GRID COMPUTING

What IS grid ? Interconnected computer systems where the machines utilize the same resources collectively. Grid computing usually consists of one main computer that distributes information and tasks to a group of networked computers to accomplish a common goal. Grid computing is often used to complete complicated or tedious mathematical or scientific calculations.

Wayne State university grid Grid handles projects requiring high speed computation, parallel and distributed computing, data management, and computationally intensive applications. Enabling users to utilize numerous processors in different systems simultaneously. High speed networks Processing power of 8,212 cores 56TB of RAM 1.2PB of disk space

Connecting to grid Double-click on Putty application Enter 'grid.wayne.edu' as 'Host Name‘ Click on Window option on the left and change the count of number of lines to scroll back as per requirement Click on Open Enter your access id when asked for ‘login as’ followed by your academica password

Basic linux commands After logging in to the grid, try these basic linux commands: 1. ls - listing files in the current directory 2. pwd - to check the present working directory 3. vi test - vi is a file editor. Opens file ‘test’ Press i - change to insert mode Enter text Press [ESC] and then :wq to exit out of vi editor 4. cat test - to display the contents of the file test 5. cp test test1 - to copy contents of test to test1 6. cat test1 7. mv test test2 - to rename the file test to test2 8. cat test2 - check the contents of test2 to be same as test 9. mkdir dir - to make a directory named dir 10. mv test1 test2 dir - to move the files test1 and test2 to directory dir 11. cd dir - to change the current directory to dir 12. pwd - check that your pwd before had given different path 13. ls 14. rm test1 - to delete the file test1 15. ls 16. cd .. - change to parent directory 17. rm -rf dir - to delete directory dir and its contents

Running a Simple Job Log in to the Grid. Copy the script from the destination to home directory as follows : cp /wsu/apps/scripts/tutorial/simple_job . Run the simple job script by typing: qsub simple_job Check to see that your job is running by typing the following command : qme You can login to the node that your job is running on by typing: ssh $HOSTNAME When your job is finished you should have an error and an output file in your home directory, check by typing: ls The job script can be viewed in the file simple_job by typing 'vim simple_job'. This is the simple_job script: #!/bin/bash ## Script is submitted to this Queue: #PBS -q wsuq ## One core and 1GB of RAM selected: #PBS -l select=1:ncpus=1:mem=1GB ## Commands to be executed: ## Sleep for 5 minutes: sleep 300

Running an interactive job Provides a shell prompt, which allows users to execute commands and scripts as they would on the login nodes  Usually used to debug the script and understand the errors Command to start : qsub -I Creates a single ssh session with 1 core and 1GB of RAM To use one node and 2 processors on that one node with queue as wsuq we type as follows: qsub -I -q wsuq -l nodes=1:ppn=2

Running an interactive job (Example) Following are the steps to follow to run an interactive job. Type ‘echo $HOSTNAME’ to notice output as ‘commodore.grid.wayne.edu’ 1. To use one node and 2 processors on that one node with queue as wsuq we type as follows: qsub -I -q wsuq -l nodes=1:ppn=2 2. You should now be on a node in the wsuq. Type these commands: date  will prompt today’s date echo $HOSTNAME  will prompt hostname which is different from ‘commodore.grid.wayne.edu’ , ensuring you are on other node. 3. ls command is used to list all files in current directory. Even if you are on different node, access to home directory still exists. Verify that using ‘ls –al’ 4. Type ‘exit’ to exit the node Following is the script we will be trying to run interactively. #!/bin/bash #PBS -l -q wsuq -l nodes=1:ppn=2 date echo $HOSTNAME

Running a Multicore Job Log in to the Grid. Copy the script from the destination to home directory as follows : cp /wsu/apps/scripts/tutorial/multicore_job . Run the multicore job script by typing: qsub multicore_job Check to see that your job is running by typing the following command : qme You can login to the node that your job is running on by typing: ssh $HOSTNAME When your job is finished you should have an error and an output file in your home directory, check by typing: ls The job script can be viewed in the file multicore_job by typing 'vim multicore_job'. This is the multicore_job script: #!/bin/bash ## Script is submitted to this Queue: #PBS -q wsuq ## Eight cores and 1GB of RAM selected: #PBS -l select=1:ncpus=8:mem=1GB:mpiprocs=8 ## Commands to be executed: ## Provides date: echo Date job ran: date ## Provides hostname: echo Host: echo $HOSTNAME ## Provides location of processes: echo Location of processes: cat $PBS_NODEFILE ## Sleep for 5 minutes: sleep 300

Running a LS-DYNA Job Log in to the Grid. Copy the script from the destination to home directory as follows : cp /wsu/apps/scripts/tutorial/tensile.k . Also copy the jobscript by typing the following: cp /wsu/apps/scripts/tutorial/jobfile.txt . Create a jobfile by typing as follows: vi jobfile.txt Make sure your jobfile.txt and tensile.k are in same directory Press the Escape key and type :wq to save and quit. To submit the job type `qsub jobfile.txt` Check to see that your job is running by typing the following command : qme The output can be found in the file named ‘outputfile.txt’ Following are the contents of jobfile.txt #!/bin/bash #PBS -N tensile #PBS -l select=1:cpu_type=Intel:ncpus=4 #PBS -j oe #PBS -m ea #PBS -M AccessID@wayne.edu module load ls-dyna-r8.0.0 ls-dyna_smp_s_r8_0_0_x64_redhat59_ifort131 i=tensile.k ncpus=4 > outputfile.txt

You can always find this information on our grid website. WWW. GRID You can always find this information on our grid website. WWW.GRID.WAYNE.EDU