Difference between revisions of "Applications/Savu"
From HPC
(→Batch Submission) |
(→Batch Submission) |
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module purge | module purge | ||
module load savu/2.0/gcc-5.2.0/openmpi-2.0.2 | module load savu/2.0/gcc-5.2.0/openmpi-2.0.2 | ||
| − | # | + | |
| + | #This line will calculate the total number of CPUs and place it in CPUs variable | ||
CPUs=$(($SLURM_NNODES * $SLURM_CPUS_ON_NODE)) | CPUs=$(($SLURM_NNODES * $SLURM_CPUS_ON_NODE)) | ||
echo " will run on $CPUs CPUs" | echo " will run on $CPUs CPUs" | ||
| Line 65: | Line 66: | ||
*/apps/savu/test/basic_tomo_process.nxs --> this is the list of processes to be performed, change it to your process list file path | */apps/savu/test/basic_tomo_process.nxs --> this is the list of processes to be performed, change it to your process list file path | ||
*/apps/savu/test --> this is the output directory | */apps/savu/test --> this is the output directory | ||
| − | * | + | *$CPUs 0 --> thats the number of CPUs and GPUs. 28 and zero should run properly on the compute partition. |
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
[username@login01 ~]$ sbatch savu.job | [username@login01 ~]$ sbatch savu.job | ||
Submitted batch job 289522 | Submitted batch job 289522 | ||
</pre> | </pre> | ||
Revision as of 15:58, 16 August 2017
Application Details
- Description: R is an open source programming language and software environment for statistical computing and graphics
- Version: 2.0
- Modules: savu/2.0/gcc-5.2.0/openmpi-2.0.2
Usage Examples
Interactive
this mode is usually used on a smaller slice of your data. to define and make sure what kind of processing you want to run and start tuning it till it shows the expected behaviour.
Note: savu supports interactive mode (as below) and execution mode running as an interpreted script.
[username@login01 ~]$ interactive salloc: Granted job allocation 402968 Job ID 402968 connecting to c059, please wait... Last login: Wed Jul 12 16:23:48 2017 from 10.254.5.246 [username@c059 ~]$ module load savu/2.0/gcc-5.2.0/openmpi-2.0.2 [username@c059~]$ savu_config
or
[username@c059~]$ savu /Path/To_input/Data/file.nxs /List/Of_processes/To_be_performed/process.nxs /path /to/output/directory
Example: this will run basic_tomo_process.nxs on file 24737.nxs and place the output in your current directory under results
[username@c059~]$ savu /trinity/clustervision/CentOS/7/apps/savu/2.0/gcc-5.2.0/openmpi-2.0.2/Savu_2.0/miniconda/pkgs/savu-2.0-h4571989_0/lib/python2.7/site-packages/savu-2.0-py2.7.egg/test_data/data/24737.nxs /trinity/clustervision/CentOS/7/apps/savu/2.0/gcc-5.2.0/openmpi-2.0.2/Savu_2.0/miniconda/pkgs/savu-2.0-h4571989_0/lib/python2.7/site-packages/savu-2.0-py2.7.egg/test_data/test_process_lists/basic_tomo_process.nxs ./results
Batch Submission
Once you are happy with the results you got. you can start submitting a bigger jobs to the cluster. Below is an example of running savu_mpi to process data on multiple nodes.
#!/bin/bash #SBATCH -J My_R_job # Job name, you can change it to whatever you want #SBATCH -N 1 # Number of nodes #SBATCH -n 28 # Number of cores #SBATCH -o %N.%j.out # Standard output will be written here #SBATCH -e %N.%j.err # Standard error will be written here #SBATCH -p compute # Slurm partition, where you want the job to be queued #SBATCH --exclusive # run on one node without any other users module purge module load savu/2.0/gcc-5.2.0/openmpi-2.0.2 #This line will calculate the total number of CPUs and place it in CPUs variable CPUs=$(($SLURM_NNODES * $SLURM_CPUS_ON_NODE)) echo " will run on $CPUs CPUs" savu_mpijob.sh /trinity/clustervision/CentOS/7/apps/savu/2.0/gcc-5.2.0/openmpi-2.0.2/Savu_2.0/miniconda/pkgs/savu-2.0-h4571989_0/lib/python2.7/site-packages/savu-2.0-py2.7.egg ./apps/savu/test/24737.nxs ./apps/savu/test/basic_tomo_process.nxs ./apps/savu/test $CPUs 0
Break down on each of the above items in the savu run command:
- savu_mpijob.sh -->this is the main run command
- /trinity/clustervision/CentOS/7/apps/savu/2.0/gcc-5.2.0/openmpi-2.0.2/Savu_2.0/miniconda/pkgs/savu-2.0-h4571989_0/lib/python2.7/site-packages/savu-2.0-py2.7.egg --> this is the path of Savu installtion, just leave it as it is
- /apps/savu/test/24737.nxs --> this is the input file, change it to your input file path
- /apps/savu/test/basic_tomo_process.nxs --> this is the list of processes to be performed, change it to your process list file path
- /apps/savu/test --> this is the output directory
- $CPUs 0 --> thats the number of CPUs and GPUs. 28 and zero should run properly on the compute partition.
[username@login01 ~]$ sbatch savu.job Submitted batch job 289522