IT wiki

VU MIF STSC

User Tools

Site Tools


en:hpc

Differences

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

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision
Previous revision
en:hpc [2022/07/18 09:43] – [Užduočių efektyvumas] grikieteen:hpc [2024/02/21 12:50] (current) – [Singularity] rolnas
Line 16: Line 16:
 ====== 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.
Line 29: Line 31:
 $ 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.
  
Line 42: Line 52:
 $ 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:
Line 60: Line 74:
 ====== 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 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 - **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 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]].
Line 77: Line 91:
  
 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.
Line 236: Line 250:
 </code> </code>
  
-All allocated processors will be used according to the number ordered. If you want to use less, you can specify the -np quantity parameter in mpirun. It is not recommended to use less CPU than reserved for a longer time period, as unused CPUs remain free.+All allocated processors will be used according to the number ordered. If you want to use less, you can specify the -np quantity parameter in **mpirun**. It is not recommended to use less CPU than reserved for a longer time period, as unused CPUs remain free.
  
 **ATTENTION** It is strictly forbidden to use more CPU than you have reserved, as this may affect the performance of other tasks. **ATTENTION** It is strictly forbidden to use more CPU than you have reserved, as this may affect the performance of other tasks.
Line 248: Line 262:
   * If you use the ''--mem=X'' parameter, the task can reserve more **CPUs** in proportion to the amount of memory it wants. For example: if you order ''--mem=14000'' in the **main** queue, at least 2 CPUs will be reserved, unless other parameters specify more. If your task uses less than this, it will be an ineffective use of resources. In addition, it may run slower because it may use other memory than the executing CPU.   * If you use the ''--mem=X'' parameter, the task can reserve more **CPUs** in proportion to the amount of memory it wants. For example: if you order ''--mem=14000'' in the **main** queue, at least 2 CPUs will be reserved, unless other parameters specify more. If your task uses less than this, it will be an ineffective use of resources. In addition, it may run slower because it may use other memory than the executing CPU.
  
-====== Resursų limitai ======+====== The Limits of Resources ======
  
-Jeigu jūsų užduotys nestartuoja su priežastimi **AssocGrpCPUMinutesLimit** arba **AssocGrpGRESMinutes**, +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.
- tai pasitikrinkite ar užduotims dar liko neišnaudotų CPU/GPU resursų iš (mėnesio) limito.+
  
-Peržiūrėti kiek išnaudota resursų+//The first way to see how much resources are used://
  
 <code> <code>
Line 259: Line 272:
 </code> </code>
  
-kur **USERNAME** jūsų MIF naudotojo vardas, o **Start** ir **End** nurodo einamojo mėnesio pradžios ir pabaigos datasJas galima nurodyti ir kaip ''$(date +%m01)'' ir ''$(date +%m31)'', kas nurodo einamojo mėnesio pirmą ir paskutines dienas.+Where the **USERNAME** - is your MIF user name. **Start** and **End** show the start and end days of the current monthYou can specify them also by ''$(date +%m01)'' and ''$(date +%m31)''.
  
-Atkreipkite dėmesįkad naudojimas pateikiamas minutėmis, o į valandas konvertuoti reikia dalinant iš 60.+**NOTE** Usage of resources is given in minutesdivide the number by 60 to get hours.
  
-Kitas būdas pažiūrėti limitus ir jų išnaudojimą+//The second way to see how much resources are used://
  
 <code> <code>
Line 269: Line 282:
 </code> </code>
  
-kur **USERNAME** MIF naudotojo vardasArba parametre **-A** nurodyti tą sąskaitą (account), kurio naudojimą norima pažiūrėti. Duomenys pateikiami minutėmis. **GrpTRESRaw** - kiek išnaudota. **GrpTRESMins** - koks yra limitas. **TRESRunMins** - likę resursai dar vis vykdomų užduočių.+Where **USERNAME** is your MIF user nameOr specify the account whose usage you want to see in **-A**. The data is also displayed in minutes:  
 +  * **GrpTRESRaw** - how much is used 
 +  * **GrpTRESMins** - what is the limit 
 +  * **GGRTRESRunMins** - the remaining resources for tasks that are still running. 
 + 
 +====== The Links ======
  
 +  * [[waldur|HPC Waldur portal description]]
 +  * [[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.
  
  
en/hpc.1658137420.txt.gz · Last modified: 2022/07/18 09:43 by grikiete

Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki