Beyond Windows: Using the Linux Servers and the Grid

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1 Beyond Windows: Using the Linux Servers and the Grid Topics Linux Overview How to Login & Remote Access Passwords Staying Up-To-Date Network Drives Server List The Grid Useful Commands Linux Overview Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. Users operate a Linux-based system through a command line interface (CLI). Note (new computers): Check TCP/IP settings How to Login & Remote Access Most offices in Blockley Hall are behind the CCEB firewall and can access the Linux machines directly. For example, I can use SecureCRT to access bioapps and biolinux directly. Access to the servers from home or any other location outside of the firewall must first go through s280r1.cceb.med.upenn.edu. Passwords Passwords must be managed on bioapps using the changepassword script. The script will change all of your passwords: LDAP, SMB, x3850 smb (SAXA), x3950 smb (shennessy) All Linux accounts have a LDAP and SMB password. The LDAP password is used to login to a host using SecureCRT. The SMB password is used when you map a network drive (user home directory or project directory). Users in the SAXA and/or shennessy group will have a password for each group.

2 Staying Up-To-Date Please run all update scripts on biolinux or bioapps All users should be using the BASH shell. Run the following commands to update your environment.. /pub/lib/docs/updates/updateme.sh. ~/.profile Network Drives Mapping drives right-click My Computer and select Map Network Drive select the drive letter you would like to use. (H: is typically used for your home drive) enter the network path using \\xnfs\ (DO NOT BROWSE) Home \\xnfs\home_username (username = your Unix username) Project \\xnfs\project_projdir (projdir = the project directory name) SAXA \\x3850\project_saxa shennessy \\x3950\project_shennessy If your Linux username is different from your Windows username: click 'Connect using a different username' check 'Reconnect at logon' click 'Finish'

3 Server List s280r1.cceb.med.upenn.edu Remote login for access to internal application servers: biolinux, bioapps, app441, app442 biolinux R, Gauss, misc. Linux apps (PLINK) Grid access bioapps StataMP, MatLab, R, Gauss, misc. Linux apps (PLINK) Grid access Change your Unix password(s) here app441 & app442 SAS, S-Plus Grid access from app441 When to use the Grid versus one of the application servers? What type of jobs should be submitted to the Grid versus being run on one of the application servers? Any CPU/memory intensive job that will run for more than minutes. If you need to run multiple jobs simultaneously. If you notice a number of people are logged in and the load is greater than 1.0. *(w)

4 The Grid The Grid is basically 60 independent CPU cores used to run a single batched program. Grid jobs are batched and may be submitted from bioapps, biolinux and app441. Jobs are batched using a wrapper script which is then submitted to the Grid using qsub. Grid commands: qsub, qstat, qdel qsub qsub is the command used for job submission to the cluster. It takes several command line arguments and can also use special directives found in the wrapper/submission scripts or command file. qsub r-example.sh qstat The qstat command is used to request the status of jobs, queues, or a batch server. The most commonly used argument is f. qstat f qdel The qdel command deletes jobs in the order in which their job identifiers are presented to the command. qdel 22690

5 Useful Commands dos2unix - DOS/MAC to UNIX text file format converter. dos2unix file ssh - connects and logs into the specified hostname. ssh bioapps pwd print working directory. pwd cd - changes the directory. Change to the projdir project directory: cd /project/projdir Change to your home directory: cd Move up two directories: cd../../ mkdir - Make a new directory. mkdir data rmdir - remove a directory (must be empty). rm data/ rm - remove a file(s). rm file.txt rm file1.txt file2.txt ls - list directory contents. ls ls l exit - allows you to exit from a program, shell or log you out of a Linux network. exit man - display manual page. man ls, man rm, man qsub *W - show who is logged on and what they are doing. w

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