2021 Cluster Instruction

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General Use Information

Logging In

The clas-compute system uses (mostly) CentOS 7 and 8 operating system. At this time, the main way of using the system is to use an SSH client to login to a terminal session on clas-compute. You will need to be on the CU Denver network (wired or CU Denver wireless, not CU Denver Guest), or using the university's VPN client.

This system uses your normal portal/email username and password.

On Windows, you will need an SSH client. There are several out there, but generally most people use PuTTY which is available for download here. You can use either 32 or 64 bit versions - computers that require the 32 bit version are rather rare (early Windows 7/Vista/XP). The Host Name is clas-compute.ucdenver.pvt. (image is from the old system, but same difference)

You can also use the Windows 10 subsystem for Linux, where you install a Linux distribution as an app and can use it to ssh out like from a terminal window on any Linux machine. This is often more stable than Putty, which tends to get stuck on some computers.

On Macintosh, you can either use a specialized SSH client or Terminal which is built into the operating system. While in Finder on your Mac, press the Option, Shift, and U keys simultaneously. The Utilities folder should appear and the Terminal is within this folder. Open terminal and at the prompt type in:

ssh awesomeperson@clas-compute.ucdenver.pvt

Whereas awesomeperson would be your UCD username. After connecting, it should ask for your UCD password and enter it at this point.

Science will then occur and you should be at the clas-compute prompt and in your home directory.

Interactive Use

Using a server ‘interactively’ (aka not scheduling a job) is often needed for troubleshooting a job or just watching what it is doing in real time. After SSH’ing into math-compute, you can type ssh math-colibri-i01 or whatever server you want to go directly to the server. Please do not run anything directly on compute nodes, which are reserved for jobs under the control of the scheduler, even if you may be able to ssh there. These are nodes with names like math-colibri-c01 with the "c" before the number. Using compute nodes, where other people run jobs through the scheduler, will interfere with their work and make you very unpopular.

Using ‘screen’ is generally a good idea both math-compute or the interactive nodes. Basically was screen does is starts a virtual terminal inside your terminal. Sound confusing? It is. The plus of this virtual terminal is if you get disconnected, whatever you were running is still going.

screen –S ‘bananaphone’ (make the name whatever you want) creates a new terminal with that name

If you want to disconnect from the screen but leave it running, hit the combination of Control-A and press the D key to disconnect. Control-A is the combo to let screen know you want to do an action.

When you want to reconnect to the screen later, log back onto wherever you started the screen and type screen –r. If you have more than one screen, it’ll complain and tell you the screens you have available to reconnect to. screen –r ‘bananaphone’ to reconnect to that screen. Sometimes there is a number in front of the screen so screen –r 3128.bananaphone. It’ll tell you the number in the screen –r info screen.

File Storage

Math home directories are on a shared server with 40TB total (right now). Projects are found in /storage/department/projects (where department may be one of many departments who use this system).

For example, the mixtures project is in /storage/math/projects/mixtures.

If you need a lot of data storage, please contact Joe before filling everything you can find.

df –h will show you the storage arrays and how much space is available. There are different types of ‘empty’ space in linux so it may say there is plenty of space in df –h yet the array is full.

Passwords

The system uses your normal UCD portal/email logon username and password. Users must be approved before using the system, so if your login is not working, you probably are not on the approved/initialized list yet.

Requesting information about the environment

Queues

There are queues for different departments on math-compute because it points to a central scheduler for all of CLAS. To see these queues type sinfo:

PARTITION AVAIL TIMELIMIT NODES STATE NODELIST

math-alderaan up 4-00:00:00 32 down* math-alderaan-c[01-32]

math-alderaan-gpu up 4-00:00:00 1 down* math-alderaan-h01

math-alderaan-gpu up 4-00:00:00 1 unk* math-alderaan-h02

math-colibri-gpu up infinite 12 unk* math-colibri-c[01-02,04-12,23]

math-colibri-gpu up infinite 12 idle math-colibri-c[03,13-22,24]

math-score up infinite 5 unk* math-score-c[01-05]

chem-xenon up infinite 6 unk* chem-xenon-c[01-06]

Nodes

To see a list of all nodes, use:

[jmandel@clas-compute ~]$ sinfo -N
NODELIST           NODES         PARTITION STATE 
chem-xenon-c01         1        chem-xenon unk*  
chem-xenon-c02         1        chem-xenon unk*  
chem-xenon-c03         1        chem-xenon unk*  
chem-xenon-c04         1        chem-xenon unk*  
chem-xenon-c05         1        chem-xenon unk*  
chem-xenon-c06         1        chem-xenon unk*  
clas-rcdesktop-01      1    clas-rcdesktop down* 
math-alderaan-c01      1     math-alderaan alloc 
math-alderaan-c02      1     math-alderaan alloc 
math-alderaan-c03      1     math-alderaan alloc 
math-alderaan-c04      1     math-alderaan alloc 
math-alderaan-c05      1     math-alderaan alloc 
math-alderaan-c06      1     math-alderaan alloc 
math-alderaan-c07      1     math-alderaan alloc 
math-alderaan-c08      1     math-alderaan alloc 
math-alderaan-c09      1     math-alderaan alloc 
math-alderaan-c10      1     math-alderaan alloc 
math-alderaan-c11      1     math-alderaan alloc 
math-alderaan-c12      1     math-alderaan alloc 
math-alderaan-c13      1     math-alderaan alloc 
math-alderaan-c14      1     math-alderaan alloc 
math-alderaan-c15      1     math-alderaan alloc 
math-alderaan-c16      1     math-alderaan mix   
math-alderaan-c17      1     math-alderaan idle  
math-alderaan-c18      1     math-alderaan idle  
math-alderaan-c19      1     math-alderaan idle  
math-alderaan-c20      1     math-alderaan idle  
math-alderaan-c21      1     math-alderaan idle  
math-alderaan-c22      1     math-alderaan idle  
math-alderaan-c23      1     math-alderaan idle  
math-alderaan-c24      1     math-alderaan idle  
math-alderaan-c25      1     math-alderaan idle  
math-alderaan-c26      1     math-alderaan idle  
math-alderaan-c27      1     math-alderaan idle  
math-alderaan-c28      1     math-alderaan idle  
math-alderaan-c29      1     math-alderaan idle  
math-alderaan-c30      1     math-alderaan idle  
math-alderaan-c31      1     math-alderaan idle  
math-alderaan-c32      1     math-alderaan idle  
math-alderaan-h01      1 math-alderaan-gpu idle  
math-alderaan-h02      1 math-alderaan-gpu idle  
math-colibri-c01       1  math-colibri-gpu idle  
math-colibri-c02       1  math-colibri-gpu idle  
math-colibri-c03       1  math-colibri-gpu idle  
math-colibri-c04       1  math-colibri-gpu unk*  
math-colibri-c05       1  math-colibri-gpu unk*  
math-colibri-c06       1  math-colibri-gpu unk*  
math-colibri-c07       1  math-colibri-gpu unk*  
math-colibri-c08       1  math-colibri-gpu unk*  
math-colibri-c09       1  math-colibri-gpu unk*  
math-colibri-c10       1  math-colibri-gpu unk*  
math-colibri-c11       1  math-colibri-gpu unk*  
math-colibri-c12       1  math-colibri-gpu unk*  
math-colibri-c13       1  math-colibri-gpu idle  
math-colibri-c14       1  math-colibri-gpu idle  
math-colibri-c15       1  math-colibri-gpu idle  
math-colibri-c16       1  math-colibri-gpu idle  
math-colibri-c17       1  math-colibri-gpu idle  
math-colibri-c18       1  math-colibri-gpu idle  
math-colibri-c19       1  math-colibri-gpu idle  
math-colibri-c20       1  math-colibri-gpu idle  
math-colibri-c21       1  math-colibri-gpu idle  
math-colibri-c22       1  math-colibri-gpu idle  
math-colibri-c23       1  math-colibri-gpu idle  
math-colibri-c24       1  math-colibri-gpu idle  
math-score-c01         1        math-score unk*  
math-score-c02         1        math-score unk*  
math-score-c03         1        math-score idle  
math-score-c04         1        math-score idle  
math-score-c05         1        math-score idle  

It looks confusing but there is a method to the madness in the naming convention. Obviously, math-colibri and math-score are the identifiers for what cluster/building the servers are in, but the –c## and –i## stand for compute and interactive. the c## servers are usually part of the queuing system and the i## ones are for interactive use. Again, never ssh to compute nodes directly.

Scheduler Instructions

Submitting a job

The qsub command is used to submit a job into a queue. Your job should be a script that is accessible to the compute nodes. There are several switches you can add to the qsub command to set the submission options - the most common ones are:

-q [queuename]	Submit the job into a certain queue (you should almost always do this)
-pe [parallel environment]	Submit the job with a specified parallel environment

By default, a job will run with one "slot" (aka core reservation). If your job is going to use more than one CPU core, use the -pe smp XX where XX is the number of cores your job will consume. (16 in the example below)

Example:

qsub -q math-all -pe smp 16 ./awesomescript.sh

Viewing queues and job status

The qstat and qhost command are used to gather information from the scheduler. Some of the most common switches are:

-q [queuename]	Request information on a certain queue. If you don't specify this option, all queues will be given
-f	Request full output - this is similar to giving a verbose output
-u [username]	Request list of jobs for a certain user. Use -u '*' to show all users.
-j [jobid]	Request information on a job. This is useful if your job throws an E (error) code.
-g c	Show status for all available queues - shows the used and available resources.

The command qhost will show information on each server managed by the scheduler - mainly number of CPUs/Threads, total memory and total memory used, and total swap memory space and swap memory space used.

Modifying Jobs

The qmod and qalter commands are used to modify job settings or statuses.

The common qmod commands are:

-sj [jobid]	suspend (pause) a job
-usj [jobid]	unsuspend (unpause) a job
-rj [jobid]	reschedule a job (restart and submit back in queue)
-cj [jobid]	clear job error state of a job

The common qalter commands are:

-q [queuename]	Change the job queue to the specified queue
-pe [parallelenvironment] [slots]	Change the parallel environment and/or number of slots used for the job