From 931decce0d015293e4e1f74922af7bbe1be159f1 Mon Sep 17 00:00:00 2001
From: Manuel Guenther <manuel.guenther@idiap.ch>
Date: Fri, 28 Mar 2014 14:16:19 +0100
Subject: [PATCH] Improved behavior when multiple jobs are re-submitted at the
same time.
---
gridtk/models.py | 4 ++--
gridtk/script/jman.py | 12 ++++++++++--
gridtk/sge.py | 3 ++-
setup.py | 2 +-
4 files changed, 15 insertions(+), 6 deletions(-)
diff --git a/gridtk/models.py b/gridtk/models.py
index 67a3017..1b1d104 100644
--- a/gridtk/models.py
+++ b/gridtk/models.py
@@ -292,9 +292,9 @@ class Job(Base):
deps = str(sorted(list(set([dep.unique for dep in self.get_jobs_we_wait_for()]))))
if dependencies < len(deps):
deps = deps[:dependencies-3] + '...'
- return format.format(self.unique, job_id, queue, status, self.name, deps, command_line)
+ return format.format(self.unique, job_id, queue[:12], status, self.name, deps, command_line)
else:
- return format.format(self.unique, job_id, queue, status, self.name, command_line)
+ return format.format(self.unique, job_id, queue[:12], status, self.name, command_line)
diff --git a/gridtk/script/jman.py b/gridtk/script/jman.py
index dc5b172..c483646 100644
--- a/gridtk/script/jman.py
+++ b/gridtk/script/jman.py
@@ -90,6 +90,14 @@ def get_ids(jobs):
return indexes
+def get_memfree(memory, parallel):
+ """Computes the memory required for the memfree field."""
+ number = int(memory.rstrip(string.ascii_letters))
+ memtype = memory.lstrip(string.digits)
+ if not memtype:
+ memtype = "G"
+ return "%d%s" % (number*parallel, memtype)
+
def submit(args):
"""Submission command"""
@@ -115,7 +123,7 @@ def submit(args):
if args.qname != 'all.q': kwargs['hvmem'] = args.memory
if args.parallel is not None:
kwargs['pe_opt'] = "pe_mth %d" % args.parallel
- kwargs['memfree'] = "%d%s" % (int(args.memory.rstrip(string.ascii_letters)) * args.parallel, args.memory.lstrip(string.digits))
+ kwargs['memfree'] = get_memfree(args.memory, args.parallel)
kwargs['dry_run'] = args.dry_run
kwargs['stop_on_failure'] = args.stop_on_failure
@@ -140,7 +148,7 @@ def resubmit(args):
kwargs['hvmem'] = args.memory
if args.parallel is not None:
kwargs['pe_opt'] = "pe_mth %d" % args.parallel
- kwargs['memfree'] = "%d%s" % (int(args.memory.rstrip(string.ascii_letters)) * args.parallel, args.memory.lstrip(string.digits))
+ kwargs['memfree'] = get_memfree(args.memory, args.parallel)
if args.io_big:
kwargs['io_big'] = True
if args.no_io_big:
diff --git a/gridtk/sge.py b/gridtk/sge.py
index 426973e..59bb8c2 100644
--- a/gridtk/sge.py
+++ b/gridtk/sge.py
@@ -154,7 +154,8 @@ class JobManagerSGE(JobManager):
logger.debug("Re-submitting job '%s' with dependencies '%s' to the grid." % (job, deps))
self._submit_to_grid(job, job.name, job.get_array(), deps, job.log_dir, **arguments)
- self.session.commit()
+ # commit after each job to avoid failures of not finding the job during execution in the grid
+ self.session.commit()
self.unlock()
diff --git a/setup.py b/setup.py
index 6399394..78b4ac7 100644
--- a/setup.py
+++ b/setup.py
@@ -9,7 +9,7 @@ if sys.version_info[:2] < (2, 7) or ((3,0) <= sys.version_info[:2] < (3,2)):
setup(
name='gridtk',
- version='1.1.3a0',
+ version='1.1.4a0',
description='SGE Grid and Local Submission and Monitoring Tools for Idiap',
url='http://github.com/idiap/gridtk',
--
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