fix images

docs.it4i/anselm/compute-nodes.md

@@ -47,7 +47,7 @@ Anselm is cluster of x86-64 Intel based nodes built with Bull Extreme Computing
 * bullx R423-E3 servers
 * cn[208-209]
 
-![](img/bullxB510.png)
+![](../img/bullxB510.png)
 **Anselm bullx B510 servers**
 
 ### Compute Node Summary

docs.it4i/anselm/hardware-overview.md

@@ -6,7 +6,7 @@ The Fat nodes are equipped with a large amount (512 GB) of memory. Virtualizatio
 
 Schematic representation of the Anselm cluster. Each box represents a node (computer) or storage capacity:
 
-![](img/Anselm-Schematic-Representation.png)
+![](../img/Anselm-Schematic-Representation.png)
 
 The cluster compute nodes cn[1-207] are organized within 13 chassis.
 

docs.it4i/anselm/resources-allocation-policy.md

@@ -40,7 +40,7 @@ Anselm users may check the current queue configuration at [https://extranet.it4i
 !!! tip
     Check the status of jobs, queues and compute nodes at [https://extranet.it4i.cz/anselm/](https://extranet.it4i.cz/anselm/)
 
-![rspbs web interface](img/rsweb.png)
+![rspbs web interface](../img/rsweb.png)
 
 Display the queue status on Anselm:
 

docs.it4i/anselm/software/debuggers/allinea-ddt.md

@@ -75,7 +75,7 @@ Then launch the debugger with the ddt command followed by the name of the execut
 
 A submission window that appears have a prefilled path to the executable to debug. You can select the number of MPI processors and/or OpenMP threads on which to run and press run. Command line arguments to a program can be entered to the "Arguments " box.
 
-![](img/ddt1.png)
+![](../../../img/ddt1.png)
 
 To start the debugging directly without the submission window, user can specify the debugging and execution parameters from the command line. For example the number of MPI processes is set by option "-np 4". Skipping the dialog is done by "-start" option. To see the list of the "ddt" command line parameters, run "ddt --help".
 

docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md

@@ -141,7 +141,7 @@ On the PuTTY Configuration screen go to Connection->SSH->Tunnels to set up the t
 
 Fill the Source port and Destination fields. **Do not forget to click the Add button**.
 
-![](img/putty-tunnel.png)
+![](../../../img/putty-tunnel.png)
 
 ### WSL (Bash on Windows)
 
@@ -159,7 +159,7 @@ Run the VNC client of your choice, select VNC server 127.0.0.1, port 5961 and co
 
 ### TigerVNC Viewer
 
-![](img/vncviewer.png)
+![](../../../img/vncviewer.png)
 
 In this example, we connect to VNC server on port 5961, via the ssh tunnel, using TigerVNC viewer. The connection is encrypted and secured. The VNC server listening on port 5961 provides screen of 1600x900 pixels.
 
@@ -167,23 +167,23 @@ In this example, we connect to VNC server on port 5961, via the ssh tunnel, usin
 
 Use your VNC password to log using TightVNC Viewer and start a Gnome Session on the login node.
 
-![](img/TightVNC_login.png)
+![](../../../img/TightVNC_login.png)
 
 ## Gnome Session
 
 You should see after the successful login.
 
-![](img/gnome_screen.png)
+![](../../../img/gnome_screen.png)
 
 ### Disable Your Gnome Session Screensaver
 
 Open Screensaver preferences dialog:
 
-![](img/gdmscreensaver.png)
+![](../../../img/gdmscreensaver.png)
 
 Uncheck both options below the slider:
 
-![](img/gdmdisablescreensaver.png)
+![](../../../img/gdmdisablescreensaver.png)
 
 ### Kill Screensaver if Locked Screen
 
@@ -222,7 +222,7 @@ The very same methods as described above, may be used to run the GUI application
 
 Open a Terminal (Applications -> System Tools -> Terminal). Run all the next commands in the terminal.
 
-![](img/gnome-terminal.png)
+![](../../../img/gnome-terminal.png)
 
 Allow incoming X11 graphics from the compute nodes at the login node:
 
@@ -244,4 +244,4 @@ $ xterm
 
 Example described above:
 
-![](img/gnome-compute-nodes-over-vnc.png)
+![](../../../img/gnome-compute-nodes-over-vnc.png)

docs.it4i/general/accessing-the-clusters/graphical-user-interface/x-window-system.md

@@ -19,7 +19,7 @@ In order to display graphical user interface GUI of various software tools, you
 
 On Windows use the PuTTY client to enable X11 forwarding. In PuTTY menu, go to Connection-SSH-X11, mark the Enable X11 forwarding checkbox before logging in.
 
-![](img/cygwinX11forwarding.png)
+![](../../../img/cygwinX11forwarding.png)
 
 Then log in as usual.
 

docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/putty.md

@@ -18,22 +18,22 @@ We recommned you to download "**A Windows installer for everything except PuTTYt
 * Run PuTTY
 * Enter Host name and Save session fields with [Login address](salomon/shell-and-data-access.md) and browse Connection -  SSH - Auth menu. The _Host Name_ input may be in the format **"username@clustername.it4i.cz"** so you don't have to type your login each time.In this example we will connect to the Salomon cluster using **"salomon.it4i.cz"**.
 
-![](img/PuTTY_host_Salomon.png)
+![](../../../img/PuTTY_host_Salomon.png)
 
 * Category - Connection -  SSH - Auth:
       Select Attempt authentication using Pageant.
       Select Allow agent forwarding.
       Browse and select your [private key](ssh-keys/) file.
 
-![](img/PuTTY_keyV.png)
+![](../../../img/PuTTY_keyV.png)
 
 * Return to Session page and Save selected configuration with _Save_ button.
 
-![](img/PuTTY_save_Salomon.png)
+![](../../../img/PuTTY_save_Salomon.png)
 
 * Now you can log in using _Open_ button.
 
-![](img/PuTTY_open_Salomon.png)
+![](../../../img/PuTTY_open_Salomon.png)
 
 * Enter your username if the _Host Name_ input is not in the format "username@salomon.it4i.cz".
 * Enter passphrase for selected [private key](general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/) file if Pageant **SSH authentication agent is not used.**
@@ -53,7 +53,7 @@ Pageant holds your private key in memory without needing to retype a passphrase
 * Enter your passphrase.
 * Now you have your private key in memory without needing to retype a passphrase on every login.
 
-![](img/PageantV.png)
+![](../../../img/PageantV.png)
 
 ## PuTTY Key Generator
 
@@ -69,7 +69,7 @@ You can change the password of your SSH key with "PuTTY Key Generator". Make sur
 * Confirm key passphrase.
 * Save your private key with _Save private key_ button.
 
-![](img/PuttyKeygeneratorV.png)
+![](../../../img/PuttyKeygeneratorV.png)
 
 ### Generate a New Public/Private Key
 
@@ -77,31 +77,31 @@ You can generate an additional public/private key pair and insert public key int
 
 * Start with _Generate_ button.
 
-![](img/PuttyKeygenerator_001V.png)
+![](../../../img/PuttyKeygenerator_001V.png)
 
 * Generate some randomness.
 
-![](img/PuttyKeygenerator_002V.png)
+![](../../../img/PuttyKeygenerator_002V.png)
 
 * Wait.
 
-![](img/PuttyKeygenerator_003V.png)
+![](../../../img/PuttyKeygenerator_003V.png)
 
 * Enter a _comment_ for your key using format 'username@organization.example.com'.
       Enter key passphrase.
       Confirm key passphrase.
       Save your new private key in "_.ppk" format with _Save private key\* button.
 
-![](img/PuttyKeygenerator_004V.png)
+![](../../../img/PuttyKeygenerator_004V.png)
 
 * Save the public key with _Save public key_ button.
       You can copy public key out of the ‘Public key for pasting into authorized_keys file’ box.
 
-![](img/PuttyKeygenerator_005V.png)
+![](../../../img/PuttyKeygenerator_005V.png)
 
 * Export private key in OpenSSH format "id_rsa" using Conversion - Export OpenSSH key
 
-![](img/PuttyKeygenerator_006V.png)
+![](../../../img/PuttyKeygenerator_006V.png)
 
 * Now you can insert additional public key into authorized_keys file for authentication with your own private key.
       You must log in using ssh key received after registration. Then proceed to [How to add your own key](general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/).

docs.it4i/general/accessing-the-clusters/vpn-access.md

@@ -17,25 +17,25 @@ It is impossible to connect to VPN from other operating systems.
 
 You can install VPN client from web interface after successful login with [IT4I credentials](general/obtaining-login-credentials/obtaining-login-credentials/#login-credentials) on address [https://vpn.it4i.cz/user](https://vpn.it4i.cz/user)
 
-![](img/vpn_web_login.png)
+![](../../img/vpn_web_login.png)
 
 According to the Java settings after login, the client either automatically installs, or downloads installation file for your operating system. It is necessary to allow start of installation tool for automatic installation. If auto install does not start, then proceed with manual installation described in next steps.
 
-![](img/vpn_web_login_2.png)
-![](img/vpn_web_install_2.png)
-![](img/copy_of_vpn_web_install_3.png)
+![](../../img/vpn_web_login_2.png)
+![](../../img/vpn_web_install_2.png)
+![](../../img/copy_of_vpn_web_install_3.png)
 
 After successful installation, VPN connection will be established and you can use available resources from IT4I network.
 
-![](img/vpn_web_install_4.png)
+![](../../img/vpn_web_install_4.png)
 
 If your Java setting doesn't allow automatic installation, you can download installation file and install VPN client manually.
 
-![](img/vpn_web_download.png)
+![](../../img/vpn_web_download.png)
 
 After you click on the link, download of installation file will start.
 
-![](img/vpn_web_download_2.png)
+![](../../img/vpn_web_download_2.png)
 
 After successful download of installation file, you have to execute this executable with administrator or root rights and install VPN client manually.
 
@@ -45,30 +45,30 @@ You can use graphical user interface or command line interface to run VPN client
 
 Before the first login to VPN, you have to fill URL **[https://vpn.it4i.cz/user](https://vpn.it4i.cz/user)** into the text field.
 
-![](img/vpn_contacting_https_cluster.png)
+![](../../img/vpn_contacting_https_cluster.png)
 
 After you click on the Connect button, you must fill your login credentials.
 
-![](img/vpn_contacting_https.png)
+![](../../img/vpn_contacting_https.png)
 
 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.
 
-![](img/anyconnecticon.jpg)
+![](../../img/anyconnecticon.jpg)
 
 If you right-click on this icon, you will see a context menu in which you can control the VPN connection.
 
-![](img/anyconnectcontextmenu.jpg)
+![](../../img/anyconnectcontextmenu.jpg)
 
 When you connect to the VPN for the first time, the client downloads the profile and creates a new item "IT4I cluster" in the connection list. For subsequent connections, it is not necessary to re-enter the URL address, but just select the corresponding item.
 
-![](img/vpn_contacting.png)
+![](../../img/vpn_contacting.png)
 
 Then AnyConnect automatically proceeds like in the case of first logon.
 
-![](img/vpn_login.png)
+![](../../img/vpn_login.png)
 
 After a successful logon, you can see a green circle with a tick mark on the lock icon.
 
-![](img/vpn_successfull_connection.png)
+![](../../img/vpn_successfull_connection.png)
 
 For disconnecting, right-click on the AnyConnect client icon in the system tray and select **VPN Disconnect**.

docs.it4i/general/obtaining-login-credentials/obtaining-login-credentials.md

@@ -4,7 +4,7 @@
 
 The computational resources of IT4I are allocated by the Allocation Committee to a Project, investigated by a Primary Investigator. By allocating the computational resources, the Allocation Committee is authorizing the PI to access and use the clusters. The PI may decide to authorize a number of her/his Collaborators to access and use the clusters, to consume the resources allocated to her/his Project. These collaborators will be associated to the Project. The Figure below is depicting the authorization chain:
 
-![](img/Authorization_chain.png)
+![](../../img/Authorization_chain.png)
 
 !!! note
     You need to either [become the PI](../applying-for-resources/) or [be named as a collaborator](obtaining-login-credentials/#authorization-by-web) by a PI in order to access and use the clusters.

docs.it4i/salomon/7d-enhanced-hypercube.md

 # 7D Enhanced Hypercube
 
-![](img/7D_Enhanced_hypercube.png)
+![](../img/7D_Enhanced_hypercube.png)
 
 | Node type                            | Count | Short name       | Long name                | Rack  |
 | ------------------------------------ | ----- | ---------------- | ------------------------ | ----- |
@@ -9,4 +9,4 @@
 
 ## IB Topology
 
-![](img/Salomon_IB_topology.png)
+![](../img/Salomon_IB_topology.png)

docs.it4i/salomon/compute-nodes.md

@@ -15,7 +15,7 @@ Compute nodes with MIC accelerator **contains two Intel Xeon Phi 7120P accelerat
 * two Intel Xeon E5-2680v3, 12-core, 2.5 GHz processors per node
 * 128 GB of physical memory per node
 
-![cn_m_cell](img/cn_m_cell.jpg)
+![cn_m_cell](../img/cn_m_cell.jpg)
 
 ### Compute Nodes With MIC Accelerator
 
@@ -26,11 +26,11 @@ Compute nodes with MIC accelerator **contains two Intel Xeon Phi 7120P accelerat
 * 128 GB of physical memory per node
 * MIC accelerator 2 x Intel Xeon Phi 7120P per node, 61-cores, 16 GB per accelerator
 
-![cn_mic](img/cn_mic-1.jpg)
+![cn_mic](../img/cn_mic-1.jpg)
 
 ![(source Silicon Graphics International Corp.)](img/sgi-c1104-gp1.jpeg)
 
-![cn_mic](img/cn_mic.jpg)
+![cn_mic](../img/cn_mic.jpg)
 
 ### Uv 2000
 
@@ -41,7 +41,7 @@ Compute nodes with MIC accelerator **contains two Intel Xeon Phi 7120P accelerat
 * 3328 GB of physical memory per node
 * 1 x NVIDIA GM200 (GeForce GTX TITAN X), 12 GB RAM
 
-![](img/uv-2000.jpeg)
+![](../img/uv-2000.jpeg)
 
 ### Compute Nodes Summary
 

docs.it4i/salomon/hardware-overview.md

@@ -6,7 +6,7 @@ The Salomon cluster consists of 1008 computational nodes of which 576 are regula
 
 [More about schematic representation of the Salomon cluster compute nodes IB topology](salomon/ib-single-plane-topology/).
 
-![Salomon](img/salomon-2.jpg)
+![Salomon](../img/salomon-2.jpg)
 
 The parameters are summarized in the following tables:
 
@@ -54,4 +54,4 @@ For large memory computations a special SMP/NUMA SGI UV 2000 server is available
 | ------ | ----- | ------------------------------------------- | ----- | --------------------- | ------------------------------------------------------------------------ |
 | UV2000 | 1     | 14 x Intel Xeon E5-4627v2, 3.3 GHz, 8 cores | 112   | 3328 GB DDR3@1866 MHz | 2 x 400GB local SSD, 1x NVIDIA GM200 (GeForce GTX TITAN X), 12 GB RAM |
 
-![](img/uv-2000.jpeg)
+![](../img/uv-2000.jpeg)

docs.it4i/salomon/ib-single-plane-topology.md

@@ -14,7 +14,7 @@ Each color in each physical IRU represents one dual-switch ASIC switch.
 
 [IB single-plane topology - ICEX Mcell.pdf](src/IB single-plane topology - ICEX Mcell.pdf)
 
-![IB single-plane topology - ICEX Mcell.pdf](img/IBsingleplanetopologyICEXMcellsmall.png)
+![IB single-plane topology - ICEX Mcell.pdf](../img/IBsingleplanetopologyICEXMcellsmall.png)
 
 ## IB Single-Plane Topology - Accelerated Nodes
 
@@ -28,4 +28,4 @@ As shown in a diagram [IB Topology](salomon/7d-enhanced-hypercube/#ib-topology)
 
 [IB single-plane topology - Accelerated nodes.pdf](src/IB single-plane topology - Accelerated nodes.pdf)
 
-![IB single-plane topology - Accelerated nodes.pdf](img/IBsingleplanetopologyAcceleratednodessmall.png)
+![IB single-plane topology - Accelerated nodes.pdf](../img/IBsingleplanetopologyAcceleratednodessmall.png)

docs.it4i/salomon/introduction.md

@@ -6,12 +6,12 @@ The cluster runs with a [CentOS Linux](http://www.bull.com/bullx-logiciels/syste
 
 ## Water-Cooled Compute Nodes With MIC Accelerators
 
-![](img/salomon.jpg)
+![](../img/salomon.jpg)
 
-![](img/salomon-1.jpeg)
+![](../img/salomon-1.jpeg)
 
 ## Tape Library T950B
 
-![](img/salomon-3.jpeg)
+![](../img/salomon-3.jpeg)
 
-![](img/salomon-4.jpeg)
+![](../img/salomon-4.jpeg)

docs.it4i/salomon/resources-allocation-policy.md

@@ -46,7 +46,7 @@ Salomon users may check current queue configuration at [https://extranet.it4i.cz
 !!! note
     Check the status of jobs, queues and compute nodes at [https://extranet.it4i.cz/rsweb/salomon/](https://extranet.it4i.cz/rsweb/salomon)
 
-![RSWEB Salomon](img/rswebsalomon.png "RSWEB Salomon")
+![RSWEB Salomon](../img/rswebsalomon.png "RSWEB Salomon")
 
 Display the queue status on Salomon:
 

docs.it4i/salomon/software/ansys/ansys-fluent.md

@@ -151,12 +151,12 @@ Fluent could be run in parallel only under Academic Research license. To do so t
 
 ANSLIC_ADMIN Utility will be run
 
-![](img/Fluent_Licence_1.jpg)
+![](../../../img/Fluent_Licence_1.jpg)
 
-![](img/Fluent_Licence_2.jpg)
+![](../../../img/Fluent_Licence_2.jpg)
 
-![](img/Fluent_Licence_3.jpg)
+![](../../../img/Fluent_Licence_3.jpg)
 
 ANSYS Academic Research license should be moved up to the top of the list.
 
-![](img/Fluent_Licence_4.jpg)
+![](../../../img/Fluent_Licence_4.jpg)

docs.it4i/salomon/storage.md

@@ -332,7 +332,7 @@ It is not recommended to allocate large amount of memory and use large amount of
 
 The Global RAM disk spans the local RAM disks of all the nodes within a single job.
 
-![Global RAM disk](img/global_ramdisk.png)
+![Global RAM disk](../img/global_ramdisk.png)
 
 The Global RAM disk deploys
 BeeGFS On Demand parallel filesystem, using local RAM disks as a storage backend.

docs.it4i/salomon/visualization.md

@@ -36,11 +36,11 @@ Remote visualization with NICE DCV software is availabe on two nodes.
 
 * Generate public fingerprint for your private key with PuTTYgen
 
-![](img/puttygen.png)
+![](../img/puttygen.png)
 
 * Add this key to `~/.ssh/authorized_keys` on the cluster
 
-![](img/addsshkey.png)
+![](../img/addsshkey.png)
 
 * Use your standard SSH key to connect to visualization server
 
@@ -49,17 +49,17 @@ Remote visualization with NICE DCV software is availabe on two nodes.
 * Install WinSCP client (user-computer) [Download WinSCP installer](https://winscp.net/download/WinSCP-5.13.3-Setup.exe)
 * Add credentials
 
-![](img/viz1-win.png)
+![](../img/viz1-win.png)
 
 * Add path to key file
 
-![](img/viz2-win.png)
+![](../img/viz2-win.png)
 
 * Save
 * Copy `~/.ssh/id_rsa` to your computer
 * Convert key to PuTTY format with PuTTYgen
 
-![](img/puttygenconvert.png)
+![](../img/puttygenconvert.png)
 
 * Use this new ssh key to connect to visualization server
 
@@ -69,12 +69,12 @@ Remote visualization with NICE DCV software is availabe on two nodes.
 * [Download PuTTY installer](https://the.earth.li/~sgtatham/putty/latest/w64/putty-64bit-0.70-installer.msi)
 * Configure PuTTY
 
-![](img/viz3-win.png)
+![](../img/viz3-win.png)
 
 * Add credentials and key file (create 3x sessions: **vizserv1.salomon.it4i.cz**, **vizserv2.salomon.it4i.cz**, **login1.salomon.it4i.cz**)
 * Config SSH tunnels (user-computer) (for sessions vizserv1 and vizserv2 only) - ports: **5901**, **5902**, **7300-7305**
 
-![](img/viz4-win.png)
+![](../img/viz4-win.png)
 
 * Save
 
@@ -110,14 +110,14 @@ $ qsub -I -q qviz -A OPEN-XX-XX -l select=1:ncpus=4:host=vizserv2,walltime=04:00
 * vizserv2: localhost:5902
 * fill password
 
-![](img/viz5-win.png)
-![](img/viz6-win.png)
+![](../img/viz5-win.png)
+![](../img/viz6-win.png)
 
 **Check DCV status (Salomon-vizservX) in VNC window**
 
 **Run glxgears (Salomon-vizservX)**
 
-![](img/viz7-win.png)
+![](../img/viz7-win.png)
 
 **LOGOUT FROM MENU: System->Logout**
 
@@ -170,13 +170,13 @@ $ qsub -I -q qviz -A OPEN-XX-XX -l select=1:ncpus=4:host=vizserv2,walltime=04:00
 * vizserv2: localhost:5902
 * fill password
 
-![](img/viz1.png)
-![](img/viz2.png)
+![](../img/viz1.png)
+![](../img/viz2.png)
 
 **Check DCV status in VNC window**
 
 **Run glxgears**
 
-![](img/viz3.png)
+![](../img/viz3.png)
 
 **LOGOUT FROM MENU: System->Logout**

docs.it4i/software/bio/bioinformatics.md

@@ -222,7 +222,7 @@ sci-libs/umfpack-5.6.2
 | libraries                               | 4      |
 | **Total**                               | **93** |
 
-![graphs](img/bio-graphs.png)
+![graphs](../img/bio-graphs.png)
 
 ## Other Applications Available Through Gentoo Linux
 

docs.it4i/software/bio/omics-master/diagnostic-component-team.md

@@ -13,6 +13,6 @@ VCF files are scanned by this diagnostic tool for known diagnostic disease-assoc
 
 TEAM (27) is an intuitive and easy-to-use web tool that fills the gap between the predicted mutations and the final diagnostic in targeted enrichment sequencing analysis. The tool searches for known diagnostic mutations, corresponding to a disease panel, among the predicted patient’s variants. Diagnostic variants for the disease are taken from four databases of disease-related variants (HGMD, HUMSAVAR , ClinVar and COSMIC) If no primary diagnostic variant is found, then a list of secondary findings that can help to establish a diagnostic is produced. TEAM also provides with an interface for the definition of and customization of panels, by means of which, genes and mutations can be added or discarded to adjust panel definitions.
 
-![Interface of the application. Panels for defining targeted regions of interest can be set up by just drag and drop known disease genes or disease definitions from the lists. Thus, virtual panels can be interactively improved as the knowledge of the disease increases.](img/fig5.png)
+![Interface of the application. Panels for defining targeted regions of interest can be set up by just drag and drop known disease genes or disease definitions from the lists. Thus, virtual panels can be interactively improved as the knowledge of the disease increases.](../../img/fig5.png)
 
 ** Figure 5. **Interface of the application. Panels for defining targeted regions of interest can be set up by just drag and drop known disease genes or disease definitions from the lists. Thus, virtual panels can be interactively improved as the knowledge of the disease increases.