436ff3c818
This commit removes the +fortran variant when building HDF5 for WRF. This seems unnecessary, and prevents building WRF with some versions of Intel MPI, as HDF5 doesn't appear to build with Fortran support and Intel MPI.
520 lines
21 KiB
Python
520 lines
21 KiB
Python
# Copyright Spack Project Developers. See COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import glob
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import re
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import sys
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import time
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from os.path import basename
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from pathlib import Path
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from subprocess import PIPE, Popen
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from spack.package import *
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if sys.platform != "win32":
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from fcntl import F_GETFL, F_SETFL, fcntl
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from os import O_NONBLOCK
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re_optline = re.compile(r"\s+[0-9]+\..*\((serial|smpar|dmpar|dm\+sm)\)\s+")
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re_paroptname = re.compile(r"\((serial|smpar|dmpar|dm\+sm)\)")
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re_paroptnum = re.compile(r"\s+([0-9]+)\.\s+\(")
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re_nestline = re.compile(r"\(([0-9]+=[^)0-9]+)+\)")
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re_nestoptnum = re.compile(r"([0-9]+)=")
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re_nestoptname = re.compile(r"=([^,)]+)")
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def setNonBlocking(fd):
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"""
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Set the given file descriptor to non-blocking
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Non-blocking pipes are not supported on windows
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"""
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flags = fcntl(fd, F_GETFL) | O_NONBLOCK
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fcntl(fd, F_SETFL, flags)
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def collect_platform_options(stdoutpipe):
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# Attempt to parse to collect options
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optiondict = {}
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for line in stdoutpipe.splitlines():
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if re_optline.match(line):
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numbers = re_paroptnum.findall(line)
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entries = re_paroptname.findall(line)
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paropts = dict(zip(entries, numbers))
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platline = re_optline.sub("", line).strip()
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optiondict[platline] = paropts
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return optiondict
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def collect_nesting_options(stdoutpipe):
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nestoptline = re_nestline.search(stdoutpipe)[0]
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nestoptnum = re_nestoptnum.findall(nestoptline)
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nestoptname = re_nestoptname.findall(nestoptline)
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nestoptname = [x.replace(" ", "_") for x in nestoptname]
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return dict(zip(nestoptname, nestoptnum))
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class Wrf(Package):
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"""The Weather Research and Forecasting (WRF) Model
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is a next-generation mesoscale numerical weather prediction system designed
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for both atmospheric research and operational forecasting applications.
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"""
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homepage = "https://www.mmm.ucar.edu/weather-research-and-forecasting-model"
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url = "https://github.com/wrf-model/WRF/archive/v4.2.tar.gz"
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maintainers("MichaelLaufer", "ptooley")
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tags = ["windows"]
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version(
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"4.6.1",
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sha256="b8ec11b240a3cf1274b2bd609700191c6ec84628e4c991d3ab562ce9dc50b5f2",
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url="https://github.com/wrf-model/WRF/releases/download/v4.6.1/v4.6.1.tar.gz",
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)
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version(
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"4.6.0",
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sha256="1bb010f9e20b40d33d9df55a602ea9eb54c5444a7316c00a95e1cc44b209021e",
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url="https://github.com/wrf-model/WRF/releases/download/v4.6.0/v4.6.0.tar.gz",
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)
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version(
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"4.5.2",
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sha256="408ba6aa60d9cd51d6bad2fa075a3d37000eb581b5d124162885b049c892bbdc",
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url="https://github.com/wrf-model/WRF/releases/download/v4.5.2/v4.5.2.tar.gz",
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)
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version(
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"4.5.1",
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sha256="9d557c34c105db4d41e727843ecb19199233c7cf82c5369b34a2ce8efe65e2d1",
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url="https://github.com/wrf-model/WRF/releases/download/v4.5.1/v4.5.1.tar.gz",
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)
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version(
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"4.5.0",
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sha256="14fd78abd4e32c1d99e2e97df0370030a5c58ec84c343591bdc5e74f163c5525",
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url="https://github.com/wrf-model/WRF/releases/download/v4.5/v4.5.tar.gz",
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)
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version(
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"4.4.2",
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sha256="488b992e8e994637c58e3c69e869ad05acfe79419c01fbef6ade1f624e50dc3a",
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url="https://github.com/wrf-model/WRF/releases/download/v4.4.2/v4.4.2.tar.gz",
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)
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version(
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"4.4",
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sha256="6b649e5ac5532f74d74ab913950b632777ce349d26ebfb7f0042b80f9f4ee83e",
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url="https://github.com/wrf-model/WRF/releases/download/v4.4/v4.4.tar.gz",
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)
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version("4.3.3", sha256="1b98b8673513f95716c7fc54e950dfebdb582516e22758cd94bc442bccfc0b86")
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version("4.3.2", sha256="2c682da0cd0fd13f57d5125eef331f9871ec6a43d860d13b0c94a07fa64348ec")
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version("4.3.1", sha256="6c9a69d05ee17d2c80b3699da173cfe6fdf65487db7587c8cc96bfa9ceafce87")
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version("4.2.2", sha256="7be2968c67c2175cd40b57118d9732eda5fdb0828edaa25baf57cc289da1a9b8")
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version("4.2", sha256="c39a1464fd5c439134bbd39be632f7ce1afd9a82ad726737e37228c6a3d74706")
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version("4.0", sha256="9718f26ee48e6c348d8e28b8bc5e8ff20eafee151334b3959a11b7320999cf65")
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version(
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"3.9.1.1",
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sha256="a04f5c425bedd262413ec88192a0f0896572cc38549de85ca120863c43df047a",
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url="https://github.com/wrf-model/WRF/archive/V3.9.1.1.tar.gz",
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)
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depends_on("c", type="build") # generated
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depends_on("fortran", type="build") # generated
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variant(
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"build_type",
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default="dmpar",
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description="Build type",
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values=("serial", "smpar", "dmpar", "dm+sm"),
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)
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variant(
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"nesting",
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default="basic",
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description="Nesting",
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values=("no_nesting", "basic", "preset_moves", "vortex_following"),
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)
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variant(
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"compile_type",
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default="em_real",
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description="Compile type",
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values=(
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"em_real",
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"em_quarter_ss",
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"em_b_wave",
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"em_les",
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"em_heldsuarez",
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"em_tropical_cyclone",
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"em_hill2d_x",
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"em_squall2d_x",
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"em_squall2d_y",
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"em_grav2d_x",
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"em_seabreeze2d_x",
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"em_scm_xy",
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),
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)
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variant("pnetcdf", default=True, description="Parallel IO support through Pnetcdf library")
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variant("chem", default=False, description="Enable WRF-Chem", when="@4:")
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variant("netcdf_classic", default=False, description="Use NetCDF without HDF5 compression")
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variant("adios2", default=False, description="Enable IO support through ADIOS2 library")
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patch("patches/3.9/netcdf_backport.patch", when="@3.9.1.1")
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patch("patches/3.9/tirpc_detect.patch", when="@3.9.1.1")
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patch("patches/3.9/add_aarch64.patch", when="@3.9.1.1")
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patch("patches/3.9/configure_aocc_2.3.patch", when="@3.9.1.1 %aocc@:2.4.0")
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patch("patches/3.9/configure_aocc_3.0.patch", when="@3.9.1.1 %aocc@3.0.0")
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patch("patches/3.9/configure_aocc_3.1.patch", when="@3.9.1.1 %aocc@3.1.0")
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patch("patches/3.9/fujitsu.patch", when="@3.9.1.1 %fj")
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# These patches deal with netcdf & netcdf-fortran being two diff things
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# Patches are based on:
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# https://github.com/easybuilders/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/w/WRF/WRF-3.5_netCDF-Fortran_separate_path.patch
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patch("patches/4.0/arch.Config.pl.patch", when="@4.0")
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patch("patches/4.0/arch.configure.defaults.patch", when="@4.0")
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patch("patches/4.0/arch.conf_tokens.patch", when="@4.0")
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patch("patches/4.0/arch.postamble.patch", when="@4.0")
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patch("patches/4.0/configure.patch", when="@4.0")
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patch("patches/4.0/external.io_netcdf.makefile.patch", when="@4.0")
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patch("patches/4.0/Makefile.patch", when="@4.0")
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patch("patches/4.0/tirpc_detect.patch", when="@4.0")
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patch("patches/4.0/add_aarch64.patch", when="@4.0")
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patch("patches/4.2/arch.Config.pl.patch", when="@4.2:4.5.1")
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patch("patches/4.2/arch.configure.defaults.patch", when="@=4.2")
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patch("patches/4.2/4.2.2_arch.configure.defaults.patch", when="@4.2.2")
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patch("patches/4.2/arch.conf_tokens.patch", when="@4.2:")
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patch("patches/4.2/arch.postamble.patch", when="@4.2")
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patch("patches/4.2/configure.patch", when="@4.2:4.3.3")
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patch("patches/4.2/external.io_netcdf.makefile.patch", when="@4.2:4.5.1")
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patch("patches/4.2/var.gen_be.Makefile.patch", when="@4.2:")
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patch("patches/4.2/Makefile.patch", when="@4.2")
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patch("patches/4.2/tirpc_detect.patch", when="@4.2")
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patch("patches/4.2/add_aarch64.patch", when="@4.2:4.3.1 target=aarch64: %gcc")
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patch("patches/4.2/add_aarch64_acfl.patch", when="@4.2:4.3.1 target=aarch64: %arm")
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patch("patches/4.2/configure_aocc_2.3.patch", when="@4.2 %aocc@:2.4.0")
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patch("patches/4.2/configure_aocc_3.0.patch", when="@4.2 %aocc@3.0.0:3.2.0")
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patch("patches/4.2/hdf5_fix.patch", when="@4.2:4.5.1 %aocc")
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patch("patches/4.2/derf_fix.patch", when="@=4.2 %aocc")
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patch(
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"patches/4.2/add_tools_flags_acfl2304.patch",
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when="@4.2:4.4.2 target=aarch64: %arm@23.04.1:",
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)
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patch("patches/4.3/add_aarch64.patch", when="@4.3.2:4.4.2 target=aarch64: %gcc")
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patch("patches/4.3/add_aarch64_acfl.patch", when="@4.3.2:4.4.2 target=aarch64: %arm")
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patch("patches/4.4/arch.postamble.patch", when="@4.4:4.5.1")
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patch("patches/4.4/configure.patch", when="@4.4:4.4.2")
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patch("patches/4.4/ifx.patch", when="@4.4: %oneapi")
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patch("patches/4.5/configure.patch", when="@4.5:")
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# Fix WRF to remove deprecated ADIOS2 functions
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# https://github.com/wrf-model/WRF/pull/1860
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patch("patches/4.5/adios2-remove-deprecated-functions.patch", when="@=4.5.0 ^adios2@2.9:")
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# Various syntax fixes found by FPT tool
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patch(
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"https://github.com/wrf-model/WRF/commit/6502d5d9c15f5f9a652dec244cc12434af737c3c.patch?full_index=1",
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sha256="c5162c23a132b377132924f8f1545313861c6cee5a627e9ebbdcf7b7b9d5726f",
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when="@4.2 %fj",
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)
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patch("patches/4.2/configure_fujitsu.patch", when="@4 %fj")
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patch("patches/4.3/Makefile.patch", when="@4.3:4.5.1")
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patch("patches/4.3/arch.postamble.patch", when="@4.3:4.3.3")
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patch("patches/4.3/fujitsu.patch", when="@4.3:4.4 %fj")
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# Syntax errors in physics routines
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patch(
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"https://github.com/wrf-model/WRF/commit/7c6fd575b7a8fe5715b07b38db160e606c302956.patch?full_index=1",
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sha256="1ce97f4fd09e440bdf00f67711b1c50439ac27595ea6796efbfb32e0b9a1f3e4",
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when="@4.3.1",
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)
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patch(
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"https://github.com/wrf-model/WRF/commit/238a7d219b7c8e285db28fe4f0c96ebe5068d91c.patch?full_index=1",
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sha256="27c7268f6c84b884d21e4afad0bab8554b06961cf4d6bfd7d0f5a457dcfdffb1",
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when="@4.3.1",
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)
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# Add ARM compiler support
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patch(
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"https://github.com/wrf-model/WRF/commit/4a084e03575da65f254917ef5d8eb39074abd3fc.patch?full_index=1",
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sha256="2d06d709074ded9bd6842aa83c0dfdad5a4e4e2df99e2e5d4a82579f0486117e",
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when="@4.5: %arm",
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)
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patch(
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"https://github.com/wrf-model/WRF/commit/6087d9192f7f91967147e50f5bc8b9e49310cf98.patch?full_index=1",
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sha256="7c6487aefaa6cda0fff3976e78da07b09d2ba6c005d649f35a0f8f1694a0b2bb",
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when="@4.5: %arm",
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)
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depends_on("pkgconfig", type=("build"))
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depends_on("libtirpc")
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depends_on("mpi")
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# According to:
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# http://www2.mmm.ucar.edu/wrf/users/docs/user_guide_v4/v4.0/users_guide_chap2.html#_Required_Compilers_and_1
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# Section: "Required/Optional Libraries to Download"
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depends_on("parallel-netcdf", when="+pnetcdf")
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depends_on("netcdf-c")
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depends_on("netcdf-fortran")
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depends_on("jasper")
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depends_on("libpng")
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depends_on("zlib-api")
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depends_on("perl")
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depends_on("jemalloc", when="%aocc")
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depends_on("hdf5+hl+mpi")
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# build script use csh
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depends_on("tcsh", type=("build"))
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# time is not installed on all systems b/c bash provides it
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# this fixes that for csh install scripts
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depends_on("time", type=("build"))
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depends_on("m4", type="build")
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depends_on("libtool", type="build")
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depends_on("adios2", when="@4.5: +adios2")
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requires(
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"%gcc",
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"%intel",
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"%arm",
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"%aocc",
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"%fj",
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"%oneapi",
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policy="one_of",
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msg="WRF supports only the GCC, Intel, AMD of Fujitsu compilers",
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)
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conflicts(
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"%oneapi", when="@:4.3", msg="Intel oneapi compiler patch only added for version 4.4"
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)
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phases = ["configure", "build", "install"]
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def setup_run_environment(self, env):
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env.set("WRF_HOME", self.prefix)
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env.append_path("PATH", self.prefix.main)
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env.append_path("PATH", self.prefix.tools)
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def setup_build_environment(self, env):
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# From 4.5.2 the split-netcdf patches are not needed,
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# just tell the build system where netcdf and netcdf-c are:
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if self.spec.satisfies("@4.5.2:"):
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env.set("NETCDF", self.spec["netcdf-fortran"].prefix)
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env.set("NETCDF_C", self.spec["netcdf-c"].prefix)
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else:
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env.set("NETCDF", self.spec["netcdf-c"].prefix)
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if "+pnetcdf" in self.spec:
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env.set("PNETCDF", self.spec["parallel-netcdf"].prefix)
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# Add WRF-Chem module
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if "+chem" in self.spec:
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env.set("WRF_CHEM", 1)
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if "+netcdf_classic" in self.spec:
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env.set("NETCDF_classic", 1)
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# This gets used via the applied patch files
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env.set("NETCDFF", self.spec["netcdf-fortran"].prefix)
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env.set("PHDF5", self.spec["hdf5"].prefix)
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env.set("JASPERINC", self.spec["jasper"].prefix.include)
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env.set("JASPERLIB", self.spec["jasper"].prefix.lib)
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if self.spec.satisfies("%aocc"):
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env.set("WRFIO_NCD_LARGE_FILE_SUPPORT", 1)
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env.set("HDF5", self.spec["hdf5"].prefix)
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env.prepend_path("PATH", ancestor(self.compiler.cc))
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if "+adios2" in self.spec:
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env.set("ADIOS2", self.spec["adios2"].prefix)
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def flag_handler(self, name, flags):
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# Force FCFLAGS/FFLAGS by adding directly into spack compiler wrappers.
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if self.spec.satisfies("@3.9.1.1: %gcc@10:") and name == "fflags":
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flags.extend(["-fallow-argument-mismatch", "-fallow-invalid-boz"])
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return (flags, None, None)
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def patch(self):
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# Let's not assume csh is intalled in bin
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files = glob.glob("*.csh")
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filter_file("^#!/bin/csh -f", "#!/usr/bin/env csh", *files)
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filter_file("^#!/bin/csh", "#!/usr/bin/env csh", *files)
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@run_before("configure", when="%aocc@4:")
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def create_aocc_config(self):
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param = {
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"MPICC": self.spec["mpi"].mpicc,
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"MPIFC": self.spec["mpi"].mpifc,
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"CTSM_SUBST": (
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"-DWRF_USE_CLM" if self.spec.satisfies("@:4.2.2") else "CONFIGURE_D_CTSM"
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),
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"NETCDFPAR_BUILD": (
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"CONFIGURE_NETCDFPAR_BUILD" if self.spec.satisfies("@4.4.0:") else ""
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),
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}
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zen_conf = (Path(__file__).parent / "aocc_config.inc").read_text().format(**param)
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if self.spec.satisfies("@4.0:"):
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filter_file("#insert new stanza here", zen_conf, "arch/configure.defaults")
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else:
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filter_file("#insert new stanza here", zen_conf, "arch/configure_new.defaults")
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def answer_configure_question(self, outputbuf):
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# Platform options question:
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if "Please select from among the following" in outputbuf:
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options = collect_platform_options(outputbuf)
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comp_pair = "%s/%s" % (
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basename(self.compiler.fc).split("-")[0],
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basename(self.compiler.cc).split("-")[0],
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)
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compiler_matches = dict((x, y) for x, y in options.items() if comp_pair in x.lower())
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if len(compiler_matches) > 1:
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tty.warn("Found multiple potential build options")
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try:
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|
compiler_key = min(compiler_matches.keys(), key=len)
|
|
tty.warn("Selected build option %s." % compiler_key)
|
|
return (
|
|
"%s\n" % compiler_matches[compiler_key][self.spec.variants["build_type"].value]
|
|
)
|
|
except KeyError:
|
|
InstallError(
|
|
"build_type %s unsupported for %s compilers"
|
|
% (self.spec.variants["build_type"].value, comp_pair)
|
|
)
|
|
|
|
if "Compile for nesting?" in outputbuf:
|
|
options = collect_nesting_options(outputbuf)
|
|
try:
|
|
return "%s\n" % options[self.spec.variants["nesting"].value]
|
|
except KeyError:
|
|
InstallError("Failed to parse correct nesting option")
|
|
|
|
def do_configure_fixup(self):
|
|
# Fix mpi compiler wrapper aliases
|
|
|
|
# In version 4.2 the file to be patched is called
|
|
# configure.defaults, while in earlier versions
|
|
# it's configure_new.defaults
|
|
if self.spec.satisfies("@3.9.1.1"):
|
|
config = FileFilter(join_path("arch", "configure_new.defaults"))
|
|
else:
|
|
config = FileFilter(join_path("arch", "configure.defaults"))
|
|
|
|
if self.spec.satisfies("@3.9.1.1 %gcc"):
|
|
# Compiling with OpenMPI requires using `-DMPI2SUPPORT`.
|
|
other_flags = " -DMPI2SUPPORT" if self.spec.satisfies("^openmpi") else ""
|
|
config.filter(
|
|
r"^DM_FC.*mpif90 -f90=\$\(SFC\)",
|
|
"DM_FC = {0}".format(self.spec["mpi"].mpifc) + other_flags,
|
|
)
|
|
config.filter(
|
|
r"^DM_CC.*mpicc -cc=\$\(SCC\)",
|
|
"DM_CC = {0}".format(self.spec["mpi"].mpicc) + other_flags,
|
|
)
|
|
|
|
if self.spec.satisfies("%aocc"):
|
|
config.filter(
|
|
"^DM_FC.*mpif90 -DMPI2SUPPORT",
|
|
"DM_FC = {0}".format(self.spec["mpi"].mpifc + " -DMPI2_SUPPORT"),
|
|
)
|
|
config.filter(
|
|
"^DM_.CC*mpicc -DMPI2SUPPORT",
|
|
"DM_CC = {0}".format(self.spec["mpi"].mpicc) + " -DMPI2_SUPPORT",
|
|
)
|
|
|
|
if self.spec.satisfies("@4.2: %intel"):
|
|
config.filter("^DM_FC.*mpif90", "DM_FC = {0}".format(self.spec["mpi"].mpifc))
|
|
config.filter("^DM_CC.*mpicc", "DM_CC = {0}".format(self.spec["mpi"].mpicc))
|
|
|
|
if self.spec.satisfies("@:4.0.3 %intel@2018:"):
|
|
config.filter(r"-openmp", "-qopenmp")
|
|
|
|
if self.spec.satisfies("%gcc@14:"):
|
|
config.filter(
|
|
"^CFLAGS_LOCAL(.*?)=([^#\n\r]*)(.*)$", r"CFLAGS_LOCAL\1= \2 -fpermissive \3"
|
|
)
|
|
config.filter("^CC_TOOLS(.*?)=([^#\n\r]*)(.*)$", r"CC_TOOLS\1=\2 -fpermissive \3")
|
|
|
|
@run_before("configure")
|
|
def fortran_check(self):
|
|
if not self.compiler.fc:
|
|
msg = "cannot build WRF without a Fortran compiler"
|
|
raise RuntimeError(msg)
|
|
|
|
def configure(self, spec, prefix):
|
|
# Remove broken default options...
|
|
self.do_configure_fixup()
|
|
|
|
p = Popen("./configure", stdin=PIPE, stdout=PIPE, stderr=PIPE)
|
|
if sys.platform != "win32":
|
|
setNonBlocking(p.stdout)
|
|
setNonBlocking(p.stderr)
|
|
|
|
# Because of WRFs custom configure scripts that require interactive
|
|
# input we need to parse and respond to questions. The details can
|
|
# vary somewhat with the exact version, so try to detect and fail
|
|
# gracefully on unexpected questions.
|
|
stallcounter = 0
|
|
outputbuf = ""
|
|
while True:
|
|
line = p.stderr.readline().decode()
|
|
if not line:
|
|
line = p.stdout.readline().decode()
|
|
if not line:
|
|
if p.poll() is not None:
|
|
returncode = p.returncode
|
|
break
|
|
if stallcounter > 300:
|
|
raise InstallError(
|
|
"Output stalled for 30s, presumably an " "undetected question."
|
|
)
|
|
time.sleep(0.1) # Try to do a bit of rate limiting
|
|
stallcounter += 1
|
|
continue
|
|
sys.stdout.write(line)
|
|
stallcounter = 0
|
|
outputbuf += line
|
|
if "Enter selection" in outputbuf or "Compile for nesting" in outputbuf:
|
|
answer = self.answer_configure_question(outputbuf)
|
|
p.stdin.write(answer.encode())
|
|
p.stdin.flush()
|
|
outputbuf = ""
|
|
|
|
if returncode != 0:
|
|
raise InstallError("Configure failed - unknown error")
|
|
|
|
@run_after("configure")
|
|
def patch_for_libmvec(self):
|
|
if self.spec.satisfies("@3.9.1.1 %aocc"):
|
|
fp = self.package_dir + "/patches/3.9/aocc_lmvec.patch"
|
|
which("patch")("-s", "-p1", "-i", "{0}".format(fp), "-d", ".")
|
|
|
|
def run_compile_script(self):
|
|
csh_bin = self.spec["tcsh"].prefix.bin.csh
|
|
csh = Executable(csh_bin)
|
|
|
|
# num of compile jobs capped at 20 in wrf
|
|
num_jobs = str(min(int(make_jobs), 20))
|
|
|
|
# Now run the compile script and track the output to check for
|
|
# failure/success We need to do this because upstream use `make -i -k`
|
|
# and the custom compile script will always return zero regardless of
|
|
# success or failure
|
|
result_buf = csh(
|
|
"./compile",
|
|
"-j",
|
|
num_jobs,
|
|
self.spec.variants["compile_type"].value,
|
|
output=str,
|
|
error=str,
|
|
)
|
|
|
|
print(result_buf)
|
|
if "Executables successfully built" in result_buf:
|
|
return True
|
|
|
|
return False
|
|
|
|
def build(self, spec, prefix):
|
|
result = self.run_compile_script()
|
|
|
|
if not result:
|
|
tty.warn("Compilation failed first time (WRF idiosyncrasies?) " "- trying again...")
|
|
result = self.run_compile_script()
|
|
|
|
if not result:
|
|
raise InstallError("Compile failed. Check the output log for details.")
|
|
|
|
def install(self, spec, prefix):
|
|
# Save all install files as many are needed for WPS and WRF runs
|
|
install_tree(".", prefix)
|