High Performance Computing

1. System Access to Eric

1.1. SSH

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

Linux 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 username@eric.loni.org

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 Linux and Mac Users.

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

Back to Top

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.

Back to Top

2. File Transfer

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

Back to Top

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)
 ...
sftp>

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.

Back to Top

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 \
        username@remotehost:/destination/dir/or/filename

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/ \
        username@remotehost:/destination/dir/ 

or

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

To receive a directory:

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

or

% 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.

Back to Top

2.4. BBCP

Using BBCP to transfer large data files without encryption.

% bbcp [opt] user@source:/path/to/data user@destination:/path/to/store/data

Possible options include:

-P 2

Give a progress report every 2 seconds

- w 2M

TCP window size of 2MBytes

-s 16

Set the number of streams to 16 (default is 4)

Other options may be necessary if bbcp is not installed in a regular location on either end of the transfer. This can lead to rather complex command lines:

$ bbcp -z -T \
  "ssh -x -a -oFallBackToRsh=no %I -l %U %H /home/user/Custom/bin/bbcp" \
  foobar-5.4.14.tbz "ruser@10.20.30.40:foo.tbz"

Back to Top

2.5 Client Software

scp and sftp

Standard Clients

The command-line scp and sftp tools come with any modern distribution of OpenSSH; this is generally installed by default on modern Linux, UNIX, and Mac OS X installs.

Windows Clients

Windows clients include:

• WinSCP,
• pscp & psftp

(puTTY-related command line utilities), and

• scp, sftp, & rsync as provided by Cygwin.

*** VERY IMPORTANT ***: if you use Filezilla, please use the Site Manager feature (under "File") to manage the profile of the cluster you use. In the "Transfer Settings" tab, make sure that the "Limit number of simultaneous comments" box is checked and the "Maximum number of connections" is set to 1. Failing to do so may result in Filezilla creating excessive ssh connections, which could lead the suspension of your user account.

Back to Top

3. Computing Environment.

3.1. Shell

Eric'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 https://allocations.loni.org.

Back to Top

3.2. Softenv

Eric 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
  +ImageMagick-6.4.6.9-intel-11.1
  +ParMetis-3.1.1-intel-11.1-mpich-1.2.7p1
  +R-2.8.1-gcc-4.3.2
  ...

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
  +ImageMagick-6.4.6.9-intel-11.1
  @default

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:

  MY_ENV=/the/value/of/your/variable

Or to append a string to an exising value:

  PATH+=/path/to/your/executable

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

Back to Top

4. File Systems

User-owned storage on the Eric system is available in two directories: home (/home/<your user name>) and work (/work/<your user name>). These directories are on separate file systems, and accessible from any node in the system. The work directory is created automatically within an hour of first login. If your work directory does 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 Eric 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.

Back to Top

4.2. Work (Scratch) Directory

The /work (/scratch) directories are created automatically once an hour after first login. The /work volume is meant for the input and output of executing batch jobs and not for long term storage. We expect files to be moved off to other locations or deleted in a timely manner, usually within 30-120 days. For performance reasons, our policy on all volumes is to limit the number of files per directory to around 10,000 and total number files to about 500,000.

The /work file system quota on Eric is 100 GB. If it becomes over utilized we will enforce a purge policy, which means that we will begin deleting files starting with the oldest last accessed date, and largest files, and continue until the volume has been reduced below 80%. An email message will be sent out weekly to users who may have files subject to purge informing them of their /work utilization. If diskspace should become critically low, more drastic measures may be required to keep the system stable.

Please do not attempt to circumvent the removal process by manually changing file dates. The /work volume capacity is not unlimited, and attempts to circumvent the purge process may adversely affect others and lead to access restrictions to the /work volume or even the cluster.

Back to Top

5. Application Development

The Intel, GNU and Portland Group (PGI) C, C++ and Fortran compilers are installed on Eric 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:

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.f90 and 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

Back to Top

module load cuda

nvcc -arch=compute_20 -code=sm_20 ...

module load pgi

pgcc -acc -ta=nvidia -Minfo=accel code.c -o code.exe

6. Running Applications

Eric 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 Eric

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<=8.
• workq - Used for jobs that will use at least one node, i.e. nodes>=1:ppn=8. Currently, this queue has a wallclock limit of 72 hours (3 days). Jobs in workq are not preemptable, which means that running jobs will not be disrupted before completion.
• checkpt - Used for jobs that will use at least one node. Jobs in the checkpt queue can be preempted if needed.

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

qstat -q -G 

Back to Top

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 along with the options for resources required, for example

  qsub -I -l walltime=hh:mm:ss,nodes=n:ppn=8 -A allocation_name

Note that you need to take the whole node when requesting an interactive job, using anything other than ppn=8 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_ENVIRONMENT: Indicates job type, PBS_BATCH or PBS_INTERACTIVE
• 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 Eric. You may copy and paste into your job script.

Single Queue Job Script Template

#!/bin/bash
#PBS -q single
#PBS -l nodes=1:ppn=1
#PBS -l walltime=HH:MM:SS
#PBS -o desired_output_file_name
#PBS -N NAME_OF_JOB

/path/to/your/executable

Workq Queue Job Script Template

#!/bin/bash
#PBS -q workq
#PBS -l nodes=1:ppn=8
#PBS -l walltime=HH:MM:SS
#PBS -o desired_output_file_name
#PBS -j oe
#PBS -N NAME_OF_JOB

# mpi jobs would execute:
#   mpirun -np 8 -machinefile $PBS_NODEFILE /path/to/your/executable
# OpenMP jobs would execute:
#   export OMP_NUM_THREADS=8; /path/to/your/executable

Checkpt Queue Job Script Template

#!/bin/bash
#PBS -q checkpt
#PBS -l nodes=1:ppn=8
#PBS -l walltime=HH:MM:SS
#PBS -o desired_output_file_name
#PBS -j oe
#PBS -N NAME_OF_JOB

# mpi jobs would execute:
#   mpirun -np 8 -machinefile $PBS_NODEFILE /path/to/your/executable
# OpenMP jobs would execute:
#   export OMP_NUM_THREADS=8; /path/to/your/executable

Save your job script (For example, script.pbs). Submit the job by executing:

$ qsub script.pbs

Back to Top

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

qstat

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

qb2:
                                                                   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.

Back to Top