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--- en:hpc [2022/04/14 13:24] – grikiete
+++ en:hpc [2022/04/15 06:35] – grikiete
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 ====== 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 13: / Line 13: @@
 The processor below = CPU = core - a single core of the processor (with all hyperthreads if they are turned on).
+====== Software ======
+In **main** and **gpu** partitions there are installed [[https://docs.qlustar.com/Qlustar/11.0/HPCstack/hpc-user-manual.html|Qlustar 11]] OS. It is based on Ubuntu 18.04 LTS. In **power** partition there is installed Ubuntu 18.04 LTS.
+You can check the list of OS package with the command ''dpkg -l'' (in login node **hpc** or in **power** nodes).
+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.
+You can prepare your container with singularity, for example:
+<code shell>
+$ singularity build --sandbox /tmp/python docker://python:3.8
+$ singularity exec -w /tmp/python pip install package
+$ singularity build python.sif /tmp/python
+$ rm -rf /tmp/python
+</code>
+Similarly, you can use R, Julia or other containers that do not require root privileges to install packages.
+If you want to add OS packages to the singularity container, you need root/superuser privileges. With fakeroot, we simulate them, and copy the required library ''libfakeroot-sysv.so'' into the container, for example:
+<code shell>
+$ singularity build --sandbox /tmp/python docker://ubuntu:18.04
+$ cp /libfakeroot-sysv.so /tmp/python/
+$ fakeroot -l /libfakeroot-sysv.so singularity exec -w /tmp/python apt-get update
+$ fakeroot -l /libfakeroot-sysv.so singularity exec -w /tmp/python apt-get install python3.8 ...
+$ fakeroot -l /libfakeroot-sysv.so singularity exec -w /tmp/python apt-get clean
+$ rm -rf /tmp/python/libfakeroot-sysv.so /tmp/python/var/lib/apt/lists (you can clean up more of what you don't need)
+$ singularity build python.sif /tmp/python
+$ rm -rf /tmp/python
+</code>
+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, for example:
+<code shell>
+$ python3.7 -m pip install --upgrade pip setuptools wheel
+$ python3.7 -m pip install --ignore-installed batchspawner jupyterlab
+</code>
+Alternatively, you can use a container that you made via JupyterHub. In that container, you need to install the ''batchswapner'' and ''jupyterlab'' packages, and to create a script ''~/.local/bin/batchspawner-singleuser'' with execution permissions (''chmod +x ~/.local/bin/batchspawner-singleuser'').
+<code shell>
+#!/bin/sh
+exec singularity exec --nv myjupyterlab.sif batchspawner-singleuser "$@"
+</code>
+====== Registration ======
+The HPC can only be used by registered users of the VU MIF computer network. Existing **VU MIF network users** can use HPC without **additional registration**.
+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.
+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]].