------------------------------------------
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
{Warning: Unable to reindex Polypeptide.abortedPolypeptides
Out of memory. Type HELP MEMORY for your options.

Error in ==> SparseMat>SparseMat.sort_subs at 2933



Error in ==> SparseMat>SparseMat.normalize at 885



Error in ==> SparseMat>SparseMat.cat at 964



Error in ==> SparseMat>SparseMat.vertcat at 975



Error in ==> DiskLogger>DiskLogger.downSample_extract_byTime at 767



Error in ==> DiskLogger>DiskLogger.loadTimecourses at 497



Error in ==> DiskLogger>DiskLogger.reindexTimeCourses at 985



Error in ==> runReindexing at 13


} 
> In DiskLogger>DiskLogger.reindexTimeCourses at 993
  In runReindexing at 13
NO DISPLAY

==============
=== status ===
==============
Job Id: 18622.covertlab-cluster.stanford.edu
    Job_Name = runReindexing-2011_10_26_19_26_15-46
    Job_Owner = jkarr@covertlab-cluster.stanford.edu
    resources_used.cput = 00:30:09
    resources_used.mem = 16557168kb
    resources_used.vmem = 18904260kb
    resources_used.walltime = 00:16:30
    job_state = R
    queue = default
    server = covertlab-cluster.stanford.edu
    Checkpoint = u
    ctime = Wed Oct 26 19:35:33 2011
    depend = beforeany:19102.covertlab-cluster.stanford.edu@covertlab-cluster.
	stanford.edu
    Error_Path = covertlab-cluster.stanford.edu:/home/projects/WholeCell/simul
	ation/output/runSimulation/2011_10_26_19_26_15/46/err.reindexing.log
    exec_host = compute-0-7/3+compute-0-7/2+compute-0-7/1+compute-0-7/0
    group_list = jkarr
    Hold_Types = n
    Join_Path = n
    Keep_Files = n
    Mail_Points = a
    Mail_Users = wholecell+pbs@lists.stanford.edu
    mtime = Wed Nov  2 08:32:17 2011
    Output_Path = covertlab-cluster.stanford.edu:/home/projects/WholeCell/simu
	lation/output/runSimulation/2011_10_26_19_26_15/46/out.reindexing.log
    Priority = 0
    qtime = Wed Oct 26 19:35:33 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 = 5915
    stagein = /state/partition1/$PBS_JOBID/@covertlab:/home/projects/WholeCell
	/simulation/output/runSimulation/2011_10_26_19_26_15/bin/runReindexing
	/,
	/state/partition1/$PBS_JOBID/@covertlab:/home/projects/WholeCell/simu
	lation/output/runSimulation/2011_10_26_19_26_15/46/
    Variable_List = PBS_O_HOME=/home/users/jkarr,PBS_O_LANG=en_US.iso885915,
	PBS_O_LOGNAME=root,PBS_O_PATH=/usr/bin:/bin,
	PBS_O_MAIL=/var/mail/jkarr,PBS_O_SHELL=/bin/bash,
	PBS_SERVER=covertlab-cluster.stanford.edu,
	PBS_O_WORKDIR=/home/projects/WholeCell/simulation,
	TMPDIR=/state/partition1,PBS_O_QUEUE=default,
	PBS_O_HOST=covertlab-cluster.stanford.edu
    etime = Fri Oct 28 12:22:11 2011
    submit_args = /home/projects/WholeCell/simulation/output/runSimulation/201
	1_10_26_19_26_15/46/job.reindexing.sh
    umask = 2
    start_time = Wed Nov  2 08:32:17 2011
    Walltime.Remaining = 259
    start_count = 1
    fault_tolerant = False
    proxy_user = jkarr