Start fixing handling GPU-reliant packages

Software packages that require a GPU (i.e. have 'GPU_reliance: required'
in their .BBSoptions file) are now ignored by the software builds (buildtype
== 'bioc') and picked up by the GPU-enabled builds (buildtype ==
'bioc-gpu').

Author: hpages

BBS-make-OUTGOING.py

@@ -99,7 +99,8 @@ def copy_outgoing_pkgs(products_in_subdir, source_node):
     meat_index_path = os.path.join(BBSvars.Central_rdir.path,
                                    BBSutils.meat_index_file)
     pkgs = bbs.parse.get_meat_packages_for_node(meat_index_path, node_hostname,
-                                                node_Arch, node_pkgType)
+                                                node_Arch, node_pkgType,
+                                                BBSvars.buildtype)
     meat_index = bbs.parse.get_meat_packages(meat_index_path, as_dict=True)
     for pkg in pkgs:
         if block_package(node_hostname, node_id, pkg):

BBS-prerun.py

@@ -117,6 +117,10 @@ def _add_or_skip_or_ignore_package(pkgsrctree, meat_index):
                 unsupported += ', win'
         if unsupported != None:
             meat_index.write('UnsupportedPlatforms: %s\n' % unsupported)
+    if options != None:
+        GPU_reliance = options.get('GPU_reliance')
+        if GPU_reliance != None:
+            meat_index.write('GPU_reliance: %s\n' % GPU_reliance)
     meat_index.write('\n')
     return 0  # package will be added to the "meat index"
 

BBS-report.py

@@ -896,8 +896,22 @@ def write_pkg_statuses_as_TDs(out, pkg, node,
         out.write('<TD %s>%s</TD>' % (TDattrs, TDcontent))
     elif not BBSreportutils.is_supported(pkg, node):
         TDattrs = 'COLSPAN="%s" class="%s"' % (ncol_to_display, TDclasses)
-        TDcontent = '... NOT SUPPORTED ...'
-        TDcontent = '%s' % TDcontent.replace(' ', '&nbsp;')
+        ## This is only a temporary hack based on the questionable assumption
+        ## that a software package unsupported on Linux is GPU-reliant, which
+        ## is of course not necessarily the case in general, but it just
+        ## happens to be true at the moment for Bioconductor software packages.
+        ## TODO: If we decide to get rid of the dedicated GPU-enabled builds
+        ## (buildtype == 'bioc-gpu') and to incorporate the GPU-capable
+        ## builders to the software builds, then we can get rid of this hack.
+        display_link_to_gpu_builds = buildtype == 'bioc' and \
+                                     sys.platform not in ['win32', 'darwin']:
+        if display_link_to_gpu_builds:
+            url = '%s/../bioc-gpu-LATEST/' % topdir
+            TDcontent = 'see GPU-enabled build/check ' + \
+                        'report <A href="%s">here</A>' % url
+        else:
+            TDcontent = '... NOT SUPPORTED ...'
+            TDcontent = '%s' % TDcontent.replace(' ', '&nbsp;')
         out.write('<TD %s>%s</TD>' % (TDattrs, TDcontent))
     else:
         for stage in BBSreportutils.stages_to_display(buildtype):

BBS-run.py

@@ -181,10 +181,9 @@ def get_list_of_target_pkgs():
     node_hostname = BBSvars.node_hostname
     node_Arch = BBSutils.getNodeSpec(node_hostname, 'Arch')
     node_pkgType = BBSutils.getNodeSpec(node_hostname, 'pkgType')
-    return bbs.parse.get_meat_packages_for_node(meat_index_path,
-                                                node_hostname,
-                                                node_Arch,
-                                                node_pkgType)
+    return bbs.parse.get_meat_packages_for_node(meat_index_path, node_hostname,
+                                                node_Arch, node_pkgType,
+                                                BBSvars.buildtype)
 
 def getSrcPkgFilesFromSuccessfulSTAGE3(stage_label):
     print('BBS> Get list of source tarballs to %s ...' % stage_label, end=' ')

BBSreportutils.py

@@ -89,7 +89,8 @@ def set_NODES(fancynames_in_one_string):
             pkgType = BBSutils.getNodeSpec(hostname, 'pkgType')
             pkgs = bbs.parse.get_meat_packages_for_node(
                                                BBSutils.meat_index_file,
-                                               hostname, arch, pkgType)
+                                               hostname, arch, pkgType,
+                                               BBSvars.buildtype)
         node = Node(hostname, node_id, os_html, arch, platform, buildbin, pkgs)
         NODES.append(node)
     if len(NODES) == 0:

bbs/parse.py

@@ -406,14 +406,23 @@ def _is_supported(unsupported_platforms, node_hostname,
 ### 'node_Arch' and 'node_pkgType' are the Arch and pkgType of node of name
 ### 'node_hostname', as specified in BBS/nodes/nodespecs.py.
 def get_meat_packages_for_node(meat_index_file, node_hostname,
-                               node_Arch=None, node_pkgType=None):
+                               node_Arch=None, node_pkgType=None,
+                               buildtype=None):
     dcf_records = parse_DCF(meat_index_file)
     pkgs = []
     for dcf_record in dcf_records:
         pkg = dcf_record['Package']
         unsupported_platforms = dcf_record.get('UnsupportedPlatforms')
-        if (_is_supported(unsupported_platforms, node_hostname,
-                          node_Arch, node_pkgType)):
+        ok1 = _is_supported(unsupported_platforms, node_hostname,
+                            node_Arch, node_pkgType)
+        GPU_reliance = dcf_record.get('GPU_reliance')
+        if buildtype == 'bioc':
+            ok2 = GPU_reliance != 'required'
+        elif buildtype == 'bioc-gpu':
+            ok2 = GPU_reliance in ['required', 'optional']
+        else:
+            ok2 = True
+        if ok1 and ok2:
             pkgs.append(pkg)
     pkgs.sort(key=str.lower)
     return pkgs