¹Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
²Center for Free-Electron Laser Science, Hamburg, Germany
³University of Southampton, Southampton, United Kingdom
Slides: https://s.gwdg.de/Ztnnel
module avail--------------- /opt_mpsd/linux-debian12/25a/sandybridge/lmod/Core ---------------
gcc/12.3.0 gcc/14.2.0 (L) intel-oneapi-compilers/2023.2.4
gcc/13.2.0 miniforge3/24.11.2-1 intel-oneapi-compilers/2025.0.0
------------ /opt_mpsd/linux-debian12/25a/sandybridge/lmod/gcc/14.2.0 ------------
boost/1.86.0 libpthread-stubs/0.5 py-h5py/3.12.1
fftw/3.3.10 libyaml/0.2.5 python/3.11.7
gettext/0.22.5 ncurses/6.5 tar/1.34
gsl/2.8 ninja/1.10.2 valgrind/3.23.0
hdf5/1.14.5 ninja/1.12.1 xcb-proto/1.17.0
kbproto/1.0.7 octopus-dependencies/full xtrans/1.5.2
knem/1.1.4 octopus-dependencies/min xz/5.4.6
krb5/1.21.3 openblas/0.3.28 zlib-ng/2.2.1
libaec/1.0.6 openmpi/4.1.5 (L) zstd/1.5.6
- /opt_mpsd/linux-debian12/25a/sandybridge/lmod/openmpi/4.1.5-jmeo3kl/gcc/14.2.0 -
berkeleygw/3.1.0 elpa/2024.03.001 netcdf-fortran/4.6.1
berkeleygw/4.0 etsf-io/1.0.4 netlib-scalapack/2.2.0
bigdft-atlab/1.9.5 fftw/3.3.10 octopus-dependencies/full
bigdft-futile/1.9.5 hdf5/1.14.5 octopus-dependencies/min
elpa-openmp/2024.03.001 netcdf-c/4.9.2 pfft/1.0.8-alpha
$ git clone https://github.com/spack/spack.git
$ cd spack && source share/spack/setup-env.sh
$ spack install zlib
[...]
==> Installing zlib-1.3.1-u37gjgxqi7fzjox4gmajk4wxj7jyisn2 [4/4]
==> No binary for zlib-1.3.1-u37gjgxqi7fzjox4gmajk4wxj7jyisn2 found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/9a/9a93b2b7dfdac77ceba5a558a580e74667dd6fede4585b91eefb60f03b72df23.tar.gz
==> No patches needed for zlib
==> zlib: Executing phase: 'edit'
==> zlib: Executing phase: 'build'
==> zlib: Executing phase: 'install'
==> zlib: Successfully installed zlib-1.3.1-u37gjgxqi7fzjox4gmajk4wxj7jyisn2
Stage: 0.24s. Edit: 0.41s. Build: 1.17s. Install: 0.04s. Post-install: 0.01s. Total: 1.97s
[+] /spack/opt/spack/linux-debian12-zen3/gcc-12.2.0/zlib-1.3.1-u37gjgxqi7fzjox4gmajk4wxj7jyisn2
$ spack find
-- linux-debian12-zen3 / gcc@12.2.0 -----------------------------
gcc-runtime@12.2.0 glibc@2.36 gmake@4.4.1 zlib@1.3.1
==> 4 installed packages
spack install hdf5@1.12.2%gcc@12.2.0+fortran~cxx ^openmpi@4.1.6
$ spack info hdf5
CMakePackage: hdf5
Description:
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
Preferred version:
1.14.5 https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_5/downloads/hdf5-1.14.5.tar.gz
Safe versions:
develop-2.0 [git] https://github.com/HDFGroup/hdf5.git on branch develop
develop-1.14 [git] https://github.com/HDFGroup/hdf5.git on branch hdf5_1_14
develop-1.12 [git] https://github.com/HDFGroup/hdf5.git on branch hdf5_1_12
develop-1.10 [git] https://github.com/HDFGroup/hdf5.git on branch hdf5_1_10
develop-1.8 [git] https://github.com/HDFGroup/hdf5.git on branch hdf5_1_8
1.14.5 https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_5/downloads/hdf5-1.14.5.tar.gz
1.14.4-3 https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/downloads/hdf5-1.14.4-3.tar.gz
1.14.3 https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_3/downloads/hdf5-1.14.3.tar.gz
1.14.2 https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_2/downloads/hdf5-1.14.2.tar.gz
1.14.1-2 https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_1/downloads/hdf5-1.14.1-2.tar.gz
1.14.0 https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_0/downloads/hdf5-1.14.0.tar.gz
1.12.3 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.3/src/hdf5-1.12.3.tar.gz
1.12.2 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.2/src/hdf5-1.12.2.tar.gz
1.12.1 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/src/hdf5-1.12.1.tar.gz
1.12.0 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0/src/hdf5-1.12.0.tar.gz
1.10.11 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.11/src/hdf5-1.10.11.tar.gz
1.10.10 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.10/src/hdf5-1.10.10.tar.gz
1.10.9 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.9/src/hdf5-1.10.9.tar.gz
1.10.8 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.8/src/hdf5-1.10.8.tar.gz
1.10.7 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.7/src/hdf5-1.10.7.tar.gz
1.10.6 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.6/src/hdf5-1.10.6.tar.gz
1.10.5 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.gz
1.10.4 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.4/src/hdf5-1.10.4.tar.gz
1.10.3 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.3/src/hdf5-1.10.3.tar.gz
1.10.2 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.2/src/hdf5-1.10.2.tar.gz
1.10.1 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz
1.10.0-patch1 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.0-patch1/src/hdf5-1.10.0-patch1.tar.gz
1.10.0 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.0/src/hdf5-1.10.0.tar.gz
1.8.23 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.23/src/hdf5-1.8.23.tar.gz
1.8.22 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.22/src/hdf5-1.8.22.tar.gz
1.8.21 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.21/src/hdf5-1.8.21.tar.gz
1.8.19 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.19/src/hdf5-1.8.19.tar.gz
1.8.18 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.18/src/hdf5-1.8.18.tar.gz
1.8.17 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.17/src/hdf5-1.8.17.tar.gz
1.8.16 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.16/src/hdf5-1.8.16.tar.gz
1.8.15 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.15/src/hdf5-1.8.15.tar.gz
1.8.14 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.14/src/hdf5-1.8.14.tar.gz
1.8.13 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.13/src/hdf5-1.8.13.tar.gz
1.8.12 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.12/src/hdf5-1.8.12.tar.gz
1.8.10 https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.10/src/hdf5-1.8.10.tar.gz
Deprecated versions:
None
Variants:
api [default] default, v110, v112, v114, v116, v16, v18
Choose api compatibility for earlier version
build_system [cmake] cmake
Build systems supported by the package
cxx [false] false, true
Enable C++ support
fortran [false] false, true
Enable Fortran support
hl [false] false, true
Enable the high-level library
mpi [true] false, true
Enable MPI support
shared [true] false, true
Builds a shared version of the library
szip [false] false, true
Enable szip support
threadsafe [false] false, true
Enable thread-safe capabilities
tools [true] false, true
Enable building tools
when build_system=cmake
build_type [Release] Debug, MinSizeRel, RelWithDebInfo, Release
CMake build type
generator [make] none
the build system generator to use
when build_system=cmake ^cmake@3.9:
ipo [false] false, true
CMake interprocedural optimization
when @1.14:
map [false] false, true
Enable MAP API support
when @1.14:+mpi
subfiling [false] false, true
Enable Subfiling VFD support
when @1.10:
java [false] false, true
Enable Java support
Build Dependencies:
cmake gmake java mpi mpich ninja szip zlib-api zlib-ng
Link Dependencies:
mpi mpich szip zlib-api zlib-ng
Run Dependencies:
java pkgconfig
Licenses:
custom
hdf5/package.py
spack install hdf5@1.12.2%gcc@12.2.0+fortran~cxx ^openmpi@4.1.6
# Copyright 2013-2024 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 os
import re
import shutil
import sys
import llnl.util.lang
import llnl.util.tty as tty
from spack.package import *
class Hdf5(CMakePackage):
"""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"
url = "https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_5/downloads/hdf5-1.14.5.tar.gz"
git = "https://github.com/HDFGroup/hdf5.git"
maintainers("lrknox", "brtnfld", "byrnHDF", "gheber", "hyoklee", "lkurz")
tags = ["e4s", "windows"]
executables = ["^h5cc$", "^h5pcc$"]
test_requires_compiler = True
license("custom")
depends_on("cxx", type="build", when="+cxx")
depends_on("fortran", type="build", when="+fortran")
# The 'develop' version is renamed so that we could uninstall (or patch) it
# without affecting other develop version.
version("develop-2.0", branch="develop")
version("develop-1.14", branch="hdf5_1_14")
version("develop-1.12", branch="hdf5_1_12")
version("develop-1.10", branch="hdf5_1_10")
version("develop-1.8", branch="hdf5_1_8")
# Odd versions are considered experimental releases
# Even versions are maintenance versions
version(
"1.14.5",
sha256="ec2e13c52e60f9a01491bb3158cb3778c985697131fc6a342262d32a26e58e44",
url="https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_5/downloads/hdf5-1.14.5.tar.gz",
preferred=True,
)
version(
"1.14.4-3",
sha256="019ac451d9e1cf89c0482ba2a06f07a46166caf23f60fea5ef3c37724a318e03",
url="https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/downloads/hdf5-1.14.4-3.tar.gz",
)
version(
"1.14.3",
sha256="09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7",
url="https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_3/downloads/hdf5-1.14.3.tar.gz",
)
version(
"1.14.2",
sha256="1c342e634008284a8c2794c8e7608e2eaf26d01d445fb3dfd7f33cb2fb51ac53",
url="https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_2/downloads/hdf5-1.14.2.tar.gz",
)
version(
"1.14.1-2",
sha256="cbe93f275d5231df28ced9549253793e40cd2b555e3d288df09d7b89a9967b07",
url="https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_1/downloads/hdf5-1.14.1-2.tar.gz",
)
version(
"1.14.0",
sha256="a571cc83efda62e1a51a0a912dd916d01895801c5025af91669484a1575a6ef4",
url="https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_0/downloads/hdf5-1.14.0.tar.gz",
)
version("1.12.3", sha256="c15adf34647918dd48150ea1bd9dffd3b32a3aec5298991d56048cc3d39b4f6f")
version("1.12.2", sha256="2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14")
version("1.12.1", sha256="79c66ff67e666665369396e9c90b32e238e501f345afd2234186bfb8331081ca")
version("1.12.0", sha256="a62dcb276658cb78e6795dd29bf926ed7a9bc4edf6e77025cd2c689a8f97c17a")
version("1.10.11", sha256="341684c5c0976b8c7e6951735a400275a90693604464cac73e9f323c696fc79c")
version("1.10.10", sha256="a6877ab7bd5d769d2d68618fdb54beb50263dcc2a8c157fe7e2186925cdb02db")
version("1.10.9", sha256="f5b77f59b705a755a5a223372d0222c7bc408fe8db6fa8d9d7ecf8bce291b8dd")
version("1.10.8", sha256="d341b80d380dd763753a0ebe22915e11e87aac4e44a084a850646ff934d19c80")
version("1.10.7", sha256="7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15")
version("1.10.6", sha256="5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa")
version("1.10.5", sha256="6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8")
version("1.10.4", sha256="8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2")
version("1.10.3", sha256="b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39")
version("1.10.2", sha256="bfec1be8c366965a99812cf02ddc97e4b708c1754fccba5414d4adccdc073866")
version("1.10.1", sha256="048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172")
version(
"1.10.0-patch1", sha256="6e78cfe32a10e6e0629393cdfddf6cfa536571efdaf85f08e35326e1b4e9eff0"
)
version("1.10.0", sha256="81f6201aba5c30dced5dcd62f5d5477a2790fd5850e02ac514ca8bf3e2bb375a")
version("1.8.23", sha256="37fa4eb6cd0e181eb49a10d54611cb00700e9537f805d03e6853503afe5abc27")
version("1.8.22", sha256="8406d96d9355ef8961d2739fb8fd5474ad4cdf52f3cfac657733defd9709bfaa")
version("1.8.21", sha256="87d8c82eba5cf766d97cd06c054f4639c1049c4adeaa3a79f77f8bd374f80f37")
version("1.8.19", sha256="a4335849f19fae88c264fd0df046bc321a78c536b2548fc508627a790564dc38")
version("1.8.18", sha256="cdb195ad8d9e6782acf24b2488061289f615628c2ccda8457b0a0c3fb7a8a063")
version("1.8.17", sha256="d9cda297ee76ade9881c4208987939250d397bae6252d0ccb66fa7d24d67e263")
version("1.8.16", sha256="ed17178abd9928a7237f30370189ba767b9e39e0db45917c2ac4665eb9cb4771")
version("1.8.15", sha256="4e963216b7d32469596bc1321a8c3f6e0c278dcbbdb7be6414c63c081b34c275")
version("1.8.14", sha256="1dbefeeef7f591897c632b2b090db96bb8d35ad035beaa36bc39cb2bc67e0639")
version("1.8.13", sha256="82f6b38eec103b4fccfbf14892786e0c27a8135d3252d8601cf5bf20066d38c1")
version("1.8.12", sha256="b5cccea850096962b5fd9e96f22c4f47d2379224bb41130d9bc038bb6c37dfcb")
version("1.8.10", sha256="4813b79c5fb8701a625b9924b8203bc7154a77f9b826ad4e034144b4056a160a")
depends_on("c", type="build") # generated
depends_on("cxx", type="build") # generated
depends_on("fortran", type="build") # generated
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("map", when="@1.14:", default=False, description="Enable MAP API support")
variant(
"subfiling", when="@1.14: +mpi", default=False, description="Enable Subfiling VFD support"
)
variant("fortran", default=False, description="Enable Fortran support")
variant("java", when="@1.10:", default=False, description="Enable Java support")
variant("threadsafe", default=False, description="Enable thread-safe capabilities")
variant("tools", default=True, description="Enable building tools")
variant("mpi", default=True, description="Enable MPI support")
variant("szip", default=False, description="Enable szip support")
# Build HDF5 with API compatibility.
variant(
"api",
default="default",
description="Choose api compatibility for earlier version",
values=("default", "v116", "v114", "v112", "v110", "v18", "v16"),
multi=False,
)
depends_on("cmake@3.12:", type="build")
depends_on("cmake@3.18:", type="build", when="@1.13:")
with when("+mpi"):
depends_on("mpi")
depends_on("mpich+fortran", when="+fortran ^[virtuals=mpi] mpich")
depends_on("java", type=("build", "run"), when="+java")
depends_on("szip", when="+szip")
depends_on("zlib-api")
# See https://github.com/HDFGroup/hdf5/pull/4147
depends_on(
"zlib-ng~new_strategies",
when="@:1.14.3,develop-1.8:develop-1.12 ^[virtuals=zlib-api] zlib-ng",
)
# The compiler wrappers (h5cc, h5fc, etc.) run 'pkg-config'.
# Skip this on Windows since pkgconfig is autotools
for plat in ["darwin", "linux"]:
depends_on("pkgconfig", when=f"platform={plat}", type="run")
conflicts("+mpi", "^mpich@4.0:4.0.3")
conflicts("api=v116", when="@1.6:1.14", msg="v116 is not compatible with this release")
conflicts(
"api=v116",
when="@develop-1.8:develop-1.14",
msg="v116 is not compatible with this release",
)
conflicts("api=v114", when="@1.6:1.12", msg="v114 is not compatible with this release")
conflicts(
"api=v114",
when="@develop-1.8:develop-1.12",
msg="v114 is not compatible with this release",
)
conflicts("api=v112", when="@1.6:1.10", msg="v112 is not compatible with this release")
conflicts(
"api=v112",
when="@develop-1.8:develop-1.10",
msg="v112 is not compatible with this release",
)
conflicts("api=v110", when="@1.6:1.8", msg="v110 is not compatible with this release")
conflicts("api=v110", when="@develop-1.8", msg="v110 is not compatible with this release")
conflicts("api=v18", when="@1.6", msg="v18 is not compatible with this release")
# The Java wrappers cannot be built without shared libs.
conflicts("+java", when="~shared")
# Fortran fails built with shared for old HDF5 versions
conflicts("+fortran", when="+shared@:1.8.15")
# See https://github.com/spack/spack/issues/31085
conflicts("+fortran+mpi", when="@1.8.22")
# See https://github.com/HDFGroup/hdf5/issues/2906#issue-1697749645
conflicts(
"+fortran", when="@1.13.3:^cmake@:3.22", msg="cmake_minimum_required is not set correctly."
)
# HDF5 searches for zlib CMake config files before it falls back to
# FindZLIB.cmake. We don't build zlib with CMake by default, so have to
# delete the first search, otherwise it may find a system zlib. See
# https://github.com/HDFGroup/hdf5/issues/4904
patch("find_package_zlib.patch", when="@1.8.16:1.14.4")
# 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')
# Patch needed for HDF5 1.14.3 to fix signaling FPE checks from triggering
# at dynamic type system initialization. The type system's builtin types
# were refactored in 1.14.3 and switched from compile-time to run-time
# initialization. This patch suppresses floating point exception checks
# that would otherwise be triggered by this code. Later HDF5 versions
# will include the patch code changes.
# See https://github.com/HDFGroup/hdf5/pull/3837
patch("hdf5_1_14_3_fpe.patch", when="@1.14.3")
# 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:",
)
# Disable MPI C++ interface when C++ is disabled, otherwise downstream
# libraries fail to link; see https://github.com/spack/spack/issues/12586
patch(
"h5public-skip-mpicxx.patch",
when="@1.8.10:1.8.21,1.10.0:1.10.5+mpi~cxx",
sha256="b61e2f058964ad85be6ee5ecea10080bf79e73f83ff88d1fa4b602d00209da9c",
)
# Fixes BOZ literal constant error when compiled with GCC 10.
# The issue is described here: https://github.com/spack/spack/issues/18625
patch(
"hdf5_1.8_gcc10.patch",
when="@:1.8.21",
sha256="0e20187cda3980a4fdff410da92358b63de7ebef2df1d7a425371af78e50f666",
)
patch("fortran-kinds.patch", when="@1.10.7")
# This patch may only be needed with GCC 11.2 on macOS, but it's valid for
# any of the head HDF5 versions as of 12/2021. Since it's impossible to
# tell what Fortran version is part of a mixed apple-clang toolchain on
# macOS (which is the norm), and this might be an issue for other compilers
# as well, we just apply it to all platforms.
# See https://github.com/HDFGroup/hdf5/issues/1157
patch("fortran-kinds-2.patch", when="@1.10.8,1.12.1")
# Patch needed for HDF5 1.14.0 where dependency on MPI::MPI_C was declared
# PUBLIC. Dependent packages using the default hdf5 package but not
# expecting to use MPI then failed to configure because they did not call
# find_package(MPI). This patch does that for them. Later HDF5 versions
# will include the patch code changes.
patch("hdf5_1_14_0_config_find_mpi.patch", when="@1.14.0")
# The argument 'buf_size' of the C function 'h5fget_file_image_c' is
# declared as intent(in) though it is modified by the invocation. As a
# result, aggressive compilers such as Fujitsu's may do a wrong
# optimization to cause an error.
def patch(self):
filter_file(
"INTEGER(SIZE_T), INTENT(IN) :: buf_size",
"INTEGER(SIZE_T), INTENT(OUT) :: buf_size",
"fortran/src/H5Fff.F90",
string=True,
ignore_absent=True,
)
filter_file(
"INTEGER(SIZE_T), INTENT(IN) :: buf_size",
"INTEGER(SIZE_T), INTENT(OUT) :: buf_size",
"fortran/src/H5Fff_F03.f90",
string=True,
ignore_absent=True,
)
if self.run_tests:
# hdf5 has ~2200 CPU-intensive tests, some of them have races:
# Often, these loop endless(at least on one Xeon and one EPYC).
# testphdf5 fails indeterministic. This fixes finishing the tests
filter_file(
"REMOVE_ITEM H5P_TESTS",
"REMOVE_ITEM H5P_TESTS t_bigio t_shapesame testphdf5",
"testpar/CMakeTests.cmake",
)
# The parallel compiler wrappers (i.e. h5pcc, h5pfc, etc.) reference MPI
# compiler wrappers and do not need to be changed.
# These do not exist on Windows.
# Enable only for supported target platforms.
if sys.platform != "win32":
filter_compiler_wrappers(
"h5cc", "h5hlcc", "h5fc", "h5hlfc", "h5c++", "h5hlc++", relative_root="bin"
)
def url_for_version(self, version):
url = "https://support.hdfgroup.org/archive/support/ftp/HDF5/releases/hdf5-{0}/hdf5-{1}/src/hdf5-{1}.tar.gz"
return url.format(version.up_to(2), version)
def flag_handler(self, name, flags):
spec = self.spec
cmake_flags = []
if name == "cflags":
if (
spec.satisfies("%gcc")
or spec.satisfies("%clang")
or spec.satisfies("%apple-clang")
or spec.satisfies("%oneapi")
):
# Quiet warnings/errors about implicit declaration of functions
# in C99:
cmake_flags.append("-Wno-error=implicit-function-declaration")
# Note that this flag will cause an error if building %nvhpc.
if spec.satisfies("@:1.8.12~shared"):
# More recent versions set CMAKE_POSITION_INDEPENDENT_CODE to
# True and build with PIC flags.
cmake_flags.append(self.compiler.cc_pic_flag)
if spec.satisfies("@1.8.21 %oneapi@2023.0.0"):
cmake_flags.append("-Wno-error=int-conversion")
elif name == "cxxflags":
if spec.satisfies("@:1.8.12+cxx~shared"):
cmake_flags.append(self.compiler.cxx_pic_flag)
elif name == "fflags":
if spec.satisfies("%cce+fortran"):
# Cray compiler generates module files with uppercase names by
# default, which is not handled by the CMake scripts. The
# following flag forces the compiler to produce module files
# with lowercase names.
cmake_flags.append("-ef")
if spec.satisfies("@:1.8.12+fortran~shared"):
cmake_flags.append(self.compiler.fc_pic_flag)
elif name == "ldlibs":
if spec.satisfies("+fortran %fj"):
cmake_flags.extend(["-lfj90i", "-lfj90f", "-lfjsrcinfo", "-lelf"])
return flags, None, (cmake_flags or None)
@property
def libs(self):
"""HDF5 can be queried for the following parameters:
- "hl": high-level interface
- "cxx": C++ APIs
- "fortran": Fortran APIs
- "java": Java APIs
:return: list of matching libraries
"""
query_parameters = self.spec.last_query.extra_parameters
shared = self.spec.satisfies("+shared")
# This map contains a translation from query_parameters
# to the libraries needed
query2libraries = {
tuple(): ["libhdf5"],
("cxx", "fortran", "hl", "java"): [
# When installed with Autotools, the basename of the real
# library file implementing the High-level Fortran interface is
# 'libhdf5hl_fortran'. Starting versions 1.8.22, 1.10.5 and
# 1.12.0, the Autotools installation also produces a symbolic
# link 'libhdf5_hl_fortran.<so/a>' to
# 'libhdf5hl_fortran.<so/a>'. Note that in the case of the
# dynamic library, the latter is a symlink to the real sonamed
# file 'libhdf5_fortran.so.<abi-version>'. This means that all
# dynamically linked executables/libraries of the dependent
# packages need 'libhdf5_fortran.so.<abi-version>' with the same
# DT_SONAME entry. However, the CMake installation (at least
# starting version 1.8.10) does not produce it. Instead, the
# basename of the library file is 'libhdf5_hl_fortran'. Which
# means that switching to CMake requires rebuilding of all
# dependant packages that use the High-level Fortran interface.
# Therefore, we do not try to preserve backward compatibility
# with Autotools installations by creating symlinks. The only
# packages that could benefit from it would be those that
# hardcode the library name in their building systems. Such
# packages should simply be patched.
"libhdf5_hl_fortran",
"libhdf5_hl_f90cstub",
"libhdf5_hl_cpp",
"libhdf5_hl",
"libhdf5_fortran",
"libhdf5_f90cstub",
"libhdf5_java",
"libhdf5",
],
("cxx", "hl"): ["libhdf5_hl_cpp", "libhdf5_hl", "libhdf5"],
("fortran", "hl"): [
"libhdf5_hl_fortran",
"libhdf5_hl_f90cstub",
"libhdf5_hl",
"libhdf5_fortran",
"libhdf5_f90cstub",
"libhdf5",
],
("hl",): ["libhdf5_hl", "libhdf5"],
("cxx", "fortran"): ["libhdf5_fortran", "libhdf5_f90cstub", "libhdf5_cpp", "libhdf5"],
("cxx",): ["libhdf5_cpp", "libhdf5"],
("fortran",): ["libhdf5_fortran", "libhdf5_f90cstub", "libhdf5"],
("java",): ["libhdf5_java", "libhdf5"],
}
# Turn the query into the appropriate key
key = tuple(sorted(query_parameters))
libraries = query2libraries[key]
return find_libraries(libraries, root=self.prefix, shared=shared, recursive=True)
@classmethod
def determine_version(cls, exe):
output = Executable(exe)("-showconfig", output=str, error=str)
match = re.search(r"HDF5 Version: (\d+\.\d+\.\d+)(\D*\S*)", output)
return match.group(1) if match else None
@classmethod
def determine_variants(cls, exes, version):
def is_enabled(text):
return text.lower() in ["t", "true", "enabled", "yes", "1", "on"]
results = []
for exe in exes:
variants = []
output = Executable(exe)("-showconfig", output=str, error=os.devnull)
match = re.search(r"High-level library: (\S+)", output)
if match and is_enabled(match.group(1)):
variants.append("+hl")
else:
variants.append("~hl")
match = re.search(r"Parallel HDF5: (\S+)", output)
if match and is_enabled(match.group(1)):
variants.append("+mpi")
else:
variants.append("~mpi")
match = re.search(r"C\+\+: (\S+)", output)
if match and is_enabled(match.group(1)):
variants.append("+cxx")
else:
variants.append("~cxx")
match = re.search(r"Fortran: (\S+)", output)
if match and is_enabled(match.group(1)):
variants.append("+fortran")
else:
variants.append("~fortran")
match = re.search(r"Java: (\S+)", output)
if match and is_enabled(match.group(1)):
variants.append("+java")
else:
variants.append("~java")
match = re.search(r"Threadsafety: (\S+)", output)
if match and is_enabled(match.group(1)):
variants.append("+threadsafe")
else:
variants.append("~threadsafe")
match = re.search(r"Build HDF5 Tools: (\S+)", output)
if match and is_enabled(match.group(1)):
variants.append("+tools")
else:
variants.append("~tools")
match = re.search(r"I/O filters \(external\): \S*(szip\(encoder\))\S*", output)
if match:
variants.append("+szip")
else:
variants.append("~szip")
match = re.search(r"Default API mapping: (\S+)", output)
if match and match.group(1) in set(["v114", "v112", "v110", "v18", "v16"]):
variants.append("api={0}".format(match.group(1)))
results.append(" ".join(variants))
return results
@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)
def setup_run_environment(self, env):
# According to related github posts and problems running test_install
# as a stand-alone test, it appears the lib path must be added to
# LD_LIBRARY_PATH.
env.append_path("LD_LIBRARY_PATH", self.prefix.lib)
@run_before("cmake")
def fortran_check(self):
if self.spec.satisfies("+fortran") and not self.compiler.fc:
msg = "cannot build a Fortran variant without a Fortran compiler"
raise RuntimeError(msg)
def cmake_args(self):
spec = self.spec
if spec.satisfies("@:1.8.15+shared"):
tty.warn("hdf5@:1.8.15+shared does not produce static libraries")
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_from_variant("HDF5_ENABLE_SUBFILING_VFD", "subfiling"),
self.define_from_variant("HDF5_ENABLE_MAP_API", "map"),
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"),
]
api = spec.variants["api"].value
if api != "default":
args.append(self.define("DEFAULT_API_VERSION", api))
# MSMPI does not provide compiler wrappers
# and pointing these variables at the MSVC compilers
# breaks CMake's mpi detection for MSMPI.
if spec.satisfies("+mpi") and "msmpi" not in spec:
args.extend(
[
"-DMPI_CXX_COMPILER:PATH=%s" % spec["mpi"].mpicxx,
"-DMPI_C_COMPILER:PATH=%s" % spec["mpi"].mpicc,
]
)
if spec.satisfies("+fortran"):
args.extend(["-DMPI_Fortran_COMPILER:PATH=%s" % spec["mpi"].mpifc])
# work-around for https://github.com/HDFGroup/hdf5/issues/1320
if spec.satisfies("@1.10.8,1.13.0"):
args.append(self.define("HDF5_INSTALL_CMAKE_DIR", "share/cmake/hdf5"))
# AOCC does not support _Float16
if spec.satisfies("@1.14.4: %aocc"):
args.append(self.define("HDF5_ENABLE_NONSTANDARD_FEATURE_FLOAT16", False))
return 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")
# 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," "1.10.6:1.10.9," "1.12.0:1.12.2" "+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")
def link_debug_libs(self):
# When build_type is Debug, the hdf5 build appends _debug to all library names.
# Dependents of hdf5 (netcdf-c etc.) can't handle those, thus make symlinks.
if self.spec.satisfies("build_type=Debug"):
libs = find(self.prefix.lib, "libhdf5*_debug.*", recursive=False)
with working_dir(self.prefix.lib):
for lib in libs:
libname = os.path.split(lib)[1]
os.symlink(libname, libname.replace("_debug", ""))
@run_after("install")
def symlink_to_h5hl_wrappers(self):
if self.spec.satisfies("+hl"):
with working_dir(self.prefix.bin):
# CMake's FindHDF5 relies only on h5cc so it doesn't find the HL
# component unless it uses h5hlcc so we symlink h5cc to h5hlcc etc
symlink_files = {"h5cc": "h5hlcc", "h5c++": "h5hlc++"}
for old, new in symlink_files.items():
if os.path.isfile(old):
os.remove(old)
symlink(new, old)
@property
@llnl.util.lang.memoized
def _output_version(self):
spec_vers_str = str(self.spec.version.up_to(3))
if "develop" in spec_vers_str:
# Remove 'develop-' from the version in spack for checking
# version against the version in the HDF5 code.
spec_vers_str = spec_vers_str.partition("-")[2]
return spec_vers_str
@run_after("install")
@on_package_attributes(run_tests=True)
def check_install(self):
self.test_check_prog()
def test_check_prog(self):
"""build, run and check output of check.c"""
print("Checking HDF5 installation...")
prog = "check.c"
spec = self.spec
checkdir = "spack-check"
# Because the release number in a develop branch is not fixed,
# only the major and minor version numbers are compared.
# Otherwise all 3 numbers are checked.
fmt = "%d.%d %u.%u"
arg_line1 = "H5_VERS_MAJOR, H5_VERS_MINOR"
arg_line2 = "majnum, minnum"
if not spec.version.isdevelop():
fmt = "%d." + fmt + ".%u"
arg_line2 = "H5_VERS_RELEASE, " + arg_line2 + ", relnum"
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 {}\n", {},
{});
return 0;
}}
"""
expected = f"HDF5 version {self._output_version} {self._output_version}\n"
with working_dir(checkdir, create=True):
with open(prog, "w") as f:
f.write(source.format(fmt, arg_line1, arg_line2))
cc = Executable(os.environ["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)
def test_version(self):
"""Perform version checks on selected installed package binaries."""
expected = f"Version {self._output_version}"
exes = [
"h5copy",
"h5diff",
"h5dump",
"h5format_convert",
"h5ls",
"h5mkgrp",
"h5repack",
"h5stat",
"h5unjam",
]
use_short_opt = ["h52gif", "h5repart", "h5unjam"]
for exe in exes:
reason = f"ensure version of {exe} is {self._output_version}"
option = "-V" if exe in use_short_opt else "--version"
with test_part(self, f"test_version_{exe}", purpose=reason):
path = join_path(self.prefix.bin, exe)
if not os.path.isfile(path):
raise SkipTest(f"{path} is not installed")
prog = which(path)
output = prog(option, output=str.split, error=str.split)
assert expected in output
def test_example(self):
"""copy, dump, and diff example hdf5 file"""
test_data_dir = self.test_suite.current_test_data_dir
with working_dir(test_data_dir, create=True):
filename = "spack.h5"
h5dump = which(self.prefix.bin.h5dump)
out = h5dump(filename, output=str.split, error=str.split)
expected = get_escaped_text_output("dump.out")
check_outputs(expected, out)
h5copy = which(self.prefix.bin.h5copy)
copyname = "test.h5"
options = ["-i", filename, "-s", "Spack", "-o", copyname, "-d", "Spack"]
h5copy(*options)
h5diff = which(self.prefix.bin.h5diff)
h5diff(filename, copyname)
Track all package versions in a dedicated git repository:
Small Python wrapper around Spack:
Install full software stack with a single command:
$ mpsd-software install 25a gcc-14_2_0
--------------- /opt_mpsd/linux-debian12/25a/sandybridge/lmod/Core ---------------
gcc/14.2.0 (L)
------------ /opt_mpsd/linux-debian12/25a/sandybridge/lmod/gcc/14.2.0 ------------
boost/1.86.0 libpthread-stubs/0.5 py-h5py/3.12.1
fftw/3.3.10 libyaml/0.2.5 python/3.11.7
gettext/0.22.5 ncurses/6.5 tar/1.34
gsl/2.8 ninja/1.10.2 valgrind/3.23.0
hdf5/1.14.5 ninja/1.12.1 xcb-proto/1.17.0
kbproto/1.0.7 octopus-dependencies/full xtrans/1.5.2
knem/1.1.4 octopus-dependencies/min xz/5.4.6
krb5/1.21.3 openblas/0.3.28 zlib-ng/2.2.1
libaec/1.0.6 openmpi/4.1.5 (L) zstd/1.5.6
- /opt_mpsd/linux-debian12/25a/sandybridge/lmod/openmpi/4.1.5-jmeo3kl/gcc/14.2.0 -
berkeleygw/3.1.0 elpa/2024.03.001 netcdf-fortran/4.6.1
berkeleygw/4.0 etsf-io/1.0.4 netlib-scalapack/2.2.0
bigdft-atlab/1.9.5 fftw/3.3.10 octopus-dependencies/full
bigdft-futile/1.9.5 hdf5/1.14.5 octopus-dependencies/min
elpa-openmp/2024.03.001 netcdf-c/4.9.2 pfft/1.0.8-alpha
Slides: https://s.gwdg.de/Ztnnel