Differences

This shows you the differences between two versions of the page.

--- en:hpc [2022/04/15 06:28] – grikiete
+++ en:hpc [2022/07/04 08:09] – grikiete
@@ Line 1: / Line 1: @@
 ====== Description of the Equipment ======
-A Distributed Computing Network (DCN) is a specially designed network of computers capable of running applications that can exchange data efficiently.
+A High Performance Computing (HPC) is a specially designed network of computers capable of running applications that can exchange data efficiently.
-VU MIF PST consists of a supercomputer from the clusters (the first number is the actual and available amount):
+VU MIF HPC consists of a supercomputer from the clusters (the first number is the actual and available amount):
 ^Title ^Nodes ^CPU ^GPU ^RAM        ^HDD    ^Network ^Notes|
@@ Line 22: / Line 22: @@
 With the command [[https://sylabs.io/guides/3.2/user-guide/index.html|singularity]] it is possible to make use of ready-made copies of container files in directories ''/apps/local/hpc'', ''/apps/local/nvidia'', ''/apps/local/intel'', ''/apps/local/lang'' or to download from singularity and docker online repositories. You can also create your own singularity containers using the MIF cloud service.
-With singularity you can prepare your container, for example:
+You can prepare your container with singularity, for example:
 <code shell>
 $ singularity build --sandbox /tmp/python docker://python:3.8
@@ Line 45: / Line 45: @@
 There are ready-made scripts to run your **hadoop** tasks using the [[https://github.com/LLNL/magpie|Magpie]] set in the directory ''/apps/local/bigdata''.
-With [[https://hpc.mif.vu.lt/hub/|JupyterHub]] you can run calculations with the python command line in a web browser and use the [[https://jupyter.org|JupyterLab]] environment. If you install your own JupyterLab environment in your home directory, you need to install the additional ''batchspawner'' package - this will start your environment, example:
+With [[https://hpc.mif.vu.lt/hub/|JupyterHub]] you can run calculations with the python command line in a web browser and use the [[https://jupyter.org|JupyterLab]] environment. If you install your own JupyterLab environment in your home directory, you need to install the additional ''batchspawner'' package - this will start your environment, for example:
 <code shell>
@@ Line 60: / Line 60: @@
 ====== Registration ======
-The PST can only be used by registered users of the VU MIF computer network. Existing **VU MIF network users** can use PST without **additional registration**.
+  * **For VU MIF network users** - HPC can be used without additional registration if the available resources are enough (monthly limit - **100 CPU-h and 6 GPU-h**). Once this limit has been reached, you can request more by filling in [[https://forms.office.com/Pages/ResponsePage.aspx?id=ghrFgo1UykO8-b9LfrHQEidLsh79nRJAvOP_wV9sgmdUM0ZMR1FINFg3TzVaNlhDSEhUN1A3QTlVUC4u|ITOAC service request form]].
-Registracijai reikia užpildyti [[http://mif.vu.lt/itapc#paslaug%C5%B3-u%C5%BEsakymas|ITAPC paslaugų užsakymo formą]] ir pateikti ten nurodytu adresu. Paraišką patenkinus, suteikiamas VU MIF kompiuterių tinklo naudotojo vardas. Jei esate VU darbuotojas ar studentas ir registracijos metu nurodėte savo VU el. pašto adresą. Tada įvesti savo pradinį slaptažodį, galite per [[https://mif.vu.lt/passwd2|pamiršto slaptažodžio]] pakeitimo procedūrą, naudodami [[https://id.vu.lt|VU E.tapatybės]] duomenis. Kitu atveju teks atvykti į VU MIF Didlaukio g. 47, 302/304 kab. darbo metu, dėl tikslaus laiko galite pasitikslinti tel. 8 5219 5005 arba 8 5219 5006.
+  * **For users of the VU computer network** - you must fill in the [[https://forms.office.com/Pages/ResponsePage.aspx?id=ghrFgo1UykO8-b9LfrHQEidLsh79nRJAvOP_wV9sgmdUM0ZMR1FINFg3TzVaNlhDSEhUN1A3QTlVUC4u|ITOAC service request form]] to get access to MIF HPC. After the confirmation of your request, you must create your account in [[https://hpc.mif.vu.lt|Waldur portal]]. More details read [[waldur|here]].
+  * **For other users (non-members of the VU community)** - you must fill in the [[https://forms.office.com/Pages/ResponsePage.aspx?id=ghrFgo1UykO8-b9LfrHQEidLsh79nRJAvOP_wV9sgmdUMDE1QUo3Slo3UVYwTjM4TDMyTEdZT0tSNi4u|ITOAC service request form]] to get access to MIF HPC. After the confirmation of your request, you must come to VU MIF Didlaukio str. 47, Room 302/304 to receive your login credentials. Please arranged the exact time by phone + 370 5219 5005. With these credentials you are able to create an account in [[https://hpc.mif.vu.lt|Waldur portal]]. More details read [[waldur|here]].
+====== Connection ======
+You need to use SSH applications (ssh, putty, winscp, mobaxterm) and Kerberos or SSH key authentication to connect to **HPC**.
+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 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).
+If **SSH keys** are used (e.g. if you need to copy big files):
+  * If you don't have SSH keys, you can find instructions on how to create them in a Windows environment **[[duk:ssh_key|here]]**
+  *     Before you can use this method, you need to log in with Kerberos at least once. Then create a ''~/.ssh'' directory in the HPC file system and put your **ssh public key** (in OpenSSH format) into the ''~/.ssh/authorized_keys'' file.
+  *     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 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.
+====== PST eilės (partition) ======
+^Eilė (partition) ^Laiko limitas ^RAM	   ^Pastabos|
+^main             ^7d            ^7000MB  ^CPU telkinys|
+^gpu              ^48h           ^12000MB ^GPU telkinys|
+^power            ^48h           ^2000MB  ^IBM Power9 telkinys|
+Visose eilėse užduotims laiko limitas yra **2h**, jei jis nebuvo nurodytas, o lentelėje yra pateiktas maksimalus leidžiamas laiko limitas.
+**RAM** stulpelyje yra pateikiamas kiekvienam rezervuotam **CPU** branduoliui skiriamas RAM kiekis.
-Su suteiktu (pasirinktu) naudotojo vardu ir savo įvestu slaptažodžiu įgyjama teisė jungtis prie serverio **uosis.mif.vu.lt**, VU MIF mokymo klasių ir dalies VU MIF darbo vietų kompiuterių.
-Adresu [[https://hpc.mif.vu.lt|Waldur]] yra savitarnos portalas, kur su savo universiteto (per **eduGAIN** arba **LITNET**) prisijungimu galima pačiam susikurti **HPC** prisijungimą. Daugiau info apie tai [[waldur|čia]].