce it. Instead, the
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# basename of the library file is 'libhdf5_hl_fortran'. Which
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# means that switching to CMake requires rebuilding of all
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# dependant packages that use the High-level Fortran interface.
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# Therefore, we do not try to preserve backward compatibility
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# with Autotools installations by creating symlinks. The only
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# packages that could benefit from it would be those that
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# hardcode the library name in their building systems. Such
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# packages should simply be patched.
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'libhdf5_hl_fortran',
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'libhdf5_hl_f90cstub',
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'libhdf5_hl_cpp',
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'libhdf5_hl',
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'libhdf5_fortran',
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'libhdf5_f90cstub',
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'libhdf5_java',
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'libhdf5',
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],
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('cxx', 'hl'): [
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@ -131,9 +266,11 @@ def libs(self):
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'libhdf5',
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],
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('fortran', 'hl'): [
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'libhdf5hl_fortran',
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'libhdf5_hl_fortran',
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'libhdf5_hl_f90cstub',
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'libhdf5_hl',
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'libhdf5_fortran',
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'libhdf5_f90cstub',
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'libhdf5',
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],
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('hl',): [
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@ -142,6 +279,7 @@ def libs(self):
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],
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('cxx', 'fortran'): [
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'libhdf5_fortran',
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'libhdf5_f90cstub',
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'libhdf5_cpp',
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'libhdf5',
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],
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@ -151,112 +289,155 @@ def libs(self):
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],
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('fortran',): [
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'libhdf5_fortran',
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'libhdf5_f90cstub',
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'libhdf5',
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],
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('java',): [
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'libhdf5_java',
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'libhdf5',
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]
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}
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# TUTORIAL: you need to fix the implementation below, and
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# return the correct list of libraries according to the
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# query parameters your dependency has used.
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||||
#
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||||
# 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 []
|
||||
# Turn the query into the appropriate key
|
||||
key = tuple(sorted(query_parameters))
|
||||
libraries = query2libraries[key]
|
||||
|
||||
@run_before('configure')
|
||||
return find_libraries(
|
||||
libraries, root=self.prefix, shared=shared, recursive=True
|
||||
)
|
||||
|
||||
@when('@:1.8.21,1.10.0:1.10.5+szip')
|
||||
def setup_build_environment(self, env):
|
||||
env.set('SZIP_INSTALL', self.spec['szip'].prefix)
|
||||
|
||||
@run_before('cmake')
|
||||
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')
|
||||
def cmake_args(self):
|
||||
spec = self.spec
|
||||
|
||||
if '+szip' in self.spec:
|
||||
extra_args.append('--with-szlib=%s' % self.spec['szip'].prefix)
|
||||
else:
|
||||
extra_args.append('--without-szlib')
|
||||
if spec.satisfies('@:1.8.15+shared'):
|
||||
tty.warn('hdf5@:1.8.15+shared does not produce static libraries')
|
||||
|
||||
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')
|
||||
args = [
|
||||
# Always enable this option. This does not actually enable any
|
||||
# features: it only *allows* the user to specify certain
|
||||
# combinations of other arguments.
|
||||
self.define('ALLOW_UNSUPPORTED', True),
|
||||
# Speed-up the building by skipping the examples:
|
||||
self.define('HDF5_BUILD_EXAMPLES', False),
|
||||
self.define(
|
||||
'BUILD_TESTING',
|
||||
self.run_tests or
|
||||
# Version 1.8.22 fails to build the tools when shared libraries
|
||||
# are enabled but the tests are disabled.
|
||||
spec.satisfies('@1.8.22+shared+tools')),
|
||||
self.define('HDF5_ENABLE_Z_LIB_SUPPORT', True),
|
||||
self.define_from_variant('HDF5_ENABLE_SZIP_SUPPORT', 'szip'),
|
||||
self.define_from_variant('HDF5_ENABLE_SZIP_ENCODING', 'szip'),
|
||||
self.define_from_variant('BUILD_SHARED_LIBS', 'shared'),
|
||||
self.define('ONLY_SHARED_LIBS', False),
|
||||
self.define_from_variant('HDF5_ENABLE_PARALLEL', 'mpi'),
|
||||
self.define_from_variant('HDF5_ENABLE_THREADSAFE', 'threadsafe'),
|
||||
self.define_from_variant('HDF5_BUILD_HL_LIB', 'hl'),
|
||||
self.define_from_variant('HDF5_BUILD_CPP_LIB', 'cxx'),
|
||||
self.define_from_variant('HDF5_BUILD_FORTRAN', 'fortran'),
|
||||
self.define_from_variant('HDF5_BUILD_JAVA', 'java'),
|
||||
self.define_from_variant('HDF5_BUILD_TOOLS', 'tools')
|
||||
]
|
||||
|
||||
# '--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')
|
||||
api = spec.variants['api'].value
|
||||
if api != 'default':
|
||||
args.append(self.define('DEFAULT_API_VERSION', api))
|
||||
|
||||
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 '+mpi' in spec:
|
||||
args.append(self.define('CMAKE_C_COMPILER', spec['mpi'].mpicc))
|
||||
|
||||
if '+cxx' in self.spec:
|
||||
extra_args.append('CXX=%s' % self.spec['mpi'].mpicxx)
|
||||
args.append(self.define('CMAKE_CXX_COMPILER',
|
||||
spec['mpi'].mpicxx))
|
||||
|
||||
if '+fortran' in self.spec:
|
||||
extra_args.append('FC=%s' % self.spec['mpi'].mpifc)
|
||||
args.append(self.define('CMAKE_Fortran_COMPILER',
|
||||
spec['mpi'].mpifc))
|
||||
|
||||
extra_args.append('--with-zlib=%s' % self.spec['zlib'].prefix)
|
||||
return args
|
||||
|
||||
return extra_args
|
||||
@run_after('install')
|
||||
def ensure_parallel_compiler_wrappers(self):
|
||||
# When installed with Autotools and starting at least version 1.8.10,
|
||||
# the package produces C compiler wrapper called either 'h5cc' (when MPI
|
||||
# support is disabled) or 'h5pcc' (when MPI support is enabled). The
|
||||
# CMake installation produces the wrapper called 'h5cc' (regardless of
|
||||
# whether MPI support is enabled) only starting versions 1.8.21, 1.10.2
|
||||
# and 1.12.0. The current develop versions also produce 'h5pcc' when MPI
|
||||
# support is enabled and the file is identical to 'h5cc'. Here, we make
|
||||
# sure that 'h5pcc' is available when MPI support is enabled (only for
|
||||
# versions that generate 'h5cc').
|
||||
if self.spec.satisfies('@1.8.21:1.8.22,1.10.2:1.10.7,1.12.0+mpi'):
|
||||
with working_dir(self.prefix.bin):
|
||||
# No try/except here, fix the condition above instead:
|
||||
symlink('h5cc', 'h5pcc')
|
||||
|
||||
@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')
|
||||
# The same as for 'h5pcc'. However, the CMake installation produces the
|
||||
# Fortran compiler wrapper called 'h5fc' only starting versions 1.8.22,
|
||||
# 1.10.6 and 1.12.0. The current develop versions do not produce 'h5pfc'
|
||||
# at all. Here, we make sure that 'h5pfc' is available when Fortran and
|
||||
# MPI support are enabled (only for versions that generate 'h5fc').
|
||||
if self.spec.satisfies('@1.8.22:1.8.999,'
|
||||
'1.10.6:1.10.999,'
|
||||
'1.12.0:1.12.999,'
|
||||
'develop:'
|
||||
'+fortran+mpi'):
|
||||
with working_dir(self.prefix.bin):
|
||||
# No try/except here, fix the condition above instead:
|
||||
symlink('h5fc', 'h5pfc')
|
||||
|
||||
@run_after('install')
|
||||
def fix_package_config(self):
|
||||
# We need to fix the pkg-config files, which are also used by the
|
||||
# compiler wrappers. The files are created starting versions 1.8.21,
|
||||
# 1.10.2 and 1.12.0. However, they are broken (except for the version
|
||||
# 1.8.22): the files are named <name>-<version>.pc but reference <name>
|
||||
# packages. This was fixed in the develop versions at some point: the
|
||||
# files started referencing <name>-<version> packages but got broken
|
||||
# again: the files got names <name>.pc but references had not been
|
||||
# updated accordingly. Another issue, which we address here, is that
|
||||
# some Linux distributions install pkg-config files named hdf5.pc and we
|
||||
# want to override them. Therefore, the following solution makes sure
|
||||
# that each <name>-<version>.pc file is symlinked by <name>.pc and all
|
||||
# references to <name>-<version> packages in the original files are
|
||||
# replaced with references to <name> packages.
|
||||
pc_files = find(self.prefix.lib.pkgconfig, 'hdf5*.pc', recursive=False)
|
||||
|
||||
if not pc_files:
|
||||
# This also tells us that the pkgconfig directory does not exist.
|
||||
return
|
||||
|
||||
# Replace versioned references in all pkg-config files:
|
||||
filter_file(
|
||||
r'(Requires(?:\.private)?:.*)(hdf5[^\s,]*)(?:-[^\s,]*)(.*)',
|
||||
r'\1\2\3', *pc_files, backup=False)
|
||||
|
||||
# Create non-versioned symlinks to the versioned pkg-config files:
|
||||
with working_dir(self.prefix.lib.pkgconfig):
|
||||
for f in pc_files:
|
||||
src_filename = os.path.basename(f)
|
||||
version_sep_idx = src_filename.find('-')
|
||||
if version_sep_idx > -1:
|
||||
tgt_filename = src_filename[:version_sep_idx] + '.pc'
|
||||
if not os.path.exists(tgt_filename):
|
||||
symlink(src_filename, tgt_filename)
|
||||
|
||||
@run_after('install')
|
||||
@on_package_attributes(run_tests=True)
|
||||
def check_install(self):
|
||||
self._check_install()
|
||||
|
||||
def _check_install(self):
|
||||
# Build and run a small program to test the installed HDF5 library
|
||||
spec = self.spec
|
||||
print("Checking HDF5 installation...")
|
||||
@ -305,3 +486,54 @@ def check_install(self):
|
||||
print('-' * 80)
|
||||
raise RuntimeError("HDF5 install check failed")
|
||||
shutil.rmtree(checkdir)
|
||||
|
||||
def _test_check_versions(self):
|
||||
"""Perform version checks on selected installed package binaries."""
|
||||
spec_vers_str = 'Version {0}'.format(self.spec.version)
|
||||
|
||||
exes = [
|
||||
'h5copy', 'h5diff', 'h5dump', 'h5format_convert', 'h5ls',
|
||||
'h5mkgrp', 'h5repack', 'h5stat', 'h5unjam',
|
||||
]
|
||||
use_short_opt = ['h52gif', 'h5repart', 'h5unjam']
|
||||
for exe in exes:
|
||||
reason = 'test: ensuring version of {0} is {1}' \
|
||||
.format(exe, spec_vers_str)
|
||||
option = '-V' if exe in use_short_opt else '--version'
|
||||
self.run_test(exe, option, spec_vers_str, installed=True,
|
||||
purpose=reason, skip_missing=True)
|
||||
|
||||
def _test_example(self):
|
||||
"""This test performs copy, dump, and diff on an example hdf5 file."""
|
||||
test_data_dir = self.test_suite.current_test_data_dir
|
||||
|
||||
filename = 'spack.h5'
|
||||
h5_file = test_data_dir.join(filename)
|
||||
|
||||
reason = 'test: ensuring h5dump produces expected output'
|
||||
expected = get_escaped_text_output(test_data_dir.join('dump.out'))
|
||||
self.run_test('h5dump', filename, expected, installed=True,
|
||||
purpose=reason, skip_missing=True,
|
||||
work_dir=test_data_dir)
|
||||
|
||||
reason = 'test: ensuring h5copy runs'
|
||||
options = ['-i', h5_file, '-s', 'Spack', '-o', 'test.h5', '-d',
|
||||
'Spack']
|
||||
self.run_test('h5copy', options, [], installed=True,
|
||||
purpose=reason, skip_missing=True, work_dir='.')
|
||||
|
||||
reason = ('test: ensuring h5diff shows no differences between orig and'
|
||||
' copy')
|
||||
self.run_test('h5diff', [h5_file, 'test.h5'], [], installed=True,
|
||||
purpose=reason, skip_missing=True, work_dir='.')
|
||||
|
||||
def test(self):
|
||||
"""Perform smoke tests on the installed package."""
|
||||
# Simple version check tests on known binaries
|
||||
self._test_check_versions()
|
||||
|
||||
# Run sequence of commands on an hdf5 file
|
||||
self._test_example()
|
||||
|
||||
# Run existing install check
|
||||
self._check_install()
|
||||
|
||||
45
var/spack/repos/tutorial/packages/hdf5/test/dump.out
Normal file
45
var/spack/repos/tutorial/packages/hdf5/test/dump.out
Normal file
@ -0,0 +1,45 @@
|
||||
HDF5 "spack.h5" {
|
||||
GROUP "/" {
|
||||
GROUP "Spack" {
|
||||
GROUP "Software" {
|
||||
ATTRIBUTE "Distribution" {
|
||||
DATATYPE H5T_STRING {
|
||||
STRSIZE H5T_VARIABLE;
|
||||
STRPAD H5T_STR_NULLTERM;
|
||||
CSET H5T_CSET_UTF8;
|
||||
CTYPE H5T_C_S1;
|
||||
}
|
||||
DATASPACE SCALAR
|
||||
DATA {
|
||||
(0): "Open Source"
|
||||
}
|
||||
}
|
||||
DATASET "data" {
|
||||
DATATYPE H5T_IEEE_F64LE
|
||||
DATASPACE SIMPLE { ( 7, 11 ) / ( 7, 11 ) }
|
||||
DATA {
|
||||
(0,0): 0.371141, 0.508482, 0.585975, 0.0944911, 0.684849,
|
||||
(0,5): 0.580396, 0.720271, 0.693561, 0.340432, 0.217145,
|
||||
(0,10): 0.636083,
|
||||
(1,0): 0.686996, 0.773501, 0.656767, 0.617543, 0.226132,
|
||||
(1,5): 0.768632, 0.0548711, 0.54572, 0.355544, 0.591548,
|
||||
(1,10): 0.233007,
|
||||
(2,0): 0.230032, 0.192087, 0.293845, 0.0369338, 0.038727,
|
||||
(2,5): 0.0977931, 0.966522, 0.0821391, 0.857921, 0.495703,
|
||||
(2,10): 0.746006,
|
||||
(3,0): 0.598494, 0.990266, 0.993009, 0.187481, 0.746391,
|
||||
(3,5): 0.140095, 0.122661, 0.929242, 0.542415, 0.802758,
|
||||
(3,10): 0.757941,
|
||||
(4,0): 0.372124, 0.411982, 0.270479, 0.950033, 0.329948,
|
||||
(4,5): 0.936704, 0.105097, 0.742285, 0.556565, 0.18988, 0.72797,
|
||||
(5,0): 0.801669, 0.271807, 0.910649, 0.186251, 0.868865,
|
||||
(5,5): 0.191484, 0.788371, 0.920173, 0.582249, 0.682022,
|
||||
(5,10): 0.146883,
|
||||
(6,0): 0.826824, 0.0886705, 0.402606, 0.0532444, 0.72509,
|
||||
(6,5): 0.964683, 0.330362, 0.833284, 0.630456, 0.411489, 0.247806
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
BIN
var/spack/repos/tutorial/packages/hdf5/test/spack.h5
Normal file
BIN
var/spack/repos/tutorial/packages/hdf5/test/spack.h5
Normal file
Binary file not shown.
Loading…
Reference in New Issue
Block a user