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slurm [2023/01/16 20:55]
popel --nodelist problems 		slurm [2024/10/02 15:22] (current)
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 ====== ÚFAL Grid Engine (LRC) ====== ====== ÚFAL Grid Engine (LRC) ======
 +
 +**IN 2024: Newly, all the documentation is at a dedicated wiki https://ufal.mff.cuni.cz/lrc (you need to use ufal and [[internal:welcome-at-ufal#small-linguistic-password|small-linguistic password]] to access the wiki from outside of the UFAL network).***
  
 LRC (Linguistic Research Cluster) is the name of ÚFAL's computational grid/cluster. The cluster is built on top of [[https://slurm.schedmd.com/|SLURM]] and is using [[https://www.lustre.org/|Lustre]] for [[internal:linux-network#directory-structure|data storage]]. LRC (Linguistic Research Cluster) is the name of ÚFAL's computational grid/cluster. The cluster is built on top of [[https://slurm.schedmd.com/|SLURM]] and is using [[https://www.lustre.org/|Lustre]] for [[internal:linux-network#directory-structure|data storage]].
 +
 +See Milan Straka's intro to Slurm (and Spark and possibly also the [[https://ufal.mff.cuni.cz/courses/npfl118#assignments|NPFL118 assingments]] if you want). Use the username=ufal and small linguistic password:
 +
 +  * https://lectures.ms.mff.cuni.cz/video/rec/npfl118/2324/npfl118-2324-winter-slurm.mp4
 +  * https://lectures.ms.mff.cuni.cz/video/rec/npfl118/2324/npfl118-2324-winter-spark.mp4
 +  * https://lectures.ms.mff.cuni.cz/video/rec/npfl118/2324/npfl118-2324-winter-assignments.mp4
  
 Currently there are following partitions (queues) available for computing: Currently there are following partitions (queues) available for computing:
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 | Node name | Thread count | Socket:Core:Thread | RAM (MB) | | Node name | Thread count | Socket:Core:Thread | RAM (MB) |
-| achilles1 | 32 | 2:8:2 | 128810 | +| achilles[1-8] | 32 | 2:8:2 | 128810 | 
-| achilles2 | 32 | 2:8:2 | 128810 | +| hector[1-8] | 32 | 2:8:2 | 128810 | 
-| achilles3 | 32 | 2:8:2 | 128810 | +| helena[1-8] | 32 | 2:8:2 | 128811 | 
-| achilles4 | 32 | 2:8:2 | 128810 | +| paris[1-8] | 32 | 2:8:2 | 128810 | 
-| achilles5 | 32 | 2:8:2 | 128810 | +| hyperion[2-8] | 64 | 2:16:2 | 257667 |
-| achilles6 | 32 | 2:8:2 | 128810 | +
-| achilles7 | 32 | 2:8:2 | 128810 | +
-| achilles8 | 32 | 2:8:2 | 128810 | +
-| hector1 | 32 | 2:8:2 | 128810 | +
-| hector2 | 32 | 2:8:2 | 128810 | +
-| hector3 | 32 | 2:8:2 | 128810 | +
-| hector4 | 32 | 2:8:2 | 128810 | +
-| hector5 | 32 | 2:8:2 | 128810 | +
-| hector6 | 32 | 2:8:2 | 128810 | +
-| hector7 | 32 | 2:8:2 | 128810 | +
-| hector8 | 32 | 2:8:2 | 128810 | +
-| helena1 | 32 | 2:8:2 | 128811 | +
-| helena2 | 32 | 2:8:2 | 128811 | +
-| helena3 | 32 | 2:8:2 | 128811 | +
-| helena4 | 32 | 2:8:2 | 128811 | +
-| helena5 | 32 | 2:8:2 | 128810 | +
-| helena6 | 32 | 2:8:2 | 128811 | +
-| helena7 | 32 | 2:8:2 | 128810 | +
-| helena8 | 32 | 2:8:2 | 128811 | +
-| paris1 | 32 | 2:8:2 | 128810 | +
-| paris2 | 32 | 2:8:2 | 128810 | +
-| paris3 | 32 | 2:8:2 | 128810 | +
-| paris4 | 32 | 2:8:2 | 128810 | +
-| paris5 | 32 | 2:8:2 | 128810 | +
-| paris6 | 32 | 2:8:2 | 128810 | +
-| paris7 | 32 | 2:8:2 | 128810 | +
-| paris8 | 32 | 2:8:2 | 128810 | +
-| hyperion2 | 64 | 2:16:2 | 257667 | +
-| hyperion3 | 64 | 2:16:2 | 257667 | +
-| hyperion4 | 64 | 2:16:2 | 257667 | +
-| hyperion5 | 64 | 2:16:2 | 257667 | +
-| hyperion6 | 64 | 2:16:2 | 257667 | +
-| hyperion7 | 64 | 2:16:2 | 257667 | +
-| hyperion8 | 64 | 2:16:2 | 257667 |+
 ==== cpu-ms ==== ==== cpu-ms ====
  
 | Node name | Thread count | Socket:Core:Thread | RAM (MB) | | Node name | Thread count | Socket:Core:Thread | RAM (MB) |
 | iridium | 16 | 2:4:2 | 515977 | | iridium | 16 | 2:4:2 | 515977 |
-| orion1 | 40 | 2:10:2 | 128799 | +| orion[1-8] | 40 | 2:10:2 | 128799 |
-| orion2 | 40 | 2:10:2 | 128799 | +
-| orion3 | 40 | 2:10:2 | 128799 | +
-| orion4 | 40 | 2:10:2 | 128799 | +
-| orion5 | 40 | 2:10:2 | 128799 | +
-| orion6 | 40 | 2:10:2 | 128799 | +
-| orion7 | 40 | 2:10:2 | 128799 | +
-| orion8 | 40 | 2:10:2 | 128799 |+
 ==== gpu-troja ==== ==== gpu-troja ====
  
 | Node name | Thread count | Socket:Core:Thread | RAM (MB) | Features | GPU type | | Node name | Thread count | Socket:Core:Thread | RAM (MB) | Features | GPU type |
-| tdll-3gpu1 | 64 | 2:16:2 | 128642 | gpuram48G gpu_cc8.6 | NVIDIA A40 | +| tdll-3gpu[1-4] | 64 | 2:16:2 | 128642 | gpuram48G gpu_cc8.6 | NVIDIA A40 | 
-| tdll-3gpu2 | 64 | 2:16:2 | 128642 | gpuram48G gpu_cc8.6 | NVIDIA A40 | +| tdll-8gpu[1,2] | 64 | 2:16:2 | 257666 | gpuram40G gpu_cc8.0 | NVIDIA A100 | 
-| tdll-3gpu3 | 64 | 2:16:2 | 128642 | gpuram48G gpu_cc8.6 | NVIDIA A40 | +| tdll-8gpu[3-7] | 32 | 2:8:2 | 253725 | gpuram16G gpu_cc7.5 | NVIDIA Quadro P5000 |
-| tdll-3gpu4 | 64 | 2:16:2 | 128642 | gpuram48G gpu_cc8.6 | NVIDIA A40 | +
-| tdll-8gpu1 | 64 | 2:16:2 | 257666 | gpuram40G gpu_cc8.0 | NVIDIA A100 | +
-| tdll-8gpu2 | 64 | 2:16:2 | 257666 | gpuram40G gpu_cc8.0 | NVIDIA A100 | +
-| tdll-8gpu3 | 32 | 2:8:2 | 253725 | gpuram16G gpu_cc7.5 | NVIDIA Quadro P5000 | +
-| tdll-8gpu4 | 32 | 2:8:2 | 253725 | gpuram16G gpu_cc7.5 | NVIDIA Quadro P5000 | +
-| tdll-8gpu5 | 32 | 2:8:2 | 253725 | gpuram16G gpu_cc7.5 | NVIDIA Quadro P5000 | +
-| tdll-8gpu6 | 32 | 2:8:2 | 253725 | gpuram16G gpu_cc7.5 | NVIDIA Quadro P5000 | +
-| tdll-8gpu7 | 32 | 2:8:2 | 253725 | gpuram16G gpu_cc7.5 | NVIDIA Quadro P5000 |+
 ==== gpu-ms ==== ==== gpu-ms ====
  
 | Node name | Thread count | Socket:Core:Thread | RAM (MB) | Features | GPU type | | Node name | Thread count | Socket:Core:Thread | RAM (MB) | Features | GPU type |
-| dll-3gpu1 | 64 | 2:16:2 | 128642 | gpuram48G gpu_cc8.6 | NVIDIA A40 | +| dll-3gpu[1-5] | 64 | 2:16:2 | 128642 | gpuram48G gpu_cc8.6 | NVIDIA A40 | 
-| dll-3gpu2 | 64 | 2:16:2 | 128642 | gpuram48G gpu_cc8.6 | NVIDIA A40 | +| dll-4gpu[1,2] | 40 | 2:10:2 | 187978 | gpuram24G gpu_cc8.6 | NVIDIA RTX 3090 | 
-| dll-3gpu3 | 64 | 2:16:2 | 128642 | gpuram48G gpu_cc8.6 | NVIDIA A40 | +| dll-4gpu3 | 62 | 1:32:2 | 515652 | gpuram48G gpu_cc8.9 | NVIDIA L40 | 
-| dll-3gpu4 | 64 | 2:16:2 | 128642 | gpuram48G gpu_cc8.6 | NVIDIA A40 | +| dll-4gpu4 | 30 | 1:16:2 | 257616 | gpuram48G gpu_cc8.6 | NVIDIA A40 | 
-| dll-3gpu5 | 64 | 2:16:2 | 128642 | gpuram48G gpu_cc8.6 | NVIDIA A40 | +| dll-8gpu[1,2] | 64 | 2:16:2 | 515838 | gpuram24G gpu_cc8.0 | NVIDIA A30 | 
-| dll-4gpu1 | 40 | 2:10:2 | 187978 | gpuram24G gpu_cc8.6 | NVIDIA RTX 3090 | +| dll-8gpu[3,4] | 32 | 2:8:2 | 257830 | gpuram16G gpu_cc8.6 | NVIDIA RTX A4000 | 
-| dll-4gpu2 | 40 | 2:10:2 | 187978 | gpuram24G gpu_cc8.6 | NVIDIA RTX 3090 | +| dll-8gpu[5,6] | 40 | 2:10:2 | 385595 | gpuram16G gpu_cc7.5 | NVIDIA Quadro RTX 5000 |
-| dll-8gpu1 | 64 | 2:16:2 | 515838 | gpuram24G gpu_cc8.0 | NVIDIA A30 | +
-| dll-8gpu2 | 64 | 2:16:2 | 515838 | gpuram24G gpu_cc8.0 | NVIDIA A30 | +
-| dll-8gpu3 | 32 | 2:8:2 | 257830 | gpuram16G gpu_cc8.6 | NVIDIA RTX A4000 | +
-| dll-8gpu4 | 32 | 2:8:2 | 253721 | gpuram16G gpu_cc8.6 | NVIDIA RTX A4000 | +
-| dll-8gpu5 | 40 | 2:10:2 | 385595 | gpuram16G gpu_cc7.5 | NVIDIA Quadro RTX 5000 | +
-| dll-8gpu6 | 40 | 2:10:2 | 385595 | gpuram16G gpu_cc7.5 | NVIDIA Quadro RTX 5000 |+
 | dll-10gpu1 | 32 | 2:8:2 | 257830 | gpuram16G gpu_cc8.6 | NVIDIA RTX A4000 | | dll-10gpu1 | 32 | 2:8:2 | 257830 | gpuram16G gpu_cc8.6 | NVIDIA RTX A4000 |
-| dll-10gpu2 | 32 | 2:8:2 | 257830 | gpuram11G gpu_cc6.1 | NVIDIA GeForce GTX 1080 Ti | +| dll-10gpu[2,3] | 32 | 2:8:2 | 257830 | gpuram11G gpu_cc6.1 | NVIDIA GeForce GTX 1080 Ti |
-| dll-10gpu3 | 32 | 2:8:2 | 257830 | gpuram11G gpu_cc6.1 | NVIDIA GeForce GTX 1080 Ti |+
  
  
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 #!/bin/bash #!/bin/bash
 #SBATCH -J helloWorld   # name of job #SBATCH -J helloWorld   # name of job
-#SBATCH -p cpu-troja   # name of partition or queue (default=cpu-ms)+#SBATCH -p cpu-troja   # name of partition or queue (default=cpu-troja)
 #SBATCH -o helloWorld.out   # name of output file for this submission script #SBATCH -o helloWorld.out   # name of output file for this submission script
 #SBATCH -e helloWorld.err   # name of error file for this submission script #SBATCH -e helloWorld.err   # name of error file for this submission script
Line 159: Line 111:
 </code> </code>
  
-==== Running jobs ====+=== Rudolf's template === 
 + 
 +The main point is for log files to have the job name and job id in them automatically. 
 + 
 +<code> 
 +#SBATCH -J RuRjob 
 +#SBATCH -o %x.%j.out 
 +#SBATCH -e %x.%j.err 
 +#SBATCH -p gpu-troja 
 +#SBATCH --gres=gpu:1 
 +#SBATCH --mem=16G 
 +#SBATCH --constraint="gpuram16G|gpuram24G" 
 + 
 +# Print each command to STDERR before executing (expanded), prefixed by "+ " 
 +set -o xtrace 
 +</code> 
 + 
 +==== Inspecting jobs ====
  
 In order to inspect all running jobs on the cluster use: In order to inspect all running jobs on the cluster use:
Line 165: Line 134:
 <code> <code>
 squeue squeue
 +</code>
 +
 +filter only my jobs
 +
 +<code>
 +squeue --me
 </code> </code>
  
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 In the example above you can see comments at all lines relevant to CPU allocation. In the example above you can see comments at all lines relevant to CPU allocation.
  
 +=== Priority ====
  
 +When running srun or sbatch, you can pass ''-q high/normal/low/preempt-low''. These represent priorities 300/200/100/100, with ''normal'' (200) being the default. Furthermore, the ''preempt-low'' QOS is actually preemptible -- if there is a job with normal or high QOS, they can interrupt your ''preempt-low'' job.
  
 +The preemption has probably not been used by anyone yet; some documentation about it is on https://slurm.schedmd.com/preempt.html, we use the REQUEUE regime (so your job is killed, very likely with some signal, so you could monitor it and for example save a checkpoint; but currently I do not know any details), and then started again when there are resources.
  
 ==== Interactive mode ==== ==== Interactive mode ====
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   * ''-''''-constraint="gpuram48G|gpuram40G"'' only consider nodes that have either ''gpuram48G'' or ''gpuram40G'' feature defined   * ''-''''-constraint="gpuram48G|gpuram40G"'' only consider nodes that have either ''gpuram48G'' or ''gpuram40G'' feature defined
  
 +
 +\\
 +**Unexpected Behavior of ''srun -c1''**
 +When you execute a command using ''srun'' and pass ''-c1'' like
 +<code>srun -c1 date</code>
 +then the command is actually executed **twice in parallel**. To avoid it, you have to either **remove the ''-c1''** or also **add explicit ''-n1''.**
 ==== Delete Job ==== ==== Delete Job ====
 <code>scancel <job_id> </code> <code>scancel <job_id> </code>
 +
 +<code>scancel -n <job_name> </code>
 +
  
 To see all the available options type: To see all the available options type:
  
-<code>man srun</code>+<code>man scancel</code> 
 + 
 +==== Basic commands on cluster machines ==== 
 + 
 +  lspci 
 +    # is any such hardware there? 
 +  nvidia-smi 
 +    # more details, incl. running processes on the GPU 
 +    # nvidia-* are typically located in /usr/bin 
 +  watch nvidia-smi 
 +    # For monitoring GPU activity in a separate terminal (thanks to Jindrich Libovicky for this!) 
 +    # You can also use nvidia-smi -l TIME 
 +  nvcc --version 
 +    # this should tell CUDA version 
 +    # nvcc is typically installed in /usr/local/cuda/bin/ 
 +  theano-test 
 +    # dela to vubec neco uzitecneho? :-) 
 +    # theano-* are typically located in /usr/local/bin/ 
 +  /usr/local/cuda/samples/1_Utilities/deviceQuery/deviceQuery 
 +    # shows CUDA capability etc. 
 +  ssh dll1; ~popel/bin/gpu_allocations 
 +    # who occupies which card on a given machine 
 +     
  
 ===== See also ===== ===== See also =====

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