Differences

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--- en:hpc [2022/04/20 07:06] – [Login] grikiete
+++ en:hpc [2022/07/04 09:48] – [Batch Processing of Tasks (SLURM)] grikiete
@@ Line 72: / Line 72: @@
 If **Kerberos** is used:
-  * Log in to the Linux environment in a VU MIF classroom or public terminal with your VU MIF username and password;
+  * Log in to the Linux environment in a VU MIF classroom or public terminal with your VU MIF username and password or login to **uosis.mif.vu.lt** with your VU MIF username and password using **ssh** or **putty**.
-  * or login to **uosis.mif.vu.lt** with your VU MIF username and password using ssh or putty.
   * Check if you have a valid Kerberos key (ticket) with the **klist** command. If the key is not available or has expired, the **kinit** command must be used.
   * Connect to the **hpc** node with the command **ssh hpc** (password must not be required).
-  * The **first time** you log in, you must wait **5 minutes** and then you can start to use HPC.
 If **SSH keys** are used (e.g. if you need to copy big files):
@@ Line 83: / Line 81: @@
   *     Connect with **ssh**, **sftp**, **scp**, **putty**, **winscp** or any other **ssh** protocol supported software to **hpc.mif.vu.lt** with your **ssh private key**, specifying your VU MIF user name. It should not require a login password, but may require your ssh private key password.
-The first time you connect, you **will not** be able to run **SLURM tasks** for the first **5 minutes**. After that, you will be automatically created as a **SLURM user** and assigned **resource limits**.
+The **first time** you connect, you **will not** be able to run **SLURM jobs** for the first **5 minutes**. After that, SLURM account will be created.
+====== Lustre - Shared File System ======
+VU MIF HPC shared file system is available in the directory ''/scratch/lustre''.
+The system creates directory ''/scratch/lustre/home/username'' for each HPC user, where **username** is the HPC username.
+The files in this file system are equally accessible on all compute nodes and on the **hpc** node.
+Please use these directories only for their purpose and clean them up after calculations.
+====== HPC Partition ======
+^Partition ^Time limit ^RAM	   ^Notes|
+^main             ^7d            ^7000MB  ^CPU cluster|
+^gpu              ^48h           ^12000MB ^GPU cluster|
+^power            ^48h           ^2000MB  ^IBM Power9 cluster|
+The time limit for tasks is **2h** in all partitions if it has not been specified. The table shows the maximum time limit.
+The **RAM** column gives the amount of RAM allocated to each reserved **CPU** core.
+====== Batch Processing of Tasks (SLURM) ======
+To use computing resources of the HPC, you need to create task scenarios (sh or csh).
+Example:
+<code shell mpi-test-job.sh>
+#!/bin/bash
+#SBATCH -p main
+#SBATCH -n4
+module load openmpi
+mpicc -o mpi-test mpi-test.c
+mpirun mpi-test
+</code>
+After submission and confirmation of your application to the ITOAC services, you need to create a user at https://hpc.mif.vu.lt/. The created user will be included in the relevant project, which will have a certain amount of resources. In order to use the project resources for calculations, you need to provide your allocation number. Below is an example with the allocation parameter "alloc_xxxx_project" (not applicable for VU MIF users, VU MIF users do not have to specify the --account parameter).
+<code shell mpi-test-job.sh>
+#!/bin/bash
+#SBATCH --account=alloc_xxxx_projektas
+#SBATCH -p main
+#SBATCH -n4
+#SBATCH --time=minutes
+module load openmpi
+mpicc -o mpi-test mpi-test.c
+mpirun mpi-test
+</code>
+It contains instructions for the task performer as special comments.
+ -p short - which queue to send to (main, gpu, power).
+ -n4 - how many processors to reserve (**NOTE:** if you set the number of cores to be used to x, but actually use fewer cores programmatically, the accounting will still count all the x "requested" cores, so we recommend to calculate this in advance).
+The initial running directory of the task is the current directory (**pwd**) on the login node from where the task is run, unless it was changed to another directory by the -D parameter. For the initial running directory, use the HPC shared filesystem directories **/scratch/lustre**, as it must exist on the compute node and the job output file **slurm-JOBID.out** is created there, unless redirected by -o or -i (for these it is advisable to use the shared filesystem as well).
+The generated script is sent with the command //sbatch//,
+''$ sbatch mpi-test-job''
+which returns the number of the submitted job **JOBID**.
+The status of a pending or ongoing task can be checked with the command //squeue//
+''$ squeue -j JOBID''
+With the //scancel// command it is possible to cancel the running of a task or to remove it from the queue
+''$ scancel JOBID''
+If you forgot your tasks **JOBID**, you can check them with the command //squeue//
+''$ squeue''
+Completed tasks are no longer displayed in **squeue**.
+If the specified number of processors is not available, your task is added to the queue. It will remain in the queue until a sufficient number of processors become available or until you remove it with **scancel**.
+The **output** of the running job is recorded in the file **slurm-JOBID.out**. The error output is written to the same file unless you specified somewhere else. The file names can be changed with the **sbatch** command parameters -o (specify the output file) and -e (specify the error file).
+More about SLURM opportunities you can read [[https://slurm.schedmd.com/quickstart.html|Quick Start User Guide]].