hdf-eos2: support version @3.0, plus assorted fixes (#41782)
1) support for version @3.0 Unfortunately, download seems to require registration now so using manual_download mechanism for @3: 2) copying from hdf-eos5 patch from @vanderwb to enable use of Spack compiler wrappers instead of h4cc 3) Patching an issue in hdf-eos2 configure script. The script will test for jpeg, libz libraries, succeed and append HAVE_LIBJPEG=1, etc to confdefs.h, and then abort because HAVE_LIBJPEG not set in running environment. 4) Add some LDFLAGS to build environment. Otherwise seems to fail to build test script due to rpc dependence in HDF4.
This commit is contained in:
Tom Payerle
GitHub
parent
00baaf868e
commit
76ec19b26e
2 changed files with 79 additions and 14 deletions
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@ -0,0 +1,25 @@
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# Fix some issues with hdf-eos2 configure script
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# configure (according to config.log) would find the jpeg
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# and libz libs, but then abort complaining they were not
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# found because HAVE_LIBJPEG, etc not set (the script just
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# appended the lines to confdefs.h but not set in the environment
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# of the running script and script tests the env variable)
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diff -Naur spack-src/configure spack-src.patched/configure
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--- spack-src/configure 2023-12-18 14:56:50.796875000 -0500
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+++ spack-src.patched/configure 2023-12-18 15:01:50.780038643 -0500
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@@ -12488,6 +12488,7 @@
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_ACEOF
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LIBS="-ljpeg $LIBS"
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+ HAVE_LIBJPEG=1
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else
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@@ -12863,6 +12864,7 @@
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_ACEOF
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LIBS="-lz $LIBS"
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+ HAVE_LIBZ=1
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else
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@ -3,8 +3,8 @@
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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 sys
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from os import chmod
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from spack.package import *
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@ -16,10 +16,15 @@ class HdfEos2(AutotoolsPackage):
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"""
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homepage = "https://hdfeos.org"
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# The download URLs are messing, and include sha256 checksum.
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# Starting with @3, download requires authentication. So reverting
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# to a manual download
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url = "file://{0}/hdf-eos2-3.0-src.tar.gz".format(os.getcwd())
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manual_download = True
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# The download URLs for @2 versions are messing, and include sha256 checksum.
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# Templates for url_for_version. 0 is sha256 checksum, 1 is filename
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# This is just a template. See version_list and url_for_version below
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# Template for url_for_version. 0 is sha256 checksum, 1 is filename
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url = "https://git.earthdata.nasa.gov/rest/git-lfs/storage/DAS/hdfeos/{0}?response-content-disposition=attachment%3B%20filename%3D%22{1}%22%3B%20filename*%3Dutf-8%27%27{1}"
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v2url = "https://git.earthdata.nasa.gov/rest/git-lfs/storage/DAS/hdfeos/{0}?response-content-disposition=attachment%3B%20filename%3D%22{1}%22%3B%20filename*%3Dutf-8%27%27{1}"
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maintainers("climbfuji")
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@ -29,15 +34,23 @@ class HdfEos2(AutotoolsPackage):
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# In basename expansions, 0 is raw version,
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# 1 is for version with dots => underscores
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version_list = [
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{
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"version": "3.0",
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"basename": "hdf-eos2-{0}-src.tar.gz",
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"sha256": "3a5564b4d69b541139ff7dfdad948696cf31d9d1a6ea8af290c91a4c0ee37188",
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"can_auto_download": False,
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},
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{
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"version": "2.20v1.00",
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"sha256": "cb0f900d2732ab01e51284d6c9e90d0e852d61bba9bce3b43af0430ab5414903",
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"basename": "HDF-EOS{0}.tar.Z",
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"can_auto_download": True,
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},
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{
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"version": "2.19b",
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"sha256": "a69993508dbf5fa6120bac3c906ab26f1ad277348dfc2c891305023cfdf5dc9d",
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"basename": "hdfeos{1}.zip",
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"can_auto_download": True,
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},
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]
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@ -63,19 +76,27 @@ class HdfEos2(AutotoolsPackage):
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depends_on("jpeg")
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depends_on("szip", when="^hdf +szip")
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# Fix some problematic logic in stock configure script
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# test succeeds, but then script aborts due to env variable not being set
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patch("hdf-eos2.configure.patch", when="@2:3.0")
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# The standard Makefile.am, etc. add a --single_module flag to LDFLAGS
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# to pass to the linker.
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# That appears to be only recognized by the Darwin linker, remove it
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# if we are not running on darwin/
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if sys.platform != "darwin":
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patch("hdf-eos2.nondarwin-no-single_module.patch")
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patch("hdf-eos2.nondarwin-no-single_module.patch", when="@2")
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def url_for_version(self, version):
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vrec = [x for x in self.version_list if x["version"] == version.dotted.string]
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if vrec:
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fname = vrec[0]["basename"].format(version.dotted, version.underscored)
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sha256 = vrec[0]["sha256"]
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myurl = self.url.format(sha256, fname)
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can_auto_download = vrec[0].get("can_auto_download", False)
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if can_auto_download:
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myurl = self.v2url.format(sha256, fname)
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else:
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myurl = self.url
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return myurl
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else:
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sys.exit(
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@ -83,12 +104,20 @@ def url_for_version(self, version):
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"version/checksum not found in version_list".format(version)
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)
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@run_before("configure")
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def fix_configure(self):
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# spack patches the configure file unless autoconf is run,
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# and this fails because configure has the wrong permissions (644)
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@run_before("configure")
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def fix_permissions(self):
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if not self.force_autoreconf:
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chmod(join_path(self.stage.source_path, "configure"), 0o755)
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os.chmod(join_path(self.stage.source_path, "configure"), 0o755)
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# The configure script as written really wants you to use h4cc.
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# This causes problems because h4cc differs when HDF is built with
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# autotools vs cmake, and we lose all the nice flags from the
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# Spack wrappers. These filter operations allow us to use the
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# Spack wrappers again
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filter_file("\\$CC -show &> /dev/null", "true", "configure")
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filter_file("CC=./\\$SZIP_CC", "", "configure")
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def flag_handler(self, name, flags):
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if self.spec.compiler.name == "apple-clang":
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@ -97,12 +126,19 @@ def flag_handler(self, name, flags):
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return flags, None, None
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def setup_build_environment(self, env):
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# Add flags to LDFLAGS for any dependencies that need it
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extra_ldflags = []
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# hdf might have link dependency on rpc, if so need to add flags
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if "rpc" in self.spec:
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tmp = self.spec["rpc"].libs.ld_flags
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extra_ldflags.append(tmp)
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# Set LDFLAGS
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env.set("LDFLAGS", " ".join(extra_ldflags))
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def configure_args(self):
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extra_args = []
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# Package really wants h4cc to be used
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extra_args.append("CC={0}/bin/h4cc -Df2cFortran".format(self.spec["hdf"].prefix))
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# We always build PIC code
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extra_args.append("--with-pic")
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extra_args.append("--enable-install_include")
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@ -114,7 +150,11 @@ def configure_args(self):
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# Provide config args for dependencies
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extra_args.append("--with-hdf4={0}".format(self.spec["hdf"].prefix))
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if "jpeg" in self.spec:
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extra_args.append("--with-jpeg={0}".format(self.spec["jpeg"].prefix))
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# Allow handling whatever provider of jpeg are using
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tmp = self.spec["jpeg"].libs.directories
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if tmp:
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tmp = tmp[0]
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extra_args.append("--with-jpeg={0}".format(tmp))
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if "szip" in self.spec:
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extra_args.append("--with-szlib={0}".format(self.spec["szip"].prefix))
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if "zlib" in self.spec:
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