Merge pull request #2486 from smoors/20210622134158_new_pr_GBkUEglHDL

update Xmipp easyblock for new version (v3.20.07)

easybuild/easyblocks/x/xmipp.py

@@ -51,23 +51,38 @@ def __init__(self, *args, **kwargs):
         """Initialize Xmipp-specific variables."""
         super(EB_Xmipp, self).__init__(*args, **kwargs)
         self.xmipp_modules = ['xmippCore', 'xmipp', 'xmippViz']
-        self.srcdir = os.path.join(self.builddir, 'src')
-        self.cfg['start_dir'] = self.builddir
+        if LooseVersion(self.version) >= LooseVersion('3.20.07'):
+            self.cfg['start_dir'] = os.path.join(self.builddir, 'xmipp-' + self.version)
+            self.srcdir = os.path.join(self.cfg['start_dir'], 'src')
+            self.cfgfile = os.path.join(self.cfg['start_dir'], 'xmipp.conf')
+            self.xmipp_exe = './xmipp'
+        else:
+            self.cfg['start_dir'] = self.builddir
+            self.srcdir = os.path.join(self.builddir, 'src')
+            self.cfgfile = os.path.join(self.builddir, 'xmipp.conf')
+            self.xmipp_exe = os.path.join(self.srcdir, 'xmipp', 'xmipp')
         self.use_cuda = False
-        self.cfgfile = os.path.join(self.builddir, 'xmipp.conf')
 
     def extract_step(self):
         """Extract Xmipp sources."""
-        # Xmipp assumes that everything is unpacked in a "src" dir
-        mkdir(self.srcdir)
-        self.cfg.update('unpack_options', '--directory %s' % os.path.basename(self.srcdir))
+        if LooseVersion(self.version) < LooseVersion('3.20.07'):
+            # Xmipp < 3.20.07 assumes that everything is unpacked in a "src" dir
+            # Xmipp >= 3.20.07 assumes that everything is unpacked in the "src" dir of Xmipp itself
+            mkdir(self.srcdir)
+            self.cfg.update('unpack_options', '--directory %s' % os.path.basename(self.srcdir))
         super(EB_Xmipp, self).extract_step()
         for module in self.xmipp_modules:
-            symlink('%s-%s' % (module, self.version), os.path.join(self.srcdir, module), use_abspath_source=False)
+            if LooseVersion(self.version) >= LooseVersion('3.20.07') and module == 'xmipp':
+                pass
+            else:
+                symlink('%s-%s' % (module, self.version), os.path.join(self.srcdir, module), use_abspath_source=False)
 
     def patch_step(self):
         """Patch files from self.srcdir dir."""
-        super(EB_Xmipp, self).patch_step(beginpath=self.srcdir)
+        if LooseVersion(self.version) >= LooseVersion('3.20.07'):
+            super(EB_Xmipp, self).patch_step()
+        else:
+            super(EB_Xmipp, self).patch_step(beginpath=self.srcdir)
 
     def setup_xmipp_env(self):
         """Setup environment before running SCons."""
@@ -88,7 +103,7 @@ def configure_step(self):
         # Initialize the config file and then patch it with the correct values
         cmd = ' '.join([
             self.cfg['preconfigopts'],
-            os.path.join(self.srcdir, 'xmipp', 'xmipp'),
+            self.xmipp_exe,
             'config',
             self.cfg['configopts'],
         ])
@@ -106,6 +121,16 @@ def configure_step(self):
             'MPI_LINKERFORPROGRAMS': os.environ.get('MPICXX', 'UNKNOWN'),
         }
 
+        if LooseVersion(self.version) >= LooseVersion('3.20.07'):
+            # Define include dirs with INCDIRFLAGS (Xmipp does not use CPPPATH directly)
+            incdirflags = os.getenv('INCDIRFLAGS', '')
+            incdirflags += '-I../ -I ' + ' -I'.join(os.environ['CPATH'].split(':'))
+            opencv_root = get_software_root('OpenCV')
+            if opencv_root:
+                incdirflags += ' -I' + opencv_root + '/include/opencv4'
+            # env.setvar('INCDIRFLAGS', incdirflags)
+            params['INCDIRFLAGS'] = incdirflags
+
         deps = [
             # Name of dependency, name of env var to set, required or not
             ('HDF5', None, True),
@@ -122,8 +147,9 @@ def configure_step(self):
             params.update({'CUDA_LIB': os.path.join(cuda_root, 'lib64')})
             params.update({'NVCC': os.environ['CUDA_CXX']})
             # Their default for NVCC is to use g++-5, fix that
-            nvcc_flags = '--x cu -D_FORCE_INLINES -Xcompiler -fPIC '
-            nvcc_flags = nvcc_flags + '-Wno-deprecated-gpu-targets -std=c++11'
+            nvcc_flags = '-v --x cu -D_FORCE_INLINES -Xcompiler -fPIC -Wno-deprecated-gpu-targets -std=c++11'
+            if LooseVersion(self.version) >= LooseVersion('3.20.07'):
+                nvcc_flags += ' --extended-lambda'
             params.update({'NVCC_CXXFLAGS': nvcc_flags})
             self.use_cuda = True
 
@@ -134,6 +160,11 @@ def configure_step(self):
                 if len(matches) == 1:
                     cufft = os.path.basename(matches[0])
                     symlink(cufft, os.path.join(self.srcdir, 'cuFFTAdvisor'), use_abspath_source=False)
+                    if LooseVersion(self.version) >= LooseVersion('3.20.07'):
+                        symlink(
+                            os.path.join(self.srcdir, cufft),
+                            os.path.join(self.srcdir, 'xmipp', 'external', 'cuFFTAdvisor')
+                        )
                 else:
                     raise EasyBuildError("Failed to isolate path to cuFFTAdvisor-*: %s", matches)
 
@@ -220,7 +251,7 @@ def install_step(self):
         # to replicate here.
         cmd = ' '.join([
             self.cfg['preinstallopts'],
-            os.path.join(self.srcdir, 'xmipp', 'xmipp'),
+            self.xmipp_exe,
             'install',
             self.installdir,
             self.cfg['installopts'],
@@ -238,9 +269,13 @@ def sanity_check_step(self):
 
         bins = ['xmipp_%s' % x for x in ['angular_rotate', 'classify_kerdensom', 'mpi_ml_refine3d']]
         libs = ['XmippCore', 'XmippJNI', 'XmippParallel', 'Xmipp']
+        cuda_root = get_software_root('CUDA')
+        if cuda_root:
+            libs.append('cuFFTAdvisor')
         custom_paths = {
             'files': [os.path.join('bin', x) for x in bins] +
             [os.path.join('bindings', 'python', 'xmippViz.py')] +
+            [os.path.join('bindings', 'java', 'lib', 'XmippJNI.jar')] +
             [os.path.join('lib', 'lib%s.%s') % (x, shlib_ext) for x in libs],
             'dirs': ['resources'],
         }