Commit c1598434 authored by David Hrbáč's avatar David Hrbáč

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......@@ -30,7 +30,9 @@ fi
In order to configure your shell for running particular application on clusters we use Module package interface.
Application modules on clusters are built using [EasyBuild](software/tools/easybuild/). The modules are divided into the following structure:
Application modules on clusters are built using [EasyBuild][1]. The modules are divided into the following structure:
[1]: software/tools/easybuild.md
```
base: Default module class
......@@ -61,4 +63,6 @@ Application modules on clusters are built using [EasyBuild](software/tools/easyb
!!! note
The modules set up the application paths, library paths and environment variables for running particular application.
The modules may be loaded, unloaded and switched, according to momentary needs. For details see [here](software/modules/lmod/).
The modules may be loaded, unloaded and switched, according to momentary needs. For details see [lmod][2].
[2]: software/modules/lmod.md
# Documentation
Welcome to the IT4Innovations documentation pages. The IT4Innovations national supercomputing center operates the supercomputers [Salomon](salomon/introduction.md) and [Anselm](anselm/introduction.md). The supercomputers are [available](general/applying-for-resources.md) to the academic community within the Czech Republic and Europe, and the industrial community worldwide. The purpose of these pages is to provide comprehensive documentation of the hardware, software and usage of the computers.
Welcome to the IT4Innovations documentation pages. The IT4Innovations national supercomputing center operates the supercomputers [Salomon][1] and [Anselm][2]. The supercomputers are [available][3] to the academic community within the Czech Republic and Europe, and the industrial community worldwide. The purpose of these pages is to provide comprehensive documentation of the hardware, software and usage of the computers.
[1]: salomon/introduction.md
[2]: anselm/introduction.md
[3]: general/applying-for-resources.md
## How to Read the Documentation
......@@ -31,7 +35,7 @@ In many cases, you will run your own code on the cluster. In order to fully expl
* **node:** a computer, interconnected via a network to other computers - Computational nodes are powerful computers, designed for, and dedicated to executing demanding scientific computations.
* **core:** a processor core, a unit of processor, executing computations
* **core-hour:** also normalized core-hour, NCH. A metric of computer utilization, [see definition](salomon/resources-allocation-policy.md#normalized-core-hours-nch).
* **core-hour:** also normalized core-hour, NCH. A metric of computer utilization, [see definition][4].
* **job:** a calculation running on the supercomputer - the job allocates and utilizes the resources of the supercomputer for certain time.
* **HPC:** High Performance Computing
* **HPC (computational) resources:** corehours, storage capacity, software licences
......@@ -41,6 +45,8 @@ In many cases, you will run your own code on the cluster. In order to fully expl
* **project:** a computational project under investigation by the PI - the project is identified by the project ID. Computational resources are allocated and charged per project.
* **jobscript:** a script to be executed by the PBS Professional workload manager
[4]: salomon/resources-allocation-policy.md#normalized-core-hours-nch
## Conventions
In this documentation, you will find a number of pages containing examples. We use the following conventions:
......
......@@ -24,7 +24,8 @@ Install development packages (gcc, g++, make, automake, autoconf, bison, flex, p
$ qsub ... -l mic_devel=true
```
Available on Salomon Perrin nodes.
!!! Warning
Available on Salomon Perrin nodes.
## Global RAM Disk
......@@ -34,7 +35,8 @@ Create global shared file system consisting of RAM disks of allocated nodes. Fil
$ qsub ... -l global_ramdisk=true
```
Available on Salomon nodes.
!!! Warning
Available on Salomon nodes only.
## Virtualization Network
......@@ -44,7 +46,9 @@ Configure network for virtualization, create interconnect for fast communication
$ qsub ... -l virt_network=true
```
[See Tap Interconnect](software/tools/virtualization/#tap-interconnect)
[See Tap Interconnect][1]
[1]: software/tools/virtualization.md#tap-interconnect
## x86 Adapt Support
......@@ -54,9 +58,11 @@ Load kernel module, that allows changing/toggling system parameters stored in MS
$ qsub ... -l x86_adapt=true
```
Hazardous, it causes CPU frequency disruption.
!!! Danger
Hazardous, it causes CPU frequency disruption.
Available on Salomon nodes.
!!! Warning
Available on Salomon nodes only.
## Disabling Intel Turbo Boost on CPU
......@@ -70,7 +76,8 @@ $ qsub ... -l cpu_turbo_boost=false
## Offlining CPU Cores
Not available.
!!! Info
Not available now.
To offline N CPU cores
......@@ -86,16 +93,16 @@ $ qsub ... -l cpu_offline_cores=PATTERN
where pattern is list of core's numbers to offline separated by character 'c' e.g. "5c11c16c23c"
Hazardous, it causes Lustre threads disruption.
!!! Danger
Hazardous, it causes Lustre threads disruption.
## Setting Intel Hyper Threading on CPU
Not available, requires changed BIOS settings.
Intel Hyper Threading is disabled by default.
To enable Intel Hyper Threading on allocated nodes CPUs
Intel Hyper Threading is disabled by default. To enable Intel Hyper Threading on allocated nodes CPUs:
```console
$ qsub ... -l cpu_hyper_threading=true
```
!!! Warning
Available on Salomon nodes only.
* ![pdf](img/pdf.png)[PBS Pro Programmer's Guide](http://www.pbsworks.com/pdfs/PBSProgramGuide13.0.pdf)
* ![pdf](img/pdf.png)[PBS Pro Quick Start Guide](http://www.pbsworks.com/pdfs/PBSQuickStartGuide13.0.pdf)
* ![pdf](img/pdf.png)[PBS Pro Reference Guide](http://www.pbsworks.com/pdfs/PBSReferenceGuide13.0.pdf)
* ![pdf](img/pdf.png)[PBS Pro User's Guide](http://www.pbsworks.com/pdfs/PBSUserGuide13.0.pdf)
* ![pdf](img/pdf.png)[PBS Pro Programmer's Guide][1]
* ![pdf](img/pdf.png)[PBS Pro Quick Start Guide][2]
* ![pdf](img/pdf.png)[PBS Pro Reference Guide][3]
* ![pdf](img/pdf.png)[PBS Pro User's Guide][4]
[1]: http://www.pbsworks.com/pdfs/PBSProgramGuide13.0.pdf
[2]: http://www.pbsworks.com/pdfs/PBSQuickStartGuide13.0.pdf
[3]: http://www.pbsworks.com/pdfs/PBSReferenceGuide13.0.pdf
[4]: http://www.pbsworks.com/pdfs/PBSUserGuide13.0.pdf
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