Katie AntypasUser Services GroupLawrence Berkeley National Lab

17 February 2012

JGI Training Series

Until all users are migrated to NERSC we plan to hold weekly Friday sessions

More on file and data management

Open Office Hours

Review of batch system policiesCrius

RheaTheia

Kronos?

Hyperion

Oceanus

Iapetus

Themis

Introduction to NIM

On NIM you can change your password, change your shell and set security questions

Login to nim.nersc.gov

Look under the actions menu to do the above tasks

File systems best practices

• Unfortunately disk is still expensive

• All of the JGI’s data can not be stored on disk within the current budget

• Archive and delete data you no longer need

• Disk usage will be controlled through quotas in some cases and purging in others

Only the “house” file system will be available on both JGI and NERSC systems initially

JGI Space NERSC SpaceCompute clusterSome submit hosts

Most web servers

NetappsNetapps “projectb”“projectb”

househouse

•If your data needs access to both servers in JGI space and the compute cluster, it MUST go into “house”•In other words – move data out of Netapps

But “house” is 90% full……

House 90%House 90%

File systems above 90% are lower performing and at higher risk of failure

We need your help deleting data from “house” and moving data from the netapps to “house”

NERSC has set up 2 fast “data transfer nodes”just for JGI users

Login to dtn03.nersc.gov or dtn04.nersc.govType >df to see all the mounted file systems Back up data to HPSS (you authenticated at last week’s training don’t remember? Type hsi and then enter your NIM password)

> cd /house/path/to/your/data> hsi put <filename>

Or archive an entire directory> htar –cvf tarname.tar directory/

There are two areas of storage within the “project” layout of the “projectb” file system

/projectb/

projectdirs/ scratch/

PI/ RD/ fungal/ metagenome/ micro/ plant/ comparative/ user/

• Group directories• Not purged• Subject to quota

• User directories• cd $SCRATCH •Purged, 12 weeks•1 TB, 500,000 inode quota

Request a projectb directory for your group through the Jira ticket system

Request a larger /scratch quota through the Jira ticket system

ssh phoebe.nersc.gov

Use the fast data transfer nodes to move data between file systems

Login to dtn03.nersc.gov or dtn04.nersc.govType >df to see all the mounted file systems You can move data to 3 file systems $HOME “project” “scratch”

> mv /old/path/filename /new/path/filename

It is important for every group to come up with a data retention policy

How long should we keep the raw data?

Can the data be deleted or should it be archived? Can we set up an

automated way to archive and delete data?

The JGI compute clusters have been consolidated into Crius with the following shares

Crius

RheaTheia

Kronos?

Hyperion

Oceanus

Iapetus

Themis

Users should submit jobs to the normal queue

Jobs running longer than 12 hours or requesting large amounts of memory could see longer wait times

Useful commands