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
|
# 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 glob
import os
from spack.package import *
from spack.util.environment import EnvironmentModifications
class Fsl(Package, CudaPackage):
"""FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI
brain imaging data."""
# NOTE: A manual download is required for FSL. Spack will search your
# current directory for the download file. Alternatively, add this file to
# a mirror so that Spack can find it. For instructions on how to set up a
# mirror, see https://spack.readthedocs.io/en/latest/mirrors.html
homepage = "https://fsl.fmrib.ox.ac.uk"
url = "file://{0}/fsl-5.0.10-sources.tar.gz".format(os.getcwd())
manual_download = True
version("6.0.5", sha256="df12b0b1161a26470ddf04e4c5d5d81580a04493890226207667ed8fd2b4b83f")
version("6.0.4", sha256="58b88f38e080b05d70724d57342f58e1baf56e2bd3b98506a72b4446cad5033e")
version("5.0.10", sha256="ca183e489320de0e502a7ba63230a7f55098917a519e8c738b005d526e700842")
depends_on("python", type=("build", "run"))
depends_on("expat")
depends_on("libx11")
depends_on("glu")
depends_on("iconv")
depends_on("openblas", when="@6:")
depends_on("vtk@:8")
conflicts("cuda_arch=none", when="+cuda", msg="must select a CUDA architecture")
conflicts("platform=darwin", msg="currently only packaged for linux")
patch("build_log.patch")
patch("eddy_Makefile.patch", when="@6.0.4")
patch("iconv.patch", when="^libiconv")
patch("fslpython_install_v5.patch", when="@:5")
patch("fslpython_install_v604.patch", when="@6.0.4")
patch("fslpython_install_v605.patch", when="@6.0.5")
# Allow fsl to use newer versions of cuda
patch(
"https://aur.archlinux.org/cgit/aur.git/plain/005-fix_cuda_thrust_include.patch?h=fsl",
sha256="9471addfc2f880350eedadcb99cb8b350abf42be1c0652ccddf49e34e5e48734",
level=2,
)
# allow newer compilers
patch("libxmlpp_bool.patch")
# These patches disable FSL's attempts to try to submit a subset of FSL
# computations to an SGE queue system. That auto-submit mechanism only
# works for SGE and requires someone to edit the fsl_sub script to
# accommodate their system. These patches disable the auto submission
# scheme and allow the fsl_sub script to behave the same on all systems,
# and without further modification, whether the computation is submitted to
# a "local" system, like a workstation, or as a batch job to a cluster
# queueing system, regardless of queue system type.
patch("fsl_sub_v5.patch", when="@:5")
patch("fsl_sub_v6.patch", when="@6:")
def patch(self):
# Uncomment lines in source file to allow building from source
with working_dir(join_path(self.stage.source_path, "etc", "fslconf")):
sourced = FileFilter("fsl.sh")
sourced.filter("#FSLCONFDIR", "FSLCONFDIR")
if self.spec.satisfies("@6:"):
sourced.filter("#FSLMACHTYPE", "FSLMACHTYPE")
else:
sourced.filter(r"#(FSLMACHTYPE).*", r"\1=linux_64-gcc4.8")
if self.spec.satisfies("@:5"):
with working_dir(join_path(self.stage.source_path, "config", "common")):
buildproj = FileFilter("buildproj")
buildproj.filter(r"(^FSLMACHTYPE).*", r"\1=linux_64-gcc4.8")
# Capture the settings file
if self.spec.satisfies("@6:"):
settings_file = join_path(self.stage.source_path, "config", "buildSettings.mk")
vtk_file = settings_file
else:
settings_file = join_path(
self.stage.source_path, "config", "linux_64-gcc4.8", "systemvars.mk"
)
externals_file = join_path(
self.stage.source_path, "config", "linux_64-gcc4.8", "externallibs.mk"
)
vtk_file = externals_file
build_settings = FileFilter(settings_file)
vtk_settings = FileFilter(vtk_file)
build_settings.filter(r"^CUDAVER", "#CUDAVER")
build_settings.filter(r"(^CC)\s*=.*", r"\1 = {0}".format(spack_cc))
build_settings.filter(r"(^CXX)\s*=.*", r"\1 = {0}".format(spack_cxx))
build_settings.filter(r"(^CXX11)\s*=.*", r"\1 = {0}".format(spack_cxx))
vtk_suffix = self.spec["vtk"].version.up_to(2)
vtk_lib_dir = self.spec["vtk"].prefix.lib64
vtk_include_dir = join_path(self.spec["vtk"].prefix.include, "vtk-{0}".format(vtk_suffix))
vtk_settings.filter(r"(^VTKDIR_INC)\s*=.*", r"\1 = {0}".format(vtk_include_dir))
vtk_settings.filter(r"(^VTKDIR_LIB)\s*=.*", r"\1 = {0}".format(vtk_lib_dir))
vtk_settings.filter(r"(^VTKSUFFIX)\s*=.*", r"\1 = -{0}".format(vtk_suffix))
if "+cuda" in self.spec:
cuda_arch = self.spec.variants["cuda_arch"].value
cuda_gencode = " ".join(self.cuda_flags(cuda_arch))
cuda_installation = self.spec["cuda"].prefix
build_settings.filter(
r"(^CUDA_INSTALLATION)\s*=.*", r"\1 = {0}".format(cuda_installation)
)
build_settings.filter(
r"(^LIB_CUDA)\s*=.*", r"\1 = {0}".format(join_path(cuda_installation, "lib64"))
)
build_settings.filter(
r"(^INC_CUDA)\s*=.*", r"\1 = {0}".format(join_path(cuda_installation, "include"))
)
build_settings.filter(
r"(^NVCC11)\s*=.*", r"\1 = {0}".format(join_path(cuda_installation, "bin", "nvcc"))
)
build_settings.filter(
r"(^NVCC)\s*=.*", r"\1 = {0}".format(join_path(cuda_installation, "bin", "nvcc"))
)
build_settings.filter(r"(^GENCODE_FLAGS)\s*=.*", r"\1 = {0}".format(cuda_gencode))
if self.spec.satisfies("@6:"):
build_settings.filter(r"(^EDDYBUILDPARAMETERS)\s*=.*", r'\1 = "cuda=1" "cpu=1"')
build_settings.filter(r"(^fdt_MASTERBUILD)\s*=.*", r"\1 = COMPILE_GPU=1")
build_settings.filter(r"(^ptx2_MASTERBUILD)\s*=.*", r"\1 = COMPILE_GPU=1")
else:
with open(settings_file, "a") as f:
f.write("COMPILE_GPU=1\n")
else:
build_settings.filter(r"^CUDA_INSTALLATION", "#CUDA_INSTALLATION")
build_settings.filter(r"^GENCODE_FLAGS", "#GENCODE_FLAGS")
build_settings.filter(r"^LIB_CUDA", "#LIB_CUDA")
build_settings.filter(r"^INC_CUDA", "#INC_CUDA")
build_settings.filter(r"^NVCC", "#NVCC")
if self.spec.satisfies("@6:"):
build_settings.filter(r"(^EDDYBUILDPARAMETERS)\s*=.*", r'\1 = "cpu=1"')
build_settings.filter(r"(^fdt_MASTERBUILD)\s*=.*", r"\1 = COMPILE_GPU=0")
build_settings.filter(r"(^ptx2_MASTERBUILD)\s*=.*", r"\1 = COMPILE_GPU=0")
filter_file(
r'(configure_opts=".*)"',
r'\1 --x-includes={0} --x-libraries={1}"'.format(
self.spec["libx11"].prefix.include, self.spec["libx11"].prefix.lib
),
join_path("extras", "src", "tk", "unix", "fslconfigure"),
)
filter_file(r" -L/lib64", r"", join_path("src", "fabber_core", "Makefile"))
def install(self, spec, prefix):
build = Executable(join_path(self.stage.source_path, "build"))
build()
rm = which("rm")
for file in glob.glob("build*"):
rm("-f", file)
rm("-r", "-f", "src")
rm("-r", "-f", join_path("extras", "src"))
rm("-r", "-f", join_path("extras", "include"))
install_tree(".", prefix)
@run_after("install")
def postinstall(self):
# The PYTHON related environment variables need to be unset here so
# the post install script does not get confused.
vars_to_unset = ["PYTHONPATH", "PYTHONHOME"]
with spack.util.environment.preserve_environment(*vars_to_unset):
for v in vars_to_unset:
del os.environ[v]
script = Executable(join_path(prefix, "etc", "fslconf", "post_install.sh"))
script("-f", prefix)
def setup_build_environment(self, env):
if not self.stage.source_path:
self.stage.fetch()
self.stage.expand_archive()
env.set("FSLDIR", self.stage.source_path)
# Below is for sourcing purposes during building
fslsetup = join_path(self.stage.source_path, "etc", "fslconf", "fsl.sh")
if os.path.isfile(fslsetup):
env.extend(EnvironmentModifications.from_sourcing_file(fslsetup))
def setup_run_environment(self, env):
# Set the environment variables after copying tree
env.set("FSLDIR", self.prefix)
fslsetup = join_path(self.prefix, "etc", "fslconf", "fsl.sh")
if os.path.isfile(fslsetup):
env.extend(EnvironmentModifications.from_sourcing_file(fslsetup))
|
