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Painter is a 4.77 TFlops Peak Performance 128 compute node cluster running the Red Hat Enterprise Linux 4 operating system. Each node contains two Dual Core Xeon 64-bit processors operating at a core frequency of 2.33 GHz. Painter is a LONI's Dell Linux cluster housed at Louisiana Tech University.

  • 128 Compute Nodes
    • Two 2.33 GHz Dual Core Xeon 64-bit Processors
    • 4 GB Ram
    • 10 Gb/sec Infiniband network interface
    • 10/100/1000 Ethernet network interface
    • Red Hat Enterprise Linux 4
  • 1 Interactive Node
    • Two 3.00 GHz Dual Core Xeon 64-bit Processors
    • 8 GB Ram
    • 10/100/1000 Ethernet network interface
    • Red Hat Enterprise Linux 4
  • Cluster Storage
    • 2.3 TB of local storage
    • 12 TB Lustre filesystem

1. System Access to Painter

1.1. SSH

To access Painter, users must connect using an Secure Shell (SSH) client.

*nix and Mac Users - SSH client is already installed and can be accessed from the command prompt using the ssh command. One would issue a command similar to the following:

$ ssh -X

The user would then be prompted for his password. The -X flags allow for X11 Forwarding to be set up automatically.

Windows Users - You will need to download and install a SSH client such as the PuTTY utility. If users need access to login with X11 Forwarding, a X-Server needs to be installed and running on your local Windows machine. Xming X Server is recommended, advanced users may also install Cygwin which also provides a command line ssh client similar to that available for *nix and Mac Users.

If you have forgotten your password, or you wish to reset it, see here (click "Forgot your password?").

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1.2. Help

To report a problem please run the ssh or gsissh command with the "-vvv" option and include the verbose information in the ticket.

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2. File Transfer to Painter

Painter supports multiple file transfer programs, common command line utilities such as scp, sftp, and rsync.

2.1. SCP

Using scp is the easiest method to use when transferring single files.

Local File to Remote Host
% scp localfile user@remotehost:/destination/dir/or/filename
Remote Host to Local File
% scp user@remotehost:/remote/filename localfile

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2.2. SFTP

Interactive Mode

One may find this mode very similar to the interactive interface offered. A login session may look similar to the following:

% sftp user@remotehost
(enter in password)

The commands are similar to those offered by the outmoded ftp client programs: get, put, cd, pwd, lcd, etc. For more information on the available set of commands, one should consult sftp the man page.

% man sftp
Batch Mode

One may use sftp interactively in two cases.

Case 1: Pull a remote file to the local host.

% sftp user@remotehost:/remote/filename localfilename

Case 2: Creating a special sftp batch file containing the set of commands one wishes to execute with out any interaction.

% sftp -b batchfile user@remotehost

Additional information on constructing a batch file is available in the sftp man page.

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2.3. rsync Over SSH (preferred)

rsync is an extremely powerful program; it can synchronize entire directory trees, only sending data about files that have changed. That said, it is rather picky about the way it is used. The rsync man page has a great deal of useful information, but the basics are explained below.

Single File Synchronization

To synchronize a single file via rsync, use the following:

To send a file:

% rsync --rsh=ssh --archive --stats --progress localfile \

To receive a file:

% rsync --rsh=ssh --archive --stats --progress \
        username@remotehost:/remote/filename localfilename

Note that --rsh=ssh is not necessary with newer versions of rsync, but older installs will default to using rsh (which is not generally enabled on modern OSes).

Directory Synchronization

To synchronize an entire directory, use the following:

To send a directory:

% rsync --rsh=ssh --archive --stats --progress localdir/ \


% rsync --rsh=ssh --archive --stats --progress localdir \

To receive a directory:

% rsync --rsh=ssh --archive --stats --progress \
        username@remotehost:/remote/directory/ /some/localdirectory/


% rsync --rsh=ssh --archive --stats --progress \
        username@remotehost:/remote/directory /some/

Note the difference with the slashes. The second command will place the files in the directory /destination/localdir; the fourth will place them in the directory /some/directory. rsync is very particular about the placement of slashes. Before running any significant rsync command, add --dry-run to the parameters. This will let rsync show you what it plans on doing without actually transferring the files.

Synchronization with Deletion

This is very dangerous; a single mistyped character may blow away all of your data. Do not synchronize with deletion if you aren't absolutely certain you know what you're doing.

To have directory synchronization delete files on the destination system that don't exist on the source system:

% rsync --rsh=ssh --archive --stats --dry-run --progress \
        --delete localdir/ username@remotehost:/destination/dir/

Note that the above command will not actually delete (or transfer) anything; the --dry-run must be removed from the list of parameters to actually have it work.

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3. Computing Environment.

3.1. Shell

Painter's default shell is bash. Other shells are available: sh, csh, tcsh, and ksh. Users may change their default shell by logging into their LONI Profile page at

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3.2. Softenv

Painter makes use of softenv to allow for adding software to the user's environment. Executing softenv on a cluster will display a list of the available software:

$ softenv

In order to add software to your environment, you'll need to add the appropriate key to your ~/.soft file. For example, to add the package ImageMagick to your user environment, you would need to add the following:

$ cat ~/.soft

The order in which you add keys to ~/.soft is important. The first occurrence of a setting takes presedence.

You can also simply set an environment variable from your .soft file. To set the value of a certain variable, add a line like this to your .soft file:


Or to append a string to an exising value:


Once the entries are to your liking, you must then execute the command resoft, i.e.:

$ resoft

If your code needs to link to a library of given package, you will find all software installed under /usr/local/packages/, e.g.:

$ ls /usr/local/packages/
  apache_ant  boost     fuse     gold      hdf5         ...
  arpack      boostjam  gamess   graphviz  hypre
  atlas       condor    git      gromacs   ImageMagick
  blacs       fftw      gnuplot  gsl       iozone

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4. File Systems

User-owned storage on the Painter system is available in two directories, identified by the home and work directories. These directories are separate Lustre (global) file systems, and accessible from any node in the system. The home and work directories are created automatically within an hour of first login. If these directories do not exist when you login, please wait at least an hour before contacting the HPC helpdesk.

4.1. Home Directory

The /home file system quota on Painter is 5 GB. Files can be stored on /home permanently, which makes it an ideal place for your source code and executables. The /home file system is meant for interactive use such as editing and active code development. Do not use /home for batch job I/O.

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4.2. Work (Scratch) Directory

The /work volume meant for the input and output of executing batch jobs and not for long term storage. We expect files to be copied to other locations or deleted in a timely manner, usually within 30-120 days. For performance reasons on all volumes, our policy is to limit the number of files per directory to around 10,000 and total files to about 500,000.

The /work file system quota on Painter is 100 GB. If it becomes over utilized we will enforce a 30 days purging policy, which means that any files that have not been accessed for the last 30 days will be permanently deleted. An email message will be sent out weekly to users targeted for a purge informing them of their /work utilization.

Please do not try to circumvent the removal process by date changing methods. We expect most files over 30 days old to disappear. If you try to circumvent the purge process, this may lead to access restrictions to the /work volume or the cluster.

Please note that the /work volume is not unlimited. Please limit your usage rate to a reasonable amount. When the utilization of /work is over 80%, a 14 day purge may be performed on users using more than 2 TB or having more than 500,000 files. Should disk space become critically low, all files not accessed in 14 days will be purged or even more drastic measures if needed. Users using the largest portions of the /work volume will be contacted when problems arise and they will be expected to take action to help resolve issues.

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5. Application Development

The Intel, GNU and Portland Group (PGI) C, C++ and Fortran compilers are installed on Painter and they can be used to create OpenMP, MPI, hybrid and serial programs. The commands you should use to create each of these types of programs are shown in the table below.

Intel compilers are loaded by default, codes can be compiled according to the following chart:

Intel Compiler Commands
Serial Codes MPI Codes OpenMP Codes Hybrid Codes
Fortran ifort mpif90 ifort -openmp mpif90 -openmp
C icc mpicc icc -openmp mpicc -openmp
C++ icpc mpiCC icpc -openmp mpiCC -openmp
GNU Compiler Commands
Serial Codes MPI Codes OpenMP Codes Hybrid Codes
Fortran gfortran mpif90 gfortran -fopenmp mpif90 -fopenmp
C gcc mpicc gcc -fopenmp mpicc -fopenmp
C++ g++ mpiCC g++ -fopenmp mpiCC -fopenmp
PGI Compiler Commands
Serial Codes MPI Codes OpenMP Codes Hybrid Codes
Fortran pgf90 mpif90 pgf90 -mp mpif90 -mp
C pgcc mpicc pgcc -mp mpicc -mp
C++ pgCC mpiCC pgCC -mp mpiCC -omp

Default MPI: mvapich 1.1 compiled with Intel compiler version 11.1

To compile a serial program, the syntax is: <your choice of compiler> <compiler flags> <source file name> . For example, the command below compiles the source file mysource.f90and generate the executble myexec.

$ ifort -o myexec mysource.f90

To compile a MPI program, the syntax is the same, except that one needs to replace the serial compiler with an MPI one listed in the table above:

$ mpif90 -o myexec_par my_parallel_source.f90

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6. Running Applications

Painter uses TORQUE, an open source version of the Portable Batch System (PBS) together with the MOAB Scheduler, to manage user jobs. Whether you run in batch mode or interactively, you will access the compute nodes using the qsub command as described below. Remember that computationally intensive jobs should be run only on the compute nodes and not the login nodes. More details on submitting jobs and PBS commands can be found here.

6.1. Available Queues on Painter

Below are the possible job queues to choose from:

  • single - Used for jobs that will only execute on a single node, i.e. nodes=1:ppn<=4.
  • workq - Used for jobs that will use at least one node, i.e. nodes>=1:ppn=4. Currently, this queue has a limit of 72 hours (3 days) of wallclock time.
  • checkpt - Used for jobs that will use at least one node.
Queue Name Max Walltime Max Nodes (per job)
workq 72 24
checkpt 72 48
single 336 1

The available queues and actual limit settings can be verified by running the command:

qstat -q -G 

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6.2. Job Submission

The command qsub is used to send a batch job to PBS. The basic usage is

qsub pbs.script 

where pbs.script is the script users write to specify their needs. qsub also accept command line arguments, which will overwrite those specified in the script, for example, the following command

qsub myscript -A my_LONI_allocation2

will direct the system to charge SUs (service units) to the allocation my_LONI_allocation2 instead of the allocation specified in myscript.

To submit an interactive job, use the -I flag to the qsub command alongwith the options for resources required, for example

qsub -I -l walltime=hh:mm:ss,nodes=n:ppn=4 -A allocation_name

Note that you need to take the whole node when requesting an interactive job, using anything other than ppn=4 will cause job submission failure. If you need to enable X-Forwarding, add the -X flag.

Your PBS submission script should be written in one of the Linux scripting languages such as bash, tcsh, csh or sh i.e. the first line of your submission script should be something like #!/bin/bash. The next section of the submission script should be PBS directives followed by the actual commands to run your job. Following are a list of useful PBS directives (can also be used as command line options to qsub) and environment variables that can be used in the submit script:

  • #PBS -q queuename: Submit job to the queuename queue.
    • Allowed values for queuename: single, workq, checkpt.
    • Depending on cluster, addition values allowed are gpu, lasigma, mwfa, bigmem.
  • #PBS -A allocationname: Charge jobs to your allocation named allocationname.
  • #PBS -l walltime=hh:mm:ss: Request resources to run job for hh hours, mm minutes and ss seconds.
  • #PBS -l nodes=m:ppn=n: Request resources to run job on n processors each on m nodes.
  • #PBS -N jobname: Provide a name, jobname to your job to identify it when monitoring job using the qstat command.
  • #PBS -o filename.out: Write PBS standard output to file filename.out.
  • #PBS -e filename.err: Write PBS standard error to file filename.err.
  • #PBS -j oe: Combine PBS standard output and error to the same file. Note you will need either #PBS -o or #PBS -e directive not both.
  • #PBS -m status: Send an email after job status status is reached. Allowed values for status are
    • a: when job aborts
    • b: when job begins
    • e: when job ends
    • The arguments can be combined, for e.g. abe will send email when job begins and either aborts or ends
  • #PBS -M your email address: Address to send email to when the status directive above is trigerred.
  • PBS_O_WORKDIR: Directory where the qsub command was executed
  • PBS_NODEFILE: Name of the file that contains a list of the HOSTS provided for the job
  • PBS_JOBID: Job ID number given to this job
  • PBS_QUEUE: Queue job is running in
  • PBS_WALLTIME: Walltime in secs requested
  • PBS_JOBNAME: Name of the job. This can be set using the -N option in the PBS script
  • PBS_O_SHELL: value of the SHELL variable in the environment in which qsub was executed
  • PBS_O_HOME: Home directory of the user running qsub

Following are templates for submitting jobs to the various queues available on Painter.

Single Queue Job Script Template
$ cat ~/script

#PBS -q single
#PBS -l nodes=1:ppn=1
#PBS -l walltime=HH:MM:SS
#PBS -o desired_output_file_name

Workq Queue Job Script Template
$ cat ~/script

#PBS -q workq
#PBS -l nodes=1:ppn=4
#PBS -l walltime=HH:MM:SS
#PBS -o desired_output_file_name
#PBS -j oe

# mpi jobs would execute:
#   mpirun -np 4 -machinefile $PBS_NODEFILE /path/to/your/executable
# OpenMP jobs would execute:
#   export OMP_NUM_THREADS=4; /path/to/your/executable
Checkpt Queue Job Script Template
$ cat ~/script

#PBS -q checkpt 
#PBS -l nodes=1:ppn=4
#PBS -l walltime=HH:MM:SS
#PBS -o desired_output_file_name
#PBS -j oe

# mpi jobs would execute:
#   mpirun -np 4 -machinefile $PBS_NODEFILE /path/to/your/executable
# OpenMP jobs would execute:
#   export OMP_NUM_THREADS=4; /path/to/your/executable

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6.3. Monitoring Jobs

qstat for checking job status

The command qstat is used to check the status of PBS jobs. The simplest usage is


which would give informations similar to the following:

[apacheco@qb4 ~]$ qstat
Job id              Name             User            Time Use S Queue
------------------- ---------------- --------------- -------- - -----
729444.qb2          job1.pbs         ebeigi3                0 Q workq          
729516.qb2          MAY2009_d        skayres         533:14:2 R workq          
729538.qb2          wallret_test222  liyuxiu         67:43:38 R workq          
729539.qb2          wallret_test223  liyuxiu         67:43:39 R workq          
729540.qb2          wallret_test228  liyuxiu         66:49:50 R workq          
729541.qb2          wallret_test231  liyuxiu         64:40:21 R workq          
729542.qb2          wallret_test232  liyuxiu         64:40:15 R workq          
729543.qb2          wallret_test233  liyuxiu         63:18:24 R workq          
729567.qb2          CaPtFeAs         cekuma          00:22:01 R workq     

The first column to the six column show the id of each job, the name of each job, the owner of each job, the time consummed by each job, the status of each job (R corresponds to running, Q correcponds to in queue ), and which queue each job is in. qstat also accepts command line arguments, for instance, the following usage gives more detailed information regarding jobs.

[apacheco@qb4 ~]$ qstat -a

                                                                   Req'd  Req'd   Elap
Job ID               Username Queue    Jobname    SessID NDS   TSK Memory Time  S Time
-------------------- -------- -------- ---------- ------ ----- --- ------ ----- - -----
729444.qb2           ebeigi3  workq    job1.pbs      --      2   1    --  06:30 Q   -- 
729516.qb2           skayres  workq    MAY2009_d    2969     8   1    --  72:00 R 66:45
729538.qb2           liyuxiu  workq    wallret_te  26259     1   1    --  70:00 R 67:44
729539.qb2           liyuxiu  workq    wallret_te   5144     1   1    --  70:00 R 67:44
729540.qb2           liyuxiu  workq    wallret_te  12445     1   1    --  70:00 R 66:50
729541.qb2           liyuxiu  workq    wallret_te   2300     1   1    --  70:00 R 64:41
729542.qb2           liyuxiu  workq    wallret_te   1809     1   1    --  70:00 R 64:41
729543.qb2           liyuxiu  workq    wallret_te   9377     1   1    --  70:00 R 63:19
729567.qb2           cekuma   workq    CaPtFeAs    10562     7   1    --  69:50 R 48:18

Other useful options to qstat:

  • -u username: To display only jobs owned by user username.
  • -n: To display list of nodes that jobs are running on.
  • -q: To summarize resources available to all queues.
qdel for cancelling a job

To cancel a PBS job, enter the following command.

qdel job_id [job_id] ...
qfree to query free nodes in PBS

One useful command for users to schedule their jobs in an optimal way is "qfree", which shows free nodes in each queue. For example,

[apacheco@qb4 ~]$ qfree
PBS total nodes: 668,  free: 6,  busy: 629,  down: 33,  use: 94%
PBS workq nodes: 529,  free: 3,  busy: 317,  queued: 2
PBS checkpt nodes: 656,  free: 1,  busy: 312,  queued: 64
(Highest priority job 729767 on queue checkpt will start in 2:34:14)

shows that there total 6 free nodes in PBS, they are available in all the two queues: checkpt and workq.

showstart for estimating the starting time for a job

The command showstart can be used to get an approximate estimation of the starting time of your job, the basic usage is

showstart job_id

The following shows an simple example:

[apacheco@qb4 ~]$ showstart 729767
job 729767 requires 32 procs for 2:00:00:00

Estimated Rsv based start in                 2:33:25 on Tue Dec 17 11:52:32
Estimated Rsv based completion in         2:02:33:25 on Thu Dec 19 11:52:32

Best Partition: base

Please note that the start time listed above is only an estimate. There is no gaurantee that the job will start at the above mentioned time.

showq to display jobs info within the batch system

The command showq can be used to display job information within the batch system.

[apacheco@qb4 ~]$ showq

active jobs------------------------
JOBID              USERNAME      STATE PROCS   REMAINING            STARTTIME                     

729538              liyuxiu    Running     8     2:11:44  Sat Dec 14 13:31:32
729539              liyuxiu    Running     8     2:11:44  Sat Dec 14 13:31:32
729607               amani1    Running   256     2:32:44  Mon Dec 16 15:52:32
729609               amani1    Running   256     2:51:13  Mon Dec 16 16:11:01
729610               amani1    Running   256     2:51:13  Mon Dec 16 16:11:01
729611               amani1    Running   256     2:51:13  Mon Dec 16 16:11:01
729613               amani1    Running   256     3:05:19  Mon Dec 16 16:25:07
... truncated ...
92 active jobs        5032 of 5064 processors in use by local jobs (99.37%)
                        629 of 633 nodes active      (99.37%)

eligible jobs----------------------
JOBID              USERNAME      STATE PROCS     WCLIMIT            QUEUETIME                     

729767             lsurampu       Idle    32  2:00:00:00  Mon Dec 16 22:54:38                     
729768             lsurampu       Idle    32  2:00:00:00  Mon Dec 16 22:54:38                     
729769             lsurampu       Idle    32  2:00:00:00  Mon Dec 16 22:54:38                     
... truncated ...
16 eligible jobs   

blocked jobs-----------------------
JOBID              USERNAME      STATE PROCS     WCLIMIT            QUEUETIME                     

0 blocked jobs   

Total jobs:  108

To display job information for a particular queue, use the command

showq -w class=<queue name>
checkjob to display detailed job state information

The command checkjob is used to display detailed information about the job state. This is very useful if your job is remaining in the queued state, and you'd like to see why PBS hasn't executed it:

[apacheco@qb4 ~]$ checkjob 729787.qb2
job 729787

AName: null
State: Idle 
Creds:  user:apacheco  group:loniadmin  account:loni_loniadmin1  class:workq  qos:userres
WallTime:   00:00:00 of 2:00:00
SubmitTime: Tue Dec 17 09:22:14
  (Time Queued  Total: 00:00:14  Eligible: 00:00:06)

NodeMatchPolicy: EXACTNODE
Total Requested Tasks: 32

Req[0]  TaskCount: 32  Partition: ALL  

Flags:          INTERACTIVE
Attr:           INTERACTIVE,checkpoint
StartPriority:  141944
available for 8 tasks     - qb[002,007,376]
rejected for Class        - (null)
rejected for State        - (null)
NOTE:  job req cannot run in partition base (available procs do not meet requirements : 24 of 32 procs found)
idle procs:  32  feasible procs:  24

Node Rejection Summary: [Class: 1][State: 667]

This job cannot be started since it requires 4 nodes (32 procs) but only 3 nodes are available.

qshow to display memory and cpu usage on the node that a job is running on

The command qshow is useful to find out how the resources on the node allocated to your job are consumed. For example, if a users job is running slow due to swapping, this command will provide you with information on how much memory (physical and virtual) is used on all processors allocated to your job.

[apacheco@qb4 ~]$ qshow 729731
PBS job: 729731, nodes: 4
Hostname  Days Load CPU U# (User:Process:VirtualMemory:Memory:Hours)
qb373       39 8.93 798 21 lsurampu:mdrun_mpi:88M:31M:10.9 lsurampu:mdrun_mpi:90M:32M:10.9 lsurampu:mdrun_mpi:117M:65M:10.6 lsurampu:mdrun_mpi:89M:31M:10.9 lsurampu:mdrun_mpi:88M:30M:10.9 lsurampu:mdrun_mpi:88M:30M:10.9 lsurampu:mdrun_mpi:89M:31M:10.9 lsurampu:mdrun_mpi:91M:33M:10.9 lsurampu:pbs_demux:3M:0M lsurampu:729731:52M:1M lsurampu:mpirun:52M:1M lsurampu:mpirun_rsh:6M:1M lsurampu:mpispawn:6M:1M
qb368       39 8.99 798 12 lsurampu:mdrun_mpi:89M:40M:10.9 lsurampu:mdrun_mpi:89M:31M:10.9 lsurampu:mdrun_mpi:88M:31M:10.9 lsurampu:mdrun_mpi:89M:32M:10.9 lsurampu:mdrun_mpi:91M:33M:10.9 lsurampu:mdrun_mpi:95M:37M:10.9 lsurampu:mdrun_mpi:91M:33M:10.9 lsurampu:mdrun_mpi:112M:50M:10.9 lsurampu:mpispawn:6M:1M
qb364       39 8.85 800 12 lsurampu:mdrun_mpi:91M:42M:10.9 lsurampu:mdrun_mpi:89M:31M:10.9 lsurampu:mdrun_mpi:93M:35M:10.9 lsurampu:mdrun_mpi:90M:32M:10.9 lsurampu:mdrun_mpi:90M:32M:10.9 lsurampu:mdrun_mpi:89M:31M:10.9 lsurampu:mdrun_mpi:90M:32M:10.9 lsurampu:mdrun_mpi:90M:32M:10.9 lsurampu:mpispawn:6M:1M
qb362       39 8.89 802 12 lsurampu:mdrun_mpi:90M:41M:10.9 lsurampu:mdrun_mpi:89M:31M:10.9 lsurampu:mdrun_mpi:89M:31M:10.9 lsurampu:mdrun_mpi:89M:31M:10.9 lsurampu:mdrun_mpi:112M:51M:10.9 lsurampu:mdrun_mpi:89M:32M:10.9 lsurampu:mdrun_mpi:89M:31M:10.9 lsurampu:mdrun_mpi:89M:31M:10.9 lsurampu:mpispawn:6M:1M
PBS_job=729731 user=lsurampu allocation=loni_poly_mic_1 queue=checkpt total_load=32 cpu_hours=320 wall_hours=10 unused_nodes=0 total_nodes=4 avg_load=8

More detailed information on the Torque PBS commands and Moab to schedule and monitor jobs can be found at Adaptive Computing on-line documentations.

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