From c6f8891cff19cf7d93b0a1d5a19b1048e88fbec0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= <lukas.krupcik@vsb.cz>
Date: Fri, 26 Oct 2018 12:51:49 +0200
Subject: [PATCH] fix images
---
docs.it4i/anselm/compute-nodes.md | 2 +-
docs.it4i/anselm/hardware-overview.md | 2 +-
.../anselm/resources-allocation-policy.md | 2 +-
.../anselm/software/debuggers/allinea-ddt.md | 2 +-
.../graphical-user-interface/vnc.md | 16 +++++------
.../x-window-system.md | 2 +-
.../shell-access-and-data-transfer/putty.md | 24 ++++++++--------
.../accessing-the-clusters/vpn-access.md | 28 +++++++++----------
.../obtaining-login-credentials.md | 2 +-
docs.it4i/salomon/7d-enhanced-hypercube.md | 4 +--
docs.it4i/salomon/compute-nodes.md | 8 +++---
docs.it4i/salomon/hardware-overview.md | 4 +--
docs.it4i/salomon/ib-single-plane-topology.md | 4 +--
docs.it4i/salomon/introduction.md | 8 +++---
.../salomon/resources-allocation-policy.md | 2 +-
.../salomon/software/ansys/ansys-fluent.md | 8 +++---
docs.it4i/salomon/storage.md | 2 +-
docs.it4i/salomon/visualization.md | 26 ++++++++---------
docs.it4i/software/bio/bioinformatics.md | 2 +-
.../omics-master/diagnostic-component-team.md | 2 +-
.../software/bio/omics-master/overview.md | 14 +++++-----
docs.it4i/software/debuggers/aislinn.md | 2 +-
docs.it4i/software/debuggers/allinea-ddt.md | 2 +-
docs.it4i/software/debuggers/cube.md | 2 +-
.../debuggers/intel-vtune-amplifier.md | 2 +-
docs.it4i/software/debuggers/total-view.md | 4 +--
docs.it4i/software/debuggers/vampir.md | 2 +-
.../intel-trace-analyzer-and-collector.md | 2 +-
.../numerical-languages/matlab_1314.md | 2 +-
.../ansys/setting-license-preferences.md | 8 +++---
docs.it4i/software/tools/ansys/workbench.md | 2 +-
docs.it4i/software/tools/virtualization.md | 2 +-
32 files changed, 97 insertions(+), 97 deletions(-)
diff --git a/docs.it4i/anselm/compute-nodes.md b/docs.it4i/anselm/compute-nodes.md
index 75b890134..a52810e60 100644
--- a/docs.it4i/anselm/compute-nodes.md
+++ b/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]
-
+
**Anselm bullx B510 servers**
### Compute Node Summary
diff --git a/docs.it4i/anselm/hardware-overview.md b/docs.it4i/anselm/hardware-overview.md
index cf8f8dadc..efcff8068 100644
--- a/docs.it4i/anselm/hardware-overview.md
+++ b/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:
-
+
The cluster compute nodes cn[1-207] are organized within 13 chassis.
diff --git a/docs.it4i/anselm/resources-allocation-policy.md b/docs.it4i/anselm/resources-allocation-policy.md
index d62656e22..ec94c08e2 100644
--- a/docs.it4i/anselm/resources-allocation-policy.md
+++ b/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/)
-
+
Display the queue status on Anselm:
diff --git a/docs.it4i/anselm/software/debuggers/allinea-ddt.md b/docs.it4i/anselm/software/debuggers/allinea-ddt.md
index 95eb4f107..8756985ae 100644
--- a/docs.it4i/anselm/software/debuggers/allinea-ddt.md
+++ b/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.
-
+
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".
diff --git a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md b/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md
index deac80094..864160517 100644
--- a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md
+++ b/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**.
-
+
### 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
-
+
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.
-
+
## Gnome Session
You should see after the successful login.
-
+
### Disable Your Gnome Session Screensaver
Open Screensaver preferences dialog:
-
+
Uncheck both options below the slider:
-
+
### 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.
-
+
Allow incoming X11 graphics from the compute nodes at the login node:
@@ -244,4 +244,4 @@ $ xterm
Example described above:
-
+
diff --git a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/x-window-system.md b/docs.it4i/general/accessing-the-clusters/graphical-user-interface/x-window-system.md
index 5381c07d4..1f87d62a5 100644
--- a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/x-window-system.md
+++ b/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.
-
+
Then log in as usual.
diff --git a/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/putty.md b/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/putty.md
index 9e9d8e4ca..b3c27ffc1 100644
--- a/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/putty.md
+++ b/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"**.
-
+
* Category - Connection - SSH - Auth:
Select Attempt authentication using Pageant.
Select Allow agent forwarding.
Browse and select your [private key](ssh-keys/) file.
-
+
* Return to Session page and Save selected configuration with _Save_ button.
-
+
* Now you can log in using _Open_ button.
-
+
* 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.
-
+
## 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.
-
+
### 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.
-
+
* Generate some randomness.
-
+
* Wait.
-
+
* 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.
-
+
* Save the public key with _Save public key_ button.
You can copy public key out of the â€Public key for pasting into authorized_keys file’ box.
-
+
* Export private key in OpenSSH format "id_rsa" using Conversion - Export OpenSSH key
-
+
* 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/).
diff --git a/docs.it4i/general/accessing-the-clusters/vpn-access.md b/docs.it4i/general/accessing-the-clusters/vpn-access.md
index a76275513..3275411fc 100644
--- a/docs.it4i/general/accessing-the-clusters/vpn-access.md
+++ b/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)
-
+
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.
-
-
-
+
+
+
After successful installation, VPN connection will be established and you can use available resources from IT4I network.
-
+
If your Java setting doesn't allow automatic installation, you can download installation file and install VPN client manually.
-
+
After you click on the link, download of installation file will start.
-
+
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.
-
+
After you click on the Connect button, you must fill your login credentials.
-
+
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.
-
+
If you right-click on this icon, you will see a context menu in which you can control the VPN connection.
-
+
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.
-
+
Then AnyConnect automatically proceeds like in the case of first logon.
-
+
After a successful logon, you can see a green circle with a tick mark on the lock icon.
-
+
For disconnecting, right-click on the AnyConnect client icon in the system tray and select **VPN Disconnect**.
diff --git a/docs.it4i/general/obtaining-login-credentials/obtaining-login-credentials.md b/docs.it4i/general/obtaining-login-credentials/obtaining-login-credentials.md
index 7f41a37ca..dadc283c5 100644
--- a/docs.it4i/general/obtaining-login-credentials/obtaining-login-credentials.md
+++ b/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:
-
+
!!! 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.
diff --git a/docs.it4i/salomon/7d-enhanced-hypercube.md b/docs.it4i/salomon/7d-enhanced-hypercube.md
index 2c434c21b..af082502d 100644
--- a/docs.it4i/salomon/7d-enhanced-hypercube.md
+++ b/docs.it4i/salomon/7d-enhanced-hypercube.md
@@ -1,6 +1,6 @@
# 7D Enhanced Hypercube
-
+
| Node type | Count | Short name | Long name | Rack |
| ------------------------------------ | ----- | ---------------- | ------------------------ | ----- |
@@ -9,4 +9,4 @@
## IB Topology
-
+
diff --git a/docs.it4i/salomon/compute-nodes.md b/docs.it4i/salomon/compute-nodes.md
index f4bbb717f..dca01b4e4 100644
--- a/docs.it4i/salomon/compute-nodes.md
+++ b/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
-
+
### 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
-
+
-
+
### 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
-
+
### Compute Nodes Summary
diff --git a/docs.it4i/salomon/hardware-overview.md b/docs.it4i/salomon/hardware-overview.md
index 5e10652b9..59c2c42ff 100644
--- a/docs.it4i/salomon/hardware-overview.md
+++ b/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/).
-
+
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 |
-
+
diff --git a/docs.it4i/salomon/ib-single-plane-topology.md b/docs.it4i/salomon/ib-single-plane-topology.md
index 4af3d3212..5da7cee75 100644
--- a/docs.it4i/salomon/ib-single-plane-topology.md
+++ b/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 - 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)
-
+
diff --git a/docs.it4i/salomon/introduction.md b/docs.it4i/salomon/introduction.md
index c60a205bc..90625624a 100644
--- a/docs.it4i/salomon/introduction.md
+++ b/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
-
+
-
+
## Tape Library T950B
-
+
-
+
diff --git a/docs.it4i/salomon/resources-allocation-policy.md b/docs.it4i/salomon/resources-allocation-policy.md
index e4af3e86e..54a231a94 100644
--- a/docs.it4i/salomon/resources-allocation-policy.md
+++ b/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)
-
+
Display the queue status on Salomon:
diff --git a/docs.it4i/salomon/software/ansys/ansys-fluent.md b/docs.it4i/salomon/software/ansys/ansys-fluent.md
index 8b8329950..9dd9dd500 100644
--- a/docs.it4i/salomon/software/ansys/ansys-fluent.md
+++ b/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
-
+
-
+
-
+
ANSYS Academic Research license should be moved up to the top of the list.
-
+
diff --git a/docs.it4i/salomon/storage.md b/docs.it4i/salomon/storage.md
index fee9f7cd1..53336d648 100644
--- a/docs.it4i/salomon/storage.md
+++ b/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.
-
+
The Global RAM disk deploys
BeeGFS On Demand parallel filesystem, using local RAM disks as a storage backend.
diff --git a/docs.it4i/salomon/visualization.md b/docs.it4i/salomon/visualization.md
index 062a17c98..9e35b4123 100644
--- a/docs.it4i/salomon/visualization.md
+++ b/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
-
+
* Add this key to `~/.ssh/authorized_keys` on the cluster
-
+
* 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
-
+
* Add path to key file
-
+
* Save
* Copy `~/.ssh/id_rsa` to your computer
* Convert key to PuTTY format with PuTTYgen
-
+
* 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
-
+
* 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**
-
+
* 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
-
-
+
+
**Check DCV status (Salomon-vizservX) in VNC window**
**Run glxgears (Salomon-vizservX)**
-
+
**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
-
-
+
+
**Check DCV status in VNC window**
**Run glxgears**
-
+
**LOGOUT FROM MENU: System->Logout**
diff --git a/docs.it4i/software/bio/bioinformatics.md b/docs.it4i/software/bio/bioinformatics.md
index 2b4a68850..91de9ca9c 100644
--- a/docs.it4i/software/bio/bioinformatics.md
+++ b/docs.it4i/software/bio/bioinformatics.md
@@ -222,7 +222,7 @@ sci-libs/umfpack-5.6.2
| libraries | 4 |
| **Total** | **93** |
-
+
## Other Applications Available Through Gentoo Linux
diff --git a/docs.it4i/software/bio/omics-master/diagnostic-component-team.md b/docs.it4i/software/bio/omics-master/diagnostic-component-team.md
index bdac047d1..f54fe184a 100644
--- a/docs.it4i/software/bio/omics-master/diagnostic-component-team.md
+++ b/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.
-
+
** 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.
diff --git a/docs.it4i/software/bio/omics-master/overview.md b/docs.it4i/software/bio/omics-master/overview.md
index 70798018d..b156ea7fe 100644
--- a/docs.it4i/software/bio/omics-master/overview.md
+++ b/docs.it4i/software/bio/omics-master/overview.md
@@ -9,7 +9,7 @@ The scope of this OMICS MASTER solution is restricted to human genomics research
The pipeline inputs the raw data produced by the sequencing machines and undergoes a processing procedure that consists on a quality control, the mapping and variant calling steps that result in a file containing the set of variants in the sample. From this point, the prioritization component or the diagnostic component can be launched.
+them, depending of the experimental design carried out.](../../img/fig1.png)
Figure 1. OMICS MASTER solution overview. Data is produced in the external labs and comes to IT4I (represented by the blue dashed line). The data pre-processor converts raw data into a list of variants and annotations for each sequenced patient. These lists files together with primary and secondary (alignment) data files are stored in IT4I sequence DB and uploaded to the discovery (candidate prioritization) or diagnostic component where they can be analyzed directly by the user that produced them, depending of the experimental design carried out.
@@ -41,7 +41,7 @@ Output: FASTQ file plus an HTML file containing statistics on the data.
FASTQ format It represents the nucleotide sequence and its corresponding quality scores.
-
+
Figure 2.FASTQ file.
#### Mapping
@@ -81,7 +81,7 @@ corresponding information is unavailable.
The standard CIGAR description of pairwise alignment defines three operations: â€M’ for match/mismatch, â€I’ for insertion compared with the reference and â€D’ for deletion. The extended CIGAR proposed in SAM added four more operations: â€N’ for skipped bases on the reference, â€S’ for soft clipping, â€H’ for hard clipping and â€P’ for padding. These support splicing, clipping, multi-part and padded alignments. Figure 3 shows examples of CIGAR strings for different types of alignments.
-
+
Figure 3 . SAM format file. The â€@SQ’ line in the header section gives the order of reference sequences. Notably, r001 is the name of a read pair. According to FLAG 163 (=1+2+32+128), the read mapped to position 7 is the second read in the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to 37 on the reverse strand (32). Read r002 has three soft-clipped (unaligned) bases. The coordinate shown in SAM is the position of the first aligned base. The CIGAR string for this alignment contains a P (padding) operation which correctly aligns the inserted sequences. Padding operations can be absent when an aligner does not support multiple sequence alignment. The last six bases of read r003 map to position 9, and the first five to position 29 on the reverse strand. The hard clipping operation H indicates that the clipped sequence is not present in the sequence field. The NM tag gives the number of mismatches. Read r004 is aligned across an intron, indicated by the N operation.
@@ -124,7 +124,7 @@ VCF (3) is a standardized format for storing the most prevalent types of sequenc
A VCF file consists of a header section and a data section. The header contains an arbitrary number of metainformation lines, each starting with characters â€##’, and a TAB delimited field definition line, starting with a single â€#’ character. The meta-information header lines provide a standardized description of tags and annotations used in the data section. The use of meta-information allows the information stored within a VCF file to be tailored to the dataset in question. It can be also used to provide information about the means of file creation, date of creation, version of the reference sequence, software used and any other information relevant to the history of the file. The field definition line names eight mandatory columns, corresponding to data columns representing the chromosome (CHROM), a 1-based position of the start of the variant (POS), unique identifiers of the variant (ID), the reference allele (REF), a comma separated list of alternate non-reference alleles (ALT), a phred-scaled quality score (QUAL), site filtering information (FILTER) and a semicolon separated list of additional, user extensible annotation (INFO). In addition, if samples are present in the file, the mandatory header columns are followed by a FORMAT column and an arbitrary number of sample IDs that define the samples included in the VCF file. The FORMAT column is used to define the information contained within each subsequent genotype column, which consists of a colon separated list of fields. For example, the FORMAT field GT:GQ:DP in the fourth data entry of Figure 1a indicates that the subsequent entries contain information regarding the genotype, genotype quality and read depth for each sample. All data lines are TAB delimited and the number of fields in each data line must match the number of fields in the header line. It is strongly recommended that all annotation tags used are declared in the VCF header section.
+this list; the reference haplotype is designated as 0. For multiploid data, the separator indicates whether the data are phased (|) or unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in this figure occur on the same chromosome in SAMPLE1. The first data line shows an example of a deletion (present in SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the second line shows a SNP and an insertion; the third a SNP; the fourth a large structural variant described by the annotation in the INFO column, the coordinate is that of the base before the variant. (b–f ) Alignments and VCF representations of different sequence variants: SNP, insertion, deletion, replacement, and a large deletion. The REF columns shows the reference bases replaced by the haplotype in the ALT column. The coordinate refers to the first reference base. (g) Users are advised to use simplest representation possible and lowest coordinate in cases where the position is ambiguous.](../../img/fig4.png)
Figure 4 . (a) Example of valid VCF. The header lines ##fileformat and #CHROM are mandatory, the rest is optional but strongly recommended. Each line of the body describes variants present in the sampled population at one genomic position or region. All alternate alleles are listed in the ALT column and referenced from the genotype fields as 1-based indexes to this list; the reference haplotype is designated as 0. For multiploid data, the separator indicates whether the data are phased (|) or unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in this figure occur on the same chromosome in SAMPLE1. The first data line shows an example of a deletion (present in SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the second line shows a SNP and an insertion; the third a SNP; the fourth a large structural variant described by the annotation in the INFO column, the coordinate is that of the base before the variant. (b–f ) Alignments and VCF representations of different sequence variants: SNP, insertion, deletion, replacement, and a large deletion. The REF columns shows the reference bases replaced by the haplotype in the ALT column. The coordinate refers to the first reference base. (g) Users are advised to use simplest representation possible and lowest coordinate in cases where the position is ambiguous.
@@ -341,19 +341,19 @@ The output folder contains all the subfolders with the intermediate data. This f
Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts. TEAM searches first for known diagnostic mutation(s) taken from four databases: HGMD-public (20), [HUMSAVAR](http://www.uniprot.org/docs/humsavar), ClinVar (29) and COSMIC (23).
-
+
Figure 7. The panel manager. The elements used to define a panel are ( A ) disease terms, ( B ) diagnostic mutations and ( C ) genes. Arrows represent actions that can be taken in the panel manager. Panels can be defined by using the known mutations and genes of a particular disease. This can be done by dragging them to the Primary Diagnostic box (action D ). This action, in addition to defining the diseases in the Primary Diagnostic box, automatically adds the corresponding genes to the Genes box. The panels can be customized by adding new genes (action F ) or removing undesired genes (action G). New disease mutations can be added independently or associated to an already existing disease term (action E ). Disease terms can be removed by simply dragging them back (action H ).
For variant discovering/filtering we should upload the VCF file into BierApp by using the following form:
-\
+\
Figure 8 . \BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description \\.
Each prioritization (â€job’) has three associated screens that facilitate the filtering steps. The first one, the â€Summary’ tab, displays a statistic of the data set analyzed, containing the samples analyzed, the number and types of variants found and its distribution according to consequence types. The second screen, in the â€Variants and effect’ tab, is the actual filtering tool, and the third one, the â€Genome view’ tab, offers a representation of the selected variants within the genomic context provided by an embedded version of the Genome Maps Tool (30).
-
+
Figure 9 . This picture shows all the information associated to the variants. If a variant has an associated phenotype we could see it in the last column. In this case, the variant 7:132481242 CT is associated to the phenotype: large intestine tumor.
diff --git a/docs.it4i/software/debuggers/aislinn.md b/docs.it4i/software/debuggers/aislinn.md
index 029ddebb2..a1fcb015e 100644
--- a/docs.it4i/software/debuggers/aislinn.md
+++ b/docs.it4i/software/debuggers/aislinn.md
@@ -79,7 +79,7 @@ $ firefox report.html
At the beginning of the report there are some basic summaries of the verification. In the second part (depicted in the following picture), the error is described.
-
+
It shows us:
diff --git a/docs.it4i/software/debuggers/allinea-ddt.md b/docs.it4i/software/debuggers/allinea-ddt.md
index 69964d186..984091fad 100644
--- a/docs.it4i/software/debuggers/allinea-ddt.md
+++ b/docs.it4i/software/debuggers/allinea-ddt.md
@@ -75,7 +75,7 @@ $ ddt test_debug
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.
-
+
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".
diff --git a/docs.it4i/software/debuggers/cube.md b/docs.it4i/software/debuggers/cube.md
index 4b5f56e72..490787e44 100644
--- a/docs.it4i/software/debuggers/cube.md
+++ b/docs.it4i/software/debuggers/cube.md
@@ -10,7 +10,7 @@ CUBE is a graphical performance report explorer for displaying data from Score-P
Each dimension is organized in a tree, for example the time performance metric is divided into Execution time and Overhead time, call path dimension is organized by files and routines in your source code etc.
-
+
\*Figure 1. Screenshot of CUBE displaying data from Scalasca.\*
diff --git a/docs.it4i/software/debuggers/intel-vtune-amplifier.md b/docs.it4i/software/debuggers/intel-vtune-amplifier.md
index d79e6e639..d3529ba98 100644
--- a/docs.it4i/software/debuggers/intel-vtune-amplifier.md
+++ b/docs.it4i/software/debuggers/intel-vtune-amplifier.md
@@ -9,7 +9,7 @@ Intel *®* VTune™ Amplifier, part of Intel Parallel studio, is a GUI profiling
* Low level specific counters, such as branch analysis and memory bandwidth
* Power usage analysis - frequency and sleep states.
-
+
## Usage
diff --git a/docs.it4i/software/debuggers/total-view.md b/docs.it4i/software/debuggers/total-view.md
index a59fe59f5..aebe91a52 100644
--- a/docs.it4i/software/debuggers/total-view.md
+++ b/docs.it4i/software/debuggers/total-view.md
@@ -140,11 +140,11 @@ $ mpirun -tv -n 5 ./test_debug
When following dialog appears click on "Yes"
-
+
At this point the main TotalView GUI window will appear and you can insert the breakpoints and start debugging:
-
+
### Debugging a Parallel Code - Option 2
diff --git a/docs.it4i/software/debuggers/vampir.md b/docs.it4i/software/debuggers/vampir.md
index 1956c9b26..3a1e9c2ee 100644
--- a/docs.it4i/software/debuggers/vampir.md
+++ b/docs.it4i/software/debuggers/vampir.md
@@ -2,7 +2,7 @@
Vampir is a commercial trace analysis and visualization tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as [Score-P](software/debuggers/score-p/)) first to collect the traces.
-
+
## Installed Versions
diff --git a/docs.it4i/software/intel/intel-suite/intel-trace-analyzer-and-collector.md b/docs.it4i/software/intel/intel-suite/intel-trace-analyzer-and-collector.md
index 308706a78..00c2c3cb7 100644
--- a/docs.it4i/software/intel/intel-suite/intel-trace-analyzer-and-collector.md
+++ b/docs.it4i/software/intel/intel-suite/intel-trace-analyzer-and-collector.md
@@ -30,7 +30,7 @@ $ traceanalyzer
The GUI will launch and you can open the produced `*`.stf file.
-
+
Please refer to Intel documenation about usage of the GUI tool.
diff --git a/docs.it4i/software/numerical-languages/matlab_1314.md b/docs.it4i/software/numerical-languages/matlab_1314.md
index 9dee602e8..8197edccb 100644
--- a/docs.it4i/software/numerical-languages/matlab_1314.md
+++ b/docs.it4i/software/numerical-languages/matlab_1314.md
@@ -46,7 +46,7 @@ Plots, images, etc... will be still available.
Recommended parallel mode for running parallel Matlab on Anselm is MPIEXEC mode. In this mode user allocates resources through PBS prior to starting Matlab. Once resources are granted the main Matlab instance is started on the first compute node assigned to job by PBS and workers are started on all remaining nodes. User can use both interactive and non-interactive PBS sessions. This mode guarantees that the data processing is not performed on login nodes, but all processing is on compute nodes.
-
+
For the performance reasons Matlab should use system MPI. On Anselm the supported MPI implementation for Matlab is Intel MPI. To switch to system MPI user has to override default Matlab setting by creating new configuration file in its home directory. The path and file name has to be exactly the same as in the following listing:
diff --git a/docs.it4i/software/tools/ansys/setting-license-preferences.md b/docs.it4i/software/tools/ansys/setting-license-preferences.md
index cd7aac3f5..e758895a4 100644
--- a/docs.it4i/software/tools/ansys/setting-license-preferences.md
+++ b/docs.it4i/software/tools/ansys/setting-license-preferences.md
@@ -12,12 +12,12 @@ $ANSYSLIC_DIR/lic_admin/anslic_admin
ANSLIC_ADMIN Utility will be run
-
+
-
+
-
+
ANSYS Academic Research license should be moved up to the top or down to the bottom of the list.
-
+
diff --git a/docs.it4i/software/tools/ansys/workbench.md b/docs.it4i/software/tools/ansys/workbench.md
index 7d2e663ac..cdbc3c799 100644
--- a/docs.it4i/software/tools/ansys/workbench.md
+++ b/docs.it4i/software/tools/ansys/workbench.md
@@ -4,7 +4,7 @@
It is possible to run Workbench scripts in batch mode. You need to configure solvers of individual components to run in parallel mode. Open your project in Workbench. Then, for example, in Mechanical, go to Tools - Solve Process Settings ...
-
+
Enable Distribute Solution checkbox and enter number of cores (e.g. 48 to run on two Salomon nodes). If you want the job to run on more then 1 node, you must also provide a so called MPI appfile. In the Additional Command Line Arguments input field, enter:
diff --git a/docs.it4i/software/tools/virtualization.md b/docs.it4i/software/tools/virtualization.md
index 9a4e44f7e..0c88936d6 100644
--- a/docs.it4i/software/tools/virtualization.md
+++ b/docs.it4i/software/tools/virtualization.md
@@ -47,7 +47,7 @@ IT4Innovations does not provide any licenses for operating systems and software
We propose this job workflow:
-
+
Our recommended solution is that job script creates distinct shared job directory, which makes a central point for data exchange between Anselm's environment, compute node (host) (e.g. HOME, SCRATCH, local scratch and other local or cluster file systems) and virtual machine (guest). Job script links or copies input data and instructions what to do (run script) for virtual machine to job directory and virtual machine process input data according instructions in job directory and store output back to job directory. We recommend, that virtual machine is running in so called [snapshot mode](virtualization/#snapshot-mode), image is immutable - image does not change, so one image can be used for many concurrent jobs.
--
GitLab