1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
|
# Copyright 2013-2023 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
from shutil import copyfile
from spack.package import *
class Nek5000(Package):
"""A fast and scalable high-order solver for computational fluid
dynamics"""
homepage = "https://nek5000.mcs.anl.gov/"
url = "https://github.com/Nek5000/Nek5000/archive/v17.0.tar.gz"
git = "https://github.com/Nek5000/Nek5000.git"
tags = [
"cfd",
"flow",
"hpc",
"solver",
"navier-stokes",
"spectral-elements",
"fluid",
"ecp",
"ecp-apps",
]
version("develop", branch="master")
version("17.0", "4d8d4793ce3c926c54e09a5a5968fa959fe0ba46bd2e6b8043e099528ee35a60")
version("19.0", "db129877a10ff568d49edc77cf65f9e732eecb1fce10edbd91ffc5ac10c41ad6")
# MPI, Profiling and Visit variants
variant("mpi", default=True, description="Build with MPI.")
variant("profiling", default=True, description="Build with profiling data.")
variant("visit", default=False, description="Build with Visit.")
# TODO: add a variant 'blas' or 'external-blas' to enable the usage of
# Spack installed/configured blas.
# Dependencies
depends_on("mpi", when="+mpi")
patch("add_fjfortran.patch", when="%fj")
@run_before("install")
def fortran_check(self):
if not self.compiler.f77:
msg = "Cannot build Nek5000 without a Fortran 77 compiler."
raise RuntimeError(msg)
@run_after("install")
def test_install(self):
with working_dir("short_tests/eddy"):
f_size = join_path(os.getcwd(), "SIZE")
f_size_legacy = join_path(os.getcwd(), "SIZE.legacy")
if not os.access(f_size, os.F_OK):
if os.access(f_size_legacy, os.F_OK):
copyfile(f_size_legacy, f_size)
else:
raise RuntimeError("Can not find {0}".format(f_size))
os.system(join_path(self.prefix.bin, "makenek") + " eddy_uv")
if not os.path.isfile(join_path(os.getcwd(), "nek5000")):
msg = "Cannot build example: short_tests/eddy."
raise RuntimeError(msg)
def install(self, spec, prefix):
bin_dir = "bin"
# Do not use the Spack compiler wrappers.
# Use directly the compilers:
fc = self.compiler.f77
cc = self.compiler.cc
fflags = spec.compiler_flags["fflags"]
cflags = spec.compiler_flags["cflags"]
if self.compiler.name in ["xl", "xl_r"]:
# Use '-qextname' to add underscores.
# Use '-WF,-qnotrigraph' to fix an error about a string: '... ??'
fflags += ["-qextname", "-WF,-qnotrigraph"]
error = Executable(fc)("empty.f", output=str, error=str, fail_on_error=False)
if "gfortran" in error or "GNU" in error or "gfortran" in fc:
# Use '-std=legacy' to suppress an error that used to be a
# warning in previous versions of gfortran.
fflags += ["-std=legacy"]
fflags = " ".join(fflags)
cflags = " ".join(cflags)
with working_dir(bin_dir):
if "+mpi" in spec:
fc = spec["mpi"].mpif77
cc = spec["mpi"].mpicc
else:
filter_file(r"^#MPI=0", "MPI=0", "makenek")
# Make sure nekmpi wrapper uses srun when we know OpenMPI
# is not built with mpiexec
if "^openmpi~legacylaunchers" in spec:
filter_file(r"mpiexec -np", "srun -n", "nekmpi")
if "+profiling" not in spec:
filter_file(r"^#PROFILING=0", "PROFILING=0", "makenek")
if "+visit" in spec:
filter_file(r"^#VISIT=1", "VISIT=1", "makenek")
filter_file(
r"^#VISIT_INSTALL=.*",
'VISIT_INSTALL="' + spec["visit"].prefix.bin + '"',
"makenek",
)
# Update the makenek to use correct compilers and
# Nek5000 source.
filter_file(r"^#FC\s*=.*", 'FC="{0}"'.format(fc), "makenek")
filter_file(r"^#CC\s*=.*", 'CC="{0}"'.format(cc), "makenek")
if self.spec.version == Version("17.0"):
filter_file(
r"^#SOURCE_ROOT\s*=\"\$H.*",
'SOURCE_ROOT="' + prefix.bin.Nek5000 + '"',
"makenek",
)
else:
filter_file(
r"^#NEK_SOURCE_ROOT\s*=\"\$H.*",
'NEK_SOURCE_ROOT="' + prefix.bin.Nek5000 + '"',
"makenek",
)
if fflags:
filter_file(r"^#FFLAGS=.*", 'FFLAGS+=" {0}"'.format(fflags), "makenek")
if cflags:
filter_file(r"^#CFLAGS=.*", 'CFLAGS+=" {0}"'.format(cflags), "makenek")
with working_dir("core"):
if self.compiler.name in ["xl", "xl_r"]:
# Patch 'core/makenek.inc' and 'makefile.template' to use
# '-qextname' when checking for underscore becasue 'xl'/'xl_r'
# use this option to enable the addition of the underscore.
filter_file(r"^\$FCcomp -c ", "$FCcomp -qextname -c ", "makenek.inc")
filter_file(
r"\$\(FC\) -c \$\(L0\)", "$(FC) -c -qextname $(L0)", "makefile.template"
)
# Install Nek5000/bin in prefix/bin
install_tree(bin_dir, prefix.bin)
# Copy Nek5000 source to prefix/bin
install_tree(self.stage.source_path, prefix.bin.Nek5000)
|