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Ported GridEngine terabyte fix and shm processors from JobTree (resolves #409) #454

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Merged
hannes-ucsc merged 1 commit into from
Oct 9, 2015
Merged

Ported GridEngine terabyte fix and shm processors from JobTree (resolves #409) #454

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7 changes: 5 additions & 2 deletions src/toil/batchSystems/gridengine.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@

class MemoryString:
def __init__(self, string):
if string[-1] == 'K' or string[-1] == 'M' or string[-1] == 'G':
if string[-1] == 'K' or string[-1] == 'M' or string[-1] == 'G' or string[-1] == 'T':
self.unit = string[-1]
self.val = float(string[:-1])
else:
Expand All @@ -54,6 +54,8 @@ def byteVal(self):
return self.val * 1048576
elif self.unit == 'G':
return self.val * 1073741824
elif self.unit == 'T':
return self.val * 1099511627776

def __cmp__(self, other):
return cmp(self.bytes, other.bytes)
Expand All @@ -76,7 +78,8 @@ def prepareQsub(cpu, mem, jobID):
if len(reqline) > 0:
qsubline.extend(["-hard", "-l", ",".join(reqline)])
if cpu is not None and math.ceil(cpu) > 1:
qsubline.extend(["-pe", "smp", str(int(math.ceil(cpu)))])
peConfig = os.getenv('TOIL_GRIDENGINE_PE') or "shm"
qsubline.extend(["-pe", peConfig, str(int(math.ceil(cpu)))])
return qsubline


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