relion: add altcpu variant and fix fftw (#30097)

This package was not setting FFTW when +mklfft was used with +cuda.
Since both were set to 'True', the default build was not linked to
any FFTW, leading to a run time error. It seems MKL support was
conflated with alternative CPU acceleration support. This PR does the
following:

- adds the altcpu variant to specify non-GPU/CPU acceleration
- sets a conflict between +altcpu and +cuda
- sets an FFTW implementation
- sets fltk+xft when +gui to get a decent looking GUI interface
- sets tbb dependency only when +altcpu
- adds dependency on ctffind
- adds variant and dependency on motioncor2
- sets defaults for
    - qsub template location
    - ctffind location
    - motioncor2 location

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

var/spack/repos/builtin/packages/relion/package.py

@@ -36,35 +36,52 @@ class Relion(CMakePackage, CudaPackage):
     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('fftw precision=float,double', when='~mklfft')
-    depends_on('fltk', when='+gui')
+
+    # 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='~cuda')
+    depends_on('tbb', when='+altcpu')
-    depends_on('mkl', when='~cuda +mklfft')
+    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')
 
     def cmake_args(self):
-
-        carch = self.spec.variants['cuda_arch'].value[0]
-
         args = [
             '-DCMAKE_C_FLAGS=-g',
             '-DCMAKE_CXX_FLAGS=-g',
@@ -72,20 +89,24 @@ def cmake_args(self):
             '-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:
-            # relion+cuda requires selecting cuda_arch
+            carch = self.spec.variants['cuda_arch'].value[0]
-            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
+            # relion+cuda requires selecting cuda_arch
-        # do not seem to cause problems with < 3
+            if carch == 'none':
-        else:
+                raise ValueError(
-            args += ['-DMKLFFT=%s' % ('+mklfft' in self.spec), '-DALTCPU=ON']
+                    'Must select a value for cuda_arch'
+                )
+            else:
+                args += [
+                    '-DCUDA=ON',
+                    '-DCudaTexture=ON',
+                    '-DCUDA_ARCH=%s' % (carch),
+                ]
 
         return args
 
@@ -93,3 +114,19 @@ 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'))