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
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
|
# 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)
from spack.package import *
from spack.util.environment import is_system_path
class Silo(AutotoolsPackage):
"""Silo is a library for reading and writing a wide variety of scientific
data to binary, disk files."""
homepage = "https://wci.llnl.gov/simulation/computer-codes/silo"
git = "https://github.com/LLNL/Silo.git"
url = "https://wci.llnl.gov/sites/wci/files/2021-01/silo-4.10.2.tgz"
maintainers("patrickb314")
version(
"4.11.1",
preferred=True,
sha256="49eddc00304aa4a19074b099559edbdcaa3532c98df32f99aa62b9ec3ea7cee2",
url="https://github.com/LLNL/Silo/releases/download/4.11.1/silo-4.11.1.tar.xz",
)
version(
"4.11.1-bsd",
sha256="51ccfdf3c09dfc98c7858a0a6f08cc3b2a07ee3c4142ee6482ba7b24e314c2aa",
url="https://github.com/LLNL/Silo/releases/download/4.11.1/silo-4.11.1-bsd.tar.xz",
)
version(
"4.11",
sha256="ab936c1f4fc158d9fdc4415965f7d9def7f4abeca596fe5a25bd8485654898ac",
url="https://github.com/LLNL/Silo/releases/download/v4.11/silo-4.11.tar.gz",
)
version(
"4.11-bsd",
sha256="6d0a85a079d48fcdcc0084ecb5fc4cfdcc64852edee780c60cb244d16f4bc4ec",
url="https://github.com/LLNL/Silo/releases/download/v4.11/silo-4.11-bsd.tar.gz",
)
version(
"4.10.2",
sha256="3af87e5f0608a69849c00eb7c73b11f8422fa36903dd14610584506e7f68e638",
preferred=True,
)
version(
"4.10.2-bsd",
sha256="4b901dfc1eb4656e83419a6fde15a2f6c6a31df84edfad7f1dc296e01b20140e",
url="https://wci.llnl.gov/sites/wci/files/2021-01/silo-4.10.2-bsd.tgz",
)
version("4.9", sha256="90f3d069963d859c142809cfcb034bc83eb951f61ac02ccb967fc8e8d0409854")
version("4.8", sha256="c430c1d33fcb9bc136a99ad473d535d6763bd1357b704a915ba7b1081d58fb21")
variant("fortran", default=True, description="Enable Fortran support")
variant("shared", default=True, description="Build shared libraries")
variant("silex", default=False, description="Builds Silex, a GUI for viewing Silo files")
variant("pic", default=True, description="Produce position-independent code (for shared libs)")
variant("mpi", default=True, description="Compile with MPI Compatibility")
variant("hdf5", default=True, description="Support HDF5 for database I/O")
variant("hzip", default=True, description="Enable hzip support")
variant("fpzip", default=True, description="Enable fpzip support")
depends_on("perl", type="build")
depends_on("m4", type="build", when="+shared")
depends_on("autoconf", type="build", when="+shared")
depends_on("autoconf-archive", type="build", when="+shared")
depends_on("automake", type="build", when="+shared")
depends_on("libtool", type="build", when="+shared")
depends_on("mpi", when="+mpi")
depends_on("hdf5@1.8:1.10", when="@:4.10+hdf5")
depends_on("hdf5@1.12:", when="@4.11:+hdf5")
depends_on("qt+gui~framework@4.8:4.9", when="+silex")
depends_on("libx11", when="+silex")
# Xmu dependency is required on Ubuntu 18-20
depends_on("libxmu", when="+silex")
depends_on("readline")
depends_on("zlib-api")
patch("remove-mpiposix.patch", when="@4.8:4.10.2")
# hdf5 1.10 added an additional field to the H5FD_class_t struct
patch("H5FD_class_t-terminate.patch", when="@:4.10.2-bsd")
# H5EPR_SEMI_COLON.patch was fixed in current dev
patch("H5EPR_SEMI_COLON.patch", when="@:4.11-bsd")
# Fix missing F77 init, fixed in 4.9
patch("48-configure-f77.patch", when="@:4.8")
# The previously used AX_CHECK_COMPILER_FLAGS macro was dropped from
# autoconf-archive in 2011
patch("configure-AX_CHECK_COMPILE_FLAG.patch", when="@:4.11-bsd")
# API changes in hdf5-1.13 cause breakage
# See https://github.com/LLNL/Silo/pull/260
patch("hdf5-113.patch", when="@4.11:4.11-bsd +hdf5 ^hdf5@1.13:")
conflicts("^hdf5@1.13:", when="@:4.10.2-bsd")
# hzip and fpzip are not available in the BSD releases
conflicts("+hzip", when="@4.10.2-bsd,4.11-bsd")
conflicts("+fpzip", when="@4.10.2-bsd,4.11-bsd")
# zfp include missing
patch("zfp_error.patch", when="@4.11:4.11-bsd +hdf5")
# use /usr/bin/env perl for portability
patch("mkinc-usr-bin-env-perl.patch", when="@:4.11-bsd")
def flag_handler(self, name, flags):
spec = self.spec
if name == "ldflags":
if "+hdf5" in spec:
if spec["hdf5"].satisfies("~shared"):
flags.append("-ldl")
if "+pic" in spec:
if name == "cflags":
flags.append(self.compiler.cc_pic_flag)
elif name == "cxxflags":
flags.append(self.compiler.cxx_pic_flag)
elif name == "fcflags":
flags.append(self.compiler.fc_pic_flag)
if name == "cflags" or name == "cxxflags":
if spec.satisfies("%oneapi"):
flags.append("-Wno-error=int")
flags.append("-Wno-error=int-conversion")
if "+hdf5" in spec:
# @:4.10 can use up to the 1.10 API
if "@:4.10" in spec:
if "@1.10:" in spec["hdf5"]:
flags.append("-DH5_USE_110_API")
elif "@1.8:" in spec["hdf5"]:
# Just in case anytone is trying to force the 1.6 api for
# some reason
flags.append("-DH5_USE_18_API")
else:
# @4.11: can use newer HDF5 APIs, so this ensures silo is
# presented with an HDF5 API consistent with the HDF5 version.
# Use the latest even-numbered API version, i.e. v1.13.1 uses
# API v1.12
maj_ver = int(spec["hdf5"].version[0])
min_ver = int(spec["hdf5"].version[1])
min_apiver = int(min_ver / 2) * 2
flags.append("-DH5_USE_{0}{1}_API".format(maj_ver, min_apiver))
if spec.compiler.name in ["clang", "apple-clang"]:
flags.append("-Wno-implicit-function-declaration")
return (flags, None, None)
@when("%clang@9:")
def patch(self):
self.clang_9_patch()
@when("%apple-clang@11.0.3:")
def patch(self):
self.clang_9_patch()
def clang_9_patch(self):
# Clang 9 and later include macro definitions in <math.h> that conflict
# with typedefs DOMAIN and RANGE used in Silo plugins.
# It looks like the upstream fpzip repo has been fixed, but that change
# hasn't yet made it into silo.
# https://github.com/LLNL/fpzip/blob/master/src/pcmap.h
if str(self.spec.version).endswith("-bsd"):
# The files below don't exist in the BSD licenced version
return
def repl(match):
# Change macro-like uppercase to title-case.
return match.group(1).title()
files_to_filter = [
"src/fpzip/codec.h",
"src/fpzip/pcdecoder.inl",
"src/fpzip/pcencoder.inl",
"src/fpzip/pcmap.h",
"src/fpzip/pcmap.inl",
"src/fpzip/read.cpp",
"src/fpzip/write.cpp",
"src/hzip/hzmap.h",
"src/hzip/hzresidual.h",
]
filter_file(r"\b(DOMAIN|RANGE|UNION)\b", repl, *files_to_filter)
@property
def force_autoreconf(self):
# Update autoconf's tests whether libtool supports shared libraries.
# (Otherwise, shared libraries are always disabled on Darwin.)
if self.spec.satisfies("@4.11-bsd") or self.spec.satisfies("@4.10.2-bsd"):
return False
else:
return self.spec.satisfies("+shared")
def configure_args(self):
spec = self.spec
config_args = [
"--enable-install-lite-headers",
"--enable-fortran" if "+fortran" in spec else "--disable-fortran",
"--enable-silex" if "+silex" in spec else "--disable-silex",
"--enable-shared" if "+shared" in spec else "--disable-shared",
"--enable-hzip" if "+hzip" in spec else "--disable-hzip",
"--enable-fpzip" if "+fpzip" in spec else "--disable-fpzip",
]
# Do not specify the prefix of zlib if it is in a system directory
# (see https://github.com/spack/spack/pull/21900).
zlib_prefix = self.spec["zlib-api"].prefix
if is_system_path(zlib_prefix):
config_args.append("--with-zlib=yes")
else:
config_args.append("--with-zlib=%s,%s" % (zlib_prefix.include, zlib_prefix.lib))
if "+hdf5" in spec:
config_args.append(
"--with-hdf5=%s,%s" % (spec["hdf5"].prefix.include, spec["hdf5"].prefix.lib)
)
if "+silex" in spec:
x = spec["libx11"]
config_args.extend(
[
"--with-Qt-dir=" + spec["qt"].prefix,
"--with-Qt-lib=QtGui -lQtCore",
"--x-includes=" + x.prefix.include,
"--x-libraries=" + x.prefix.lib,
]
)
if "+mpi" in spec:
config_args.append("CC=%s" % spec["mpi"].mpicc)
config_args.append("CXX=%s" % spec["mpi"].mpicxx)
config_args.append("FC=%s" % spec["mpi"].mpifc)
return config_args
@property
def libs(self):
shared = "+shared" in self.spec
return find_libraries("libsilo*", root=self.prefix, shared=shared, recursive=True)
|
