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Linux Cluster User Guide
This is a user guide with some of the basic commands to use the Cluster.
Accessing the Cluster
Note: There are now two clusters:
- pleiades.bc.edu. Installed in the Fall of 2012
To login to the pleiades cluster:
ssh -l -p Port-Number email@example.com
From on campus, you do not need to specify the port number (i.e. you do not need the "-p Port-number" option). You must enter a port number from off campus. Contact firstname.lastname@example.org for the port number
To login to the scorpio cluster:
where user-name is your BC user name. Enter your password.
If you are using an X11 client,
ssy -Y -p Port-Number email@example.com
ssh -Y firstname.lastname@example.org
will allow you to run graphical applications on scorpio from your workstation.
Changing your password
Please change your intitial password after you login. To change your password, type:
then follow instructions.
We use "Environment Modules" to keep the environment clean. For application software, there will be a module to load before you can use the software. The module will set all paths and environment variables necessary to use the software. Environment Modules are simple to use. For example, to use the software called glide, first load the glide module by typing:
module load glide
If you use a module frequently, you can add the module to the existing "module load" command in your .tcshrc or your .bash_profile, depending on which shell you are using.The default shell is the tcsh.
There are some basic commands:
module avail - lists all currently available modules
module list - lists all modules currently loaded.
module load modulefile - add/load one or more modulefile
module unload modulefile - unload modulefile.
module switch mod1 mod2 - replace mod1 with mod2
There should be no need for you to set a path yourself to run application software that is available to all users of the system.
The gnu, Intel and other compilers are installed on scorpio. For Intel , the C, C++, and FORTRAN 77/90/95 compilers are icc, icc, and ifort, respectively. To compile and link a C program, for example, you may type from your shell prompt:
gcc -o hello hello.c
The intell module needs to be loaded to use the pathscale compilers (module load pathscale)
Each account has a home directory. Home directories are backed up nightly. If a file in your home directory exists, there will be a copy on the backup system. For files that exist and change, we save the current file, and, for 15 days, the previous version. We can restore either the current file or, if the requested is made within 15 days of the last change to the file, the previous version of the file. If a file is deleted, then we can recover the file for up to 30 days from the day it was deleted.
Home directories will have a quota. The default quota will be 100 GB. If you need more space, please keep in mind there is a file system called /scratch that can be used for temporary files. You may also request a larger quota by sending email to email@example.com.
For temporary files, please create a directory for your work in /scratch and put your temporary files there. Files in /scratch are not backed up.
Running a program (Queues)
Other than short test jobs on scorpio.bc.edu, all jobs must be submitted to the queuing system. For information on the queue structure, see the Cluster Queue Web page. We are using PBS(Torque), along with the Moab scheduler to dispatch jobs to the compute nodes. For more information and instructions see the Torque User Guide. The most common PBS and Moab commands are as follows:
qsub submit jobs
qdel delete a job(s) job from the queue.
showq show the jobs waiting to run, and the running
showstart displays an estimated start time of a job waiting to run
Parameters such as memory, the number of cores and wallclock time requested are specified in a command file. Here is an example of a command file.
#PBS -l mem=500mb,nodes=1:ppn=1,walltime=1:00:00
#PBS -m abe -M your-email-address
This will request 500 MB of memory and one core for 1 hour
To submit the job via the script file sample.pbs, you may type
Specifing the maximum wall clock time (walltime=hh:mm:ss) helps schedule your job promptly. Wall clock time is the elapsed time from when your job starts running to the time it completes. We have one queue, the scheduler will determine where to run your job so that it gets started as soon as possible. We have reserved some nodes for short jobs. By having one queue and letting the scheduler determine where to run the job means that you won't submit your job to the wrong queue (meaning a queue that is full, when there are available processors in another). Likewise, we have nodes with different amounts of memory and the scheduler will guarantee that you get the memory you requested for yourself alone.
Unfortunately, both the memory and wall-clock time parameters require you to over estimate the amount. If you under estimate, your job may be killed. Use this to get better estimates on future job submissions. For assistance, contact researchservices (firstname.lastname@example.org).
To view all jobs in the system, type:
You may want to kill your job with job id 901, you may type:
To view the estimated start time of job id 901, type:
This is only an estimate of the start time, and the start time may change as other jobs are submitted.
The following options may generate more faster code:
In order to use OpenMP, your program must be compiled and linkied with
For assistance please contact Research Services at: email@example.com