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authorDouglas Duckworth <quackmaster@protonmail.com>2018-08-16 11:51:58 -0400
committerAdam J. Stewart <ajstewart426@gmail.com>2018-08-16 10:51:58 -0500
commitbe11608732f1d54cd856940519149eac36f0f8fc (patch)
tree0c5304f6a4026a8df6655831a5117854c52532f4
parentcd446a9668c0248e3240a1531f537fb4e0b3a411 (diff)
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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
-rw-r--r--var/spack/repos/builtin/packages/relion/package.py53
1 files 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 @@ class Relion(CMakePackage, CudaPackage):
'-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