# Copyright Spack Project Developers. See COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack_repo.builtin.build_systems.cmake import CMakePackage from spack_repo.builtin.build_systems.cuda import CudaPackage 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 = "https://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("5.0.1", sha256="3253230cd4b3d9633a5cac906937039b9971eb9430c3e2d838473777fb811f4c") version("5.0.0", sha256="800ad0c0aa778cbf584fcf8986976645f2b25d677a80f168e5397975b9db6e47") 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", ) variant("python", default=False, description="Build Python environment for RELION", when="@5:") 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@11:12.8", when="@:5.0.0 +cuda") # 5.0.0 is not compatible with cuda 12.9+ depends_on("cuda@11:13", when="@5.0.1: +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", ) # New? for 5.0 depends_on("xz", when="@5:", type="run") depends_on("bzip2", when="@5:", type="run") # should be pbzip2 but thats not really maintained depends_on("zstd", when="@5:", type="run") # Python stuff for Tomo on 5.0.0 depends_on("python@3.10", when="@5.0 +python") depends_on("py-torch@2.0.1", when="@5.0 +python") # TODO how to define Cuda? depends_on("py-torchvision@0.15.2", when="@5.0 +python") depends_on("py-tqdm@4.65.0", when="@5.0 +python") depends_on("py-mrcfile@1.4.3", when="@5.0 +python") depends_on("py-starfile@0.5.6:", when="@5.0 +python") depends_on("py-loguru@0.7.0", when="@5.0 +python") depends_on("py-scikit-learn@1.3.0", when="@5.0 +python") depends_on("py-umap-learn@0.5.3", when="@5.0 +python") depends_on("py-matplotlib@3.7.2", when="@5.0 +python") depends_on("py-pydantic@1.10.19", when="@5.0 +python") # Should be .18 but that doesn't exist in Spack # depends_on("py-napari+all@0.4.18", when="@5.0 +python") # TODO create package depends_on("tsne-cuda@3.0.1 +cuda +python", when="@5.0 +python +cuda") # Only when cuda depends_on("py-pyqt5@5.15.9", when="@5.0 +python") depends_on("py-typer@0.9.0", when="@5.0 +python") depends_on("py-biopython@1.81", when="@5.0 +python") depends_on("py-fastcluster@1.2.6", when="@5.0 +python") depends_on("py-seaborn@0.12.2", when="@5.0 +python") depends_on("py-dill@0.3.7", when="@5.0 +python") depends_on("py-numpy@:2", when="@5.0 +python") depends_on("py-click@:8.1", when="@5.0 +python") # Plus some more packages from custom git reposistories 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)] if "+python" in self.spec: args.append(self.define("PYTHON_EXE_PATH", self["python"].command.path)) 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"), )