techstaff:slurm
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techstaff:slurm [2017/11/13 10:02] – kauffman | techstaff:slurm [2018/05/04 12:32] – kauffman | ||
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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. | ||
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+ | |||
===== Where to begin ===== | ===== Where to begin ===== | ||
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ssh user@linux.cs.uchicago.edu | ssh user@linux.cs.uchicago.edu | ||
+ | ===== Mailing List ===== | ||
+ | If you are going to be a user of this cluster please sign up for the mailing list. Downtime and other relevant information will be announced here. | ||
+ | |||
+ | [[ https:// | ||
===== Documentation ===== | ===== Documentation ===== | ||
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* [[https:// | * [[https:// | ||
* [[http:// | * [[http:// | ||
+ | |||
+ | |||
===== Infrastructure ===== | ===== Infrastructure ===== | ||
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Request interactive shell | Request interactive shell | ||
< | < | ||
+ | |||
+ | Create a directory on the scratch partition if you don't already have one: | ||
+ | < | ||
Change into my scratch directory: | Change into my scratch directory: | ||
- | < | + | < |
Get the files I need: | Get the files I need: | ||
< | < | ||
- | user@research2:/ | + | user@slurm1:/ |
foo | foo | ||
</ | </ | ||
Check that the file now exists: | Check that the file now exists: | ||
< | < | ||
- | user@research2:/ | + | user@slurm1:/ |
-rw------- 1 user user 105121 Dec 29 2015 foo | -rw------- 1 user user 105121 Dec 29 2015 foo | ||
</ | </ | ||
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== Performance is slow == | == 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. | 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:// | Sometimes it is useful to see how much of the cluster is utilized. You can do that via the following URL: http:// | ||
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====== Using the GPU ====== | ====== Using the GPU ====== | ||
+ | |||
+ | ===== GRES Multiple GPU's on one system ===== | ||
+ | GRES: Generic Resource. As of 2018-05-04 these only include GPU's. | ||
+ | |||
+ | Jobs will not be allocated any generic resources unless specifically requested at job submit time using the '' | ||
+ | < | ||
+ | |||
+ | Jobs will be allocated specific generic resources as needed to satisfy the request. If the job is suspended, those resources do not become available for use by other jobs. | ||
+ | |||
+ | Job steps can be allocated generic resources from those allocated to the job using the '' | ||
+ | |||
+ | ==== Ok, but I don't want to read the wall of text above ==== | ||
+ | Fine. | ||
+ | |||
+ | The '' | ||
+ | |||
+ | < | ||
+ | --gpu=gpu: | ||
+ | # Please try to limit yourself to one GPU per person. | ||
+ | </ | ||
+ | |||
+ | Example when using tensorflow: | ||
+ | |||
+ | Give the file ' | ||
+ | Depends on: | ||
+ | '' | ||
+ | '' | ||
+ | < | ||
+ | # | ||
+ | from tensorflow.python.client import device_lib | ||
+ | print(device_lib.list_local_devices()) | ||
+ | </ | ||
+ | |||
+ | Here we can see that no GPU was allocated to us because we did not specify the '' | ||
+ | < | ||
+ | kauffman3@bulldozer: | ||
+ | kauffman3@gpu3: | ||
+ | kauffman3@gpu3: | ||
+ | </ | ||
+ | |||
+ | If we request only 1 GPU. | ||
+ | < | ||
+ | kauffman3@bulldozer: | ||
+ | kauffman3@gpu3: | ||
+ | physical_device_desc: | ||
+ | </ | ||
+ | |||
+ | If we request 2 GPUs. | ||
+ | < | ||
+ | kauffman3@bulldozer: | ||
+ | kauffman3@gpu3: | ||
+ | physical_device_desc: | ||
+ | physical_device_desc: | ||
+ | </ | ||
+ | |||
+ | If we request more GPUs then are available. | ||
+ | < | ||
+ | kauffman3@bulldozer: | ||
+ | srun: error: Unable to allocate resources: Requested node configuration is not available | ||
+ | </ | ||
+ | |||
+ | ==== Cool, but how do I know where and what resources are available ==== | ||
+ | Turns out the '' | ||
+ | < | ||
+ | $ sinfo -O partition, | ||
+ | PARTITION | ||
+ | debug* | ||
+ | general | ||
+ | pascal | ||
+ | titan | ||
+ | </ | ||
+ | |||
+ | FEATURES: Is actually just an arbitrary string in the configuration file that defines a node. However, techstaff hopes it actually provides some useful info. | ||
+ | |||
+ | GRES: Don't depend on this being accurate, however it will definitely give you a clue as to how many generic resources are in a partition. | ||
+ | |||
+ | |||
+ | |||
===== Paths ===== | ===== Paths ===== | ||
You will need to add the following to your $PATH and $LD_LIBRARY_PATH. | You will need to add the following to your $PATH and $LD_LIBRARY_PATH. |
/var/lib/dokuwiki/data/pages/techstaff/slurm.txt · Last modified: 2021/01/06 16:13 by kauffman