------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/bin/MATLAB/MATLAB_Compiler_Runtime/v714/runtime/glnxa64:/usr/local/bin/MATLAB/MATLAB_Compiler_Runtime/v714/bin/glnxa64:/usr/local/bin/MATLAB/MATLAB_Compiler_Runtime/v714/sys/os/glnxa64:/usr/local/bin/MATLAB/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/bin/MATLAB/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/bin/MATLAB/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/bin/MATLAB/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64
NO DISPLAY

==============
=== status ===
==============
Job Id: 23382.covertlab-cluster.stanford.edu
    Job_Name = runReindexing-2011_11_11_21_25_46-404
    Job_Owner = jkarr@covertlab-cluster.stanford.edu
    resources_used.cput = 00:23:45
    resources_used.mem = 2089976kb
    resources_used.vmem = 3124708kb
    resources_used.walltime = 00:15:49
    job_state = R
    queue = default
    server = covertlab-cluster.stanford.edu
    Checkpoint = u
    ctime = Fri Nov 18 18:02:26 2011
    Error_Path = covertlab-cluster.stanford.edu:/home/projects/WholeCell/simul
	ation/output/runSimulation/2011_11_11_21_25_46/404/err.reindexing.log
    exec_host = compute-0-4/3+compute-0-4/2+compute-0-4/1+compute-0-4/0
    group_list = jkarr
    Hold_Types = n
    Join_Path = n
    Keep_Files = n
    Mail_Points = a
    Mail_Users = jkarr@stanford.edu
    mtime = Thu Dec  1 07:40:02 2011
    Output_Path = covertlab-cluster.stanford.edu:/home/projects/WholeCell/simu
	lation/output/runSimulation/2011_11_11_21_25_46/404/out.reindexing.log
	
    Priority = 0
    qtime = Fri Nov 18 18:02:26 2011
    Rerunable = True
    Resource_List.mem = 20gb
    Resource_List.nodect = 1
    Resource_List.nodes = 1:ppn=4
    Resource_List.vmem = 20gb
    Resource_List.walltime = 01:00:00
    session_id = 31101
    stagein = /state/partition1/$PBS_JOBID/@covertlab:/home/projects/WholeCell
	/simulation/output/runSimulation/2011_11_11_21_25_46/bin/runReindexing
	/,
	/state/partition1/$PBS_JOBID/@covertlab:/home/projects/WholeCell/simu
	lation/output/runSimulation/2011_11_11_21_25_46/404/
    Variable_List = PBS_O_HOME=/root,PBS_O_LANG=en_US.iso885915,
	PBS_O_LOGNAME=jkarr,
	PBS_O_PATH=/usr/kerberos/sbin:/usr/java/latest/bin:/home/users/jkarr/
	.local/bin:/usr/NX/bin:/opt/openmpi/bin:/usr/kerberos/bin:/usr/java/la
	test/bin:/usr/local/bin:/bin:/usr/bin:/opt/bio/ncbi/bin:/opt/bio/mpibl
	ast/bin/:/opt/bio/hmmer/bin:/opt/bio/EMBOSS/bin:/opt/bio/clustalw/bin:
	/opt/bio/tcoffee/bin:/opt/bio/phylip/exe:/opt/bio/mrbayes:/opt/bio/fas
	ta:/opt/bio/glimmer/bin://opt/bio/glimmer/scripts:/opt/bio/gromacs/bin
	:/opt/bio/gmap/bin:/opt/bio/tigr/bin:/opt/bio/autodocksuite/bin:/opt/b
	io/wgs/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/maui/b
	in:/opt/torque/bin:/opt/torque/sbin:/opt/rocks/bin:/opt/rocks/sbin:/ho
	me/users/jkarr/bin:/opt/bio/ncbi/bin:/opt/bio/mpiblast/bin/:/opt/bio/h
	mmer/bin:/opt/bio/EMBOSS/bin:/opt/bio/clustalw/bin:/opt/bio/tcoffee/bi
	n:/opt/bio/phylip/exe:/opt/bio/mrbayes:/opt/bio/fasta:/opt/bio/glimmer
	/bin://opt/bio/glimmer/scripts:/opt/bio/gromacs/bin:/opt/bio/gmap/bin:
	/opt/bio/tigr/bin:/opt/bio/autodocksuite/bin:/opt/bio/wgs/bin:/opt/ecl
	ipse:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/maui/bin:/opt/torque/bin:
	/opt/torque/sbin:/opt/rocks/bin:/opt/rocks/sbin,
	PBS_O_MAIL=/var/spool/mail/jkarr,PBS_O_SHELL=/bin/bash,
	PBS_SERVER=covertlab-cluster.stanford.edu,
	PBS_O_WORKDIR=/home/projects/WholeCell/simulation/output/runSimulatio
	n/2011_11_11_21_25_46,TMPDIR=/state/partition1,PBS_O_QUEUE=default,
	PBS_O_HOST=covertlab-cluster.stanford.edu
    etime = Wed Nov 30 11:26:43 2011
    submit_args = 404/job.reindexing.sh
    umask = 2
    start_time = Thu Dec  1 07:40:02 2011
    Walltime.Remaining = 258
    start_count = 1
    fault_tolerant = False
    proxy_user = jkarr