DiCOSApps

DiCOSApp Introduction

DiCOSApp is web based micro-service that handles different application individually. Here is the document to introduce its SPEC for each APP.

Use DiCOSApp

Login in to DiCOS web and then go to https://dicos.grid.sinica.edu.tw/dockerapps/ to start using DiCOSApps. The remaining resources are displayed for each DiCOSApp. Like the image below, click launch button (and choose proper lifetime of the application if applicable), and then start to use the application.

CryoEM Specific APPs

CryoEM specific APPs
APP name	CPU cores	GPU	Memory	SSD
CisTEM	32	0	100GB	no
RELION3	16	4 (1080Ti)	380GB	yes
RELION2	16	4 (1080Ti)	380GB	yes
CisTEM-cluster	40 per job, max to 600	0	256GB ~ 3840GB	no
CryoSPARC(no longer up2date)	16	1 (1080Ti)	380GB	yes

Jupyter Notebooks

Jupyter Notebooks
APP name	CPU coures	GPU	Memory	SSD
JupyterLab(CPU)	12	0	64GB	yes
JupyterLab(GPU)	12	1 (P100)	128GB	yes

RELION Job Configuration

What’s the ideal MPI number and thread number with current RELION APP?

4 MPI with 4 threads. If it’s GPU accelerated process, please use 5 MPI with 4 threads

What’s the ideal MPI number and thread number with Premium RELION v100 app?

The v100 GPU is relatively powerful GPU against GTX-1080Ti. So, it can bear much load than 1080ti. In principle, with following job setup, user can get pretty nice speed up when dealing 2D and 3D classifications:

2D: Number of MPI procs: 16, Number of Threads: 1
3D: Number of MPI procs: 9, Number of Threads: 2

What if RELION encounters error?

RELION is often stable. When error occurs, it would usually caused by:

Memory or resources are not enough. For such error, simply reducing Thread number would just help. If the error lasts, then try reducing MPI number.
Input file error. Checking log and removing problematic file indicated in log may just solve this issue.

DiCOSApp Data Handling

The DiCOSApp is ephemeral and isolated application, everything changed or created in APP will be wiped out after the APP is terminated. However, there are three persistent spaces, everything storing there will be kept:

Note

The CryoEM data from ASCEM to ASGC will be stored at /cryoEM/tmp

1. User HOME space

The user home space is connected inside the APP by following paths:

-  ~/data/
-  $HOME/data
-  /dicos_ui_home/<user_name>/data

Please note, the user home space doesn’t guarantee any data protection or space for every user. So, please be careful what you store on it. And please make backup by yourself, if you will only use home space.
All data in user home space can be also accessible from outside APP by sftp (using filezilla or sftp client) with following endpoints:

- dicos-ui02.grid.sinica.edu.tw
- dicos-ui04.grid.sinica.edu.tw

2. DiCOSBOX(Cloud storage) space

DiCOSBOX is Dropbox-like storage, it is also connected inside the APP by following path:

- ~/DiCOSBox
- $HOME/DiCOSBox
- /dicos_ui_home/[ your username ]/DiCOSBox

DiCOSBOX can be also accessible from outside APP by login to following page:
- https://dicosbox.twgrid.org

3. CryoEM group space (CryoEM user only)

CryoEM group space is for CryoEM user only, which must be requested by PI.
CryoEM group space is connected inside the APP by following path:

- /cryoEM/

All data in CryoEM group space can be also accessible from outside APP by sftp( using filezilla or sftp client) with following endpoints:

- dicos-ui02.grid.sinica.edu.tw
- dicos-ui04.grid.sinica.edu.tw

The path is also /cryoEM/

Request for Specific Application Installation

If you have special requirement for the application installation, please contact to DiCOS-Support@twgrid.org.