Introduction to MSI* for PubH 8403

Transcription

1 Introduction to MSI* for PubH 8403 Sep 30, 2015 Nancy Rowe *The Minnesota Supercomputing Institute for Advanced Computational Research

2 Overview MSI at a Glance MSI Resources Access System Access - Physical Additional Assistance

3 MSI at a Glance Facilitate research, help attract funding, contribute to education Access through eligible PI Serves more than 500 PI groups; users About 40 fulltime staff; student workers A unit of the Office of the VP for Research Access to HPC, labs, storage and support 300+ software packages Basic resources at no charge

4 Questions?

5 Location Main offices 5 th floor Walter Library HPC systems basement of Walter Library Computer labs Walter, Hasselmo, 717 Delaware (East Bank) Cargill (St. Paul)

6 Resources HPC systems Labs Software Storage Support

7 HPC systems Mesabi new this year; HP Linux cluster; 100 fastest in the world; about 18K cores, 67 TB memory Itasca HP Linux cluster about 9500 cores, 31TB memory Several other specialized systems

8 Laboratories Scientific Development and Visualization 575 and 585 Walter Library Basic Sciences Computing Nils Hasselmo Hall Computational Genetics 138 Cargill Building Biomedical Modeling, Simulation, and Design Delaware Building LCSE-MSI Visualization Virtual reality Large screen Remote visualization 125 Walter Library

9 Storage High Performance Storage 2.8 PB 25GB/s read/write 150 GB/group default; more w/ justification Second Tier Storage 1.4 PB CEPH Globally available Scratch < 30 days, not backed up Can get extensions

10 UNIX/Linux UNIX is the operating system of choice for engineering and scientific workstations. For our purposes UNIX/Linux are the same. Most software at MSI will run faster on UNIX Worth the effort to learn to use UNIX The variant of UNIX found at MSI and most widely in use around the world is GNU/Linux. MSI currently uses CentOS Linux. There are many other distributions (RedHat, Ubuntu, Debian)

11 Access building and system System access is through Professor Carlin For building Access to BSCL (use appropriate lab name) Full legal name, your student ID number, U Card number, phone number Your instructor and/or class For other labs include whether you have access to AHC facilities Information can be found in the General Information page for each lab ( )

12 Remote Connection to MSI Several options for remote connection NICE From inside UMN From outside UMN use VPN first

13 Accessing machines while at MSI ssh [options] machine [options] -X set up environment to port graphics -Y for Macs machine User itasca, mesabi, etc. Encrypted login to remote machines $> man ssh See the MSI home page for a full lis:ng of lab and core machines scp scp [[user@]host1:]filename1[[user@]host2:]filename2 Examples: scp temp.ps login.msi.umn.edu:/scratch/temp.ps ssh Y rowe@itasca.msi.umn.edu - File transfer section

14 Remote Login from outside MSI Requires VPN it.umn.edu/services/all/data-network/vpn/ Terminal login to the bastion host* login.msi.umn.edu Use ssh to connect to other machines Syntax: ssh [-X][-Y] Examples: Use NICE Remote graphical connection Fastest Download client You can launch software directly on NICE ssh Y rowe@login.msi.umn.edu ssh itasca or isub *Users cannot launch software directly on login.msi.umn.edu

15 Getting Started MSI account. Open a terminal while sitting at the machine. A shell provides an interface for the user to interact with the operating system. BASH is the default shell at MSI. Alternatively, see the following link for information concerning remote access from your machine.

16 isub isub is an MSI specific command to connect to MSI machines from login.msi.umn.edu or NX Expects bash shell Examples: isub isub n nodes=1:ppn=4 m 16GB w 24:00:0 Check for more details *Users cannot launch software directly on login.msi.umn.edu or from NX

17 Linux software (modules) see web page module load R start software R module avail R see available versions

18 Queueing system HPC system generally are not interactive Jobs are submitted to queues PBS Each HPC system has a Quickstart page

19 Caveats If you delete a file, it s GONE! There is no Recycle Bin step. The file may be able to be recovered from a backup by contacting help@msi.umn.edu. See Access question 7 If you overwrite a file it has been changed forever. Home directories are backed up nightly. The scratch spaces are not backed up.

20 MSI home page Software Password reset Tutorials FAQ MSI web pages

21 For help By Web: Phone: In person: Room 587 Walter Staffed 8:30AM to 6:00PM or by appointment Nancy Rowe or The University of Minnesota is an equal opportunity educator and employer. This PowerPoint is available in alternative formats upon request. Direct requests to Minnesota, 599 Walter library, 117 Pleasant St. SE, Minneapolis, Minnesota, 55455,