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SSH Matlab Julia Sagemath Maple Mathematica

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SSH Matlab Julia Sagemath Maple Mathematica

Currently one can use the following programs with SSH:

  • Matlab

  • Julia

  • Sagemath

  • Maple

  • Mathematica

Further programs will follow.

Be aware: Probably you will not be the only user on the device. Therefore please try to keep the workload  as low as possible!


Furthermore please keep in mind, that once every morning all SSH connections will be terminated.

ATTENTION: For the use of the server a working Math-Cip-Pool-Account is necessary !! (Only math students get a Cip-Pool-Account)

Using Matlab from outside

First steps

As students cannot use the math department’s  computer lab (the CIP Pool) right now due to the current pandemic, one can access Matlab from outside. To do so proceed as follows:

1. Establish a VPN connection to the university network
A detailed instruction can be found here: https://www.anleitungen.rrze.fau.de/internet-zugang/vpn/.

2. Log into the CIP’s SSH server
Therefore a SSH client is needed, which one might need to install. For Windows one can use for example PuTTY (​https://putty.org/)
To open a SSH connection with PuTTY one needs to enter the following Host-IP and credentials.
Host address: 131.188.54.22
User name: IDM identification (e.g. ab01cdef)
Password: CIP password (by default identical to IDM password)
Detailed instructions on how to use the SSH connection can be found here. Now you are connected to the CIP server and in a command line window in your home directory.

3. Optional: Set up the text editor nano in a “MATLAB friendly” way 
To do this, use this command to load/copy the configuration file into ones .nanorc:

mkdir -p  ~/.nano && wget -O ~/.nano/octave.nanorc https://www.math.fau.de/download/colorcodes --no-check-certificate&& echo "include ~/.nano/octave.nanorc" >> ~/.nanorc

4. Starting MATLAB 
With the following command one can start MATLAB without a graphical user interface and nano as ones text editor:

matlab -nodisplay -r "setenv('EDITOR','nano')"

After executing the command you are in the MATLAB console. First of all, when using script files, as in the desktop version, one should set the current path relative to which all the entered file names are interpreted. In order to navigate with the terminal window, one can use pwd to have the current path shown or  cd to navigate within the folders.

 

Executing a script

To do this start MATLAB as explained above. The following should appear on your screen:

MATLAB is selecting SOFTWARE OPENGL rendering.

                            < M A T L A B (R) >
                  Copyright 1984-2019 The MathWorks, Inc.
                  R2019a (9.6.0.1072779) 64-bit (glnxa64)
                               March 8, 2019

 
To get started, type doc.
For product information, visit www.mathworks.com.
 

	Classroom License -- for classroom instructional use only.
>>

Now you can run MATLAB scripts as usual by typing

>> run NameOfTheFile.m 

into the command line. Pay attention that you started MATLAB in the folder of your script.

To edit scripts, please consult the explanations above under First Steps. By

>>edit NameOfTheFile.m

files can be edited.

Plotting graphs is not as easy as when using the regular Matlab graphic interface. The command ‘plot’ can still be used, but no graphical plot will be shown. But in the background, a normal plot command is still executed. You can save said plotted file as a svg-file by typing

print('a_file_name_without_ending','-dsvg')

It will be saved in your current folder. Other file extensions like ‘-dpng’ are also possible. For further explanation and refined control, see the print documentation from MATLAB (https://www.mathworks.com/help/matlab/ref/print.html). To view the file, copy the files on your personal computer as described in the following part. The path on the CIP computer mostly look like:

ab12cdef@131.188.54.22:/home/stud/ab12cdef/Often_here_is_a_folder_in_between/a_file_name_without_a_ending.svg

You can exit Matlab by typing ‘exit’.

Copy files from the CIP computer to your own computer

It is assumed that the m-files are on your personal computer. You must be able to use the command ‘scp’ for the following instructions. On Mac and Linux, this is built into the operating system.

(Windows) For Windows, the program WinSCP can be used. To log in, first select scp as transmission protocol, secondly enter “131.188.54.22” in the server address (without ” “) and finally port 22 should be used as port. The user name is the IdM identifier (eg. ab01cdef) and the password is your regular IdM password.

After installing Drag and Drop is possible in between the server and your device at home.

Another way to approach this issue: PuTTY provides the tool pscp for this purpose (https://the.earth.li/~sgtatham/putty/0.73/htmldoc/Chapter5.html#psv)

(Mac/Linux) To copy files, enter

scp /Ordner/Filename ab01cdef@131.188.54.22:~/Ordner

in your command line. Be aware that the paths have to be absolute, so you have to give the entire path.

Option Resultat
-nojvm Starting MATLAB without Java® Virtual Machine (JVM™) Software. It reduces the starting time and the workload of the RAM.
-nodisplay Starting  JVM Software without MATLAB Desktop.
-logfile filename Writing the complete output in the file named filename (also the logs)
-r For interactive working.
-h  Shows the start options.

 

> nano’s shortcuts <

External usage of Julia

To start the program, use the following command

julia

An introduction to Julia:

Julia at the Department of Mathematics

 

External usage of  Sagemath

To start the program, use the following command

sagemath

An introduction to Sagemath:Sagemath at the Department of Mathematics

 

 

External usage of  Maple

To start the program, use the following command

maple

An introduction to Maple:Maple at the Department of Mathematics

External usage of Mathematica

To start the program, use the following command

mathematica

An introduction to mathematica:

Wolfram Mathematica: Using a Text‐Based Interface

Glossar

account

An account on a “UNIX”-System. It consists of the pair of username and user ID, also called login and UID.

BSD

Berkeley Software Distribution
Family of mostly free unix derivates like FreeBSD, OpenBSD and NetBSD.

Bash

(Bourne-again shell) is the standard shell in many unix and linux systems. Contrasting to the PowerShell/PowerShell Core is the bash not object-oriented, but purely text-based.

C

is the programming language in which the platform independent part of the Linux kernel and most of the applications has been developed.

CLI

(Command Line Interface). A programme that enables the user to issue commands to the operating system. Under Linux the CLI is realized in the form of the different shell-implementations.

Compiler

A compiler serves as a tool for the creation of programmes. More precisely, it translates source code into object files.

Copy-On-Write

Describes a feature of file systems where blocks are not over-written directly, but instead a copy of the new data is stored in a different block. After finishing a new block, the corresponding pointer is adjusted. Hence, in the case of a system crash during the write-operation no inconsistent file system state is created. Only the data that was written in that moment would be lost, but the previous version of the block is still intact. Apart from that, this concept makes the easy and fast creation of snapshots possible.

CPU
(Central Processing Unit). The primary micro-processor. A processor is an (albeit very small and freely) programmable arithmetic unit, i. e. a machine or electrical circuit that controls other machines or electrical circuits according to the instructions it is being passed.

Dataset

(in the context of ZFS) is a term for ZFS-file systems, volumes and snapshots. Datasets are organised in a hereditary hierarchy and always assigned to a zpool. They serve as structuring unit of the pool and can be tailored to many different applications. The compression, check sum algorithm, logical block size and many more features and properties of any dataset can be changed individually by setting corresponding parameters. All datasets share the storage space of the whole pool, hence they should not be considered as a partition with its own storage space.

Daemon processes

processes running in the background and mostly performing special tasks.

Device (file)

A device interface that is mapped to a device file in the virtual file system. These files usually reside under the directory /dev.

Debian

Debian Linux is also a collaboratively developed free operating system. Debian GNU/Linux is based on the basic system tools of the GNU project and the Linux kernel.

ext2/ext3/ext4

The file systems primarily used under linux. The newer ext3 featuires journaling, in contrast to ext2, however it is backwards-compatible. Using an ext2-driver one can still access an ext3 partition. ext4 is has been developed as successor to ext3.

FIFO

(First-In-First-Out). A FIFO is a queue. Data that has been written into it has to be retrieved in the same order.

Firewall

A computer or application that protectes the local network from attacks from the internet.

FQDN

(Fully Qualified Domain Name). The full domain name of a system, consisting of hostname and domain. The full name of a (web) domain is called the Fully Qualified Domain Name (FQDN). In that case, it is an absolute address.

The FQDN www.example.com. consists of: 3rd-level-label. 2nd-level-label.
Top-Level-Domain(com). and hence is: www.example.com

FTP

(File Transfer Protocol). A protocol for the communication with file servers.

GPL

(GNU General Public License). Licence under which linux and a lot of other free software is distributed.

HTTP (HyperText Transfer Protocol).

A protocol describing the interaction with web-servers.

HTTPS

HTTPS (HTTP Secure) is an encrypted version of HTTP. Most of the times it uses SSL (en-US) or TLS in order to encrypt the whole communication between a client and a server. This safe connection enables clients to safely exchange sensitive information with the server, like e. g. in online banking or online shopping.

Interpreter

An interpreter executes a script written in a programming language without having to compile it beforehand.

ISO 9660

This standard describes a file system for CD-ROMs and DVDs. Typical characteristics are the limits on the length of filenames. Also there is no information about the file owners and permissions.

Journaling

In journaling file systems, every transaction is logged, so that after a crash the often-times cumbersome repair of the file system can be omitted.

Kernel

The kernel is the core component of the operating system and responsible for important tasks like process and memory management or supporting the hardware.

Kernel-Module

Loadable kernel modules (LKM) are components that can be dynamically integrated into the kernel and often provide driver code. Thanks to such LKMs a re-compilation of the kernel is often not necessary.

Kernelspace

Memory region in the RAM for the kernel and all kernel modules, like hardware drivers.

LKM

(Loadable Kernel Module). See Kernel-Module.

Linux

is an operating system based on the linux (operating system) kernel an free GNU software. Linus was developed in 1991 by the Finn Linus Torvalds on the basis of the operating system UNIX.

Multitasking

Ability to execute multiple processes simultaneously.

Multiuser

A multiuser systems is an operating system that is capable of providing and keeping seperated working environments for multiple users.

NFS

The Network File System (NFS) is a protocol developed by Sun Microsystems which allows accessing files over a network connection.

NNTP

NNTP (Network News Transfer Protocol) is a transfer protocol for new in newsgroups. It is used e. g. in Usenet.

NTP

The Network Time Protocol (NTP) is a standard for the synchronization of clocks in computer systems over packet-based communication networks. NTP uses the connection-less transfer protocol UDP or the connection-oriented TCP. Is was developed specifically to make the transmission of reliable time stamps possible over networks with variable packet runtime.

Open Source

Movement for the promotion of free software. Free software is defined by its free use and the availability of the source code.

Proxyserver

A proxy server is a server between many clients and one server. In general its task is to buffer requests so that the server is not being overloaded.

Process

A process in Linux is ideally representing a running programme. Apart from the executable programme code also the environment, consisting but not restricted to shell variables, is included in this concept.

Pseudo File System

A file system that typically resides in memory and has to be access via a pseudo interface. Examples are procfs and swapfs.

Quota

Disk Quota (quite literally) is a limit for the storage on storage devices like hard drives, that a single user or group of users can use. It limits the storage use of a user.

RAM

(Random Access Memory). The main memory.

ROM

(Read Only Memory). A memory that can only be written once. It is e. g. installed on the mainboard for storing the BIOS.

SMB

A protocol for file shares in a network. Primarily used in the Windows ecosystem.

SMTP

(Simple Mail Transfer Protocol). The standard protocol for sending E-mail.

Snapshot

freezes the state of a filesystem at a certain point in time. If data in the file system is changed, both the current version and the version of the snapshot are stored. At a later time either the state of the snapshot can be restored ore single files of the snapshot can be accessed for recovery purposes.

Secure Shell (SSH)

is a protocol and the corresponding client and server programmes for establishing an encrypted network connection. SHH features mutual authentication and an encrypted file transfer. Initially only for UNIX-based systems, there are nowadays also implementations for Windows and others.

Swap

Parts of the main memory relocated onto the hard drive.

Syscall

A system-call, i. e. a call of a particular kernel function by a programme running in user space.

TCP/IP

Transmission Control Protocol/Internet Protocol
The TCP/IP-protocol family consists of many important protocols for network
communication.
The Transmission Control Protocol (TCP) is a network protocol which defines
how data should be exchanged between network components.
Unlike the connection-less UDP (User Datagram Protocol) in TCP a connection
is established between the end-points of a network connection (sockets). Using that connection data can be transmitted in both directions. Most of the times TCP is stacked onto the IP (Internet Protocol). That is why sometimes people (mostly imprecisely) talk about a “TCP/IP”-protocol.

Ubuntu

also Ubuntu Linux, is a Linux distribution derived from Debian. The name comes from the Nguni philosophy of ubuntu, which means something in the direction of “humanity to others.”

Userspace

Part of the RAM which is used for all programmes and data that are not directly associated to the kernel. Hence, these programmes have no access to the memory region of the kernel.

VFS

(Virtual File System). The virtual file system forms the basis of file system management. All other file systems are integrated by so-called mount points and are hence transparent to the user.

WLAN

(Wireless LAN). Connect to the network over radio connections.

X11

The X window system 11 release 7 (X11R7) provides a graphical user interface for Unix systems.

Zombie-Process

A process which has already terminated but still resides in memory. That way, the parent process can still evaluate the return status of the process later even though it has been neglected at the time.

ZFS

ZFS is a transactional file system developed by Sun Microsystems.

zpool

Concept of ZFS. In practical applications several physical storage devices are pooled into logical units, the zpools, which can optionally be configured more fail-safe. In order to generate a pool stretching over multple hard drives and then create partitions on it, only two relatively simple instructions are needed. Partitioning, creating the logical volume and subsequent mounting in an existing file systems is done automatically.

System Administration Glossar
account An account on a “UNIX”-System. It consists of the pair of username and user ID, also called login and UID. BSD Berkeley Software Distribution Family of mostly free unix derivates like FreeBSD, OpenBSD and NetBSD. Bash (Bourne-again shell) is the standard shell in many unix and linux systems. Contrasting to the PowerShell/PowerShell Core is the bash not object-oriented, but purely text-based. C is the programming language in which the platform independent part of the Linux kernel and most of the applications has been developed. CLI (Command Line Interface). A programme that enables the user to issue commands to the operating system. Under Linux the CLI is realized in the form of the different shell-implementations. Compiler A compiler serves as a tool for the creation of programmes. More precisely, it translates source code into object files. Copy-On-Write Describes a feature of file systems where blocks are not over-written directly, but instead a copy of the new data is stored in a different block. After finishing a new block, the corresponding pointer is adjusted. Hence, in the case of a system crash during the write-operation no inconsistent file system state is created. Only the data that was written in that moment would be lost, but the previous version of the block is still intact. Apart from that, this concept makes the easy and fast creation of snapshots possible. CPU (Central Processing Unit). The primary micro-processor. A processor is an (albeit very small and freely) programmable arithmetic unit, i. e. a machine or electrical circuit that controls other machines or electrical circuits according to the instructions it is being passed. Dataset (in the context of ZFS) is a term for ZFS-file systems, volumes and snapshots. Datasets are organised in a hereditary hierarchy and always assigned to a zpool. They serve as structuring unit of the pool and can be tailored to many different applications. The compression, check sum algorithm, logical block size and many more features and properties of any dataset can be changed individually by setting corresponding parameters. All datasets share the storage space of the whole pool, hence they should not be considered as a partition with its own storage space. Daemon processes processes running in the background and mostly performing special tasks. Device (file) A device interface that is mapped to a device file in the virtual file system. These files usually reside under the directory /dev. Debian Debian Linux is also a collaboratively developed free operating system. Debian GNU/Linux is based on the basic system tools of the GNU project and the Linux kernel. ext2/ext3/ext4 The file systems primarily used under linux. The newer ext3 featuires journaling, in contrast to ext2, however it is backwards-compatible. Using an ext2-driver one can still access an ext3 partition. ext4 is has been developed as successor to ext3. FIFO (First-In-First-Out). A FIFO is a queue. Data that has been written into it has to be retrieved in the same order. Firewall A computer or application that protectes the local network from attacks from the internet. FQDN (Fully Qualified Domain Name). The full domain name of a system, consisting of hostname and domain. The full name of a (web) domain is called the Fully Qualified Domain Name (FQDN). In that case, it is an absolute address. The FQDN www.example.com. consists of: 3rd-level-label. 2nd-level-label. Top-Level-Domain(com). and hence is: www.example.com FTP (File Transfer Protocol). A protocol for the communication with file servers. GPL (GNU General Public License). Licence under which linux and a lot of other free software is distributed. HTTP (HyperText Transfer Protocol). A protocol describing the interaction with web-servers. HTTPS HTTPS (HTTP Secure) is an encrypted version of HTTP. Most of the times it uses SSL (en-US) or TLS in order to encrypt the whole communication between a client and a server. This safe connection enables clients to safely exchange sensitive information with the server, like e. g. in online banking or online shopping. Interpreter An interpreter executes a script written in a programming language without having to compile it beforehand. ISO 9660 This standard describes a file system for CD-ROMs and DVDs. Typical characteristics are the limits on the length of filenames. Also there is no information about the file owners and permissions. Journaling In journaling file systems, every transaction is logged, so that after a crash the often-times cumbersome repair of the file system can be omitted. Kernel The kernel is the core component of the operating system and responsible for important tasks like process and memory management or supporting the hardware. Kernel-Module Loadable kernel modules (LKM) are components that can be dynamically integrated into the kernel and often provide driver code. Thanks to such LKMs a re-compilation of the kernel is often not necessary. Kernelspace Memory region in the RAM for the kernel and all kernel modules, like hardware drivers. LKM (Loadable Kernel Module). See Kernel-Module. Linux is an operating system based on the linux (operating system) kernel an free GNU software. Linus was developed in 1991 by the Finn Linus Torvalds on the basis of the operating system UNIX. Multitasking Ability to execute multiple processes simultaneously. Multiuser A multiuser systems is an operating system that is capable of providing and keeping seperated working environments for multiple users. NFS The Network File System (NFS) is a protocol developed by Sun Microsystems which allows accessing files over a network connection. NNTP NNTP (Network News Transfer Protocol) is a transfer protocol for new in newsgroups. It is used e. g. in Usenet. NTP The Network Time Protocol (NTP) is a standard for the synchronization of clocks in computer systems over packet-based communication networks. NTP uses the connection-less transfer protocol UDP or the connection-oriented TCP. Is was developed specifically to make the transmission of reliable time stamps possible over networks with variable packet runtime. Open Source Movement for the promotion of free software. Free software is defined by its free use and the availability of the source code. Proxyserver A proxy server is a server between many clients and one server. In general its task is to buffer requests so that the server is not being overloaded. Process A process in Linux is ideally representing a running programme. Apart from the executable programme code also the environment, consisting but not restricted to shell variables, is included in this concept. Pseudo File System A file system that typically resides in memory and has to be access via a pseudo interface. Examples are procfs and swapfs. Quota Disk Quota (quite literally) is a limit for the storage on storage devices like hard drives, that a single user or group of users can use. It limits the storage use of a user. RAM (Random Access Memory). The main memory. ROM (Read Only Memory). A memory that can only be written once. It is e. g. installed on the mainboard for storing the BIOS. SMB A protocol for file shares in a network. Primarily used in the Windows ecosystem. SMTP (Simple Mail Transfer Protocol). The standard protocol for sending E-mail. Snapshot freezes the state of a filesystem at a certain point in time. If data in the file system is changed, both the current version and the version of the snapshot are stored. At a later time either the state of the snapshot can be restored ore single files of the snapshot can be accessed for recovery purposes. Secure Shell (SSH) is a protocol and the corresponding client and server programmes for establishing an encrypted network connection. SHH features mutual authentication and an encrypted file transfer. Initially only for UNIX-based systems, there are nowadays also implementations for Windows and others. Swap Parts of the main memory relocated onto the hard drive. Syscall A system-call, i. e. a call of a particular kernel function by a programme running in user space. TCP/IP Transmission Control Protocol/Internet Protocol The TCP/IP-protocol family consists of many important protocols for network communication. The Transmission Control Protocol (TCP) is a network protocol which defines how data should be exchanged between network components. Unlike the connection-less UDP (User Datagram Protocol) in TCP a connection is established between the end-points of a network connection (sockets). Using that connection data can be transmitted in both directions. Most of the times TCP is stacked onto the IP (Internet Protocol). That is why sometimes people (mostly imprecisely) talk about a “TCP/IP”-protocol. Ubuntu also Ubuntu Linux, is a Linux distribution derived from Debian. The name comes from the Nguni philosophy of ubuntu, which means something in the direction of “humanity to others.” Userspace Part of the RAM which is used for all programmes and data that are not directly associated to the kernel. Hence, these programmes have no access to the memory region of the kernel. VFS (Virtual File System). The virtual file system forms the basis of file system management. All other file systems are integrated by so-called mount points and are hence transparent to the user. WLAN (Wireless LAN). Connect to the network over radio connections. X11 The X window system 11 release 7 (X11R7) provides a graphical user interface for Unix systems. Zombie-Process A process which has already terminated but still resides in memory. That way, the parent process can still evaluate the return status of the process later even though it has been neglected at the time. ZFS ZFS is a transactional file system developed by Sun Microsystems. zpool Concept of ZFS. In practical applications several physical storage devices are pooled into logical units, the zpools, which can optionally be configured more fail-safe. In order to generate a pool stretching over multple hard drives and then create partitions on it, only two relatively simple instructions are needed. Partitioning, creating the logical volume and subsequent mounting in an existing file systems is done automatically.
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