Differences

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

--- en:hpc [2022/09/12 14:59] – [Registration] grikiete
+++ en:hpc [2025/03/31 12:36] (current) – [Registration] mif28585
@@ Line 16: / Line 16: @@
 ====== 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.
+In **main** and **gpu** partitions there are installed [[https://docs.qlustar.com/Qlustar/11.0/HPCstack/hpc-user-manual.html|Qlustar 12]] OS. It is based on Ubuntu 20.04 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).
+===== Singularity =====
 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.
@@ Line 29: / Line 31: @@
 $ rm -rf /tmp/python
 </code>
+To use this container, it is advised to use different directory instead of home directory (for python packages don't mixup with installed to home directory).
+<code shell>
+$ mkdir ~/workdir
+$ singularity exec -H ~/workdir:$HOME python.sif python3 ...
+</code>
 Similarly, you can use R, Julia or other containers that do not require root privileges to install packages.
@@ Line 42: / Line 52: @@
 $ rm -rf /tmp/python
 </code>
+===== Hadoop =====
 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''.
+===== JupyterHub =====
 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:
@@ Line 60: / Line 74: @@
 ====== Registration ======
-  * **For VU MIF network users** - HPC can be used without additional registration if the available resources are enough (monthly limit - **500 CPU-h and 60 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]].
+  * **For VU MIF network users** - HPC can be used without additional registration if the available resources are enough (monthly limit - **1000 CPU-h and 100 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]].
   * **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]].
@@ Line 77: / Line 91: @@
 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]]**
+  * If you don't have SSH keys, you can find instructions on how to create them in a Windows environment **[[en: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.