Difference between revisions of "Applications/Savu"

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(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             # Job name, you can change it to whatever you want
+
#SBATCH -J My_R_job       # Job name, you can change it to whatever you want
#SBATCH -N 1               # Number of nodes  
+
#SBATCH -N 1               # Number of nodes  
#SBATCH -o %N.%j.out       # Standard output will be written here
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#SBATCH -o %N.%j.out       # Standard output will be written here
#SBATCH -e %N.%j.err       # Standard error 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 -p compute         # Slurm partition, where you want the job to be queued  
#SBATCH --exclusive           # run on one node without any other users
+
#SBATCH --exclusive       # run on one node without any other users
#SBATCH --mem=64G       # reserve 64Gbytes of RAM for my job (optional)
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#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