en:hpc
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en:hpc [2022/07/04 08:36] – [Batch Processing of Tasks (SLURM)] grikiete | en:hpc [2022/07/18 15:00] – [The Links] grikiete | ||
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- | Jame kaip specialūs komentarai yra nurodymai užduočių vykdytojui. | + | It contains instructions for the task performer as special |
- | -p short - į kokią eilę siųsti | + | -p short - which queue to send to (main, gpu, power). |
- | -n4 - kiek procesorių rezervuoti | + | -n4 - how many processors to reserve |
- | Užduoties pradinis einamasis katalogas yra dabartinis katalogas | + | The initial running directory of the task is the current directory |
- | Suformuotą scenarijų siunčiame su komanda | + | The generated script is sent with the command //sbatch//, |
'' | '' | ||
- | kuri gražina pateiktos užduoties numerį | + | which returns the number of the submitted job **JOBID**. |
- | Laukiančios arba vykdomos užduoties būseną galima sužinoti su komanda | + | The status of a pending or ongoing task can be checked with the command //squeue// |
'' | '' | ||
- | Su komanda | + | With the //scancel// command it is possible to cancel the running of a task or to remove it from the queue |
'' | '' | ||
- | Jeigu neatsimenate savo užduočių | + | If you forgot your tasks **JOBID**, |
'' | '' | ||
- | Užbaigtų užduočių | + | Completed tasks are no longer displayed in **squeue**. |
- | Jeigu nurodytas procesorių kiekis nėra pasiekiamas, tai jūsų užduotis yra įterpiama į eilę. Joje ji bus kol atsilaisvins pakankamas kiekis procesorių arba kol jūs ją pašalinsite su **scancel**. | + | If the specified number of processors is not available, your task is added to the queue. It will remain in the queue until a sufficient number of processors become available or until you remove it with **scancel**. |
- | Vykdomos užduoties išvestis (**output**) yra įrašoma į failą | + | The **output** |
- | Daugiau apie SLURM galimybes galite paskaityti | + | More about SLURM opportunities you can read [[https:// |
+ | ====== Interactive Tasks (SLURM) ====== | ||
+ | |||
+ | Interactive tasks can be done with the //srun// command: | ||
+ | |||
+ | < | ||
+ | $ srun --pty $SHELL | ||
+ | </ | ||
+ | |||
+ | The above command will connect you to the compute node environment assigned to SLURM and allow you to directly run and debug programs on it. | ||
+ | |||
+ | After the commands are done disconnect from the compute node with the command | ||
+ | |||
+ | < | ||
+ | $ exit | ||
+ | </ | ||
+ | |||
+ | If you want to run graphical programs, you need to connect to **ssh -X** to **uosis.mif.vu.lt** and **hpc**: | ||
+ | |||
+ | < | ||
+ | $ ssh -X uosis.mif.vu.lt | ||
+ | $ ssh -X hpc | ||
+ | $ srun --pty $SHELL | ||
+ | </ | ||
+ | |||
+ | In **power** cluster interactive tasks can be performed with | ||
+ | |||
+ | < | ||
+ | $ srun -p power --mpi=none --pty $SHELL | ||
+ | </ | ||
+ | |||
+ | ====== GPU Tasks (SLURM) ====== | ||
+ | |||
+ | To use GPU you need to specify additionally < | ||
+ | |||
+ | With '' | ||
+ | |||
+ | Example of an interactive task with 1 GPU: | ||
+ | < | ||
+ | $ srun -p gpu --gres gpu --pty $SHELL | ||
+ | </ | ||
+ | |||
+ | ====== Introduction to OpenMPI ====== | ||
+ | |||
+ | Ubuntu 18.04 LTS is the packet of **2.1.1** OpenMPI version. | ||
+ | To use the newer version **4.0.1** you need to use | ||
+ | < | ||
+ | module load openmpi/4.0 | ||
+ | </ | ||
+ | before running MPI commands. | ||
+ | |||
+ | ===== MPI Compiling Programs ===== | ||
+ | |||
+ | An example of a simple MPI program is in the directory ''/ | ||
+ | |||
+ | < | ||
+ | $ mpicc -o foo foo.c | ||
+ | $ mpif77 -o foo foo.f | ||
+ | $ mpif90 -o foo foo.f | ||
+ | </ | ||
+ | ===== Implementation of MPI Programmes ===== | ||
+ | |||
+ | MPI programs are started with **mpirun** or **mpiexec**. You can learn more about them with the **man mpirun** or **man mpiexec** command. | ||
+ | |||
+ | A simple (SPMD) program can be started with the following mpirun command line. | ||
+ | |||
+ | < | ||
+ | $ mpirun foo | ||
+ | </ | ||
+ | |||
+ | 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. | ||
+ | |||
+ | Find more information on [[https:// | ||
+ | |||
+ | ====== Task Efficiency ====== | ||
+ | |||
+ | * Please use at least 50% of the ordered CPU quantity. | ||
+ | * Using more CPUs than ordered will not improve performance, | ||
+ | * If you use the '' | ||
+ | |||
+ | ====== The Limits of Resources ====== | ||
+ | |||
+ | If your tasks don't start because of **AssocGrpCPUMinutesLimit** or **AssocGrpGRESMinutes**, | ||
+ | |||
+ | //The first way to see how much resources are used:// | ||
+ | |||
+ | < | ||
+ | sreport -T cpu, | ||
+ | </ | ||
+ | |||
+ | Where the **USERNAME** - is your MIF user name. **Start** and **End** show the start and end days of the current month. You can specify them also by '' | ||
+ | |||
+ | **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:// | ||
+ | |||
+ | < | ||
+ | sshare -l -A USERNAME_mif -p -o GrpTRESRaw, | ||
+ | </ | ||
+ | |||
+ | 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** - 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:// | ||
+ | * [[https:// | ||
+ | * [[https:// | ||
+ | * [[http:// | ||
+ | * [[pagalba@mif.vu.lt]] - registration of the **HPC** problems. | ||
en/hpc.txt · Last modified: 2024/02/21 12:50 by rolnas