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techstaff:slurm [2015/12/04 13:58] – kauffmantechstaff:slurm [2016/01/05 09:01] – [More] kauffman
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-====== DRAFT | Peanut Job Submission Cluster | DRAFT ======+====== DRAFT | Peanut Job Submission Cluster ======
  
 We are currently **alpha** testing and gauging user interest in a cluster of machines that allows for the submission of long running compute jobs. Think of these machines as a dumping ground for discrete computing tasks that might have been rude or disruptive to execute on the main (shared) shell servers (i.e., linux1, linux2, linux3). We are currently **alpha** testing and gauging user interest in a cluster of machines that allows for the submission of long running compute jobs. Think of these machines as a dumping ground for discrete computing tasks that might have been rude or disruptive to execute on the main (shared) shell servers (i.e., linux1, linux2, linux3).
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 SLURM is similar to most other queue systems in that you write a batch script, then submit it to the queue manager. The queue manager schedules your job to run on the queue (or partition in SLURM parlance) that you designate. Below is an outline of how to submit jobs to SLURM, how SLURM decides when to schedule your job, and how to monitor progress. SLURM is similar to most other queue systems in that you write a batch script, then submit it to the queue manager. The queue manager schedules your job to run on the queue (or partition in SLURM parlance) that you designate. Below is an outline of how to submit jobs to SLURM, how SLURM decides when to schedule your job, and how to monitor progress.
 +
 +===== Where to begin =====
 +SLURM is a set of command line utilities that can be accessed via the command line from **most** any computer science system you can login to. Using our main shell servers (linux.cs.uchicago.edu) is expected to be our most common use case, so you should start there.
 +
 +  ssh user@linux.cs.uchicago.edu
 +
  
 ===== Documentation ===== ===== Documentation =====
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 ==== Storage ==== ==== Storage ====
-Shared scratch storage is being planned, but not yet available. Techstaff hopes to have this done in time for the winter quarter.+There is slow scratch space mounted to ''%%/scratch%%''. It is a ZFS pool consisting of 10x 2TB 7200RPM SAS drives connected via a LSI 9211-8i and is made up of 5 mirrored VDEVs, which is similar to a RAID10. The servers uplink is 1G ethernet. 
  
 +  * Files older than 90 days will be deleted automatically.
 +  * Scratch space is shared by all users.
 +
 +=== Access ===
 +Scratch space is only mounted on nodes associated with the cluster. If you want to be able to transfer files to the scratch space you will want to run an [[techstaff:slurm#interactive_jobs|interactive shell]]. Now you will be able to use standard tools such as ''%%scp%%'' or ''%%rsync%%'' to transfer files.
 +
 +  - You should only do a file transfer via the debug partition: ''%% srun -p debug --pty --mem 500 /bin/bash%%''
 +  - Now you can create a directory of your own: ''%%mkdir /scratch/$USER%%'' You should store any files you create in this directory.
 +
 +== Example ==
 +
 +Request interactive shell
 +<code>user@csilcomputer:~$ srun --pty --mem 500 /bin/bash </code>
 +
 +Change into my scratch directory:
 +<code>user@research2:~$ cd /scratch/user/</code>
 +
 +Get the files I need:
 +<code>
 +user@research2:/scratch/user$ scp user@csilcomputer:~/foo .
 +foo                         100%  103KB 102.7KB/s   00:00    
 +</code>
 +Check that the file now exists:
 +<code>
 +user@research2:/scratch/user$ ls -l foo 
 +-rw------- 1 user user 105121 Dec 29  2015 foo
 +</code>
 +
 +I can now exit my interactive shell.
 +
 +== Performance is slow ==
 +This is expected. The maximum speed this server will ever be able to achieve is 1Gb/s because of its single 1G ethernet uplink. If this cluster gains in popularity we plan on upgrading the network and storage server.
 ==== Utilization Dashboard ==== ==== Utilization Dashboard ====
 Sometimes it is useful to see how much of the cluster is utilized. You can do that via the following URL: http://peanut.cs.uchicago.edu Sometimes it is useful to see how much of the cluster is utilized. You can do that via the following URL: http://peanut.cs.uchicago.edu
  
 ==== Partitions / Queues ==== ==== Partitions / Queues ====
-As of December, 2015 we have 3 partitions in our cluster.+To find out what partitions we offer, checkout the [[techstaff:slurm#sinfo|sinfo]] command. 
 + 
 +As of December, 2015 we have will have at least 2 partitions in our cluster; 'debug' and 'general'.
  
 ^ Partition Name ^ Description ^ ^ Partition Name ^ Description ^
 | **debug** | The partition your job will be submitted to if none is specified. The purpose of this partition is to make sure your code is running as it should before submitting a long running job to the general queue. | | **debug** | The partition your job will be submitted to if none is specified. The purpose of this partition is to make sure your code is running as it should before submitting a long running job to the general queue. |
 | **general** | All jobs that have been thoroughly tested can be submitted here. This partition will have access to more nodes and will process most of the jobs. If you need to use the ''%%--exclusive%%'' flag it should be done here.| | **general** | All jobs that have been thoroughly tested can be submitted here. This partition will have access to more nodes and will process most of the jobs. If you need to use the ''%%--exclusive%%'' flag it should be done here.|
-| **hardware** | The purpose of this partition is to set aside nodes that do not use the virtualization layer. This is important if you need true hardware access. | 
  
  
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 PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
 debug*       up      30:00      1   idle research2 debug*       up      30:00      1   idle research2
-general      up   infinite      5   idle research[3-7] +general      up 1-00:00:00      6   idle research[3-8]
-hardware     up    1:00:00      1   idle research8+
 </code> </code>
  
  
-===== Monitoring Jobs =====+====== Monitoring Jobs ======
  
 ''%%squeue%%'' and ''%%sacct%%'' are two different commands that allow you to monitor job activity in SLURM. ''%%squeue%%'' is the primary and most accurate monitoring tool since it queries the SLURM controller directly. ''%%sacct%%'' gives you similar information for running jobs, and can also report on previously finished jobs, but because it accesses the SLURM database, there are some circumstances when the information is not in sync with squeue. ''%%squeue%%'' and ''%%sacct%%'' are two different commands that allow you to monitor job activity in SLURM. ''%%squeue%%'' is the primary and most accurate monitoring tool since it queries the SLURM controller directly. ''%%sacct%%'' gives you similar information for running jobs, and can also report on previously finished jobs, but because it accesses the SLURM database, there are some circumstances when the information is not in sync with squeue.
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-===== Interactive Jobs =====+====== Interactive Jobs ======
  
 Though batch submission is the best way to take full advantage of the compute power in the job submission cluster, foreground, interactive jobs can also be run. Though batch submission is the best way to take full advantage of the compute power in the job submission cluster, foreground, interactive jobs can also be run.
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 will start a command line shell (''%%/bin/bash%%'') on the 'general' queue with 500 MB of RAM for 6 hours; 1 core on 1 node is assumed as these parameters (''%%-n 1 -N 1%%'') were left out. When the interactive session starts, you will notice that you are no longer on a login node, but rather one of the compute nodes dedicated to this queue. The ''%%--pty%%'' option allows the session to act like a standard terminal. will start a command line shell (''%%/bin/bash%%'') on the 'general' queue with 500 MB of RAM for 6 hours; 1 core on 1 node is assumed as these parameters (''%%-n 1 -N 1%%'') were left out. When the interactive session starts, you will notice that you are no longer on a login node, but rather one of the compute nodes dedicated to this queue. The ''%%--pty%%'' option allows the session to act like a standard terminal.
  
-===== Job Scheduling =====+====== Job Scheduling ======
  
 We use a [[http://slurm.schedmd.com/priority_multifactor.html|multifactor]] method of job scheduling. Job priority is assigned by a combination of fair-share, partition priority, and length of time a job has been sitting in the queue. The priority of the queue is the highest factor in the job priority calculation. For certain queues this will cause jobs on lower priority queues which overlap with that queue to be requeued. The second most important factor is fair-share score. You can find a description of how SLURM calculates Fair-share [[http://slurm.schedmd.com/priority_multifactor.html#fairshare|here]]. The third most important is how long you have been sitting in the queue. The longer your job sits in the queue the higher its priority grows. If everyone’s priority is equal then FIFO is the scheduling method. If you want to see what your current priority is just do ''%%sprio -j JOBID%%'' which will show you the calculation it does to figure out your job priority. If you do ''%%sshare -u USERNAME%%'' you can see your current fair-share and usage.((https://rc.fas.harvard.edu/resources/running-jobs)) We use a [[http://slurm.schedmd.com/priority_multifactor.html|multifactor]] method of job scheduling. Job priority is assigned by a combination of fair-share, partition priority, and length of time a job has been sitting in the queue. The priority of the queue is the highest factor in the job priority calculation. For certain queues this will cause jobs on lower priority queues which overlap with that queue to be requeued. The second most important factor is fair-share score. You can find a description of how SLURM calculates Fair-share [[http://slurm.schedmd.com/priority_multifactor.html#fairshare|here]]. The third most important is how long you have been sitting in the queue. The longer your job sits in the queue the higher its priority grows. If everyone’s priority is equal then FIFO is the scheduling method. If you want to see what your current priority is just do ''%%sprio -j JOBID%%'' which will show you the calculation it does to figure out your job priority. If you do ''%%sshare -u USERNAME%%'' you can see your current fair-share and usage.((https://rc.fas.harvard.edu/resources/running-jobs))
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-===== Common Issues =====+====== Common Issues ======
  
 ^Error ^What does it mean? ^ ^Error ^What does it mean? ^
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 | JOB <jobid> CANCELLED AT <time> DUE TO NODE FAILURE | There can be many reasons for this message, but most often it means that the node your job was set to run on can no longer be contacted by the the SLURM controller.| | JOB <jobid> CANCELLED AT <time> DUE TO NODE FAILURE | There can be many reasons for this message, but most often it means that the node your job was set to run on can no longer be contacted by the the SLURM controller.|
 | error: Unable to allocate resources: More processors requested than permitted | It usually has **nothing** to do with priviledges you may or may not have. Rather, it usually means that you have allocated more processors than one compute node actually has. | | error: Unable to allocate resources: More processors requested than permitted | It usually has **nothing** to do with priviledges you may or may not have. Rather, it usually means that you have allocated more processors than one compute node actually has. |
 +
 +====== More ======
 +If you feel this documentation is lacking in some way please let techstaff know. Email [[techstaff@cs.uchicago.edu]], call (773-702-1031), or stop by our office (Ryerson 154).
/var/lib/dokuwiki/data/pages/techstaff/slurm.txt · Last modified: 2021/01/06 16:13 by kauffman
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