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en:hpc [2022/07/18 12:18] – [The Limits of Resources] grikieteen:hpc [2025/03/31 12:36] (current) – [Registration] mif28585
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 ====== Software ====== ====== 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). 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. 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.
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 $ rm -rf /tmp/python $ rm -rf /tmp/python
 </code> </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. Similarly, you can use R, Julia or other containers that do not require root privileges to install packages.
  
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 $ rm -rf /tmp/python $ rm -rf /tmp/python
 </code> </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''. 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: 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:
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 ====== Registration ====== ====== 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]].   * **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]].
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 If **SSH keys** are used (e.g. if you need to copy big files): 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.   *     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.   *     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.
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 If your tasks don't start because of **AssocGrpCPUMinutesLimit** or **AssocGrpGRESMinutes**, you need to check if there are any unused CPU/GPU resources left from your monthly limit. If your tasks don't start because of **AssocGrpCPUMinutesLimit** or **AssocGrpGRESMinutes**, you need to check if there are any unused CPU/GPU resources left from your monthly limit.
  
-**The first way to see how much resources are used:**+//The first way to see how much resources are used://
  
 <code> <code>
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 **NOTE** Usage of resources is given in minutes, divide the number by 60 to get hours. **NOTE** Usage of resources is given in minutes, divide the number by 60 to get hours.
  
-**The second way to see how much resources are used:**+//The second way to see how much resources are used://
  
 <code> <code>
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 </code> </code>
  
-Where **USERNAME** is your MIF user name. Arba parametre **-A** nurodyti tą paskyrą, kurios naudojimą reikia pažiūrėti. Duomenys yra pateikiami taip pat minutėmis:  +Where **USERNAME** is your MIF user name. Or specify the account whose usage you want to see in **-A**. The data is also displayed in minutes:  
-  * **GrpTRESRaw** - kiek išnaudota.  +  * **GrpTRESRaw** - how much is used.  
-  * **GrpTRESMins** - koks yra limitas.  +  * **GrpTRESMins** - what is the limit.  
-  * **TRESRunMins** - likę resursai dar vis vykdomų užduočių.+  * **GGRTRESRunMins** - the remaining resources for tasks that are still running.
  
-====== Nuorodos ======+====== The Links ======
  
-  * [[waldur|HPC Waldur portalo aprašymas]] +  * [[waldur|HPC Waldur portal description]] 
-  * [[http://mif.vu.lt/itapc#paslaug%C5%B3-u%C5%BEsakymas|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://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)]]   * [[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 standartas]] +  * [[http://www.mcs.anl.gov/research/projects/mpi/|MPI standart]] 
-  * pagalba@mif.vu.lt - problemų su **HPC** registracija+  * [[pagalba@mif.vu.lt]] - registration of the **HPC** problems.
  
  
en/hpc.1658146726.txt.gz · Last modified: 2022/07/18 12:18 by grikiete
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