High Performance Computing (HPC) Centre forms a key part of the infrastructure backbone enabling scientific discovery, driving innovation and ensuring the competitive over any cutting edge technology used in societal development.The HPC infrastructure is a platform for various application scaling environments such as maintaining comprehensive process and product profile digital database,use of image processing technology for crop disease identification, development of Omics platform for the analysis of genomics,transcriptomics and proteomics data for pattern discovery and predicting crop simulation models for enhancement of production and productivity in agricultural and its allied sectors.
Omics data analysis platform Omics-based research and application development provide crucial resources to promote research in model and applied plant and animal species.To facilitate Omics based research in the agricultural and allied sector, high performance computing clusters are required for carrying out the parallel computing in order to generate patterns in data.
What is HPC cluster
An HPC cluster is a collection of many separate servers (computers), called nodes, which are connected via a fast interconnect. There may be different types of nodes for different types of tasks. Each of the HPC clusters listed on this site has
headnode or login node, where users log in
specialized data transfer node
regular compute nodes (where majority of computations is run)
“fat” compute nodes that have at least 1TB of memory
GPU nodes (on these nodes computations can be run both on CPU cores and on a Graphical Processing Unit)
- an Infiniband switch to connect all nodes
All cluster nodes have the same components as a laptop or desktop: CPU cores, memory and disk space. The difference between personal computer and a cluster node is in quantity, quality and power of the components.
Users login from their computers to the cluster headnode using the ssh program.
HPC Cluster at OUAT
OUAT HPC Enviornment
OUAT HPC ENVIORNMENT
1. Master Node ( HPE DL380 Gen10 8SFF CTO Server) : 1 No
Processor :- 2 X Intel Xeon-G 6238
Memory :- 288 GB
HDD :- 2 X 480GB SATA MU SFF SC MV SSD (Approx. 450 GB
Usable Capacity)
Computing Capacity :- 2.9 TF
2. Compute Node ( HPE ProLiant XL170r) : 4 Nos
Processor :- 2 X XL1x0r Gen10 Xeon-G 6238
Memory :- 288 GB
HDD :- 2TB SATA 7.2K LFF LP DS HDD (Approx. 1.8 TB Usable
Capacity)
Computing Capacity :- 2.9 TF(HPL)
Total Computing Capacity :- 2.9 X 4 = 11.6 TFLOPS
3. GPU Node ( HPE DL380 Gen10 8SFF CTO Server) (AI ) : 1 No
Processor :- 2 X Intel Xeon-G 6238
Memory :- 288 GB
HDD :- 2TB SATA 7.2K SFF SC 512e DS HDD (Approx. 1.8 TB Usable
Capacity)
Graphics :- 2 X NVIDIA Tesla T4 16GB Module
Computing Capacity :- 8.1 TF
Total Computing Capacity :- 8.1 X 2 = 16.2 TFLOPS
4. OSS ( HPE DL360 Gen10 8SFF CTO Server) : 2 Nos
Processor :- 2 X Intel Xeon-G 6246
Memory :- 384 GB
HDD :- 2 X 600GB SAS 10K SFF SC DS HD (Approx. 540GB Usable
Capacity)
5. MDS ( HPE DL360 Gen10 8SFF CTO Server) : 2 Nos
Processor :- 2 X Intel Xeon-S 4215R
Memory :- 96 GB
HDD :- 2 X 600GB SAS 10K SFF SC DS HD (Approx. 540GB Usable
Capacity)
6. STORAGE Node ( HPE D8000 2 I_O Mod Density Enclosure) : 1 No
Storage Capacity :- 100 TB
Reserve Capacity : 200 TB
7. IB Switch ( Mellanox IB EDR v2 36p Switch) : 1 No
8. GIGABIT Ethernet Switch ( Aruba 2930F 24G 4SFP Switch) : 1 No
OUAT HPC INFRA SCHEMATIC DIAGRAM
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Linux Command for HPC
Here we will provide more details on commands needed to copy, move, see contents, edit and delete files (and directories). Note that a directory is a type of file that contains information about its contents, which may be a mixture of other directories (subdirectories) and ordinary files.
Most of the commands take different options and arguments. For example, earlier in this guide we used “cp” command with two arguments.
To get complete information about a command, you can use “man” command (“man” stands for manual). You can even use this command on itself: “man man” will provide information about man command. The “man” command will list only one page of the manual at a time. To navigate between pages, use PgDn, PgUp and arrow keys. Alternatively, you can use Space, ‘b’ and Enter keys. To search for a term, type ‘/’, term and hit Enter. E.g., to find examples in the manual for man command, type ‘/examples’ within the manual. The search is case-insensitive. To close manual, use ‘q’ key.
Some programs may not have a man page available, but they may have ‘–help’ option to list help information about the program/command. This information is usually shorter than the one in the manual. For example, issue “man –help” or “man -h” to get condensed information about arguments and options of the man command.
pwd and ls
The “pwd” command prints the full name (the full path) of current/working directory. By default, right after ssh-ing to a Linux machine you would find yourself in your home directory, usually /home/. ssh to a cluster, type “pwd” and see if it returns ‘/home/’, where is your ISU NetID.
The “ls” command lists directory contents. ls command can be used with many options and has one optional argument. If you issue “ls -a” command in your home directory, you should see several files listed, some of the names starting with a dot. Now try issuing “ls” command without any options. You may not see any files at all. The ‘-a’ option tells ls to display hidden files – those files, whose name start with a dot.
Issue again the “ls -a” command. The first two directories in the list should be ‘.’ and ‘..’. Every directory on a Linux machine will have those two directories. The ‘.’ directory means current directory and the ‘..’ directory means parent directory, e.g. the directory one level up, that contains the current directory. For example, for /home/abc directory ‘.’ will mean /home/abc and the ‘..’ will mean /home. With no arguments “ls” command prints contents of the current directory. To see contents of the parent directory, issue “ls ..”. You should see a list of users on the system. You may guess that “ls .” command will provide same output as the “ls” command. To see contents of the root directory, issue “ls /”.
‘-l’ option tells ls command to use a long listing format, providing additional information about directory contents. Issue “ls -la” in your home directory. For each file the following information will be listed: file type, file permissions, file owner, group associated with the file (group owner), size, last modification date. File permissions are shown as three triplets: for the file owner, for the group owner and for everyone else on the system. For more information about file permissions, refer to the man page of chmod command: “man chmod”.
You can also use “ls” command on a regular file (non-directory). Usually you will use it with ‘-l’ option to get file information.
mkdir and cd
To create new directory use “mkdir” command. For example, to create directory TMP in the current directory issue either “mkdir TMP” or “mkdir ./TMP”. It’s a good practice to organize files by creating directories and putting files inside of them instead of having all files in one directory. Try to avoid using spaces and other special characters (except “_”) in file names on Linux. While almost any character can be used in a file name, it’s more complicated to refer to such names in CLI commands. Now, that you’ve created directory TMP in the current directory, what output do you think you will get if you issue “ls -a TMP” command? Check yourself.
In a graphical desktop environment to go to a different directory (folder), you would just click on the directory name. In the CLI you will use “cd” command (which stands for “change directory”). To go to the newly created TMP directory, issue “cd TMP”. Issue “pwd” to verify that you’re now in the new directory.
“cd ..” command will take you one level up. “cd /” will change current directory to root directory, while “cd” with no arguments will take you to your home directory.
Sometimes you may need to change directory to somewhere else, and then go back to the directory you were in. In this case you can use “cd -“ command which is equivalent to “cd $OLDPWD”.
Creating, editing and displaying files
There are several ways to create new file. Since usually you would want to write something in the new file, you can just use one of the text editors available on the cluster.
If you don’t know how to use vi/vim, we recommend using nano, which is a small and friendly editor. If you’re used to emacs, it’s also installed on our clusters.
Whether to create a new file or edit an existing file in the current directory, issue “nano ” command, where is the name of the file you would like to create/edit. Within nano use PgDn, PgUp and arrow keys to move cursor to the different part of the file. Pressing Enter key will create new line. At the bottom of the editor window you will find the list of hot keys for various actions with ‘^’ meaning Ctrl key. For example, among the commands you will see:
That means that to exit editor, you need to press Ctrl-X. Read carefully the questions that editor will ask. For example, it may ask if you would like to save changes that you’ve made to the file before closing the editor.
If you don’t need to edit file and just want to see the contents, you can use one of the following commands: “cat”, “less”, “head”, “tail”.
“cat ” will print contents of the file on the screen. Usually you would use it on small files. For larger files it’s better to use “less” command which initially will print only the first page. As in the “man” command, to navigate between pages, use PgDn, PgUp and arrow keys. Alternatively, you can use Space, ‘b’ and Enter keys. To search for a term, type ‘/’ and hit Enter. To repeat the same search, type ‘/’ and press Enter. To exit “less” command, use ‘q’ key.
If you need to see only the first N lines of a file, use “head -N” command. If number of lines is not specified, 10 lines will be displayed. Similarly, “tail -N” command will display last N lines of the file. It’s useful to display the end of a log file that is being actively written to.
cp, mv, rm
“cp” command is used to copy files and directories. It requires at least two arguments.
To copy file file1 to a new file file2, issue “cp file1 file2” command. file2 will have the same contents as file1, but it will have new date stamp. Modifying one of the files will not affect the other file.
To copy file1 and file2 to a different directory, issue “cp file1 file2 ”. File /file1 will have the same contents as file1, and file /file2 will have the same contents as file2, but they will have new date stamps.
To copy directory dir1 with all the files and subdirectories to a different directory, issue “cp -r dir1 ”.
“mv” command is used to move or rename files and directories. It also requires at least two arguments.
- To rename file file1 to file2, issue “mv file1 file2” command. Note that after being renamed, file will still have old time stamp.
To move file1 and file2 to a different directory, issue “mv file1 file2 ”. To move directory dir1 with all the files and subdirectories to a different directory, issue “mv dir1 ”.
“rm” command is used to remove files and directories. It requires at least one argument. Be careful with this command so that you don’t delete files that you meant to keep. To remove directory dir1 with all the files and subdirectories, issue “rm -r dir1”.