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# 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 *
class Relion(CMakePackage, CudaPackage):
"""RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a
stand-alone computer program that employs an empirical Bayesian approach to
refinement of (multiple) 3D reconstructions or 2D class averages in
electron cryo-microscopy (cryo-EM)."""
homepage = "http://www2.mrc-lmb.cam.ac.uk/relion"
git = "https://github.com/3dem/relion.git"
url = "https://github.com/3dem/relion/archive/4.0.0.zip"
maintainers("dacolombo")
license("GPL-2.0-only")
version("4.0.1", sha256="7e0d56fd4068c99f943dc309ae533131d33870392b53a7c7aae7f65774f667be")
version("4.0.0", sha256="0987e684e9d2dfd630f1ad26a6847493fe9fcd829ec251d8bc471d11701d51dd")
# 3.1.4 latest release in 3.1 branch
version("3.1.4", sha256="3bf3449bd2d71dc85d2cdbd342e772f5faf793d8fb3cda6414547cf34c98f34c")
version("3.1.3", sha256="e67277200b54d1814045cfe02c678a58d88eb8f988091573453c8568bfde90fc")
version("3.1.2", sha256="dcdf6f214f79a03d29f0fed2de58054efa35a9d8401543bdc52bfb177987931f")
version("3.1.1", sha256="63e9b77e1ba9ec239375020ad6ff631424d1a5803cba5c608c09fd44d20b1618")
version("3.1.0", sha256="8a7e751fa6ebcdf9f36046499b3d88e170c4da86d5ff9ad1914b5f3d178867a8")
# 3.0.8 latest release in 3.0 branch
version("3.0.8", sha256="18cdd58e3a612d32413eb37e473fe8fbf06262d2ed72e42da20356f459260973")
version("3.0.7", sha256="a6d37248fc4d0bfc18f4badb7986dc1b6d6849baa2128b0b4dade13cb6991a99")
# relion master contains development code
# contains 3.0 branch code
version("master")
variant("gui", default=True, description="build the gui")
variant("cuda", default=True, description="enable compute on gpu")
variant("double", default=True, description="double precision (cpu) code")
variant("double-gpu", default=False, description="double precision gpu")
# if built with purpose=cluster then relion will link to gpfs libraries
# if that's not desirable then use purpose=desktop
variant(
"purpose",
default="cluster",
values=("cluster", "desktop"),
description="build relion for use in cluster or desktop",
)
variant(
"build_type",
default="RelWithDebInfo",
description="The build type to build",
values=("Debug", "Release", "RelWithDebInfo", "Profiling", "Benchmarking"),
)
# these new values were added in relion 3
# do not seem to cause problems with < 3
variant("mklfft", default=True, description="Use MKL rather than FFTW for FFT")
variant(
"allow_ctf_in_sagd",
default=True,
description=(
"Allow CTF-modulation in SAGD, " "as specified in Claim 1 of patent US10,282,513B2"
),
)
variant("altcpu", default=False, description="Use CPU acceleration", when="~cuda")
variant(
"external_motioncor2",
default=False,
description="Have external motioncor2 available in addition to " "Relion builtin",
)
depends_on("mpi")
depends_on("cmake@3:", type="build")
depends_on("binutils@2.32:", type="build")
depends_on("fftw precision=float,double", when="~mklfft")
# use the +xft variant so the interface is not so horrible looking
depends_on("fltk+xft", when="+gui")
depends_on("libtiff")
depends_on("libpng", when="@4:")
depends_on("cuda", when="+cuda")
depends_on("cuda@9:", when="@3: +cuda")
depends_on("tbb", when="+altcpu")
depends_on("mkl", when="+mklfft")
depends_on("ctffind", type="run")
depends_on("motioncor2", type="run", when="+external_motioncor2")
# TODO: more externals to add
# Spack packages needed
# - Gctf
# - ResMap
patch("0002-Simple-patch-to-fix-intel-mkl-linking.patch", when="@:3.1.1 os=ubuntu18.04")
patch(
"https://github.com/3dem/relion/commit/2daa7447c1c871be062cce99109b6041955ec5e9.patch?full_index=1",
sha256="4995b0d4bc24a1ec99042a4b73e9db84918eb6f622dacb308b718146bfb6a5ea",
when="@4.0.0",
)
def cmake_args(self):
args = [
"-DCMAKE_C_FLAGS=-g",
"-DCMAKE_CXX_FLAGS=-g",
"-DGUI=%s" % ("+gui" in self.spec),
"-DDoublePrec_CPU=%s" % ("+double" in self.spec),
"-DDoublePrec_GPU=%s" % ("+double-gpu" in self.spec),
"-DALLOW_CTF_IN_SAGD=%s" % ("+allow_ctf_in_sagd" in self.spec),
"-DMKLFFT=%s" % ("+mklfft" in self.spec),
"-DALTCPU=%s" % ("+altcpu" in self.spec),
]
if "+cuda" in self.spec:
carch = self.spec.variants["cuda_arch"].value[0]
# relion+cuda requires selecting cuda_arch
if carch == "none":
raise ValueError("Must select a value for cuda_arch")
else:
args += ["-DCUDA=ON", "-DCudaTexture=ON", "-DCUDA_ARCH=%s" % (carch)]
return args
def patch(self):
# Remove flags not recognized by the NVIDIA compilers
if self.spec.satisfies("%nvhpc"):
filter_file("-std=c99", "-c99", "src/apps/CMakeLists.txt")
# set up some defaults
filter_file(
r"(#define DEFAULTQSUBLOCATION).*",
r'\1 "{0}"'.format(join_path(self.spec.prefix.bin, "relion_qsub.csh")),
join_path("src", "pipeline_jobs.h"),
)
filter_file(
r"(#define DEFAULTCTFFINDLOCATION).*",
r'\1 "{0}"'.format(join_path(self.spec["ctffind"].prefix.bin, "ctffind")),
join_path("src", "pipeline_jobs.h"),
)
if "+external_motioncor2" in self.spec:
filter_file(
r"(#define DEFAULTMOTIONCOR2LOCATION).*",
r'\1 "{0}"'.format(join_path(self.spec["motioncor2"].prefix.bin, "MotionCor2")),
join_path("src", "pipeline_jobs.h"),
)
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