always honor TOIL_GRIDENGINE_PE and never assume a site-dependent def…

…ault (#3041)

* always honor TOIL_GRIDENGINE_PE and never assume a site-dependent default

* requite TOIL_GRIDENGINE_PE if multiple CPUs are used

* give hints on where to look for coorrent PE values

src/toil/batchSystems/gridengine.py

@@ -134,9 +134,12 @@ def prepareQsub(self, cpu, mem, jobID):
                     if arg.startswith(("vf=", "hvmem=", "-pe")):
                         raise ValueError("Unexpected CPU, memory or pe specifications in TOIL_GRIDGENGINE_ARGs: %s" % arg)
                 qsubline.extend(sgeArgs)
-            if cpu is not None and math.ceil(cpu) > 1:
-                peConfig = os.getenv('TOIL_GRIDENGINE_PE') or 'shm'
-                qsubline.extend(['-pe', peConfig, str(int(math.ceil(cpu)))])
+            if os.getenv('TOIL_GRIDENGINE_PE') is not None:
+                peCpu = int(math.ceil(cpu)) if cpu is not None else 1
+                qsubline.extend(['-pe', os.getenv('TOIL_GRIDENGINE_PE'), str(peCpu)])
+            elif (cpu is not None) and (cpu > 1):
+                raise RuntimeError("must specify PE in TOIL_GRIDENGINE_PE environment variable when using multiple CPUs. "
+                                   "Run qconf -spl and your local documentation for possible values")
 
             stdoutfile = self.boss.formatStdOutErrPath(jobID, 'gridengine', '$JOB_ID', 'std_output')
             stderrfile = self.boss.formatStdOutErrPath(jobID, 'gridengine', '$JOB_ID', 'std_error')