quick:start
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quick:start [2019/07/31 08:34] ccrosby [Queues] |
quick:start [2026/06/11 11:17] (current) kevin [Logging in for the First Time] |
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| This guide is intended for experienced HPC users and provides a summary of the essential components of the systems available at the CHPC. For more detailed information on the subjects below see the full [[guide: | This guide is intended for experienced HPC users and provides a summary of the essential components of the systems available at the CHPC. For more detailed information on the subjects below see the full [[guide: | ||
| - | |||
| - | **NOTE: the new system is still under construction and information here and in the User Guide is incomplete and subject to sudden change.** | ||
| //docti cave// | //docti cave// | ||
| + | |||
| + | ==== Video tutorials for newcomers ==== | ||
| + | If you are a new user to the CHPC, please watch these videos: | ||
| + | * [[https:// | ||
| + | * [[https:// | ||
| + | * [[https:// | ||
| + | * [[https:// | ||
| + | |||
| + | ====Mailing List==== | ||
| + | |||
| + | The **[[https:// | ||
| =====Overview: | =====Overview: | ||
| - | The CHPC' | + | The CHPC's Dell Linux cluster |
| - | The new system is an homogeneous cluster, comprising Intel 5th generation CPUs. As of March 2017 it has 1368 compute nodes with 24 cores and 128 GiB* memory | + | The new system is an homogeneous cluster, comprising Intel 5th generation CPUs. As of May 2025 it has 41 nodes with 24 cores and 256 GiB memory, 784 compute nodes with 24 cores and 128 GiB* memory, 355 nodes with 24 cores and 64 GiB memory, and four large memory " |
| - | * Maximum available memory on each type of node: '' | + | * Maximum available memory on each type of node: '' |
| ====GPU nodes==== | ====GPU nodes==== | ||
| - | There are 9 compute nodes that contain a total of 24 Nvidia V100 GPUs. For more information see the [[guide: | + | There are 9 compute nodes that contain a total of 30 Nvidia V100 GPUs. For more information see the [[guide: |
| =====Logging in===== | =====Logging in===== | ||
| Line 29: | Line 38: | ||
| </ | </ | ||
| + | ====Logging in for the First Time==== | ||
| - | The new system is running CentOS 7.0 and uses the //Bash// shell by default. | + | :!: You will use a password only for the **first time** you log in using ssh. And the first step will be to set up your ssh key. After this, you **can only log in using ssh keys and your password will be disabled.** |
| - | You should change | + | Please read carefully and follow the procedure to set up your [[guide: |
| - | To change | + | |
| - | Rules are: 10 characters, with at least one of the following character types: upper and lower case, numbers, and special characters. | + | |
| + | ====Long Interactive Sessions==== | ||
| + | |||
| + | Once you have logged | ||
| + | |||
| + | The new system is running [[quick: | ||
| + | |||
| + | ====Trouble Logging in?==== | ||
| + | Many users have their login blocked at some point. Usually this is because an incorrect password was entered more times than permitted (5 times). This restriction was put in place to prevent brute-force attacks by malicious individuals who want to gain access to your account. | ||
| + | |||
| + | * If you cannot log in, the first step is to make sure that you typed your username, hostname (lengau.chpc.ac.za or scp.chpc.ac.za) and password | ||
| + | * Next, check that you are not experiencing a network problem. If you see a message along the lines of " | ||
| + | * If your network connection is fine, wait 30 minutes before attempting to log in again. After this period, | ||
| + | * If for some reason this does not work, you should go to your user page on users.chpc.ac.za. There is a link at that address, to the left, which allows you to change your password | ||
| + | * If even changing the password does not help, please contact our helpdesk, and ask for our assistance. | ||
| - | Once you have logged in, give some consideration to how you will be using your session on the login node. If you are going to spend a long time logged in, doing a variety of tasks, it is best to get yourself [[http:// | ||
| ==== Transferring Data ==== | ==== Transferring Data ==== | ||
| Line 62: | Line 85: | ||
| subdirectory of your scratch directory /// | subdirectory of your scratch directory /// | ||
| (where // | (where // | ||
| + | |||
| + | |||
| + | === Downloading files from other servers === | ||
| + | You may need to download data from a server at another site. Do not do this on ** //login2// **! Use ** // scp.chpc.ac.za// | ||
| + | |||
| + | < | ||
| + | wget http:// | ||
| + | </ | ||
| + | |||
| + | Very large files may be transferred more quickly by using a multi-threaded downloader. The easiest of these is **axel**, see [[https:// | ||
| + | |||
| + | < | ||
| + | module load chpc/ | ||
| + | axel -n 4 -a http:// | ||
| + | </ | ||
| + | |||
| + | |||
| [[guide: | [[guide: | ||
| Line 70: | Line 110: | ||
| ^ Mount point ^ File System ^ Size ^ Quota ^ Backup ^ Access | ^ Mount point ^ File System ^ Size ^ Quota ^ Backup ^ Access | ||
| - | | ''/ | + | | ''/ |
| - | | ''/ | + | | ''/ |
| - | | ''/ | + | | ''/ |
| - | | ''/ | + | | ''/ |
| - | | ''/ | + | |
| + | :!: **IMPORTANT NOTE:** Files older than 90 days on ''/ | ||
| + | |||
| + | **Note [1]** Unfortunately, | ||
| + | |||
| + | **Note [2]** Create a support ticket on Helpdesk if you would like to request | ||
| + | |||
| + | **Note [3]** Access to ''/ | ||
| + | |||
| + | It is essential that all files that your job script writes to be on Lustre, apart from scheduler errors you will lose performance because your home directory is on NFS which is not a parallel file system. It is also recommended that all files your jobs scripts reads, especially if large or read more than once, be on Lustre for the same reason. | ||
| + | It is usually okay to keep binaries and libraries on home since they are read once and loaded into RAM when your executable launches. But you may notice improved performance if they are also on Lustre. | ||
| ====Quotas==== | ====Quotas==== | ||
| Line 137: | Line 187: | ||
| The module command may be abbreviated and optionally be given a search term, eg.: | The module command may be abbreviated and optionally be given a search term, eg.: | ||
| module ava chpc/open | module ava chpc/open | ||
| + | Or, more flexibly, you can pipe stderr to grep, and search for a phrase, such as mpi: | ||
| + | module avail 2>&1 | grep mpi | ||
| To see a synopsis of a particular modulefile' | To see a synopsis of a particular modulefile' | ||
| module help < | module help < | ||
| Line 202: | Line 254: | ||
| ^ Queue Name ^ Max. cores ^ Min. cores ^ Max. jobs ^^ Max. time ^ Notes ^ Access | ^ Queue Name ^ Max. cores ^ Min. cores ^ Max. jobs ^^ Max. time ^ Notes ^ Access | ||
| ^ ::: ^ per job ^^ in queue ^ running | ^ ::: ^ per job ^^ in queue ^ running | ||
| - | | serial | + | | serial |
| - | | seriallong | + | | seriallong |
| | smp | 24 | 24 | 20 | 10 | 96 | For single-node parallel jobs. | | | | smp | 24 | 24 | 20 | 10 | 96 | For single-node parallel jobs. | | | ||
| - | ^ normal | + | ^ normal |
| - | | large | 2400 | 264 | 10 | 5 | | + | | large | 2400 | 264 | 10 | 5 | |
| + | | xlarge | ||
| | express | | express | ||
| | bigmem | | bigmem | ||
| | vis | 12 | 1 | 1 | 1 | 3 | Visualisation node | | | | vis | 12 | 1 | 1 | 1 | 3 | Visualisation node | | | ||
| | test | 24 | 1 | 1 | 1 | 3 | Normal nodes, for testing only | | | | test | 24 | 1 | 1 | 1 | 3 | Normal nodes, for testing only | | | ||
| + | | gpu_1 | 10 | 1 | | 2 | 12 | Up to 10 cpus, 1 GPU | | | ||
| + | | gpu_2 | 20 | 1 | | 2 | 12 | Up to 20 cpus, 2 GPUs | | | ||
| + | | gpu_3 | 36 | 1 | | 2 | 12 | Up to 36 cpus, 3 GPUs | | | ||
| + | | gpu_4 | 40 | 1 | | 2 | 12 | Up to 40 cpus, 4 GPUs | | | ||
| + | | gpu_long | 20 | 1 | | 1 | 24 | Up to 20 cpus, 1 or 2 GPUs | // | ||
| + | |||
| + | |||
| ===Notes: | ===Notes: | ||
| Line 294: | Line 354: | ||
| <code bash> | <code bash> | ||
| #!/bin/bash | #!/bin/bash | ||
| - | #PBS -l ncpus=24: | + | #PBS -l select=1:ncpus=24: |
| #PBS -P PRJT1234 | #PBS -P PRJT1234 | ||
| #PBS -q smp | #PBS -q smp | ||
| Line 301: | Line 361: | ||
| #PBS -e / | #PBS -e / | ||
| #PBS -m abe | #PBS -m abe | ||
| - | #PBS -M your.email@address | + | #PBS -M youremail@ddress |
| ulimit -s unlimited | ulimit -s unlimited | ||
| Line 327: | Line 387: | ||
| #PBS -e / | #PBS -e / | ||
| #PBS -m abe | #PBS -m abe | ||
| - | #PBS -M your.email@address | + | #PBS -M youremail@ddress |
| ulimit -s unlimited | ulimit -s unlimited | ||
| . / | . / | ||
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