Difference between revisions of "Applications/Savu"
From HPC
(→Interactive) |
(→Batch Submission) |
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=== Batch Submission === | === 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. | ||
| + | |||
<pre style="background-color: #C8C8C8; color: black; font-family: monospace, sans-serif;"> | <pre style="background-color: #C8C8C8; color: black; font-family: monospace, sans-serif;"> | ||
#!/bin/bash | #!/bin/bash | ||
| − | #SBATCH -J My_R_job | + | #SBATCH -J My_R_job # Job name, you can change it to whatever you want |
| − | #SBATCH -N 1 | + | #SBATCH -N 1 # Number of nodes |
| − | #SBATCH -o %N.%j.out | + | #SBATCH -o %N.%j.out # Standard output will be written here |
| − | #SBATCH -e %N.%j.err | + | #SBATCH -e %N.%j.err # Standard error will be written here |
| − | #SBATCH -p compute | + | #SBATCH -p compute # Slurm partition, where you want the job to be queued |
| − | #SBATCH --exclusive | + | #SBATCH --exclusive # run on one node without any other users |
| − | #SBATCH --mem=64G | + | #SBATCH --mem=64G # reserve 64Gbytes of RAM for my job (optional) |
module purge | module purge | ||
Revision as of 14:23, 15 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 -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 #SBATCH --mem=64G # reserve 64Gbytes of RAM for my job (optional) module purge module add R/3.4.1 R CMD BATCH Random.R
[username@login01 ~]$ sbatch Rtest.job Submitted batch job 289522