From 2b3d6a0c1f1ec93827f9172a3c08f0fe890393de Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20Hrb=C3=A1=C4=8D?= <david@hrbac.cz>
Date: Wed, 31 Oct 2018 15:01:24 +0100
Subject: [PATCH] Links OK
---
docs.it4i/environment-and-modules.md | 3 +-
docs.it4i/index.md | 27 +++++++-----
docs.it4i/job-features.md | 4 +-
docs.it4i/prace.md | 62 +++++++++++++++-------------
4 files changed, 52 insertions(+), 44 deletions(-)
diff --git a/docs.it4i/environment-and-modules.md b/docs.it4i/environment-and-modules.md
index 31b4bfcb8..0c8c2a056 100644
--- a/docs.it4i/environment-and-modules.md
+++ b/docs.it4i/environment-and-modules.md
@@ -32,8 +32,6 @@ In order to configure your shell for running particular application on clusters
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
bio: Bioinformatics, biology and biomedical
@@ -65,4 +63,5 @@ Application modules on clusters are built using [EasyBuild][1]. The modules are
The modules may be loaded, unloaded and switched, according to momentary needs. For details see [lmod][2].
+[1]: software/tools/easybuild.md
[2]: software/modules/lmod.md
diff --git a/docs.it4i/index.md b/docs.it4i/index.md
index 748c56c3f..b018a997b 100644
--- a/docs.it4i/index.md
+++ b/docs.it4i/index.md
@@ -2,10 +2,6 @@
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
1. Read the list in the left column. Select the subject of interest. Alternatively, use the Search tool in the upper right corner.
@@ -15,21 +11,21 @@ Welcome to the IT4Innovations documentation pages. The IT4Innovations national s
## Getting Help and Support
!!! note
- Contact [support\[at\]it4i.cz](mailto:support@it4i.cz) for help and support regarding the cluster technology at IT4Innovations. Please use **Czech**, **Slovak** or **English** language for communication with us. Follow the status of your request to IT4Innovations at [support.it4i.cz/rt](http://support.it4i.cz/rt). The IT4Innovations support team will use best efforts to resolve requests within thirty days.
+ Contact [support\[at\]it4i.cz][a] for help and support regarding the cluster technology at IT4Innovations. Please use **Czech**, **Slovak** or **English** language for communication with us. Follow the status of your request to IT4Innovations at [support.it4i.cz/rt][b]. The IT4Innovations support team will use best efforts to resolve requests within thirty days.
-Use your IT4Innovations username and password to log in to the [support](http://support.it4i.cz/) portal.
+Use your IT4Innovations username and password to log in to the [support][b] portal.
## Required Proficiency
!!! note
You need basic proficiency in Linux environments.
-In order to use the system for your calculations, you need basic proficiency in Linux environments. To gain this proficiency we recommend you read the [introduction to Linux](http://www.tldp.org/LDP/intro-linux/html/) operating system environments, and install a Linux distribution on your personal computer. A good choice might be the [CentOS](http://www.centos.org/) distribution, as it is similar to systems on the clusters at IT4Innovations. It's easy to install and use. In fact, any Linux distribution would do.
+In order to use the system for your calculations, you need basic proficiency in Linux environments. To gain this proficiency we recommend you read the [introduction to Linux][c] operating system environments, and install a Linux distribution on your personal computer. A good choice might be the [CentOS][d] distribution, as it is similar to systems on the clusters at IT4Innovations. It's easy to install and use. In fact, any Linux distribution would do.
!!! note
Learn how to parallelize your code!
-In many cases, you will run your own code on the cluster. In order to fully exploit the cluster, you will need to carefully consider how to utilize all the cores available on the node and how to use multiple nodes at the same time. You need to **parallelize** your code. Proficieny in MPI, OpenMP, CUDA, UPC or GPI2 programming may be gained via [training provided by IT4Innovations.](http://prace.it4i.cz)
+In many cases, you will run your own code on the cluster. In order to fully exploit the cluster, you will need to carefully consider how to utilize all the cores available on the node and how to use multiple nodes at the same time. You need to **parallelize** your code. Proficieny in MPI, OpenMP, CUDA, UPC or GPI2 programming may be gained via [training provided by IT4Innovations][e].
## Terminology Frequently Used on These Pages
@@ -45,8 +41,6 @@ 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:
@@ -66,8 +60,19 @@ local $
## Errors
Although we have taken every care to ensure the accuracy of the content, mistakes do happen.
-If you find an inconsistency or error, report it by visiting [http://support.it4i.cz/rt](http://support.it4i.cz/rt), creating a new ticket, and entering the details.
+If you find an inconsistency or error, report it by visiting [support][b], creating a new ticket, and entering the details.
By doing so, you can save other readers from frustration and help us improve.
!!! tip
We will fix the problem as soon as possible.
+
+[1]: salomon/introduction.md
+[2]: anselm/introduction.md
+[3]: general/applying-for-resources.md
+[4]: salomon/resources-allocation-policy.md#normalized-core-hours-nch
+
+[a]: mailto:support@it4i.cz
+[b]: http://support.it4i.cz/rt
+[c]: http://www.tldp.org/LDP/intro-linux/html/
+[d]: http://www.centos.org/
+[e]: http://prace.it4i.cz
diff --git a/docs.it4i/job-features.md b/docs.it4i/job-features.md
index 82b452df1..904a555f7 100644
--- a/docs.it4i/job-features.md
+++ b/docs.it4i/job-features.md
@@ -48,8 +48,6 @@ $ qsub ... -l virt_network=true
[See Tap Interconnect][1]
-[1]: software/tools/virtualization.md#tap-interconnect
-
## x86 Adapt Support
Load kernel module, that allows changing/toggling system parameters stored in MSR and PCI registers of x86 processors.
@@ -106,3 +104,5 @@ $ qsub ... -l cpu_hyper_threading=true
!!! Warning
Available on Salomon nodes only.
+
+[1]: software/tools/virtualization.md#tap-interconnect
diff --git a/docs.it4i/prace.md b/docs.it4i/prace.md
index 45351de17..4c6732937 100644
--- a/docs.it4i/prace.md
+++ b/docs.it4i/prace.md
@@ -4,18 +4,14 @@
PRACE users coming to the TIER-1 systems offered through the DECI calls are in general treated as standard users and so most of the general documentation applies to them as well. This section shows the main differences for quicker orientation, but often uses references to the original documentation. PRACE users who don't undergo the full procedure (including signing the IT4I AuP on top of the PRACE AuP) will not have a password and thus access to some services intended for regular users. This can lower their comfort, but otherwise they should be able to use the TIER-1 system as intended. Please see the [Obtaining Login Credentials section][1], if the same level of access is required.
-[1]: general/obtaining-login-credentials/obtaining-login-credentials.md
-
-All general [PRACE User Documentation](http://www.prace-ri.eu/user-documentation/) should be read before continuing reading the local documentation here.
+All general [PRACE User Documentation][a] should be read before continuing reading the local documentation here.
## Help and Support
-If you have any troubles, need information, request support or want to install additional software, use [PRACE Helpdesk](http://www.prace-ri.eu/helpdesk-guide264/).
+If you have any troubles, need information, request support or want to install additional software, use [PRACE Helpdesk][b].
Information about the local services are provided in the [introduction of general user documentation Salomon][2] and [introduction of general user documentation Anselm][3]. Please keep in mind, that standard PRACE accounts don't have a password to access the web interface of the local (IT4Innovations) request tracker and thus a new ticket should be created by sending an e-mail to support[at]it4i.cz.
-[2]: salomon/introduction.md
-[3]: anselm/introduction.md
## Obtaining Login Credentials
In general PRACE users already have a PRACE account setup through their HOMESITE (institution from their country) as a result of rewarded PRACE project proposal. This includes signed PRACE AuP, generated and registered certificates, etc.
@@ -32,11 +28,11 @@ The user will need a valid certificate and to be present in the PRACE LDAP (cont
Most of the information needed by PRACE users accessing the TIER-1 systems can be found here:
-* [General user's FAQ](http://www.prace-ri.eu/Users-General-FAQs)
-* [Certificates FAQ](http://www.prace-ri.eu/Certificates-FAQ)
-* [Interactive access using GSISSH](http://www.prace-ri.eu/Interactive-Access-Using-gsissh)
-* [Data transfer with GridFTP](http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
-* [Data transfer with gtransfer](http://www.prace-ri.eu/Data-Transfer-with-gtransfer)
+* [General user's FAQ][c]
+* [Certificates FAQ][d]
+* [Interactive access using GSISSH][e]
+* [Data transfer with GridFTP][f]
+* [Data transfer with gtransfer][g]
Before you start to use any of the services don't forget to create a proxy certificate from your certificate:
@@ -135,8 +131,6 @@ $ gsissh `prace_service -e -s anselm`
Although the preferred and recommended file transfer mechanism is [using GridFTP][5], the GSI SSH
implementation supports also SCP, so for small files transfer gsiscp can be used:
-[5]: #file-transfers
-
```console
$ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ salomon.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_
$ gsiscp -P 2222 salomon.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
@@ -157,8 +151,6 @@ If the user needs to run X11 based graphical application and does not have a X11
If the user uses GSI SSH based access, then the procedure is similar to the [SSH based access][6], only the port forwarding must be done using GSI SSH:
-[6]: general/accessing-the-clusters/graphical-user-interface/x-window-system.md
-
```console
$ gsissh -p 2222 salomon.it4i.cz -L 5961:localhost:5961
```
@@ -171,9 +163,6 @@ After successful obtainment of login credentials for the local IT4Innovations ac
PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, see [the section in the general documentation for Salomon][8] and [the section in general documentation for Anselm][9].
-[8]: salomon/shell-and-data-access.md
-[9]: anselm/shell-and-data-access.md
-
Apart from the standard mechanisms, for PRACE users to transfer data to/from Salomon cluster, a GridFTP server running Globus Toolkit GridFTP service is available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).
There's one control server and three backend servers for striping and/or backup in case one of them would fail.
@@ -331,16 +320,11 @@ There are some limitations for PRACE user when using the cluster. By default PRA
For production runs always use scratch file systems. The available file systems are described [for Salomon here][10] and [for Anselm here][11].
-[10]: salomon/storage.md
-[11]: anselm/storage.md
-
### Software, Modules and PRACE Common Production Environment
All system wide installed software on the cluster is made available to the users via the modules. The information about the environment and modules usage is in this [section of general documentation][12].
-[12]: environment-and-modules.md
-
-PRACE users can use the "prace" module to use the [PRACE Common Production Environment](http://www.prace-ri.eu/prace-common-production-environment/).
+PRACE users can use the "prace" module to use the [PRACE Common Production Environment][h].
```console
$ ml prace
@@ -374,15 +358,12 @@ For Anselm:
The resources that are currently subject to accounting are the core hours. The core hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. See [example in the general documentation for Salomon][13] and [example in the general documentation for Anselm][14].
-[13]: salomon/resources-allocation-policy.md
-[14]: anselm/resources-allocation-policy.md
-
-PRACE users should check their project accounting using the [PRACE Accounting Tool (DART)](http://www.prace-ri.eu/accounting-report-tool/).
+PRACE users should check their project accounting using the [PRACE Accounting Tool (DART)][i].
Users who have undergone the full local registration procedure (including signing the IT4Innovations Acceptable Use Policy) and who have received local password may check at any time, how many core-hours have been consumed by themselves and their projects using the command "it4ifree". You need to know your user password to use the command and that the displayed core hours are "system core hours" which differ from PRACE "standardized core hours".
!!! note
- The **it4ifree** command is a part of it4i.portal.clients package, [located here](https://pypi.python.org/pypi/it4i.portal.clients).
+ The **it4ifree** command is a part of it4i.portal.clients package, [located here][j].
```console
$ it4ifree
@@ -402,4 +383,27 @@ $ lfs quota -u USER_LOGIN /scratch
If the quota is insufficient, contact the [support][15] and request an increase.
+[1]: general/obtaining-login-credentials/obtaining-login-credentials.md
+[2]: salomon/introduction.md
+[3]: anselm/introduction.md
+[5]: #file-transfers
+[6]: general/accessing-the-clusters/graphical-user-interface/x-window-system.md
+[8]: salomon/shell-and-data-access.md
+[9]: anselm/shell-and-data-access.md
+[10]: salomon/storage.md
+[11]: anselm/storage.md
+[12]: environment-and-modules.md
+[13]: salomon/resources-allocation-policy.md
+[14]: anselm/resources-allocation-policy.md
[15]: #help-and-support
+
+[a]: http://www.prace-ri.eu/user-documentation/
+[b]: http://www.prace-ri.eu/helpdesk-guide264/
+[c]: http://www.prace-ri.eu/Users-General-FAQs
+[d]: http://www.prace-ri.eu/Certificates-FAQ
+[e]: http://www.prace-ri.eu/Interactive-Access-Using-gsissh
+[f]: http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details
+[g]: http://www.prace-ri.eu/Data-Transfer-with-gtransfer
+[h]: http://www.prace-ri.eu/prace-common-production-environment/
+[i]: http://www.prace-ri.eu/accounting-report-tool/
+[j]: https://pypi.python.org/pypi/it4i.portal.clients
--
GitLab