add

docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.md

@@ -6,10 +6,10 @@ Storage
   
 
 There are two main shared file systems on Anselm cluster, the
-[HOME](#home) and [SCRATCH](#scratch). All
-login and compute nodes may access same data on shared filesystems.
-Compute nodes are also equipped with local (non-shared) scratch, ramdisk
-and tmp filesystems.
+[HOME](../storage.html#home) and
+[SCRATCH](../storage.html#scratch). All login and compute
+nodes may access same data on shared filesystems. Compute nodes are also
+equipped with local (non-shared) scratch, ramdisk and tmp filesystems.
 
 Archiving
 ---------
@@ -17,19 +17,19 @@ Archiving
 Please don't use shared filesystems as a backup for large amount of data
 or long-term archiving mean. The academic staff and students of research
 institutions in the Czech Republic can use [CESNET storage
-service](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage),
-which is available via SSHFS.
+service](../storage-1/cesnet-data-storage.html), which
+is available via SSHFS.
 
 Shared Filesystems
 ------------------
 
 Anselm computer provides two main shared filesystems, the [HOME
-filesystem](#home) and the [SCRATCH
-filesystem](#scratch). Both HOME and SCRATCH filesystems
-are realized as a parallel Lustre filesystem. Both shared file systems
-are accessible via the Infiniband network. Extended ACLs are provided on
-both Lustre filesystems for the purpose of sharing data with other users
-using fine-grained control.
+filesystem](../storage.html#home) and the [SCRATCH
+filesystem](../storage.html#scratch). Both HOME and
+SCRATCH filesystems are realized as a parallel Lustre filesystem. Both
+shared file systems are accessible via the Infiniband network. Extended
+ACLs are provided on both Lustre filesystems for the purpose of sharing
+data with other users using fine-grained control.
 
 ### Understanding the Lustre Filesystems
 
@@ -206,7 +206,7 @@ The HOME filesystem should not be used to archive data of past Projects
 or other unrelated data.
 
 The files on HOME filesystem will not be deleted until end of the [users
-lifecycle](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials).
+lifecycle](../../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html).
 
 The filesystem is backed up, such that it can be restored in case of 
 catasthropic failure resulting in significant data loss. This backup

docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md

@@ -11,7 +11,7 @@ Accessing IT4Innovations internal resources via VPN
 **Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS
 patch**
 Workaround can be found at
-<https://docs.it4i.cz/vpn-connection-fail-in-win-8.1>
+[https://docs.it4i.cz/vpn-connection-fail-in-win-8.1](../../vpn-connection-fail-in-win-8.1.html)
 
  
 
@@ -35,7 +35,7 @@ It is impossible to connect to VPN from other operating systems.
 You can install VPN client from web interface after successful login
 with LDAP credentials on address <https://vpn1.it4i.cz/anselm>
 
-![](https://docs.it4i.cz/anselm-cluster-documentation/login.jpg/@@images/30271119-b392-4db9-a212-309fb41925d6.jpeg)
+![](../login.jpg/@@images/30271119-b392-4db9-a212-309fb41925d6.jpeg)
 
 According to the Java settings after login, the client either
 automatically installs, or downloads installation file for your
@@ -43,29 +43,29 @@ operating system. It is necessary to allow start of installation tool
 for automatic installation.
 
 ![Java
-detection](https://docs.it4i.cz/anselm-cluster-documentation/java_detection.jpg/@@images/5498e1ba-2242-4b9c-a799-0377a73f779e.jpeg "Java detection")
+detection](../java_detection.jpg/@@images/5498e1ba-2242-4b9c-a799-0377a73f779e.jpeg "Java detection")
 
 ![Execution
-access](https://docs.it4i.cz/anselm-cluster-documentation/executionaccess.jpg/@@images/4d6e7cb7-9aa7-419c-9583-6dfd92b2c015.jpeg "Execution access")![Execution
+access](../executionaccess.jpg/@@images/4d6e7cb7-9aa7-419c-9583-6dfd92b2c015.jpeg "Execution access")![Execution
 access
-2](https://docs.it4i.cz/anselm-cluster-documentation/executionaccess2.jpg/@@images/bed3998c-4b82-4b40-83bd-c3528dde2425.jpeg "Execution access 2")
+2](../executionaccess2.jpg/@@images/bed3998c-4b82-4b40-83bd-c3528dde2425.jpeg "Execution access 2")
 
 After successful installation, VPN connection will be established and
 you can use available resources from IT4I network.
 
 ![Successfull
-instalation](https://docs.it4i.cz/anselm-cluster-documentation/successfullinstalation.jpg/@@images/c6d69ffe-da75-4cb6-972a-0cf4c686b6e1.jpeg "Successfull instalation")
+instalation](../successfullinstalation.jpg/@@images/c6d69ffe-da75-4cb6-972a-0cf4c686b6e1.jpeg "Successfull instalation")
 
 If your Java setting doesn't allow automatic installation, you can
 download installation file and install VPN client manually.
 
 ![Installation
-file](https://docs.it4i.cz/anselm-cluster-documentation/instalationfile.jpg/@@images/202d14e9-e2e1-450b-a584-e78c018d6b6a.jpeg "Installation file")
+file](../instalationfile.jpg/@@images/202d14e9-e2e1-450b-a584-e78c018d6b6a.jpeg "Installation file")
 
 After you click on the link, download of installation file will start.
 
 ![Download file
-successfull](https://docs.it4i.cz/anselm-cluster-documentation/downloadfilesuccessfull.jpg/@@images/69842481-634a-484e-90cd-d65e0ddca1e8.jpeg "Download file successfull")
+successfull](../downloadfilesuccessfull.jpg/@@images/69842481-634a-484e-90cd-d65e0ddca1e8.jpeg "Download file successfull")
 
 After successful download of installation file, you have to execute this
 tool with administrator's rights and install VPN client manually.
@@ -76,50 +76,47 @@ Working with VPN client
 You can use graphical user interface or command line interface to run
 VPN client on all supported operating systems. We suggest using GUI.
 
-![Icon](https://docs.it4i.cz/anselm-cluster-documentation/icon.jpg "Icon")
+![Icon](../icon.jpg "Icon")
 
 Before the first login to VPN, you have to fill
 URL **https://vpn1.it4i.cz/anselm** into the text field.
 
-![First
-run](https://docs.it4i.cz/anselm-cluster-documentation/firstrun.jpg "First run")
+![First run](../firstrun.jpg "First run")
 
 After you click on the Connect button, you must fill your login
 credentials.
 
-![Login -
-GUI](https://docs.it4i.cz/anselm-cluster-documentation/logingui.jpg "Login - GUI")
+![Login - GUI](../logingui.jpg "Login - GUI")
 
 After a successful login, the client will minimize to the system tray.
 If everything works, you can see a lock in the Cisco tray icon.
 
 ![Successfull
-connection](https://docs.it4i.cz/anselm-cluster-documentation/anyconnecticon.jpg "Successfull connection")
+connection](../anyconnecticon.jpg "Successfull connection")
 
 If you right-click on this icon, you will see a context menu in which
 you can control the VPN connection.
 
 ![Context
-menu](https://docs.it4i.cz/anselm-cluster-documentation/anyconnectcontextmenu.jpg "Context menu")
+menu](../anyconnectcontextmenu.jpg "Context menu")
 
 When you connect to the VPN for the first time, the client downloads the
 profile and creates a new item "ANSELM" in the connection list. For
 subsequent connections, it is not necessary to re-enter the URL address,
 but just select the corresponding item.
 
-![Anselm
-profile](https://docs.it4i.cz/anselm-cluster-documentation/Anselmprofile.jpg "Anselm profile")
+![Anselm profile](../Anselmprofile.jpg "Anselm profile")
 
 Then AnyConnect automatically proceeds like in the case of first logon.
 
 ![Login with
-profile](https://docs.it4i.cz/anselm-cluster-documentation/loginwithprofile.jpg/@@images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpeg "Login with profile")
+profile](../loginwithprofile.jpg/@@images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpeg "Login with profile")
 
 After a successful logon, you can see a green circle with a tick mark on
 the lock icon.
 
 ![successful
-login](https://docs.it4i.cz/anselm-cluster-documentation/successfullconnection.jpg "successful login")
+login](../successfullconnection.jpg "successful login")
 
 For disconnecting, right-click on the AnyConnect client icon in the
 system tray and select **VPN Disconnect**.

docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.md

@@ -12,7 +12,7 @@ The X Window system is a principal way to get GUI access to the
 clusters.
 
 Read more about configuring [**X Window
-System**](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc).
+System**](../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
 
 VNC
 ---
@@ -27,5 +27,5 @@ to remotely control another <span
 class="link-external">[computer](http://en.wikipedia.org/wiki/Computer "Computer")</span>.
 
 Read more about configuring
-**[VNC](https://docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc)**.
+**[VNC](../../salomon/accessing-the-cluster/graphical-user-interface/vnc.html)**.
 

docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md

@@ -192,14 +192,14 @@ nodes.****
  
 
 
-**![](https://docs.it4i.cz/anselm-cluster-documentation/bullxB510.png)**
+**![](bullxB510.png)**
 
 ****Figure Anselm bullx B510 servers****
 
 ### Compute Nodes Summary********
 
-  Node type                    Count   Range           Memory   Cores         [Access](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy)
-  ---------------------------- ------- --------------- -------- ------------- -----------------------------------------------------------------------------------------------------------------------------------------------
+  Node type                    Count   Range           Memory   Cores         [Access](resource-allocation-and-job-execution/resources-allocation-policy.html)
+  ---------------------------- ------- --------------- -------- ------------- --------------------------------------------------------------------------------------------------
   Nodes without accelerator    180     cn[1-180]     64GB     16 @ 2.4Ghz   qexp, qprod, qlong, qfree
   Nodes with GPU accelerator   23      cn[181-203]   96GB     16 @ 2.3Ghz   qgpu, qprod
   Nodes with MIC accelerator   4       cn[204-207]   96GB     16 @ 2.3GHz   qmic, qprod

docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md

@@ -49,7 +49,8 @@ We have also second modules repository. This modules repository is
 created using tool called EasyBuild. On Salomon cluster, all modules
 will be build by this tool. If you want to use software from this
 modules repository, please follow instructions in section [Application
-Modules Path Expansion](#EasyBuild).
+Modules
+Path Expansion](environment-and-modules.html#EasyBuild).
 
 The modules may be loaded, unloaded and switched, according to momentary
 needs.
@@ -112,3 +113,4 @@ This command expands your searched paths to modules. You can also add
 this command to the .bashrc file to expand paths permanently. After this
 command, you can use same commands to list/add/remove modules as is
 described above.
+

docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md

@@ -327,17 +327,16 @@ There are four types of compute nodes:
     5110P
 -   2 fat nodes - equipped with 512GB RAM and two 100GB SSD drives
 
-[More about Compute
-nodes](https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes).
+[More about Compute nodes](compute-nodes.html).
 
 GPU and accelerated nodes are available upon request, see the [Resources
 Allocation
-Policy](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy).
+Policy](resource-allocation-and-job-execution/resources-allocation-policy.html).
 
 All these nodes are interconnected by fast <span
 class="WYSIWYG_LINK">InfiniBand <span class="WYSIWYG_LINK">QDR</span>
 network</span> and Ethernet network.  [More about the <span
-class="WYSIWYG_LINK">Network</span>](https://docs.it4i.cz/anselm-cluster-documentation/network).
+class="WYSIWYG_LINK">Network</span>](network.html).
 Every chassis provides Infiniband switch, marked **isw**, connecting all
 nodes in the chassis, as well as connecting the chassis to the upper
 level switches.
@@ -347,11 +346,11 @@ shared /scratch storage is available for the scratch data. These file
 systems are provided by Lustre parallel file system. There is also local
 disk storage available on all compute nodes /lscratch.  [More about
 <span
-class="WYSIWYG_LINK">Storage</span>](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage).
+class="WYSIWYG_LINK">Storage</span>](storage.html).
 
 The user access to the Anselm cluster is provided by two login nodes
 login1, login2, and data mover node dm1. [More about accessing
-cluster.](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster)
+cluster.](accessing-the-cluster.html)
 
  The parameters are summarized in the following tables:
 
@@ -362,8 +361,7 @@ Architecture of compute nodes
 x86-64
 Operating system
 Linux
-[**Compute
-nodes**](https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes)
+[**Compute nodes**](compute-nodes.html)
 Totally
 209
 Processor cores
@@ -397,8 +395,7 @@ Total amount of RAM
   Fat compute node   2x Intel Sandy Bridge E5-2665, 2.4GHz   512GB    -
 
   For more details please refer to the [Compute
-nodes](https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes),
-[Storage](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage),
-and
-[Network](https://docs.it4i.cz/anselm-cluster-documentation/network).
+nodes](compute-nodes.html),
+[Storage](storage.html), and
+[Network](network.html).
 

docs.it4i.cz/anselm-cluster-documentation/introduction.md

@@ -13,30 +13,29 @@ cores, at least 64GB RAM, and 500GB harddrive. Nodes are interconnected
 by fully non-blocking fat-tree Infiniband network and equipped with
 Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA
 Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in [Hardware
-Overview](https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview).
+Overview](hardware-overview.html).
 
 The cluster runs bullx Linux [<span
 class="WYSIWYG_LINK"></span>](http://www.bull.com/bullx-logiciels/systeme-exploitation.html)[operating
-system](https://docs.it4i.cz/anselm-cluster-documentation/software/operating-system),
-which is compatible with the <span class="WYSIWYG_LINK">RedHat</span>
-[<span class="WYSIWYG_LINK">Linux
+system](software/operating-system.html), which is
+compatible with the <span class="WYSIWYG_LINK">RedHat</span> [<span
+class="WYSIWYG_LINK">Linux
 family.</span>](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
 We have installed a wide range of
-[software](https://docs.it4i.cz/anselm-cluster-documentation/software)
-packages targeted at different scientific domains. These packages are
-accessible via the [modules
-environment](https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules).
+[software](software.1.html) packages targeted at
+different scientific domains. These packages are accessible via the
+[modules environment](environment-and-modules.html).
 
 User data shared file-system (HOME, 320TB) and job data shared
 file-system (SCRATCH, 146TB) are available to users.
 
 The PBS Professional workload manager provides [computing resources
 allocations and job
-execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution).
+execution](resource-allocation-and-job-execution.html).
 
 Read more on how to [apply for
-resources](https://docs.it4i.cz/get-started-with-it4innovations/applying-for-resources),
+resources](../get-started-with-it4innovations/applying-for-resources.html),
 [obtain login
-credentials,](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials)
-and [access the
-cluster](https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster).
+credentials,](../get-started-with-it4innovations/obtaining-login-credentials.html)
+and [access the cluster](accessing-the-cluster.html).
+

docs.it4i.cz/anselm-cluster-documentation/prace.md

@@ -18,7 +18,7 @@ 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](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials),
+section](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html),
 if the same level of access is required.
 
 All general [PRACE User
@@ -33,8 +33,7 @@ install additional software, please use [PRACE
 Helpdesk](http://www.prace-ri.eu/helpdesk-guide264/).
 
 Information about the local services are provided in the [introduction
-of general user
-documentation](https://docs.it4i.cz/anselm-cluster-documentation/introduction).
+of general user documentation](introduction.html).
 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
@@ -53,7 +52,7 @@ account at IT4Innovations. To get an account on the Anselm cluster, the
 user needs to obtain the login credentials. The procedure is the same as
 for general users of the cluster, so please see the corresponding
 [section of the general documentation
-here](https://docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials).
+here](../get-started-with-it4innovations/obtaining-login-credentials.html).
 
 Accessing the cluster
 ---------------------
@@ -147,9 +146,9 @@ class="monospace">prace_service</span> script can be used:
  
 
 Although the preferred and recommended file transfer mechanism is [using
-GridFTP](#file-transfers), the GSI SSH implementation on
-Anselm supports also SCP, so for small files transfer gsiscp can be
-used:
+GridFTP](prace.html#file-transfers), the GSI SSH
+implementation on Anselm supports also SCP, so for small files transfer
+gsiscp can be used:
 
     $ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ anselm.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_
 
@@ -165,11 +164,11 @@ 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, please see the [section in
 general
-documentation](resolveuid/11e53ad0d2fd4c5187537f4baeedff33).
+documentation](https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/11e53ad0d2fd4c5187537f4baeedff33).
 
 If the user uses GSI SSH based access, then the procedure is similar to
 the SSH based access ([look
-here](resolveuid/11e53ad0d2fd4c5187537f4baeedff33)),
+here](https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/11e53ad0d2fd4c5187537f4baeedff33)),
 only the port forwarding must be done using GSI SSH:
 
     $ gsissh -p 2222 anselm.it4i.cz -L 5961:localhost:5961
@@ -180,7 +179,7 @@ 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 please see the [section in
 general
-documentation](resolveuid/5d3d6f3d873a42e584cbf4365c4e251b).
+documentation](https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/5d3d6f3d873a42e584cbf4365c4e251b).
 
 []()File transfers
 ------------------
@@ -188,7 +187,7 @@ documentation](resolveuid/5d3d6f3d873a42e584cbf4365c4e251b).
 PRACE users can use the same transfer mechanisms as regular users (if
 they've undergone the full registration procedure). For information
 about this, please see [the section in the general
-documentation](resolveuid/5d3d6f3d873a42e584cbf4365c4e251b).
+documentation](https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/5d3d6f3d873a42e584cbf4365c4e251b).
 
 Apart from the standard mechanisms, for PRACE users to transfer data
 to/from Anselm cluster, a GridFTP server running Globus Toolkit GridFTP
@@ -263,7 +262,7 @@ Generally both shared file systems are available through GridFTP:
   /scratch                  Lustre       Shared SCRATCH mounted on the whole cluster
 
 More information about the shared file systems is available
-[here](https://docs.it4i.cz/anselm-cluster-documentation/storage).
+[here](storage.html).
 
 Usage of the cluster
 --------------------
@@ -278,14 +277,14 @@ because of insufficient amount of licenses.
 
 For production runs always use scratch file systems, either the global
 shared or the local ones. The available file systems are described
-[here](https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview).
+[here](hardware-overview.html).
 
 ### 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](https://docs.it4i.cz/anselm-cluster-documentation/environment-and-modules).
+documentation](environment-and-modules.html).
 
 PRACE users can use the "prace" module to use the [PRACE Common
 Production
@@ -299,7 +298,7 @@ Environment](http://www.prace-ri.eu/PRACE-common-production).
 
 General information about the resource allocation, job queuing and job
 execution is in this [section of general
-documentation](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction).
+documentation](resource-allocation-and-job-execution/introduction.html).
 
 For PRACE users, the default production run queue is "qprace". PRACE
 users can also use two other queues "qexp" and "qfree".
@@ -334,7 +333,7 @@ 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](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy).
+documentation](resource-allocation-and-job-execution/resources-allocation-policy.html).
 
 PRACE users should check their project accounting using the [PRACE
 Accounting Tool
@@ -368,7 +367,8 @@ the quota use
     $ lfs quota -u USER_LOGIN /scratch
 
 If the quota is insufficient, please contact the
-[support](#help-and-support) and request an increase.
+[support](prace.html#help-and-support) and request an
+increase.
 
  
 

docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md

@@ -16,7 +16,7 @@ Currently two compute nodes are dedicated for this service with
 following configuration for each node:
 
 [**Visualization node
-configuration**](https://docs.it4i.cz/anselm-cluster-documentation/compute-nodes)
+configuration**](compute-nodes.html)
 CPU
 2x Intel Sandy Bridge E5-2670, 2.6GHz
 Processor cores
@@ -32,9 +32,9 @@ InfiniBand QDR
 Schematic overview
 ------------------
 
-![rem_vis_scheme](https://docs.it4i.cz/anselm-cluster-documentation/scheme.png "rem_vis_scheme")
+![rem_vis_scheme](scheme.png "rem_vis_scheme")
 
-![rem_vis_legend](https://docs.it4i.cz/anselm-cluster-documentation/legend.png "rem_vis_legend")
+![rem_vis_legend](legend.png "rem_vis_legend")
 
 How to use the service 
 ----------------------
@@ -55,7 +55,7 @@ The procedure is:
 #### 1. Connect to a login node. {#1-connect-to-a-login-node}
 
 Please [follow the
-documentation](resolveuid/5d3d6f3d873a42e584cbf4365c4e251b).
+documentation](https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/5d3d6f3d873a42e584cbf4365c4e251b).
 
 #### 2. Run your own instance of TurboVNC server. {#2-run-your-own-instance-of-turbovnc-server}
 
@@ -120,7 +120,7 @@ $ ssh login2.anselm.it4i.cz -L 5901:localhost:5901
 
 *If you use Windows and Putty, please refer to port forwarding setup
 <span class="internal-link">in the documentation</span>:*
-<https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc#section-12>
+[https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc#section-12](accessing-the-cluster/x-window-and-vnc.html#section-12)
 
 #### 7. If you don't have Turbo VNC installed on your workstation. {#7-if-you-don-t-have-turbo-vnc-installed-on-your-workstation}
 
@@ -281,19 +281,19 @@ Tips and Tricks
 If you want to increase the responsibility of the visualization, please
 adjust your TurboVNC client settings in this way:
 
-![rem_vis_settings](https://docs.it4i.cz/anselm-cluster-documentation/turbovncclientsetting.png "rem_vis_settings")
+![rem_vis_settings](turbovncclientsetting.png "rem_vis_settings")
 
 To have an idea how the settings are affecting the resulting picture
 quality three levels of "JPEG image quality" are demonstrated:
 
 1. JPEG image quality = 30
 
-![rem_vis_q3](https://docs.it4i.cz/anselm-cluster-documentation/quality3.png "rem_vis_q3")
+![rem_vis_q3](quality3.png "rem_vis_q3")
 
 2. JPEG image quality = 15
 
-![rem_vis_q2](https://docs.it4i.cz/anselm-cluster-documentation/quality2.png "rem_vis_q2")
+![rem_vis_q2](quality2.png "rem_vis_q2")
 
 3. JPEG image quality = 10
 
-![rem_vis_q1](https://docs.it4i.cz/anselm-cluster-documentation/quality1.png "rem_vis_q1")
+![rem_vis_q1](quality1.png "rem_vis_q1")

docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.md

@@ -5,17 +5,15 @@ Resource Allocation and Job Execution
 
   
 
-To run a
-[job](https://docs.it4i.cz/anselm-cluster-documentation/introduction),
-[computational
-resources](https://docs.it4i.cz/anselm-cluster-documentation/introduction)
-for this particular job must be allocated. This is done via the PBS Pro
-job workload manager software, which efficiently distributes workloads
-across the supercomputer. Extensive informations about PBS Pro can be
-found in the [official documentation
-here](https://docs.it4i.cz/pbspro-documentation),
-especially in the [PBS Pro User's
-Guide](https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide).
+To run a [job](introduction.html), [computational
+resources](introduction.html) for this particular job
+must be allocated. This is done via the PBS Pro job workload manager
+software, which efficiently distributes workloads across the
+supercomputer. Extensive informations about PBS Pro can be found in the
+[official documentation
+here](../pbspro-documentation.html), especially in the
+[PBS Pro User's
+Guide](../pbspro-documentation/pbspro-users-guide.1).
 
 Resources Allocation Policy
 ---------------------------
@@ -23,7 +21,7 @@ Resources Allocation Policy
 The resources are allocated to the job in a fairshare fashion, subject
 to constraints set by the queue and resources available to the Project.
 [The
-Fairshare](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority)
+Fairshare](resource-allocation-and-job-execution/job-priority.html)
 at Anselm ensures that individual users may consume approximately equal
 amount of resources per week. The resources are accessible via several
 queues for queueing the jobs. The queues provide prioritized and
@@ -39,7 +37,7 @@ available to Anselm users:
 Check the queue status at <https://extranet.it4i.cz/anselm/>
 
 Read more on the [Resource Allocation
-Policy](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy)
+Policy](resource-allocation-and-job-execution/resources-allocation-policy.html)
 page.
 
 Job submission and execution
@@ -56,7 +54,7 @@ resources are allocated the jobscript or interactive shell is executed
 on first of the allocated nodes.**
 
 Read more on the [Job submission and
-execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution)
+execution](resource-allocation-and-job-execution/job-submission-and-execution.html)
 page.
 
 Capacity computing
@@ -74,6 +72,6 @@ huge number of jobs, including **ways to run huge number of single core
 jobs**.
 
 Read more on [Capacity
-computing](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing)
+computing](resource-allocation-and-job-execution/capacity-computing.html)
 page.
 

docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md

@@ -23,21 +23,23 @@ per user, 1000 per job array**
 Please follow one of the procedures below, in case you wish to schedule
 more than <span>100</span> jobs at a time.
 
--   Use [Job arrays](#job-arrays) when running huge number
-    of [multithread](#shared-jobscript-on-one-node) (bound
-    to one node only) or multinode (multithread across several nodes)
-    jobs
--   Use [GNU parallel](#gnu-parallel) when running single
-    core jobs
+-   Use [Job arrays](capacity-computing.html#job-arrays)
+    when running huge number of
+    [multithread](capacity-computing.html#shared-jobscript-on-one-node)
+    (bound to one node only) or multinode (multithread across
+    several nodes) jobs
+-   Use [GNU
+    parallel](capacity-computing.html#gnu-parallel) when
+    running single core jobs
 -   Combine[GNU parallel with Job
-    arrays](#combining-job-arrays-and-gnu-parallel)  when
-    running huge number of single core jobs
+    arrays](capacity-computing.html#combining-job-arrays-and-gnu-parallel) 
+    when running huge number of single core jobs
 
 Policy
 ------
 
 1.  A user is allowed to submit at most 100 jobs. Each job may be [a job
-    array](#job-arrays).
+    array](capacity-computing.html#job-arrays).
 2.  The array size is at most 1000 subjobs.
 
 []()Job arrays
@@ -124,8 +126,8 @@ run has to be used properly.
 ### Submit the job array
 
 To submit the job array, use the qsub -J command. The 900 jobs of the
-[example above](#array_example) may be submitted like
-this:
+[example above](capacity-computing.html#array_example) may
+be submitted like this:
 
 ``` 
 $ qsub -N JOBNAME -J 1-900 jobscript
@@ -203,7 +205,7 @@ $ qstat -u $USER -tJ
 ```
 
 Read more on job arrays in the [PBSPro Users
-guide](https://docs.it4i.cz/pbspro-documentation).
+guide](../../pbspro-documentation.html).
 
 []()GNU parallel
 ----------------
@@ -283,7 +285,8 @@ $TASK.out name.
 ### Submit the job
 
 To submit the job, use the qsub command. The 101 tasks' job of the
-[example above](#gp_example) may be submitted like this:
+[example above](capacity-computing.html#gp_example) may be
+submitted like this:
 
 ``` 
 $ qsub -N JOBNAME jobscript
@@ -393,8 +396,9 @@ Select  subjob walltime and number of tasks per subjob  carefully
 ### Submit the job array
 
 To submit the job array, use the qsub -J command. The 992 tasks' job of
-the [example above](#combined_example) may be submitted
-like this:
+the [example
+above](capacity-computing.html#combined_example) may be
+submitted like this:
 
 ``` 
 $ qsub -N JOBNAME -J 1-992:32 jobscript
@@ -414,7 +418,7 @@ Examples
 --------
 
 Download the examples in
-[capacity.zip](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing-examples), 
+[capacity.zip](capacity-computing-examples), 
 illustrating the above listed ways to run huge number of jobs. We
 recommend to try out the examples, before using this for running
 production jobs.

docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md

@@ -5,30 +5,27 @@ Resource Allocation and Job Execution
 
   
 
-To run a
-[job](https://docs.it4i.cz/anselm-cluster-documentation/introduction),
-[computational
-resources](https://docs.it4i.cz/anselm-cluster-documentation/introduction)
-for this particular job must be allocated. This is done via the PBS Pro
-job workload manager software, which efficiently distributes workloads
-across the supercomputer. Extensive informations about PBS Pro can be
-found in the [official documentation
-here](https://docs.it4i.cz/pbspro-documentation),
-especially in the [PBS Pro User's
-Guide](https://docs.it4i.cz/pbspro-documentation/pbspro-users-guide).
+To run a [job](../introduction.html), [computational
+resources](../introduction.html) for this particular job
+must be allocated. This is done via the PBS Pro job workload manager
+software, which efficiently distributes workloads across the
+supercomputer. Extensive informations about PBS Pro can be found in the
+[official documentation
+here](../../pbspro-documentation.html), especially in
+the [PBS Pro User's
+Guide](../../pbspro-documentation/pbspro-users-guide.1).
 
 Resources Allocation Policy
 ---------------------------
 
 The resources are allocated to the job in a fairshare fashion, subject
 to constraints set by the queue and resources available to the Project.
-[The
-Fairshare](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority)
-at Anselm ensures that individual users may consume approximately equal
-amount of resources per week. The resources are accessible via several
-queues for queueing the jobs. The queues provide prioritized and
-exclusive access to the computational resources. Following queues are
-available to Anselm users:
+[The Fairshare](job-priority.html) at Anselm ensures
+that individual users may consume approximately equal amount of
+resources per week. The resources are accessible via several queues for
+queueing the jobs. The queues provide prioritized and exclusive access
+to the computational resources. Following queues are available to Anselm
+users:
 
 -   **qexp**, the Express queue
 -   **qprod**, the Production queue****
@@ -39,8 +36,7 @@ available to Anselm users:
 Check the queue status at <https://extranet.it4i.cz/anselm/>
 
 Read more on the [Resource Allocation
-Policy](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy)
-page.
+Policy](resources-allocation-policy.html) page.
 
 Job submission and execution
 ----------------------------
@@ -56,8 +52,7 @@ resources are allocated the jobscript or interactive shell is executed
 on first of the allocated nodes.**
 
 Read more on the [Job submission and
-execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution)
-page.
+execution](job-submission-and-execution.html) page.
 
 Capacity computing
 ------------------
@@ -74,8 +69,7 @@ huge number of jobs, including **ways to run huge number of single core
 jobs**.
 
 Read more on [Capacity
-computing](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing)
-page.
+computing](capacity-computing.html) page.
 
 
 

docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md

@@ -38,7 +38,7 @@ Fairshare priority is used for ranking jobs with equal queue priority.
 
 Fairshare priority is calculated as
 
-![](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png)
+![](fairshare_formula.png)
 
 where MAX_FAIRSHARE has value 1E6,
 usage~Project~ is cumulated usage by all members of selected project,
@@ -74,7 +74,7 @@ job.</span></span>
 
 Job execution priority (job sort formula) is calculated as:
 
-![](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png)
+![](job_sort_formula.png)
 
 ### Job backfilling
 

docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md

@@ -80,8 +80,8 @@ the first node in the allocation.
  
 
 All qsub options may be [saved directly into the
-jobscript](#PBSsaved). In such a case, no options to qsub
-are needed.
+jobscript](job-submission-and-execution.html#PBSsaved). In
+such a case, no options to qsub are needed.
 
 ``` 
 $ qsub ./myjob
@@ -143,18 +143,16 @@ with Intel Xeon E5-2665 CPU.
 
 Groups of computational nodes are connected to chassis integrated
 Infiniband switches. These switches form the leaf switch layer of the
-[Infiniband 
-network](https://docs.it4i.cz/anselm-cluster-documentation/network)
-<span class="internal-link">fat</span> tree topology. Nodes sharing the
-leaf switch can communicate most efficiently. Sharing the same switch
+[Infiniband  network](../network.html) <span
+class="internal-link">fat</span> tree topology. Nodes sharing the leaf
+switch can communicate most efficiently. Sharing the same switch
 prevents hops in the network and provides for unbiased, most efficient
 network communication.
 
 Nodes sharing the same switch may be selected via the PBS resource
 attribute ibswitch. Values of this attribute are iswXX, where XX is the
 switch number. The node-switch mapping can be seen at [Hardware
-Overview](https://docs.it4i.cz/anselm-cluster-documentation/hardware-overview)
-section.
+Overview](../hardware-overview.html) section.
 
 We recommend allocating compute nodes of a single switch when best
 possible computational network performance is required to run the job
@@ -449,8 +447,7 @@ directory. The mympiprog.x is executed as one process per node, on all
 allocated nodes.
 
 Consider preloading inputs and executables onto [shared
-scratch](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage)
-before the calculation starts.
+scratch](../storage.html) before the calculation starts.
 
 In some cases, it may be impractical to copy the inputs to scratch and
 outputs to home. This is especially true when very large input and
@@ -497,9 +494,8 @@ allocated nodes. If mympiprog.x implements OpenMP threads, it will run
 16 threads per node.
 
 More information is found in the [Running
-OpenMPI](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI)
-and [Running
-MPICH2](https://docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2)
+OpenMPI](../software/mpi-1/Running_OpenMPI.html) and
+[Running MPICH2](../software/mpi-1/running-mpich2.html)
 sections.
 
 ### Example Jobscript for Single Node Calculation[]()
@@ -508,8 +504,7 @@ Local scratch directory is often useful for single node jobs. Local
 scratch will be deleted immediately after the job ends.
 
 Example jobscript for single node calculation, using [local
-scratch](https://docs.it4i.cz/anselm-cluster-documentation/storage-1/storage)
-on the node:
+scratch](../storage.html) on the node:
 
 ``` 
 #!/bin/bash
@@ -541,10 +536,8 @@ may use threads.
 ### Other Jobscript Examples
 
 Further jobscript examples may be found in the
-[Software](https://docs.it4i.cz/anselm-cluster-documentation/software)
-section and the [Capacity
-computing](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing)
-section.
+[Software](../software.1.html) section and the [Capacity
+computing](capacity-computing.html) section.
 
  
 

docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md

@@ -12,12 +12,11 @@ The resources are allocated to the job in a fairshare fashion, subject
 to constraints set by the queue and resources available to the Project.
 The Fairshare at Anselm ensures that individual users may consume
 approximately equal amount of resources per week. Detailed information
-in the [Job
-scheduling](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority)
-section. The resources are accessible via several queues for queueing
-the jobs. The queues provide prioritized and exclusive access to the
-computational resources. Following table provides the queue partitioning
-overview:     
+in the [Job scheduling](job-priority.html) section. The
+resources are accessible via several queues for queueing the jobs. The
+queues provide prioritized and exclusive access to the computational
+resources. Following table provides the queue partitioning overview:   
+ 
 
 <table>
 <colgroup>
@@ -110,12 +109,12 @@ Free resource queue</td>
 </table>
 
 **The qfree queue is not free of charge**. [Normal
-accounting](#resources-accounting-policy) applies.
-However, it allows for utilization of free resources, once a Project
-exhausted all its allocated computational resources. This does not apply
-for Directors Discreation's projects (DD projects) by default. Usage of
-qfree after exhaustion of DD projects computational resources is allowed
-after request for this queue.
+accounting](resources-allocation-policy.html#resources-accounting-policy)
+applies. However, it allows for utilization of free resources, once a
+Project exhausted all its allocated computational resources. This does
+not apply for Directors Discreation's projects (DD projects) by default.
+Usage of qfree after exhaustion of DD projects computational resources
+is allowed after request for this queue.
 
 **The qexp queue is equipped with the nodes not having the very same CPU
 clock speed.** Should you need the very same CPU speed, you have to
@@ -179,7 +178,7 @@ select the proper nodes during the PSB job submission.
 
 The job wall clock time defaults to **half the maximum time**, see table
 above. Longer wall time limits can be  [set manually, see
-examples](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution).
+examples](job-submission-and-execution.html).
 
 Jobs that exceed the reserved wall clock time (Req'd Time) get killed
 automatically. Wall clock time limit can be changed for queuing jobs
@@ -194,8 +193,7 @@ Anselm users may check current queue configuration at
 Check the status of jobs, queues and compute nodes at
 <https://extranet.it4i.cz/anselm/>
 
-![rspbs web
-interface](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/rsweb.png)
+![rspbs web interface](rsweb.png)
 
 Display the queue status on Anselm:
 
@@ -275,8 +273,7 @@ of whether the cores are actually used for any calculation. 1 core-hour
 is defined as 1 processor core allocated for 1 hour of wall clock time.
 Allocating a full node (16 cores) for 1 hour accounts to 16 core-hours.
 See example in the  [Job submission and
-execution](https://docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution)
-section.
+execution](job-submission-and-execution.html) section.
 
 ### Check consumed resources
 

docs.it4i.cz/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2.md

@@ -189,7 +189,8 @@ Intel MPI on Xeon Phi
 ---------------------
 
 The[MPI section of Intel Xeon Phi
-chapter](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi)
-provides details on how to run Intel MPI code on Xeon Phi architecture.
+chapter](../../../intel-xeon-phi.html) provides details
+on how to run Intel MPI code on Xeon Phi architecture.
+
 
 

docs.it4i.cz/anselm-cluster-documentation/software/ansys.md

@@ -16,7 +16,7 @@ of license is realized on command line respectively directly in user's
 pbs file (see individual products). [<span id="result_box"
 class="short_text"><span class="hps">More</span> <span class="hps">about
 licensing</span> <span
-class="hps">here</span></span>](https://docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing)
+class="hps">here</span></span>](ansys/licensing.html)
 
 To load the latest version of any ANSYS product (Mechanical, Fluent,
 CFX, MAPDL,...) load the module:
@@ -32,3 +32,4 @@ solution to the Anselm directly from the client's Workbench project
 (see ANSYS RSM service).
 
 
+

docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view.md

 
+