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techstaff:slurm [2015/12/29 15:53] – [sinfo] kauffmantechstaff:slurm [2016/12/20 11:00] – kauffman
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 ====== DRAFT | Peanut Job Submission Cluster ====== ====== 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 be rude or disruptive to execute on the main (shared) shell servers (i.e., linux1, linux2, linux3).
  
 For job submission we will be using a piece of software called [[http://slurm.schedmd.com|SLURM]]. Simply put, SLURM is a queue management system and stands for **S**imple **L**inux **U**tility for **R**esource **M**anagement; it was developed at the Lawrence Livermore National Lab. It currently supports some of the largest compute clusters in the world. The best description of SLURM can be found on its homepage: For job submission we will be using a piece of software called [[http://slurm.schedmd.com|SLURM]]. Simply put, SLURM is a queue management system and stands for **S**imple **L**inux **U**tility for **R**esource **M**anagement; it was developed at the Lawrence Livermore National Lab. It currently supports some of the largest compute clusters in the world. The best description of SLURM can be found on its homepage:
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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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   * Files older than 90 days will be deleted automatically.   * Files older than 90 days will be deleted automatically.
   * Scratch space is shared by all users.   * 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
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 | **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.|
 +| **gpu** | Contains servers with graphics cards. As of May 2016 there is only one node containing a Tesla M2090. You will be forced to use this server exclusively for now. Please keep your time in interactive mode to a minimum.|
  
 ====== Job Submission ====== ====== Job Submission ======
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 #!/bin/bash #!/bin/bash
 # #
-#SBATCH --mail-user=user@cs.uchicago.edu+#SBATCH --mail-user=cnetid@cs.uchicago.edu
 #SBATCH --mail-type=ALL #SBATCH --mail-type=ALL
-#SBATCH --output=/home/user/slurm/slurm_out/%j.%N.stdout +#SBATCH --output=/home/cnetid/slurm/slurm_out/%j.%N.stdout 
-#SBATCH --error=/home/user/slurm/slurm_out/%j.%N.stderr +#SBATCH --error=/home/cnetid/slurm/slurm_out/%j.%N.stderr 
-#SBATCH --workdir=/home/user/slurm+#SBATCH --workdir=/home/cnetid/slurm
 #SBATCH --partition=debug #SBATCH --partition=debug
 #SBATCH --job-name=check_hostname_of_node #SBATCH --job-name=check_hostname_of_node
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   man sbatch   man sbatch
  
-Make sure to replace all instances of the word ''%%user%%'' with your CNETID.+Make sure to replace all instances of the word ''%%cnetid%%'' with your CNETID.
  
 +=== Submitting job script ===
 +Using the above example you will want to place your tested code into a file. 'hostname.job' is the file name in this example.
 +<code>
 +sbatch hostname.job
 +</code>
 +
 +You can then check the status via squeue or see the output in the output directory '$HOME/slurm/slurm_out'.
 ==== srun ==== ==== srun ====
 Used to submit a job to the cluster that doesn't necessarily need a script. Used to submit a job to the cluster that doesn't necessarily need a script.
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 This command: This command:
-   srun -p general --pty --mem 500 -t 0-06:00 /bin/bash+   srun -p general --pty --cpus-per-task 1 --mem 500 -t 0-06:00 /bin/bash
 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 ======
  
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 | 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. |
  
 +====== Using the GPU ======
 +===== Paths =====
 +You will need to add the following to your $PATH and $LD_LIBRARY_PATH.
 +
 +  export PATH=$PATH:/usr/local/cuda/bin
 +  export LD_LIBRARY_PATH=$LD_LIBRARY_PATH=/usr/local/cuda/lib
 +
 +
 +===== Example =====
 +This sbatch script will get device information from the installed Tesla gpu.
 +<code>
 +#!/bin/bash
 +#
 +#SBATCH --mail-user=cnetid@cs.uchicago.edu
 +#SBATCH --mail-type=ALL
 +#SBATCH --output=/home/cnetid/slurm/slurm_out/%j.%N.stdout
 +#SBATCH --error=/home/cnetid/slurm/slurm_out/%j.%N.stderr
 +#SBATCH --workdir=/home/cnetid/slurm
 +#SBATCH --partition=gpu
 +#SBATCH --job-name=get_tesla_info
 +
 +export PATH=$PATH:/usr/local/cuda/bin
 +export LD_LIBRARY_PATH=$LD_LIBRARY_PATH=/usr/local/cuda/lib
 +
 +cat << EOF > /tmp/getinfo.cu
 +#include <stdio.h>
 +
 +int main() {
 +  int nDevices;
 +
 +  cudaGetDeviceCount(&nDevices);
 +  for (int i = 0; i < nDevices; i++) {
 +    cudaDeviceProp prop;
 +    cudaGetDeviceProperties(&prop, i);
 +    printf("Device Number: %d\n", i);
 +    printf("  Device name: %s\n", prop.name);
 +    printf("  Memory Clock Rate (KHz): %d\n",
 +           prop.memoryClockRate);
 +    printf("  Memory Bus Width (bits): %d\n",
 +           prop.memoryBusWidth);
 +    printf("  Peak Memory Bandwidth (GB/s): %f\n\n",
 +           2.0*prop.memoryClockRate*(prop.memoryBusWidth/8)/1.0e6);
 +  }
 +}
 +EOF
 +
 +/usr/local/cuda/bin/nvcc /tmp/getinfo.cu -o /tmp/a.out
 +/tmp/a.out
 +rm /tmp/a.out
 +rm /tmp/getinfo.cu
 +</code>
 +==== Output ====
 +STDOUT will look something like this:
 +<code>
 +cnetid@linux1:~$ cat $HOME/slurm/slurm_out/12567.gpu1.stdout 
 +Device Number: 0
 +  Device name: Tesla M2090
 +  Memory Clock Rate (KHz): 1848000
 +  Memory Bus Width (bits): 384
 +  Peak Memory Bandwidth (GB/s): 177.408000
 +</code>
 +STDERR should be blank.
 ====== More ====== ====== 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).+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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