add sge

rabit-learn/linear/Makefile

@@ -1,4 +1,9 @@
-# specify tensor path
+ifneq ("$(wildcard ../config.mk)","")
+	config = ../config.mk
+else
+	config = ../make/config.mk
+endif
+
 BIN = linear.rabit
 MOCKBIN= linear.mock
 MPIBIN = 
@@ -6,7 +11,6 @@ MPIBIN =
 OBJ = linear.o
 
 # common build script for programs
-include ../make/config.mk
 include ../make/common.mk
 CFLAGS+=-fopenmp
 linear.o: linear.cc ../../src/*.h linear.h ../solver/*.h

rabit-learn/make/config.mk

@@ -6,7 +6,7 @@
 #
 #  - copy this file to the root of rabit-learn folder
 #  - modify the configuration you want
-#  - type make or make -j n for parallel build
+#  - type make or make -j n on each of the folder
 #----------------------------------------------------
 
 # choice of compiler

tracker/README.md

@@ -9,4 +9,4 @@ the example guidelines are in the script themselfs
 * Yarn (Hadoop): [rabit_yarn.py](rabit_yarn.py)
   - It is also possible to submit via hadoop streaming with rabit_hadoop_streaming.py
   - However, it is higly recommended to use rabit_yarn.py because this will allocate resources more precisely and fits machine learning scenarios
-
+* Sun Grid engine: [rabit_sge.py](rabit_sge.py)

tracker/rabit_mpi.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python
 """
 This is the demo submission script of rabit, it is created to
-submit rabit jobs using hadoop streaming
+submit rabit jobs using MPI
 """
 import argparse
 import sys

tracker/rabit_sge.py

@@ -0,0 +1,70 @@
+#!/usr/bin/python
+"""
+This is the demo submission script of rabit, it is created to
+submit rabit jobs to Sun Grid Engine
+"""
+import argparse
+import sys
+import os
+import subprocess
+import rabit_tracker as tracker
+
+parser = argparse.ArgumentParser(description='Rabit script to submit rabit job using MPI')
+parser.add_argument('-n', '--nworker', required=True, type=int,
+                    help = 'number of worker proccess to be launched')
+parser.add_argument('-q', '--queue', default='default', type=str,
+                    help = 'the queue we want to submit the job to')
+parser.add_argument('-hip', '--host_ip', default='auto', type=str,
+                    help = 'host IP address if cannot be automatically guessed, specify the IP of submission machine')
+parser.add_argument('--vcores', default = 1, type=int,
+                    help = 'number of vcpores to request in each mapper, set it if each rabit job is multi-threaded')
+parser.add_argument('--jobname', default='auto', help = 'customize jobname in tracker')
+parser.add_argument('--logdir', default='auto', help = 'customize the directory to place the logs')
+parser.add_argument('-v', '--verbose', default=0, choices=[0, 1], type=int,
+                    help = 'print more messages into the console')
+parser.add_argument('command', nargs='+',
+                    help = 'command for rabit program')
+args = parser.parse_args()
+
+if args.jobname == 'auto':
+    args.jobname = ('rabit%d.' % args.nworker) + args.command[0].split('/')[-1];
+if args.logdir == 'auto':
+    args.logdir = args.jobname + '.log'
+
+if os.path.exists(args.logdir):
+    if not os.path.isdir(args.logdir):
+        raise RuntimeError('specified logdir %s is a file instead of directory' % args.logdir)
+else:
+    os.mkdir(args.logdir)
+    
+runscript = '%s/runrabit.sh' % args.logdir
+fo = open(runscript, 'w')
+fo.write('\"$@\"')
+fo.close()
+#
+# submission script using MPI
+#
+def sge_submit(nslave, worker_args, worker_envs):
+    """
+      customized submit script, that submit nslave jobs, each must contain args as parameter
+      note this can be a lambda function containing additional parameters in input
+      Parameters
+         nslave number of slave process to start up
+         args arguments to launch each job
+              this usually includes the parameters of master_uri and parameters passed into submit
+    """    
+    env_arg = ','.join(['%s=\"%s\"' % (k, str(v)) for k, v in worker_envs.items()])
+    cmd = 'qsub -cwd -t 1-%d -S /bin/bash' % nslave
+    if args.queue != 'default':
+        cmd += '-q %s' % args.queue
+    cmd += ' -N %s ' % args.jobname
+    cmd += ' -e %s -o %s' % (args.logdir, args.logdir)
+    cmd += ' -pe orte %d' % (args.vcores)
+    cmd += ' -v %s,PATH=${PATH}:.' % env_arg
+    cmd += ' %s %s' % (runscript, ' '.join(args.command + worker_args))
+    print cmd
+    subprocess.check_call(cmd, shell = True)
+    print 'Waiting for the jobs to get up...' % args.jobname
+
+# call submit, with nslave, the commands to run each job and submit function
+tracker.submit(args.nworker, [], fun_submit = sge_submit, verbose = args.verbose)