diff gaussian_job_rules.py @ 2:ed472dc06c20 draft default tip

Uploaded 1.0.0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gaussian_job_rules.py	Tue Sep 18 23:03:01 2012 -0400
@@ -0,0 +1,54 @@
+def gaussian(job):
+    inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] )
+    inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] )
+    src_comfile = inp_data[ "infile" ].file_name
+    comfile = open(src_comfile, 'r')
+    ppn='1'
+    pmem = '900mb'
+    overhead = 200
+    walltime = '11:59:59'
+    for line in comfile:
+        line = line.strip().lower()
+        if ( "%nproc=" in line):
+            try:
+                ppn = line.split('=')[1]
+            except Exception, e:
+                log.debug(e)
+                sys.stdout.write(e)
+        if ("%mem=" in line):
+            try:
+                mem_str = line.split('=')[1]
+                if ( "kb" in mem_str ):
+                    mem_num = mem_str.split('kb')[0]
+                    mem_num = int(int(mem_num) / 1024.0) + overhead
+                if ( "mb" in mem_str ):
+                    mem_num = mem_str.split('mb')[0]
+                    mem_num = int(mem_num) + overhead
+                elif ( "gb" in mem_str ):
+                    mem_num = mem_str.split('gb')[0]
+                    mem_num = (int(mem_num) * 1024) + overhead
+                elif ( "kw" in mem_str ):
+                    mem_num = mem_str.split('kw')[0]
+                    mem_num = int(int(mem_num) * 8 / 1024.0) + overhead
+                elif ( "mw" in mem_str ):
+                    mem_num = mem_str.split('mw')[0]
+                    mem_num = (int(mem_num) * 8) + overhead
+                elif ( "gw" in mem_str ):
+                    mem_num = mem_str.split('gw')[0]
+                    mem_num = (int(mem_num) * 8 * 1024) + overhead
+                else:
+                    #Assume words
+                    mem_num = int(int(mem_str) * 8 / 1024.0 / 1024.0) + overhead
+                pmem_num = int(mem_num / int(ppn))
+                pmem = str(pmem_num) + 'mb'
+            except Exception, e:
+                log.debug(e)
+                sys.stdout.write(e)
+        if ("!walltime=" in line):
+            try:
+                walltime = line.split('=')[1]
+            except Exception, e:
+                log.debug(e)
+                sys.stdout.write(e)
+    request = "-l nodes=1:ppn=%s,pmem=%s,walltime=%s" % (ppn, pmem, walltime)
+    return 'drmaa://%s/' % request