DiCOSApps

DiCOSApp Introduction

DiCOSApp is web-based SaaS cloud computing service. In this document, we will introduce how to access the service and the computing resources its provides.

Use DiCOSApp

Login in to DiCOS web and go to https://dicos.grid.sinica.edu.tw/dockerapps/ to start DiCOSApps. Each DiCOSApp shows its software and the availability of its computing resources as the image below. Press launch button (and choose proper lifetime of the application if applicable) to start the computing instance.

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

Every user has their home space and each group has a group space.
You can download and access your data via the endpoints, slurm-ui.twgrid.org and dicos-sftp.twgrid.org by sftp client(like FileZilla).
All the space can be accessed in your DiCOSApp instance as well.
Please check more information as below:

1. User Home space

The user home space is in following paths:

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

Please make a remote backup periodically to secure it

2. Group space

The group space is shared among group members and PI has full access rights and responsibility to manage it.
This space is served as the computing working directory for your jobs.
Please find the space as below:

-  /ceph/work/{group_name}

Please make a remote backup your data periodically to secure it

4. CryoEM group space (CryoEM user only)

CryoEM user & group space is in the following path:

- /activeEM/

Data Transfer Endpoint

Please transfer your data by dicos-sftp.twgrid.org``(recommended) or ``slurm-ui.twgrid.org endpoint.( using filezilla or sftp client):

- dicos-sftp.twgrid.org
- slurm-ui.twgrid.org

Restore your DiCOSApp Instance

Your DiCOSApp instance might be lost when our service experiences accidental or scheduled downtime. Please restore your DiCOSApp instance by following the instructions.

Go to DiCOSApp page to see if there are any open DiCOSApp(s).
Click Delete button to delete the opened DiCOSApp(s).
Launch a new DiCOSApp

Specific Software Installation

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