MTM Toolkit Running on Windows Via Cygwin and Remote X Client 1 Follow Installation Notes

Total Page：16

File Type：pdf, Size：1020Kb

SSA-MTM Toolkit running on Windows via Cygwin and remote X client 1 Follow installation notes: http://x.cygwin.com/docs/ug/cygwin-x-ug.pdf 2 Install Cygwin/X (Page 4 of pdf) a Follow steps 1-15. b In addition – install selected: tcsh, Grace, Gv, Ssh and X11 3 Continue with installation steps 16-19 to complete setup. 4 Follow the ‘Display remote clients’ instructions (page 17) to launch a remote X client on a ssh session. a Launch ‘Cygwin64 terminal’ icon on desktop b Set the display environment (export DISPLAY=:0.0) c Run the ssh command to connect to a known remote host (ssh –Y username@remote_hostname_or_ip_address): d Enter password 5 Type in ‘xterm’ to open a xterm shell 6 Type in ‘spectra’ and then the SSA-MTM toolkit opens. SSA-MTM toolkit has previously been installed/setup on remote host. 7 File transferring between PC and external/remote client (i.e. to access the result/computed files on the external/remote server): - Install Filezilla – (FileZilla Client for Windows) https://filezilla-project.org - Once installed, connect to the external/remote location as sftp://external source; that allows to drag and drop files from the external source to PC. SSA-MTM Toolkit running on Windows and VMWare Another option for Window OS users is to run Linux (such as Ubuntu) under VMWare, such as a free VMWare Workstation Player. Having VMWare provides ‘virtual machine’ environment and allows for the Ubunutu OS system to operate/run. It has the bonus of being able to move (select copy, drag etc.) data files (for SSA-MTM toolkit) and result files between the Windows and Ubuntu environment – via using ‘files’ or ‘my computer/explorer’. One also needs to install ‘grace’: “sudo apt install grace” or see https://ubuntuforums.org/showthread.php?t=442322) .

Copy Link

Recommended publications

Cygwin User's Guide
Cygwin User’s Guide Cygwin User’s Guide ii Copyright © Cygwin authors Permission is granted to make and distribute verbatim copies of this documentation provided the copyright notice and this per- mission notice are preserved on all copies. Permission is granted to copy and distribute modiﬁed versions of this documentation under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this documentation into another language, under the above conditions for modiﬁed versions, except that this permission notice may be stated in a translation approved by the Free Software Foundation. Cygwin User’s Guide iii Contents 1 Cygwin Overview 1 1.1 What is it? . .1 1.2 Quick Start Guide for those more experienced with Windows . .1 1.3 Quick Start Guide for those more experienced with UNIX . .1 1.4 Are the Cygwin tools free software? . .2 1.5 A brief history of the Cygwin project . .2 1.6 Highlights of Cygwin Functionality . .3 1.6.1 Introduction . .3 1.6.2 Permissions and Security . .3 1.6.3 File Access . .3 1.6.4 Text Mode vs. Binary Mode . .4 1.6.5 ANSI C Library . .4 1.6.6 Process Creation . .5 1.6.6.1 Problems with process creation . .5 1.6.7 Signals . .6 1.6.8 Sockets . .6 1.6.9 Select . .7 1.7 What’s new and what changed in Cygwin . .7 1.7.1 What’s new and what changed in 3.2 .
[Show full text]
A Brief Introduction to the Use of Shell Variables
A Brief Introduction to the Use of Shell Variables Norman Matloff July 25, 2001 Contents 1 Two Popular Shells: tcsh and bash 1.1 Overview There are many different shells available for Unix systems. Here we focus on two of the most popular ones, tcsh and bash. Other shells tend to be very similar to one or both of these. Your Unix account has a preset login shell for you, typically tcsh in academic settings and bash in Linux. When you log in, a shell of the given type is automatically started for you. (This can be seen in the ﬁle /etc/passwd.) If you wish to temporarily run a different shell, just type its name. If you wish to change your login shell, run the chsh command. 1.2 Command Commonality Among Shells Most of what people tend to think of as “basic Unix commands” are actually shell commands which are common to almost all of the shells. So for example you could type cd /abc/def to change to the directory /abc/def in either tcsh or bash.1 2 Shell Variables 2.1 Introduction to Shell Variable Syntax The tcsh shell uses “set” and = for the assignment operation. For example, 1Technically speaking, the “change directory” command for Unix itself is chdir(), a function which must be called from a program. A shell is a program, and when for example you issue the cd command to a shell, that program in turn calls chdir(). 1 set x = 3 would assign the value 3 to the shell variable x.
[Show full text]
Shell Variables
Shell Using the command line Orna Agmon ladypine at vipe.technion.ac.il Haifux Shell – p. 1/55 TOC Various shells Customizing the shell getting help and information Combining simple and useful commands output redirection lists of commands job control environment variables Remote shell textual editors textual clients references Shell – p. 2/55 What is the shell? The shell is the wrapper around the system: a communication means between the user and the system The shell is the manner in which the user can interact with the system through the terminal. The shell is also a script interpreter. The simplest script is a bunch of shell commands. Shell scripts are used in order to boot the system. The user can also write and execute shell scripts. Shell – p. 3/55 Shell - which shell? There are several kinds of shells. For example, bash (Bourne Again Shell), csh, tcsh, zsh, ksh (Korn Shell). The most important shell is bash, since it is available on almost every free Unix system. The Linux system scripts use bash. The default shell for the user is set in the /etc/passwd ﬁle. Here is a line out of this ﬁle for example: dana:x:500:500:Dana,,,:/home/dana:/bin/bash This line means that user dana uses bash (located on the system at /bin/bash) as her default shell. Shell – p. 4/55 Starting to work in another shell If Dana wishes to temporarily use another shell, she can simply call this shell from the command line: [dana@granada ˜]$ bash dana@granada:˜$ #In bash now dana@granada:˜$ exit [dana@granada ˜]$ bash dana@granada:˜$ #In bash now, going to hit ctrl D dana@granada:˜$ exit [dana@granada ˜]$ #In original shell now Shell – p.
[Show full text]
UNIX Essentials (Hands-On)
UNIX essentials (hands-on) • the directory tree • running programs • the shell (using the T-shell) → command line processing → special characters → command types → shell variables → environment variables → wildcards → shell scripts → shell commands → pipes and redirection • OS commands • special files 1 • The Directory Tree → directories contain files and/or directories → / : means either the root directory, or a directory separator • consider /home/afniuser/AFNI_data3 afniuser/suma_demo → an "absolute" pathname begins with '/', a "relative" pathname does not • a relative pathname depends on where you start from • in the directories above, note which is a relative pathname → every directory has a parent directory • the relative pathname for the parent directory is '..' • the relative pathname for the current directory is '.' • consider './run_this_script' and '/bin/ls ../../suma_demo' → many commands can be used to return to the home directory (of "afniuser") • cd, cd ~, cd ~afniuser, cd $HOME, cd /home/afniuser • note the 2 special characters, '~' and '$' → while you work, keep your location within the directory tree in mind 2 → class work: • open a terminal window • commands: cd, pwd, ls, ls -al • use the "cd" command to go to the given directories e.g. for directory /usr/bin, use the command: cd /usr/bin once there, use the commands "pwd", "ls", and "ls -al" note that you can always return to the home directory via: cd / home/afniuser AFNI_data3 .. AFNI_data3/afni /usr/bin ~/abin ../../afniuser/../afniuser • first example (starting with the '/'directory), use the commands: cd / pwd ls ls -al 3 • Running Programs → a program is something that gets "executed", or "run" → the first element of a command line is generally a program (followed by a space) → most shells are case sensitive when processing a command → command examples: /bin/ls $HOME ~/AFNI_data3 count -digits 2 1 10 → script: an interpreted program (interpreted by another program) • e.g.
[Show full text]
Unix Tools 1 Jeff Freymueller Resources
Unix Tools 1 Jeff Freymueller Resources • Unix and Linux – It comes with the package • Macintosh – Really a Unix machine with fancy wrapping – Terminal.app • Windows – VirtualBox: hFp://www.virtualbox.org/ – Or you could try Cygwin: hFp://www.cygwin.com/ Outline • What is Unix, what is the shell? • Directories, files, wildcards • RedirecPng input/output, pipes • Variables and control • Power tools: GMT, etc. in future lectures • Need more power? Upgrade to perl! • perl = PracPcal ExtracPon and ReporPng Language • perl = Pathologically Extensible Rubbish Lister! Unix • Unix is the most common operang system for “serious computers” – Developed in 1969 at Bell Labs (of the old AT&T) – At first, could support two simultaneous users! – RewriFen in C in 1973 (before that, assembly language) • From Wikipedia: – Unix was designed to be portable, mulP-tasking and mulP-user in a Pme-sharing configuraon. Unix systems are characterized by various concepts: the use of plain text for storing data; a hierarchical file system; treang devices and certain types of inter-process communicaon (IPC) as files; and the use of a large number of sodware tools, small programs that can be strung together through a command line interpreter using pipes, as opposed to using a single monolithic program that includes all of the same func6onality. These concepts are known as the Unix philosophy. Unix, Unices, Linux • Numerous Unix variants have sprung up over the years, some academic and some commercial. – BSD, Solaris, HP-UX, … – Linux is unix-like, not Unix • Started as a hobby project by Linus Torvalds • Made useful by existence of free, open source sodware tools (like the Gnu project) • OS consists of two major parts: kernel and everything else – Kernel: master control program, starts and stops processes, handles low-level file/disk access, etc.
[Show full text]
A Crash Course on UNIX
AA CCrraasshh CCoouurrssee oonn UUNNIIXX UNIX is an "operating system". Interface between user and data stored on computer. A Windows-style interface is not required. Many flavors of UNIX (and windows interfaces). Solaris, Mandrake, RedHat (fvwm, Gnome, KDE), ... Most UNIX users use "shells" (or "xterms"). UNIX windows systems do provide some Microsoft Windows functionality. TThhee SShheellll A shell is a command-line interface to UNIX. Also many flavors, e.g. sh, bash, csh, tcsh. The shell provides commands and functionality beyond the basic UNIX tools. E.g., wildcards, shell variables, loop control, etc. For this tutorial, examples use tcsh in RedHat Linux running Gnome. Differences are minor for the most part... BBaassiicc CCoommmmaannddss You need these to survive: ls, cd, cp, mkdir, mv. Typically these are UNIX (not shell) commands. They are actually programs that someone has written. Most commands such as these accept (or require) "arguments". E.g. ls -a [show all files, incl. "dot files"] mkdir ASTR688 [create a directory] cp myfile backup [copy a file] See the handout for a list of more commands. AA WWoorrdd AAbboouutt DDiirreeccttoorriieess Use cd to change directories. By default you start in your home directory. E.g. /home/dcr Handy abbreviations: Home directory: ~ Someone else's home directory: ~user Current directory: . Parent directory: .. SShhoorrttccuuttss To return to your home directory: cd To return to the previous directory: cd - In tcsh, with filename completion (on by default): Press TAB to complete filenames as you type. Press Ctrl-D to print a list of filenames matching what you have typed so far. Completion works with commands and variables too! Use ↑, ↓, Ctrl-A, & Ctrl-E to edit previous lines.
[Show full text]
Configuring Your Login Session
SSCC Pub.# 7-9 Last revised: 5/18/99 Configuring Your Login Session When you log into UNIX, you are running a program called a shell. The shell is the program that provides you with the prompt and that submits to the computer commands that you type on the command line. This shell is highly configurable. It has already been partially configured for you, but it is possible to change the way that the shell runs. Many shells run under UNIX. The shell that SSCC users use by default is called the tcsh, pronounced "Tee-Cee-shell", or more simply, the C shell. The C shell can be configured using three files called .login, .cshrc, and .logout, which reside in your home directory. Also, many other programs can be configured using the C shell's configuration files. Below are sample configuration files for the C shell and explanations of the commands contained within these files. As you find commands that you would like to include in your configuration files, use an editor (such as EMACS or nuTPU) to add the lines to your own configuration files. Since the first character of configuration files is a dot ("."), the files are called "dot files". They are also called "hidden files" because you cannot see them when you type the ls command. They can only be listed when using the -a option with the ls command. Other commands may have their own setup files. These files almost always begin with a dot and often end with the letters "rc", which stands for "run commands".
[Show full text]
Cygwin User's Guide
Cygwin User’s Guide i Cygwin User’s Guide Cygwin User’s Guide ii Copyright © 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012 Red Hat, Inc. Permission is granted to make and distribute verbatim copies of this documentation provided the copyright notice and this per- mission notice are preserved on all copies. Permission is granted to copy and distribute modiﬁed versions of this documentation under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this documentation into another language, under the above conditions for modiﬁed versions, except that this permission notice may be stated in a translation approved by the Free Software Foundation. Cygwin User’s Guide iii Contents 1 Cygwin Overview 1 1.1 What is it? . .1 1.2 Quick Start Guide for those more experienced with Windows . .1 1.3 Quick Start Guide for those more experienced with UNIX . .1 1.4 Are the Cygwin tools free software? . .2 1.5 A brief history of the Cygwin project . .2 1.6 Highlights of Cygwin Functionality . .3 1.6.1 Introduction . .3 1.6.2 Permissions and Security . .3 1.6.3 File Access . .3 1.6.4 Text Mode vs. Binary Mode . .4 1.6.5 ANSI C Library . .5 1.6.6 Process Creation . .5 1.6.6.1 Problems with process creation . .5 1.6.7 Signals . .6 1.6.8 Sockets . .6 1.6.9 Select .
[Show full text]
Shells and Shell Programming
Shells & Shell Programming (Part A) Software Tools EECS2031 Winter 2018 Manos Papagelis Thanks to Karen Reid and Alan J Rosenthal for material in these slides SHELLS 2 What is a Shell • A shell is a command line interpreter that is the interface between the user and the OS. • The shell: – analyzes each command – determines what actions are to be performed – performs the actions • Example: wc –l file1 > file2 3 Which shell? • sh – Bourne shell – Most common, other shells are a superset – Good for programming • csh or tcsh – command-line default on EECS labs – C-like syntax – Best for interactive use. • bash – default on Linux (Bourne again shell) – Based on sh, with some csh features. • korn – written by David Korn – Based on sh – Some claim best for programming. – Commercial product. 4 bash versus sh • On EECS labs, when you run sh, you are actually running bash. • bash is a superset of sh. • For EECS2031, you will be learning only the features of the language that belong to sh. 5 Changing your shell • I recommend changing your working shell on EECS to bash – It will make it easier to test your shell programs. – You will only need to learn one set of syntax. • What to do: – echo $SHELL (to check your current shell) – chsh <userid> bash – Logout and log back in. – .profile is executed every time you log in, so put your environment variables there 6 Standard Streams • Preconnected input and output channels between a computer program and its environment. There are 3 I/O connections: – standard input (stdin) – standard output (stdout) – standard
[Show full text]
An Introduction to the C Shell
-- -- An Introduction to the C shell William Joy (revised for 4.3BSD by Mark Seiden) Computer Science Division Department of Electrical Engineering and Computer Science University of California, Berkeley Berkeley, California 94720 ABSTRACT Csh is a newcommand language interpreter for UNIX†systems. It incorporates good features of other shells and a history mechanism similar to the redo of INTERLISP. While incorporating manyfeatures of other shells which makewriting shell programs (shell scripts) easier,most of the features unique to csh are designed more for the interac- tive UNIX user. UNIX users who have read a general introduction to the system will ﬁnd a valuable basic explanation of the shell here. Simple terminal interaction with csh is possible after reading just the ﬁrst section of this document. The second section describes the shell’s capabilities which you can explore after you have begun to become acquainted with the shell. Later sections introduce features which are useful, but not necessary for all users of the shell. Additional information includes an appendix listing special characters of the shell and a glossary of terms and commands introduced in this manual. Introduction A shell is a command language interpreter. Csh is the name of one particular command interpreter on UNIX.The primary purpose of csh is to translate command lines typed at a terminal into system actions, such as invocation of other programs. Csh is a user program just likeany you might write. Hopefully, csh will be a very useful program for you in interacting with the UNIX system. In addition to this document, you will want to refer to a copyofthe UNIX User Reference Manual.
[Show full text]
Intro to Unix 2018
Introduction to *nix Bill Renaud, OLCF ORNL is managed by UT-Battelle for the US Department of Energy Background • UNIX operating system was developed in 1969 by Ken Thompson and Dennis Ritchie • Many “UNIX-like” OSes developed over the years • UNIX® is now a trademark of The Open Group, which maintains the Single UNIX Specification • Linux developed by Linus Torvalds in 1991 • GNU Project started by Richard Stallman in 1983 w/aim to provide free, UNIX-compatible OS • Many of the world’s most powerful computers use Linux kernel + software from the GNU Project References: 1www.opengroup.org/unix 2https://en.wikipedia.org/wiki/Linux 2 3https://www.gnu.org/gnu/about-gnu.html This Presentation • This presentation will focus on using *nix operating systems as a non-privileged user in an HPC environment – Assumes you’re using a ‘remote’ system – No info on printing, mounting disks, etc. • We’ll focus on systems using the Linux kernel + system software from the GNU project since that’s so prevalent • Two-Part – Basics: general information, commands – Advanced: advanced commands, putting it all together, scripts, etc. 3 This Presentation • May seem a bit disjoint at first – Several basic concepts that don’t flow naturally but later topics build upon – Hopefully everything will come together, but if not… • I’ll cover (what I hope is) some useful info but can’t cover it all – People write thousand-page books on this, after all • Please ask questions! 4 Basics Terminology • User – An entity that interacts with the computer. Typically a person but could also be for an automated task.
[Show full text]
Lmod Documentation Release 8.5.16
Lmod Documentation Release 8.5.16 Robert McLay Sep 24, 2021 Contents 1 PURPOSE 1 2 OVERVIEW 3 3 Lmod Web Sites 5 4 Introduction to Lmod 7 5 Installing Lmod 27 6 Advanced Topics 55 7 Topics yet to be written 119 8 Indices and tables 121 i ii CHAPTER 1 PURPOSE Lmod is a Lua based module system that easily handles the MODULEPATH Hierarchical problem. Environment Modules provide a convenient way to dynamically change the users’ environment through modulefiles. This includes easily adding or removing directories to the PATH environment variable. Modulefiles for Library packages provide environment variables that specify where the library and header files can be found. 1 Lmod Documentation, Release 8.5.16 2 Chapter 1. PURPOSE CHAPTER 2 OVERVIEW This guide is written to explain what Environment Modules are and why they are very useful for both users and system administrators. Lmod is an implementation of Environment Modules, much of what is said here is true for any environment modules system but there are many features which are unique to Lmod. Environment Modules provide a convenient way to dynamically change the users’ environment through modulefiles. This includes easily adding or removing directories to the PATH environment variable. A modulefile contains the necessary information to allow a user to run a particular application or provide access to a particular library. All of this can be done dynamically without logging out and back in. Modulefiles for applications modify the user’s path to make access easy. Modulefiles for Library packages provide environment variables that specify where the library and header files can be found.
[Show full text]