HPC - User contributions [en-gb]

Applications/HyPhy

2018-03-26T14:57:14Z

Seif: /* Batch Script */

==Application Details==
*Description: HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning
*Version: 2.2.7
*Module: hyphy/2.2.7/gcc-6.3.0/openmpi-2.0.2
*Licence: Open source
==Usage Examples==
Currently its available only after through interactive session. its not possible to run it on login nodes of Viper
===Module===

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@c001 ~]$ module add hyphy/2.2.7/gcc-6.3.0/openmpi-2.0.2
</pre>

or

<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@c001 ~]$ module add hyphy/2.2.7/gcc-6.3.0/openmpi-2.0.2
</pre>

===Description===

There are two binaries available.
* HYPHYMP is openMP implementation that could utilise more than 1 processors.
* HYPHYMPI is MPI implementation that could run on single or multiple nodes.
you can use the openmp version in side an interactive session to define your input arrguments that you can run later as batch job below
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@c001 ~]$ interactive
[username@c001 ~]$ HYPHYMP
</pre>

===Batch Script===

once you know the input arguments (sections) that you have made to HYPHY using interactive session. you can then create a submission script. below is an example of HYPHY slurm submission script
<pre style="background-color: #C8C8C8; color: black; border: 2px solid #C8C8C8; font-family: monospace, sans-serif;">

#!/bin/bash

#SBATCH -J amphibio_meme # Job Name
#SBATCH -N 1 # Number of Nodes to use
#SBATCH -n 28 # Number of CPUs
#SBATCH -o %N.%j.%a.out # Output file name
#SBATCH -e %N.%j.%a.err # Error file name
#SBATCH -p compute # Partition to run on
#SBATCH --exclusive # Request exclusive access to a node (all 28 cores, 128GB of RAM)

module load hyphy/2.2.7/gcc-6.3.0/openmpi-2.0.2

(echo "10"; echo "4"; echo "2"; echo "/pass/to/input1/example.fas"; echo "/pass/to/input2/example.tre"; echo "1"; echo "d") | HYPHYMP
</pre>

2018-01-30T12:01:59Z

Seif: /* Introduction */

Training/Matlab-Viper-plugin

2018-01-26T11:54:20Z

Seif: /* Matlab to Viper */

=Matlab viper plugin=
==Introduction==
There is a feature in Matlab that enables you to submit jobs to clusters directly from your matlab client (normal desktop matlab). we were able to develop Matlab-Viper plugin that utilise this feature and integrate Matlab with viper to enable all our Matlab users to submit some Matlab jobs to viper easily without the need to know much about hpc. Everything could be done from the normal desktop Matlab version that many users are already using.
This guide should explain more on how to use viper through the Matlab viper plugin. in-general the toolbox that could utilise such integration is the Matlab parallel computing toolbox. we will try to explain the main concepts here and point you to some Mathworks tutorial that you could use and try on viper.
*If you don't have Matlab-Viper plugin installed and tested on your Matlab contact help@hull.ac.uk or viper@hull.ac.uk and we will help you to install it and configure it.
*This is only available for Matlab 2017a , we will try to support all the upcoming versions starting from 2017a. if you have a special use case that requires the usage of older version you could check the possibility of creating a plugin for it by emailing us : viper@hull.ac.uk
* this link https://uk.mathworks.com/products/ineligible_programs.html shows a list of Ineligible programs that couldn't run on Matlab distributed computing server.

==Matlab to Viper==
using parallel tool box, you can run your matlab code on viper using 2 modes.
#'''Batch job'''
#*This is the main way to utilize the Matlab-viper -plugin. this submit your job to Viper queening system (SLURM) and send back the results to your client once everything is done.
#*This is very useful for time consuming job that need hours or even days to finish. you will submit your job and you don't need to keep your Matlab running or even the whole computer could be shutdown.
# '''Parallel pool'''
#* Another mode of operation that is easier if you are testing piece of code or running a small job that you expect to finish in few minutes.
#* This requires a running connection to be in place between your computer and viper. at any point you shutdown your Matlab, Wifi or even your laptop everything will be lost and you will need to rerun your code/simulation.

== Further Information ==

* [http://www.ee.surrey.ac.uk/Teaching/Unix/ http://www.ee.surrey.ac.uk/Teaching/Unix/]
{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

Training/Linux - command line

2018-01-26T10:31:32Z

Seif: /* Further Information */

== Introduction ==

This represents a series of teaching pages to allow you to learn more about Viper's Linux command line interface

== Command Line ==

Like other operating systems Linux does have a window’s type environment too called X and hopefully in the future its successor Wayland. (Linux refers to X and Wayland with the term Display Server). However, with VIPER the vast majority of work will be carried out on the command line.

The command line in Linux is referred to as a shell. The shell is a program that allows the user to interact with Linux at the command line. In true Linux style there are a few different ones to choose from, however the one used predominantly is BASH. The name BASH is an acronym for “Bourne Again SHell”, a reference to BASH is an enhanced replacement for sh, the original Unix shell program written by Steve Bourne.

Below is an example of Viper's command line interface using the terminal program [http://mobaxterm.mobatek.net/ MobaXterm].

[[File:commandline.jpg]]

== Man pages ==

This will explain the use of man pages (also called manual pages) on Linux. Most Linux files and commands have pretty good man pages to explain their use.
Type man followed by a command (for which you want help) and start reading. Press q to quit the man page. See below:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ man whois (shows manual page for the command whois)
username@viper:~$ man syslog.config (shows the manual page for a configuration file)
username@viper:~$ man syslogd (show the manual for a daemon (background program))
username@viper:~$ man –k syslog (an apropos which shows a list of available man pages with this string contained within it)

</pre>

== Working with directories ==

As with other operating systems such as Microsoft Windows the filesystem is based around files and directories. Linux is no exception to this and uses a number of commands for the user to navigate around its own filesystem.

This module is a brief overview of the most common commands to work with directories: '''pwd, cd, ls, mkdir''' and '''rmdir'''. These commands are available on any Linux system.

This section will also discuss absolute and relative paths and path completion in the bash shell.

=== pwd ===

On the command line pwd (or print working directory) basically displays the current directory you are in. This would appear as:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ pwd
/home/dbird

</pre>

=== cd ===

On the command line cd (or change directory) changes your current directory to the one specified:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cd /var
username@viper:~$ pwd
/var
username@viper:~$ cd /home/user
username@viper:~$ pwd
/home/user

</pre>

There is also a shortcut back to your home directory by typing the character ~ (tilda) which has the same effect as typing (for example) /home/user.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cd ~
username@viper:~$ pwd
/home/user

</pre>

To go to the directory above (or parent directory), we use the characters ..

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ pwd
/home/user

username@viper:~$ cd ..
username@viper:~$ pwd
/home

</pre>

There is also the character . which means the current directory. This is not useful for the cd command but is very useful for copying files to your current directory.

=== Absolute and relative paths ===
{|
|style="width:5%; border-width: 0" | [[File:icon_pencil.png]]
|style="width:95%; border-width: 0" | Although an important concept to understand the rule here is very simple. When you type a path starting with a slash (/), then the root of the file tree is assumed. If you don't start your path with a slash, then the current directory is the assumed starting point.

Here are two examples, firstly of absolute path:
|-
|}
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ pwd
/home/user

user@viper:~$ cd /var
user@viper:~$ pwd
/var

</pre>

And relative path

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ pwd
/home/user

username@viper:~$ cd myfiles
username@viper:~$ pwd
/home/user/myfiles

</pre>

The command line will help you in typing a path without errors. If you type a partial command such as:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cd /home/user/my

</pre>

Pressing the '''TAB''' key will fill in the rest of the directory name, if that directory exists and it is unique). So the following would appear

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cd /home/user/myfiles

</pre>

=== ls ===

This command lists the contents of a directory:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ ls
myfile1.txt myfile2.txt mydirectory1

</pre>

'''ls''' has a number of useful different options

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ ls –l (show a long listing with more information)
username@viper:~$ ls –a (show all files including those that are hidden)
username@viper:~$ ls –la (combines both of the options above)

</pre>

=== mkdir ===

This commands makes a directory from the specified directory:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ mkdir mydirectory1
username@viper:~$ cd mydirectory1
username@viper:~$ pwd
/home/user/mydirectory1

</pre>

=== rmdir ===

This command removes the specified directory, note the directory must be empty and must not be the directory you are currently in:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ rmdir mydirectory1

</pre>

== Working with files ==

In this section we learn how to recognise, create, remove, copy and move files using commands like '''file''', '''touch''', '''rm''', '''cp''', '''mv''' and '''rename'''.

Just before we start looking at these commands we need to cover two important areas:

* Files on Linux are case sensitive. This means that FILE1 is different from file1, and /etc/hosts is different from /etc/Hosts (the latter one does not exist on a typical Linux computer).
* Everything on Linux is a file. A directory is a special kind of file, but it is still a (case sensitive!) file. Each terminal window (for example /dev/pts/4), any hard disk or partition (for example /dev/sdb1) and any process are all represented somewhere in the file system as a file.

=== file ===

This command determines the file type. Unlike Windows, Linux does not determine the file type from the extension but from examining the file header/contents itself.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ file mypicture.png
pic33.png: PNG image data, 3840 x 1200, 8-bit/color RGBA, non-interlaced

username@viper:~$ file parallel.c
parallel.c: ASCII C program text

</pre>

=== touch ===

This creates an empty file, which can be useful for various uses.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ touch newfile.c
username@viper:~$ ls
newfile.c

</pre>

=== rm ===

Remove a file, as always be very careful with this command and without a backup this file will be lost forever.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ ls
newfile.c backup.c
username@viper:~$ rm newfile.c
username@viper:~$ ls
backup.c

</pre>

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ rm –i backup.c (this is interactive delete and will ask you to delete the file before it occurs)
username@viper:~$ rm –r mydirectory (works recursively down the specified directory but not removing any non-empty directories)
username@viper:~$ rm –rf mydirectory (works recursively down the specified directory however the –f option means force. This option is very powerful but also needs to be used with extreme care!)

</pre>

As with many Linux commands there are a few options with can be used with '''rm''' (these can be view by typing '''man rm''').

=== cp ===

Copy files or directories from a source to a destination:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cp parallel.c mybackup.c (copies parallel.c to mybackup.c)
username@viper:~$ cp parallel.c mydirectory1 (copies parallel.c to mydirectory1)
username@viper:~$ cp *c backupdirectory/ (copies all *.c files to backupdirectory)
username@viper:~$ cp –r mydirectory1 mydirectory2 (copies one directory to another, note the option –r for recursive copying)

</pre>

As with many Linux commands there are a few options with can be used with '''cp''' (these can be view by typing '''man cp''').

=== mv ===

Move files from a source to a destination. A versatile command that can rename a file too:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ mv file1.c testfile.c (rename file1.c to testfile.c)
username@viper:~$ mv directory1 directory2 (rename directory)
username@viper:~$ mv file1.c /home/user/myrepo (mv file1.c to /home/user/myrepo/file1.c)

</pre>

=== rename ===

Although preferably to use the '''mv''' command, this command does exist to rename files

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ touch file1.c file2.c file3.c
username@viper:~$ ls
file1.c file2.c file3.c

username@viper:~$ rename .c .backup *.c
username@viper:~$ ls
file1.backup file2.backup file3.backup

</pre>

== Working with file contents ==

This section will look at working with file contents themselves, such commands are '''head''', '''tail''', '''cat''', '''tac''', '''more''' and '''less'''.

=== head ===

By default head will show the first ten lines of a file.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ head /etc/passwd

root:x:0:0:root:/root:/bin/bash
daemon:x:1:1:daemon:/usr/sbin:/bin/sh
bin:x:2:2:bin:/bin:/bin/sh
sys:x:3:3:sys:/dev:/bin/sh
sync:x:4:65534:sync:/bin:/bin/sync
games:x:5:60:games:/usr/games:/bin/sh
man:x:6:12:man:/var/cache/man:/bin/sh
lp:x:7:7:lp:/var/spool/lpd:/bin/sh
mail:x:8:8:mail:/var/mail:/bin/sh
news:x:9:9:news:/var/spool/news:/bin/sh

</pre>

=== tail ===

Similar to '''head''' but this time it will show the last 10 lines of file by default.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ tail /etc/services
vboxd 20012/udp
binkp 24554/tcp # binkp fidonet protocol
asp 27374/tcp # Address Search Protocol
asp 27374/udp
csync2 30865/tcp # cluster synchronization tool
dircproxy 57000/tcp # Detachable IRC Proxy
tfido 60177/tcp # fidonet EMSI over telnet
fido 60179/tcp # fidonet EMSI over TCP

</pre>

=== cat ===

The '''cat''' command (short for concatenate) one of the most universal tools, yet all it does is copy standard input to standard output. In combination with the shell this can be very powerful and diverse. Some examples will give a glimpse into the possibilities.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cat /etc/resolv.conf

domain example.com
search example.com
nameserver 192.168.1.42

username@viper:~$ cat file1.c file2.c >file3.all (concatenate c files into file3.all)

</pre>

=== tac ===

Works the same as '''cat''' but will show you the file backwards:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cat numbers
one
two
three

username@viper:~$ tac numbers
three
two
one

</pre>

=== more ===

The more command is useful for displaying files that take up more than one screen. More will allow you to see the contents of the file page by page. Use the space bar to see the next page, or q to quit. Some people prefer the less command to more.

=== less ===

Very similar to more but with some additional features

== Basic Linux Tools ==

This chapter introduces commands to find or locate files and to compress files, together with other common tools that were not discussed before.

=== find ===

This command is very useful to find files, more options are provided on the command line by typing '''man find'''. Here are some useful examples below:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ find /etc (find all files in the /etc directory)
username@viper:~$ find . –name “*.conf” (find all files that end in .conf from the current directory)
username@viper:~$ find . –newer file1.c (find all files newer than file1.c)
username@viper:~$ find /etc >etcfiles.txt (find all files but this time put them in (pipe) to the file etcfiles.txt)

</pre>

=== locate ===

The '''locate''' command is very different from find in that it uses an index to locate files. This is a lot faster than traversing all the directories, but it also means that it may be outdated too.

=== date ===

The '''date''' command can display the date, time, time zone and more.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ date
Sat Feb 23 12:44:30 BST 2017

</pre>

=== cal ===

The '''cal''' command displays the current month, with the current day highlighted.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ cal
April 2016
Su Mo Tu We Th Fr Sa
1 2
3 4 5 6 7 8 9
10 11 12 13 14 15 16
17 18 19 20 21 22 23
24 25 26 27 28 29 30

</pre>

=== sleep ===

The '''sleep''' command is sometimes used in scripts to wait a number of seconds. This example shows a five second sleep.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ sleep 5 (five seconds later)
username@viper:~$

</pre>

=== sort ===

The command '''sort''' will sort lines of text files. By default the output is to the screen but this can be piped to a file or another program.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ sort myfile.txt
apple
banana
cherry

</pre>

=== time ===

The time command can display how long it takes to execute a command. The date command takes only a little time.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ time date
Sat Feb 23 13:08:27 BST 2016
real 0m0.014s
user 0m0.008s
sys 0m0.006s

</pre>

=== gzip – gunzip ===

This is a useful compression program (like '''zip''' which also exists in Linux). The '''gzip''' command can make files take up less space.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ gzip myfile.c (will create myfile.c.gz)
username@viper:~$ gunzip myfile.c.gz (will create myfile.c again)

</pre>

=== bzip2 – bunzip2 ===

Files can also be compressed with '''bzip2''' which takes a little more time than '''gzip''', but compresses better.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ bzip2 myfile.c (will create myfile.c.bz2)
username@viper:~$ bunzip2 myfile.c.bz2 (will create myfile.c again)

</pre>

=== zip – unzip ===

A compression program which is compatible with other '''zip''' programs found in MS Windows and other OSes.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ zip myfile.c (will create myfile.c.zip)
username@viper:~$ unzip myfile.c.zip (will create myfile.c again)

</pre>

=== grep ===

The '''grep''' filter is famous among Linux (and UNIX) users. The most common use of '''grep''' is to filter lines of text containing (or not containing) a certain string.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ grep “Darren” /etc/passwd
user:x:1000:1000:Darren Bird,,,:/home/user:/bin/bash

</pre>

As with most Linux commands there are also a large amount of useful options that will go with each command and '''grep''' is certainly no exception here

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ grep –i “Darren” /etc/passwd (search in a case insensitive way)
username@viper:~$ grep –r “Darren” /etc/passwd (search recursively down any directories too)
username@viper:~$ grep –v “Darren” /etc/passwd (search for everything not containing “Darren”)

</pre>

=== wc ===

Counting words, lines and characters is easy with '''wc'''.

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ wc myfile.c (show number of words, lines and characters)
5 10 100 tennis.txt

</pre>

== File Permissions ==

=== Introduction ===

Similar to many other operating systems Linux uses a method of access rights on files and directories. These can be view by using the ls command

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ ls –l (option l is for long listing)

-rw-r--r-- 1 dbird admin 12211 May 11 2016 template.countries
-rw-r--r-- 1 dbird admin 3097 May 11 2016 template.languages (1)
drwxr-x--- 2 dbird admin 4096 Dec 1 10:54 Templates (2)
-rw-r--r-- 1 dbird admin 8087 Feb 12 14:05 temp.txt
-rwx------ 1 dbird admin 1110 Mar 8 10:53 test4pisignage.pl (3)

</pre>

Each file and directory has access rights that are associated with each one. When we look at the 10 symbol string above on the left hand side (e.g. '''drwxr-xr-x''').

* The first letter present whether the file is a directory or not.
* The next three represents the file permission for the user that owns that file (i.e. dbird in this example).
* The next three represent the file permission of the group to whom that user belongs to (i.e. group admin).
* The last three represent the file permissions for everyone else (i.e. all users).

For each of the permission parts the letters mean the following in their groups:

* r indicates read permission to read and copy the file, its absence indicates this is not available.
* w indicates write permission to write the file, its absence indicates this is not available.
* x indicates execution permission to allow the file to be executed, its absence indicates this is not available.

Using the example above would mean:

* Example '''(1)''' has read/write access for user dbird and read access only for everyone else.
* Example '''(2)''' is a directory with full access for user dbird and read access for only users in the admin group.
* Example '''(3)''' is an application which is only accessible by the user dbird, note not only is it read and write but it also has its ‘execution’ permission set for that user also.

=== Changing access rights ===

This command allows the user to change file (and directory) permissions.

* u User
* g Group
* o Other
* a All
* r Read
* w Write (and erase)
* x Execution (and access directory
* + Add permission
* - Remove permission

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

username@viper:~$ chmod go-rwx myfile.c (remove read, write and execute permissions removed for group and other)
username@viper:~$ chmod u+x myapp.pl (make the program myapp.pl executable to user (i.e. the owner of the file))

</pre>

== Further Information ==

* [https://uk.mathworks.com/products/parallel-computing.html?s_tid=srchtitle Mathworks parallel computing toolbox home page]
{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

2018-01-19T16:39:03Z

Seif: /* Introduction */

Training/Matlab-Viper-plugin

2018-01-19T16:02:28Z

Seif: /* Introduction */

Training/Matlab-Viper-plugin

2018-01-19T14:29:42Z

Seif: /* introduction */

Training/Matlab-Viper-plugin

2018-01-19T14:29:29Z

Seif: Created page with "=Matlab viper plugin= ==introduction== There is a feature in Matlab that enables you to submit jobs to clusters directly from your matlab client (normal desktop matlab). we we..."

=Matlab viper plugin=
==introduction==
There is a feature in Matlab that enables you to submit jobs to clusters directly from your matlab client (normal desktop matlab). we were able to develop Matlab-Viper plugin that utilise this feature and integrate Matlab with viper to enable all our Matlab users to submit some Matlab jobs to viper easily without the need to know much about hpc. Everything could be done from the normal desktop Matlab version that many users are already using.
This guide should explain more on how to use viper through the Matlab viper plugin. in-general the toolbox that could utilise such integration is the Matlab parallel computing toolbox. we will try to explain the main concepts here and point you to some Mathworks tutorial that you could use and try on viper.
If you don't have Matlab-Viper plugin installed and tested on your Matlab contact help@hull.ac.uk or viper@hull.ac.uk and we will help you to install it and configure it.

Training

2018-01-19T14:20:57Z

Seif: /* Training */

== Training ==

{| class="wikitable"
| style="width:25%" | Training Area
| style="width:75%" | Description
|-
| [[Training/Getting Connected|Getting Connected]]
| Learn how to connect to Viper
|-
| [[Training/XQuartz|XQuartz - macOS X11 ]]
| Learn how to enable X11 window support on macOS
|-
| [[Training/X2Go macOS|X2Go - macOS]]
| Learn how to install X2Go on macOS for use with Viper's Visualisation Nodes
|-
| [[Training/Transferring Data|Transferring Data]]
| Learn how to download and upload data.
|-
| [[Training/Working Remotely on Viper|Working Remotely on Viper]]
| Learn how to remotely connect to Viper.
|-
| [[Training/Linux - command line|Linux command line]]
| Learn the Linux command line with this extensive guide.
|-
| [[Training/Linux_-_vi_editor|Linux vi editor]]
| Learn the Linux editor vi for editing files
|-
| [[Training/Linux - Nano editor|Linux nano editor]]
| Learn the Linux editor nano for editing files
|-
| [[Training/Matlab-Viper-plugin|parallel computing in matlab]]
| Learn about Matlab parallel toolbox that speed up your calculations on viper.
|-
|}

* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[Libraries|Library support]]
* [[Programming|Development support]]
* [[General|General]]
* [[Training|Training]]

Training/Matlab-add-on

2018-01-19T12:19:58Z

Training

2018-01-18T14:49:35Z

Seif: /* Training */

== Training ==

{| class="wikitable"
| style="width:25%" | Training Area
| style="width:75%" | Description
|-
| [[Training/Getting Connected|Getting Connected]]
| Learn how to connect to Viper
|-
| [[Training/XQuartz|XQuartz - macOS X11 ]]
| Learn how to enable X11 window support on macOS
|-
| [[Training/X2Go macOS|X2Go - macOS]]
| Learn how to install X2Go on macOS for use with Viper's Visualisation Nodes
|-
| [[Training/Transferring Data|Transferring Data]]
| Learn how to download and upload data.
|-
| [[Training/Working Remotely on Viper|Working Remotely on Viper]]
| Learn how to remotely connect to Viper.
|-
| [[Training/Linux - command line|Linux command line]]
| Learn the Linux command line with this extensive guide.
|-
| [[Training/Linux_-_vi_editor|Linux vi editor]]
| Learn the Linux editor vi for editing files
|-
| [[Training/Linux - Nano editor|Linux nano editor]]
| Learn the Linux editor nano for editing files
|-
| [[Training/Matlab-add-on|parallel computing in matlab]]
| Learn about Matlab parallel toolbox that speed up your calculations on viper.
|-
|}

* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[Libraries|Library support]]
* [[Programming|Development support]]
* [[General|General]]
* [[Training|Training]]

Applications/RaXML

2017-11-16T17:11:02Z

Seif: /* Interactive */

==Application Details==
*A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
*Version: MPI AVX 8.2.11
*Licence: Open source

==usage==
===Interactive===

While logged into viper login node:
you could find the example file used in this path /home/ViperAdmin/software/source/iqtree/iqtree-mpi-1.4.4-Linux/example.phy copy it to the location where you would like to run the below steps

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ interactive
salloc: Granted job allocation 296769
Job ID 296769 connecting to c170, please wait...
Last login: Wed Jan 25 09:10:51 2017 from 10.254.5.246
[username@c170 ~]$ module add openmpi/gcc/1.10.2
[username@c170 ~]$ /trinity/clustervision/CentOS/7/apps/raxml/8.2.11/openmpi-1.10.2/gcc-4.9.3/bin/raxmlHPC-MPI-AVX -N 10 -m GTRCAT -s myalign.phy -n myalign.phy pause

</pre>

====Batch Session====

Below is how to submit the same example using our scheduler slurm.
please replace /home/USERNAME/PATH/OF/DIR to the path of the directory where you copied the example.phy file or to the file that you want to use.
<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
#!/bin/bash
#SBATCH -J raxml_example # Job name, you can change it to whatever you want
#SBATCH -o %N.%j.out # Standard output will be written here
#SBATCH -e %N.%j.err # Standard error will be written here
#SBATCH -n 14 # number of cores
#SBATCH -N 1 # Number of nodes
#SBATCH -p highmem # Slurm partition, where you want the job to be queued
#SBATCH --exclusive # Request exclusive access to a node (all 28 cores, 128GB of RAM)

module load openmpi/gcc/1.10.2
cd /home/USERNAME/PATH/OF/DIR
/trinity/clustervision/CentOS/7/apps/raxml/8.2.11/openmpi-1.10.2/gcc-4.9.3/bin/raxmlHPC-MPI-AVX -N 10 -m GTRCAT -s myalign.phy -n myalign.phy pause

</pre>

Then the next step is to submit the above script to slurm
for example if you name the above text file raxml.sh
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

[user@login01 ~]$ sbatch raxml.sh
Submitted batch job 409671

</pre>

==Further Information==

* https://sco.h-its.org/exelixis/web/software/raxml/cluster.html

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

Applications/RaXML

2017-11-16T17:10:52Z

Seif: /* Batch Session */

==Application Details==
*A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
*Version: MPI AVX 8.2.11
*Licence: Open source

===Interactive===

While logged into viper login node:
you could find the example file used in this path /home/ViperAdmin/software/source/iqtree/iqtree-mpi-1.4.4-Linux/example.phy copy it to the location where you would like to run the below steps

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ interactive
salloc: Granted job allocation 296769
Job ID 296769 connecting to c170, please wait...
Last login: Wed Jan 25 09:10:51 2017 from 10.254.5.246
[username@c170 ~]$ module add openmpi/gcc/1.10.2
[username@c170 ~]$ /trinity/clustervision/CentOS/7/apps/raxml/8.2.11/openmpi-1.10.2/gcc-4.9.3/bin/raxmlHPC-MPI-AVX -N 10 -m GTRCAT -s myalign.phy -n myalign.phy pause

</pre>

====Batch Session====

Below is how to submit the same example using our scheduler slurm.
please replace /home/USERNAME/PATH/OF/DIR to the path of the directory where you copied the example.phy file or to the file that you want to use.
<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
#!/bin/bash
#SBATCH -J raxml_example # Job name, you can change it to whatever you want
#SBATCH -o %N.%j.out # Standard output will be written here
#SBATCH -e %N.%j.err # Standard error will be written here
#SBATCH -n 14 # number of cores
#SBATCH -N 1 # Number of nodes
#SBATCH -p highmem # Slurm partition, where you want the job to be queued
#SBATCH --exclusive # Request exclusive access to a node (all 28 cores, 128GB of RAM)

module load openmpi/gcc/1.10.2
cd /home/USERNAME/PATH/OF/DIR
/trinity/clustervision/CentOS/7/apps/raxml/8.2.11/openmpi-1.10.2/gcc-4.9.3/bin/raxmlHPC-MPI-AVX -N 10 -m GTRCAT -s myalign.phy -n myalign.phy pause

</pre>

Then the next step is to submit the above script to slurm
for example if you name the above text file raxml.sh
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

[user@login01 ~]$ sbatch raxml.sh
Submitted batch job 409671

</pre>
==Further Information==

* https://sco.h-its.org/exelixis/web/software/raxml/cluster.html

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

Applications/iqtree

2017-11-16T17:09:11Z

Seif: /* Application Details */

==Application Details==
*Description: Allows maximum likelihood analysis of large phylogenetic data. IQ-TREE explores the tree space efficiently and often achieves higher likelihoods than RAxML and PhyML. Other key features of IQ-TREE are (i) very fast model selection procedure including partition scheme finding, (ii) partitioned analysis for phylogenomic data, (iii) ultrafast bootstrap approximation, (iv) implementation of several branch tests and (v) tree topology tests. W-IQ-TREE an intuitive and user-friendly web interface and server for IQ-TREE is also available.
*Version: MPI 1.4.4
*Licence: Open source

==usage==

===Interactive===

While logged into viper login node:
you could find the example file used in this path /home/ViperAdmin/software/source/iqtree/iqtree-mpi-1.4.4-Linux/example.phy copy it to the location where you would like to run the below steps

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ interactive
salloc: Granted job allocation 296769
Job ID 296769 connecting to c170, please wait...
Last login: Wed Jan 25 09:10:51 2017 from 10.254.5.246
[username@c170 ~]$ module add openmpi/gcc/1.10.2
[username@c170 ~]$ mpirun /trinity/clustervision/CentOS/7/apps/iqtree/1.4.4/openmpi-1.10.2/gcc-4.9.3/bin/iqtree-mpi -s example.phy

</pre>

====Batch Session====

Below is how to submit the same example using our scheduler slurm.
please replace /home/USERNAME/PATH/OF/DIR to the path of the directory where you copied the example.phy file or to the file that you want to use.
<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
#!/bin/bash
#SBATCH -J IQtree_example # Job name, you can change it to whatever you want
#SBATCH -o %N.%j.out # Standard output will be written here
#SBATCH -e %N.%j.err # Standard error will be written here
#SBATCH -n 14 # number of cores
#SBATCH -N 1 # Number of nodes
#SBATCH -p highmem # Slurm partition, where you want the job to be queued
#SBATCH --exclusive # Request exclusive access to a node (all 28 cores, 128GB of RAM)

module load openmpi/gcc/1.10.2
cd /home/USERNAME/PATH/OF/DIR
mpirun /trinity/clustervision/CentOS/7/apps/iqtree/1.4.4/openmpi-1.10.2/gcc-4.9.3/bin/iqtree-mpi -s example.phy

</pre>

Then the next step is to submit the above script to slurm
for example if you name the above text file iqtree.sh
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

[user@login01 ~]$ sbatch iqtree.sh
Submitted batch job 409671

</pre>

==Further Information==

* http://www.iqtree.org/doc/

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

2017-11-10T15:41:36Z

Seif: /* Further Information */

==Application Details==
*Description: Allows maximum likelihood analysis of large phylogenetic data. IQ-TREE explores the tree space efficiently and often achieves higher likelihoods than RAxML and PhyML. Other key features of IQ-TREE are (i) very fast model selection procedure including partition scheme finding, (ii) partitioned analysis for phylogenomic data, (iii) ultrafast bootstrap approximation, (iv) implementation of several branch tests and (v) tree topology tests. W-IQ-TREE an intuitive and user-friendly web interface and server for IQ-TREE is also available.
*Version: MPI 1.4.4
*Licence: Open source
==usage==

===Interactive===

While logged into viper login node:
you could find the example file used in this path /home/ViperAdmin/software/source/iqtree/iqtree-mpi-1.4.4-Linux/example.phy copy it to the location where you would like to run the below steps

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ interactive
salloc: Granted job allocation 296769
Job ID 296769 connecting to c170, please wait...
Last login: Wed Jan 25 09:10:51 2017 from 10.254.5.246
[username@c170 ~]$ module add openmpi/gcc/1.10.2
[username@c170 ~]$ mpirun -n 14 /trinity/clustervision/CentOS/7/apps/iqtree/1.4.4/open^Ci-1.10.2/gcc-4.9.3/bin/iqtree-mpi -s example.phy
</pre>

====Batch Session====

Below is how to submit the same example using our scheduler slurm.
please replace /home/USERNAME/PATH/OF/DIR to the path of the directory where you copied the example.phy file or to the file that you want to use.
<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
#!/bin/bash
#SBATCH -J IQtree_example # Job name, you can change it to whatever you want
#SBATCH -o %N.%j.out # Standard output will be written here
#SBATCH -e %N.%j.err # Standard error will be written here
#SBATCH -n 14 # number of cores
#SBATCH -N 1 # Number of nodes
#SBATCH -p highmem # Slurm partition, where you want the job to be queued
#SBATCH --exclusive # Request exclusive access to a node (all 28 cores, 128GB of RAM)
module load openmpi/gcc/1.10.2
cd /home/USERNAME/PATH/OF/DIR
mpirun /trinity/clustervision/CentOS/7/apps/iqtree/1.4.4/openmpi-1.10.2/gcc-4.9.3/bin/iqtree-mpi -s example.phy

</pre>

Then the next step is to submit the above script to slurm
for example if you name the above text file iqtree.sh
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

[user@login01 ~]$ sbatch iqtree.sh
Submitted batch job 409671

</pre>

==Further Information==

* http://www.iqtree.org/doc/

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}