Differences

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--- en:hpc [2022/07/18 14:36] – [The Links] grikiete
+++ en:hpc [2026/01/22 12:24] (current) – [Software] mif28585
@@ Line 7: / Line 7: @@
 ^Title ^Nodes ^CPU ^GPU ^RAM        ^HDD    ^Network ^Notes|
 ^main        ^35/36  ^48  ^0   ^384GiB     ^0      ^1Gbit/s, 2x10Gbit/s, 4xEDR(100Gbit/s) infiniband ^[[https://ark.intel.com/content/www/us/en/ark/products/192447/intel-xeon-gold-6252-processor-35-75m-cache-2-10-ghz.html|CPU]]|
-^gpu         ^3/3    ^40  ^8   ^512GB/32GB  ^7TB   ^2x10Gbit/s, 4xEDR(100Gbit/s) infiniband ^[[https://ark.intel.com/content/www/us/en/ark/products/91753/intel-xeon-processor-e5-2698-v4-50m-cache-2-20-ghz.html|CPU]] [[https://en.wikipedia.org/wiki/Nvidia_DGX#DGX-1|NVIDIA DGX-1]]|
+^gpu         ^3/3    ^40  ^8xV100   ^512GB/32GB  ^7TB   ^2x10Gbit/s, 4xEDR(100Gbit/s) infiniband ^[[https://ark.intel.com/content/www/us/en/ark/products/91753/intel-xeon-processor-e5-2698-v4-50m-cache-2-20-ghz.html|CPU]] [[https://en.wikipedia.org/wiki/Nvidia_DGX#DGX-1|NVIDIA DGX-1]]|
 ^power       ^2/2    ^32  ^4   ^1024GB/32GB ^1.8TB ^2x10Gbit/s, 4xEDR(100Gbit/s) infiniband ^[[https://www.ibm.com/products/power-systems-ac922|IBM Power System AC922]]|
@@ 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/13/HPCstack/hpc-user-manual.html|Qlustar 13]] 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 - **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]].
+  * **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.
@@ Line 273: / Line 287: @@
   * **GGRTRESRunMins** - the remaining resources for tasks that are still running.
+**
+How are monthly limits assigned?**
+Once an application has been submitted to get more CPU or GPU hours, a decision is usually made within 5 business days. The monthly limit is increased on the day the decision is made in the current month, minus the limit already used up that month. For example, if a user who has used 100 GPU-h requests that the limits be increased to 600 GPU-h per month, they will be granted an additional 500 GPU-h for that month. The following month, the user will again have 600 GPU-h, so the unused balance from the previous month is not carried over to the following month.
 ====== The Links ======
   * [[waldur|HPC Waldur portal description]]
-  * [[https://mif.vu.lt/lt3/en/about/structure/it-research-center#ordering|ITAPC paslaugų užsakymas]]
+  * [[https://mif.vu.lt/lt3/en/about/structure/it-research-center#ordering|ITOAC service ordering]]
   * [[https://slurm.schedmd.com/quickstart.html|Quick Start User Guide (SLURM)]]
   * [[https://docs.qlustar.com/Qlustar/11.0/HPCstack/hpc-user-manual.html|HPC User Manual (Qlustar)]]
   * [[http://www.mcs.anl.gov/research/projects/mpi/|MPI standart]]
-  * pagalba@mif.vu.lt - registration of the **HPC** problems.
+  * [[pagalba@mif.vu.lt]] - registration of the **HPC** problems.