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5 merge requests!368Update prace.md to document the change from qprace to qprod as the default...,!367Update prace.md to document the change from qprace to qprod as the default...,!366Update prace.md to document the change from qprace to qprod as the default...,!323extended-acls-storage-section,!219Virtual environment, upgrade MKdocs, upgrade Material design
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## Introduction
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](general/obtaining-login-credentials/obtaining-login-credentials/), if the same level of access is required.
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](general/obtaining-login-credentials/obtaining-login-credentials.md), if the same level of access is required.
All general [PRACE User Documentation](http://www.prace-ri.eu/user-documentation/) should be read before continuing reading the local documentation here.
......@@ -10,13 +10,13 @@ All general [PRACE User Documentation](http://www.prace-ri.eu/user-documentation
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/).
Information about the local services are provided in the [introduction of general user documentation Salomon](salomon/introduction/) and [introduction of general user documentation Anselm](anselm/introduction/). 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.
Information about the local services are provided in the [introduction of general user documentation Salomon](salomon/introduction.md) and [introduction of general user documentation Anselm](anselm/introduction.md). 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.
## 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.
If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on a cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so see the corresponding [section of the general documentation here](general/obtaining-login-credentials/obtaining-login-credentials/).
If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on a cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so see the corresponding [section of the general documentation here](general/obtaining-login-credentials/obtaining-login-credentials.md).
## Accessing the Cluster
......@@ -128,7 +128,7 @@ $ gsissh `prace_service -e -s salomon`
$ gsissh `prace_service -e -s anselm`
```
Although the preferred and recommended file transfer mechanism is [using GridFTP](prace/#file-transfers), the GSI SSH
Although the preferred and recommended file transfer mechanism is [using GridFTP](prace.md#file-transfers), the GSI SSH
implementation supports also SCP, so for small files transfer gsiscp can be used:
```console
......@@ -147,9 +147,9 @@ $ gsiscp -P 2222 anselm-prace.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_
### Access to X11 Applications (VNC)
If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, see the [section in general documentation](general/accessing-the-clusters/graphical-user-interface/x-window-system/).
If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, see the [section in general documentation](general/accessing-the-clusters/graphical-user-interface/x-window-system.md).
If the user uses GSI SSH based access, then the procedure is similar to the SSH based access ([look here](general/accessing-the-clusters/graphical-user-interface/x-window-system/)), only the port forwarding must be done using GSI SSH:
If the user uses GSI SSH based access, then the procedure is similar to the SSH based access ([look here](general/accessing-the-clusters/graphical-user-interface/x-window-system.md)), only the port forwarding must be done using GSI SSH:
```console
$ gsissh -p 2222 salomon.it4i.cz -L 5961:localhost:5961
......@@ -157,11 +157,11 @@ $ gsissh -p 2222 salomon.it4i.cz -L 5961:localhost:5961
### Access With SSH
After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information see [the section in general documentation for Salomon](salomon/shell-and-data-access/) and [the section in general documentation for Anselm](anselm/shell-and-data-access/).
After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information see [the section in general documentation for Salomon](salomon/shell-and-data-access.md) and [the section in general documentation for Anselm](anselm/shell-and-data-access.md).
## File Transfers
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](salomon/shell-and-data-access/) and [the section in general documentation for Anselm](anselm/shell-and-data-access/).
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](salomon/shell-and-data-access.md) and [the section in general documentation for Anselm](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).
......@@ -302,7 +302,7 @@ Generally both shared file systems are available through GridFTP:
| /home | Lustre | Default HOME directories of users in format /home/prace/login/ |
| /scratch | Lustre | Shared SCRATCH mounted on the whole cluster |
More information about the shared file systems is available [for Salomon here](salomon/storage/) and [for anselm here](anselm/storage).
More information about the shared file systems is available [for Salomon here](salomon/storage.md) and [for Anselm here](anselm/storage.md).
!!! hint
`prace` directory is used for PRACE users on the SCRATCH file system.
......@@ -318,11 +318,11 @@ Only Salomon cluster /scratch:
There are some limitations for PRACE user when using the cluster. By default PRACE users aren't allowed to access special queues in the PBS Pro to have high priority or exclusive access to some special equipment like accelerated nodes and high memory (fat) nodes. There may be also restrictions obtaining a working license for the commercial software installed on the cluster, mostly because of the license agreement or because of insufficient amount of licenses.
For production runs always use scratch file systems. The available file systems are described [for Salomon here](salomon/storage/) and [for Anselm here](anselm/storage).
For production runs always use scratch file systems. The available file systems are described [for Salomon here](salomon/storage.md) and [for Anselm here](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](environment-and-modules/).
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](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/).
......@@ -332,7 +332,7 @@ $ ml prace
### Resource Allocation and Job Execution
General information about the resource allocation, job queuing and job execution is in this [section of general documentation for Salomon](salomon/resources-allocation-policy/) and [section of general documentation for Anselm](anselm/resources-allocation-policy/).
General information about the resource allocation, job queuing and job execution is in this [section of general documentation for Salomon](salomon/resources-allocation-policy.md) and [section of general documentation for Anselm](anselm/resources-allocation-policy.md).
For PRACE users, the default production run queue is "qprace". PRACE users can also use two other queues "qexp" and "qfree".
......@@ -356,7 +356,7 @@ For Anselm:
### Accounting & Quota
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](salomon/resources-allocation-policy/) and [example in the general documentation for Anselm](anselm/resources-allocation-policy/).
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](salomon/resources-allocation-policy.md) and [example in the general documentation for Anselm](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/).
......@@ -381,4 +381,4 @@ $ quota
$ lfs quota -u USER_LOGIN /scratch
```
If the quota is insufficient, contact the [support](prace/#help-and-support) and request an increase.
If the quota is insufficient, contact the [support](prace.md#help-and-support) and request an increase.
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