From be11608732f1d54cd856940519149eac36f0f8fc Mon Sep 17 00:00:00 2001 From: Douglas Duckworth Date: Thu, 16 Aug 2018 11:51:58 -0400 Subject: [PATCH] added relion version 3 (beta) (#8872) * added relion 3 beta - WIP * added relion 3 beta - WIP * more relion changes - still WIP * more changes for relion * more changes * now correctly handling cuda_arch * now correctly handling cuda_arch * fixed flake8 syntax errors * fixed flake8 syntax errors * merge * fixed flake8 errors again * relion 3 finished * added print message to cuda_arch exception * relion - shortened explination * still need tag=2.0.3 for v 2.0.3 - removed @develop since it no longer exists * correct cuda versions now used properly * relion 3 done * added tags back * fixed exception message * relion - added develop back as master --- .../repos/builtin/packages/relion/package.py | 53 +++++++++++++------ 1 file changed, 36 insertions(+), 17 deletions(-) diff --git a/var/spack/repos/builtin/packages/relion/package.py b/var/spack/repos/builtin/packages/relion/package.py index 120ef6bd83..62a0b2c0a0 100644 --- a/var/spack/repos/builtin/packages/relion/package.py +++ b/var/spack/repos/builtin/packages/relion/package.py @@ -34,29 +34,45 @@ class Relion(CMakePackage, CudaPackage): homepage = "http://http://www2.mrc-lmb.cam.ac.uk/relion" git = "https://github.com/3dem/relion.git" - version('develop') - version('2.1', tag='2.1') + version('3.0_beta', + git='https://bitbucket.org/scheres/relion-3.0_beta.git') + version('2.1', preferred='true', tag='2.1') version('2.0.3', tag='2.0.3') + # relion has no develop branch though pulling from master + # should be considered the same as develop + version('develop', branch='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) 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')) depends_on('mpi') + # relion will not build with newer versions of cmake + # per https://github.com/3dem/relion/issues/380 + depends_on('cmake@3:3.9.4', type='build') depends_on('fftw+float+double') depends_on('fltk', when='+gui') - # cuda 9 not yet supported - # https://github.com/3dem/relion/issues/296 - depends_on('cuda@8.0:8.99', when='+cuda') - # use gcc < 5 when compiled with cuda 8 - conflicts('%gcc@5:', when='+cuda') + depends_on('libtiff') + + # relion 3 supports cuda 9 + # relion < 3 does not + depends_on('cuda', when='+cuda') + depends_on('cuda@9:', when='@3: +cuda') + depends_on('cuda@8.0:8.99', when='@:2 +cuda') def cmake_args(self): + + carch = self.spec.variants['cuda_arch'].value[0] + args = [ '-DCMAKE_C_FLAGS=-g', '-DCMAKE_CXX_FLAGS=-g', @@ -65,14 +81,17 @@ def cmake_args(self): '-DDoublePrec_GPU=%s' % ('+double-gpu' in self.spec), ] - carch = self.spec.variants['cuda_arch'].value - if '+cuda' in self.spec: - args += [ - '-DCUDA=on', - ] - if carch is not None: - args += [ - '-DCUDA_ARCH=%s' % (carch), - ] + # relion+cuda requires selecting cuda_arch + if not carch: + raise ValueError("select cuda_arch when building with +cuda") + else: + args += ['-DCUDA=ON', '-DCudaTexture=ON', + '-DCUDA_ARCH=%s' % (carch)] + + # these new values were added in relion 3 + # do not seem to cause problems with < 3 + else: + args += ['-DMKLFFT=ON', '-DFORCE_OWN_TBB=ON', '-DALTCPU=ON'] + return args