Installation Guide TopSpin 2.1 Red Hat Enterprise Linux WS 4 Version 2.1.
Copyright (C) 2007 by Bruker BioSpin GmbH INDEX Part-No: H9556SL2/10 DONE INDEX revision state: 19/10/2007 (Version 2.1.0) The information in this manual may be altered without notice. BRUKER accepts no liability for any mistakes contained in the manual, leading to coincidental damage, whether during installation or operation of the instrument.
Contents Chapter 1 1.1 1.2 1.3 1.4 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 About this manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Safety Regulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.3 Installing TOPSPIN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 4.3.1 4.3.2 Installation in parallel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 What do you want to do with TOPSPIN? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 4.6.1 4.6.2 4.6.3 Requirements for NMR Guide 4.0 . . . . . . . . . . . . . . . . . . .
7.1.1 7.1.2 7.1.3 7.1.4 7.1.5 7.1.6 Chapter 8 Plotting and printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 Print/Plot from the Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 Plot data from the Processing guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 Plot INDEX data with the TOPSPIN PLOT EDITOR . . . . .
11.2.2 Installation of a Unix network printer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151 11.2.3 Installation of a Windows network printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156 11.2.4 Installation of a Jet Direct printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
13.1.7 find . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13.1.8 ps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13.1.9 kill . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13.1.10 compress, gzip. . . . . . . . . . . . . .
16.1.1 Automatic notification for helium refill . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257 16.1.1.1 Set minimum limit of helium level . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257 16.1.1.2 Create shell script ’heliumwarn’ for email notification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258 16.2 Script for saving important files . . . . . . . . . . . . . . . . . . . . . . .
Chapter 1 Introduction 1.1 About this manual This manual describes the installation of the TOPSPIN 2.1 under RED HAT ENTERPRISE LINUX WS 4. It is available: • as a hard copy ’Installation Guide for TOPSPIN RED HAT ENTERPRISE LINUX WS 4’. The print-version of the Installation Guide is actualized in planned intervals. • as pdf file on the toplevel of the TOPSPIN 2.1 DVD • as TOPSPIN 2.
Introduction The first part shows how to install and configure TOPSPIN and some essential additional software packages. It is recommended to follow the instructions step by step. INDEX Part two describes the scratch installation of RED HAT ENTERPRISE LINUX WS 4 INDEX and some configuration steps likeDONE setup for network and printers. If you want to install Bruker BioSpin TOPSPIN on a PC which is already in use, you can skip this part.
Introduction 11 1.3 Safety Regulations INDEX In order to work safety in laboratories with NMR-spectrometers all users have to follow the safety regulations for magnetic, electrical, cryogenic and chemical INDEX DONE safety. For detailed information please refer to the safety instructions in the Beginners Guide Manual provided on the TOPSPIN DVD. 1.4 Hardware and software requirements for TopSpin 1.4.1 Supported operating systems TOPSPIN 2.
Introduction that Bruker cannot support the use of above-named systems. For detailed information please look up the software support matrix, provided in pdf-format, on the Bruker Web server under following address: INDEX http://www.bruker-biospin.com/documentation_general.html DONE INDEX 1.4.2 Special PC Hardware requirements To run TOPSPIN 2.
Introduction 13 Hardware components that are TOPSPIN version or operating system dependent are listed below. Components that are not listed here do not need an upgrade for TOPSPIN 2.1. INDEX If your Avance INDEX spectrometer does not meet the above specifications, please get in DONE touch with your local Bruker BioSpin representative for your upgrade options. 1.4.3.
Introduction • FCU 4: FCU 4 required minimum EC Level part # H9727 any part # H9773 INDEX DONE INDEX any • RCU: RCUa EC level RCU 1/2 (part # Z003678) any RCU 1/3 (part # Z022488) any a.
• TCU 3: TCU 3 required minimum EC Level part # H5813, EC level 00 to 19 09 (recommended 12) part # H5813, EC level > 20 28 (recommended 31) part # H5813V1 any (recommended 01) part # H5813F2 any (recommended 01) part # H5813F3 any (recommended 01) RX22 EC Level part # HZ002810 any (recommended 08) part # Z012810 any (recommended 02) part # Z032810 any (recommended 01) • RX22: 1.4.3.
Introduction • IPSO-AQSS H9984 IPSO-AQSS H9984 required minimum EC Level INDEX Ipso-ACQ host part # H12547 Ipso-ACQ acq part # H12549 PCI adapter board part # H12557 Hr-board part # H12553 FTMS-board part # H 12555 DONE INDEX any any any any any • DPP1: DPP1 required minimum EC Level part # H12513f1 any 1.4.4 Software requirements ! Because of the variety of Linux systems and their possible problems with some PC-hardware components, Bruker BioSpin can not support all of them.
1.5 Important Red Hat Linux Enterprise WS 4 configurations 1.5.1 KDE - desktop manager: recommended by Bruker BioSpin ! All information described in this manual is based on the desktop manager KDE. If you use GNOME, there will be some differences in handling. In the login window, type in: • your login name • your password • choose as Session KDE1 and press Enter 1. You can define your default login session with the command switchdesk when you are logged in.
Introduction INDEX DONE INDEX
Express Installation and Configuration of TOPSPIN 19 Chapter 2 INDEX INDEX DONE Express Installation and Configuration of TOPSPIN 2.1 About this chapter This chapter gives a brief description of how to install Bruker BioSpin’s TOPSPIN. In order to provide installation impressively and short, this chapter only handles with the main aspects of installation. The following is dressed to users who would like to install TOPSPIN 2.
Express Installation and Configuration of TOPSPIN 2.2 Installing TOPSPIN INDEX is where do you want to The main decision you have to make during installation install the new TOPSPIN version. If you a have previous NMR SUITE or TOPSPIN DONE INDEX installation on this PC available, you can either: • install the new version in parallel to the previous one (e.g. old version in /opt/topspin2.0, new in /opt/topspin2.1) or • install the new version in the same directory as the previous one (e.g.
Express Installation and Configuration of TOPSPIN 21 5. The window TOPSPIN Installation Manager appears. 6. The window Welcome! appear. INDEX • Click Next DONE 7. The windowINDEX TOPSPIN Release Letter will appear: Please read the NMR Release letter! You can find therein all information about new features and bug fixes of the current version . • When you have finished reading the Release Letter please click Next. 8.
Express Installation and Configuration of TOPSPIN dow.1 12. If a previous TOPSPIN installation is available in the global environment variaINDEX ble Path, you will be asked if you want to define the current installation path instead. It is recommended to DONE set the current INDEX installation into the PATH variable, so enable:2 Yes, add the new TOPSPIN installation directory to the global PATH • Click Next 13. A window appear that asks for the installation path of FlexLM.
Express Installation and Configuration of TOPSPIN 23 a) Type in the NMR ADMINISTRATION PASSWORD b) Re-enter the NMR ADMINISTRATION PASSWORD INDEX c) Click Next 17. If Data Processing, and automation or Customized with the DiskINDEXacquisition DONE less package was selected in step 8 a window will appear to inform that the spectrometer has to be shut down. a) If the PC is not yet connected to a spectrometer or if the CCU is not booted1 you can promptly.
Express Installation and Configuration of TOPSPIN windows (e.g. an editor window) and check if no other users are logged in into this PC) then click Yes. INDEX • If you have not installed DISKLESS a window will appear that informs you to log out and log back in before you start TOPSPIN, click Seen. DONE INDEX 20. The window wherein you entered the root password informs you that you have to press Enter to close this window. • Press Enter 21.
Express Installation and Configuration of TOPSPIN 25 When a user starts a new TOPSPIN version for the first time, a window LICENSE will appear: INDEX a) Please read the license agreement for Bruker TOPSPIN ! b) If you agree, please clickDONE I Accept. INDEX Now the window Configuration check will appear, that allows you to configure the software. If you have to click on Cf or Expinstall depends on what you want to do with TOPSPIN. You are mainly in one of the following situations: 1.
2.3.2 If your PC controls a spectrometer: 1. Be sure that the spectrometer is booted (see chapter 9.3.2 and 12.3.1.7) 2. Open a dataset • Type new and create a new dataset. • You can also select a dataset (e.g. exam1d_1H) acquired with another TOPSPIN or XWIN-NMR version 3. Enter cf (The command cf now configures the software according to the hardware of your spectrometer.) a) A window will appear: Password request. Please enter the NMR ADMINISTRATION PASSWORD Type in the NMR ADMINISTRATION PASSWORD.
f) A window will appear: Additional configuration. Security check. Enable peak power check (POWCHK). Enable puls power check (PULCHK). Choose the options if you want to use this security options. Powchk and Pulchk require special probes and cortab. If in doubt contact your local Bruker BioSpin representative, please.
d) In the appearing window: Check the required system → Click Next e) In the appearing dialog box: Select the spectrometer configuration name → Click Next f) In the appearing dialog box: Check the items you want to install or, accept the default selection → Click Next g) In the appearing dialog box: Select the default printer and plotter and the desired paper format → Click Next h) In the appearing window: Enter the desired spectrometer frequency, acquisition mode and pre-scan-delay or, accept the default v
After cf, expinstall,... have finished insert a sample and make sure that you can lock on the lock solvent. Type ii and read with rpar a standard Bruker BioSpin parameter file (e.g. 'rpar PROTON all'), type getprosol, rga, wobb and zg and collect a normal 1H NMR spectrum. 2.3.3 If you want to configure a processing-PC like your spectrometer-PC: If the PC does not control a spectrometer but is used in connection with a particular spectrometer, e.g.
Express Installation and Configuration of TOPSPIN INDEX DONE INDEX
Express Installation and Configuration of TOPSPIN Part I INDEX INDEX DONE TopSpin Installation and Configuration 31
Express Installation and Configuration of TOPSPIN INDEX DONE INDEX
General Installation Information 33 Chapter 3 INDEX INDEX DONE General Installation Information 3.1 Installation order A complete new installation on a PC connected to a spectrometer involves the following steps: 1. Installing RED HAT ENTERPRISE LINUX WS 4 (see chapter 9.1) 2. Installing additional packages (see chapter 9.2) Step 1 to 2 are normally already done by the manufacturer. 3. Configuring the network (see chapter Chapter 10) 4. Installing TOPSPIN (see chapter 4.3) 5.
General Installation Information INDEX DONE INDEX
Installing TOPSPIN 35 Chapter 4 INDEX INDEX DONE Installing TOP SPIN 4.1 NMR SUPERUSER and NMR ADMINISTRATION PASSWORD TOPSPIN offers a complete new password check for the configuration tools of TOPSPIN. During the TOPSPIN installation, you are prompted to define: 1. The username for the so called NMR SUPERUSER. The NMR SUPERUSER can be nmrsu (this is the default) or any other user (if the user does not exists so far, it will automatically be created during installation process).
Installing TOPSPIN them does not affect the other. With the information about the NMR ADMINISTRATION PASSWORD and NMR INDEX NMR ADMINISTRATION PASSSUPERUSER TOPSPIN is ready to be configured. The WORD will be asked for every time a configuration type command is entered. If this DONE INDEX password is typed in correctly, the command will be executed regardless of which user is logged in the operating system.
Installing TOPSPIN 37 4.1.2 How to define a new NMR ADMINSTRATION PASSWORD To define a new NMR ADMINISTRATION PASSWORD, for example because you INDEX have forgotten it, you have to: INDEX 1. Open a Linux shell DONE 2. Login as root with the command su 3. Delete the file /conf/nmradminpassword 4. Enter the command prog/bin/installnmr 5. Enter new password as requested.
Installing TOPSPIN 3. NMR-GLP: Program for ’Good Laboratory Practice’ tests 4. FLEXLM: License manager required for starting TOPSPIN programs. 5. AUREMOL INDEX DONEabout theINDEX Please note that all version information different programs can be found on the TOPSPIN DVD and in the latest version of the Release Letter. 4.3 Installing TOPSPIN This chapter describes the installation of the TOPSPIN.
Installing TOPSPIN 39 • If the shell of the next step does not appear automatically you have click on the DVD icon on your desktop and click on the file install 1 INDEX 4. If you are not logged in as root, a Linux shell will appear that asks you for the root password: INDEX DONE Please enter root password if prompted for it: Password: • Enter root password and press enter 5. The windows TOPSPIN Installation Manager and Welcome to the Bruker Software Installation Manager will appear: • Click Next 6.
Installing TOPSPIN 7. A window Please select a target directory for TOPSPIN will appear: INDEX DONE Enter an installation /opt/topspin2.1 path which INDEX does not exists so far, e.g. • Click Next 8. If the installation directory does not exist you will be asked if the installation process should create it automatically • Click Yes 9. A window Please select the setup type will appear: a) Select the setup type.
Installing TOPSPIN 9.1. 41 If Customized was selected in step 9 ... INDEX INDEX DONE ... a window Please select products to install will appear: • Select the packages which you want to install (note that DISKLESS is only required if your PC controls a spectrometer or you want to configure it like this (see chapter 6.2.2).
Installing TOPSPIN • FLEXlm: License manager required for starting TOPSPIN programs. • NMR-GLP: Program for’Good Laboratory INDEX Practice’ tests (requires separate license) • Click Next DONE INDEX 10. The window Select a spectrometer configuration to import will appear. You can either import no spectrometer configuration, or browse for a spectrometer configuration or select one of the configurations you get offered within this window.
Installing TOPSPIN 43 recommended to accept the default path! 1 INDEX INDEX DONE • Click Next 13. A window appear that displays the programs which will be installed • Click Next 14. A window will appear that prompted for a definition of an NMR SUPERUSER a) Do one of the following: • Accept the default NMR SUPERUSER (nmrsu) or • Enter a special user for this purpose, e.g. named nmr-admin or 1.
Installing TOPSPIN • Enter any other user If the user does not exists, installation will create it. For further details see chapter 4.1 or the TOPSPIN Users Guide. INDEX b) Click Next DONE INDEX 15. A window Password Input will appear and asks for the NMR ADMINISTRATION PASSWORD1 (for more details about this feature see chapter 4.1) • Type in the NMR ADMINISTRATION PASSWORD • Re-enter in the NMR ADMINISTRATION PASSWORD c) Click Next → The installation of TOPSPIN will start now. 16.
b) If your PC is currently connected to a spectrometer and the CCU is booted (see chapter 9.3.2 and 12.3.1.7) a) Open a Linux shell b) enter the command: telnet spect c) login as root d) enter the command: init 5 → this will shut down the CCU e) Close the Linux shell f) Click Next in the window that asked you about shutdown the CCU Note: The CCU is now either down or switched off and should be turned on again at the end of this procedure. → The installation of TOPSPIN will start now. 17.
Installing TOPSPIN windows (e.g. an editor window) and check if no other users are logged in into this PC) then click on Yes INDEX DONE INDEX • If you have not installed DISKLESS a window will appear that informs you to log out and log back in before you start TOPSPIN, click Seen 19. The window wherein you entered the root password informs you that you have to press Enter to close this window • Press Enter 20.
Installing TOPSPIN 47 4.4 Perl and GCC The packages INDEX Perl and GCC are automatically installed in the directory /gnu and /perl where INDEX DONE is the directory where TOPSPIN is installed (default /opt/topspin). Perl and GCC are needed for compiling TOPSPIN AU programs. 4.5 Installing TopSpin patches TOPSPIN patches are parts of TOPSPIN which contain bug fixes. They are available on the Bruker BioSpin WWW server.
Installing TOPSPIN We will then send you the information by email. 4.6 The usage of the NMR-GUIDE DONE INDEX INDEX NMR-GUIDE 4.0 that comes with TOPSPIN 2.1 uses an own web server and the TOPSPIN internal java package. Therefore it is not necessary anymore to have these packages installed/configured separately! 4.6.1 Requirements for NMR Guide 4.0 The using of NMR-GUIDE 4.0 requires the installation of TOPSPIN 2.1. Also be sure that the following components are installed: 1. Web browser 2.
Installing TOPSPIN 49 4.6.2 Java Requirements for NMR-GUIDE 4.0 For using NMR-GUIDE 4.0 that comes with the TOPSPIN 2.1 version it is not necesINDEX a special Java package. NMR-GUIDE uses the TOPSPIN sary to install/configure internal Java package that is automatically INDEX DONE installed and configured during installation of TOPSPIN. 4.6.3 Working with the NMR-GUIDE In order to work with the NMR-GUIDE, the following procedure must be followed. 4.6.3.1 Start up of the NMR-GUIDE 1.
Installing TOPSPIN http://localhost:6600/guide/index.html INDEX DONE INDEX You can now use the functionality of NMR-GUIDE 4.6.3.2 Using the NMR-GUIDE search engine One of the very important and useful tools of NMR-GUIDE is its search engine. It offers the possibility to search within thousands of html pages that contain a huge amount of information about NMR spectroscopy.
The TOPSPIN license 51 Chapter 5 INDEX INDEX The TOP SPINDONE license 5.1 Questions and answers about the TOPSPIN license 1. Which programs need a license? TOPSPIN, NMR-SIM and NMR-GUIDE need a license. If you do not have a license for TOPSPIN, it will start up in an emergency mode if your PC is connected to a spectrometer. However, NMR-SIM and NMR-GUIDE will not run without a valid license. ICON-NMR is always used in connection with TOPSPIN and does not need an individual license.
https://www.bruker-biospin.de/NMR/nmrsoftw/licenses or contact your local Bruker BioSpin representative.
If more than one license is available, as many copies of the program as are covered by the license can be started simultaneously. 4. Which licensing program is used for TOPSPIN? The Flexlm license manager is used and is delivered on the TOPSPIN DVD. It contains the ’bruker_lmgr’ license manager, the ’lmutil’ program, Help files and example license.dat file. 5. What are the requirements for the Flexlm to function: Your PC must have an Ethernet card 6.
The TOPSPIN license • The operating system on the three computers can be the same or can be different (Linux, Windows). 8. What is a Node Locked license? INDEX A node-locked license allows DONE you to start theINDEX respective program only on the computer with the Host-ID for which that license was generated. Typically, this license form is used for Demo and Teaching licenses. No other computer can use the license in the way described above for floating licenses. 9.
The TOPSPIN license 55 No, a Demo license is Node Locked uncounted and therefore only requires FEATURE lines. If SERVER and/or DAEMON lines exist, they are ignored. INDEX 14. I have a Floating license. Must the file license.dat be identical on all hosts, server and clients? INDEX DONE Yes, you have to install the license.dat on the server and copy it to all clients. 15. Must the Flexlm license manager run on all hosts in the network? No, it only needs to run on the license server.
The TOPSPIN license • the number of licenses and your order number (not necessary for demo license) Licenses can be ordered from the German BrukerINDEX BioSpin web server: https://www.bruker-biospin.de/NMR/nmrsoftw/licenses DONE INDEX 5.2.2 How do I determine the correct hostid The hostid is a 12-digit hexadecimal number. It is the physical address (also called Mac address or Node address) of the Ethernet card.
The TOPSPIN license 57 DAEMON bruker_ls /usr/local/flexlm/Bruker/bruker_ls FEATURE TOPSPIN1 bruker_ls 0.0 6-aug-2018 3 0B0E4011FF0CD32FBFF1 \ vendor_info=" INDEX for hostid(s) : 0060080e830d" ISSUER=00047573d35e FEATURE TOPSPIN_1D bruker_ls 0.0 6-aug-2018 3 9B3EA021818829E2716A \ INDEX DONE vendor_info=" for hostid(s) : 0060080e830d" ISSUER=00047573d35e FEATURE TOPSPIN_2D bruker_ls 0.
The TOPSPIN license INDEX DONE INDEX
Configuration of TOPSPIN 59 Chapter 6 INDEX INDEX DONE Configuration of TOPSPIN The idea of this chapter is to give you some guidelines to full spectrometer or workstation configuration. We do not discuss the commands in detail here. For a full description refer to the TOPSPIN manual. 6.1 Take over the configuration of XWIN-NMR/TOPSPIN into TOPSPIN 2.1 The decision how to install TOPSPIN is very important in case you have already XWIN-NMR or TOPSPIN installed on the same or another PC.
Configuration of TOPSPIN 6.1.1 You have a TopSpin/XWIN-NMR configuration that you like to use for TopSpin (on the same PC) INDEX You can take over the configuration during the Installation of TOPSPIN 2.1 (see chapter 4.3) or after the installation with the TOPSINDEX PIN command nmr_save. DONE During the installation you will be asked if you want to import a spectrometer configuration.
Configuration of TOPSPIN 61 6.1.2 You have a TopSpin/XWIN-NMR configuration that you like to use for TOPSPIN (on another PC) INDEX Before you start installation of TOPSPIN on PC-A you have to copy the two directories: INDEX DONE conf , plot and exp from the TOPSPIN/XWIN-NMR installation on the PC-B into the directory where TOPSPIN will be installed.
Configuration of TOPSPIN software. If you have to click on Cf or Expinstall depends on what you want to do INDEX DONE INDEX with TOPSPIN. You are mainly in one of the following situations: 1. You want to configure a processing-only-PC with a default configuration on a datastation → go to chapter 2.3.1 (for details see chapter 6.2.3) 2.
Configuration of TOPSPIN 63 b) A window Cf will appear: INDEX INDEX DONE Most likely you will select an existing configuration and press Edit to confirm this configuration. c) A window will appear: The selected configuration is displayed. Choose the type of your spectrometer e.g. AVANCE → ENTER. Check or type in the 1H frequency of the magnet e.g. 500.13 → ENTER.
Configuration of TOPSPIN of trouble-shooting. INDEX DONE INDEX d) In case the information window mod hconfserver appears: • your spectrometer has not a BSMS rack with ECLB board: you may ignore this warning → ENTER. Nevertheless please check the configuration summary (uxnmr.info file) if all units are listed. • your spectrometer has a BSMS rack with ECLB board and the DHCP server might not work correctly. For troubleshooting information see chapter 12.3.
Configuration of TOPSPIN 65 nected. The RS232/485 channel for external devicesTable appears. CheckINDEX if the tty-numbers of the hardware components are set correctly. f) A window will appear:DONE INDEX Additional configuration. Security check. Enable peak power check (POWCHK). Enable puls power check (PULCHK). Choose the options if you need this security options.
Configuration of TOPSPIN the NMR ADMINISTRATION PASSWORD a couple of times): INDEX DONE INDEX • Continue with expinstall a) Type in the NMR ADMINISTRATION PASSWORD and ENTER b) Click Next if you either have no modified Bruker BioSpin-Parameterfiles,
Configuration of TOPSPIN 67 AU-programs and Pulse-programs (If you have some, you have to archive them in a different directory before executing expinstall).
Configuration of TOPSPIN In the dialog box that appears → Check the items you want to install or, accept the default selection → Click Next INDEX DONE INDEX f) In the dialog box that appears → Select the default printer and plotter and the desired paper format → Click Next g) In the window that appears → Enter the desired spectrometer frequency, acquisition mode and pre-scan-delay or accept the default values
Configuration of TOPSPIN 69 → Click Next INDEX INDEX DONE h) In the information box that appears → Check the configuration selection and, if it is correct → Click Finish When expinstall is finished you can go ahead with the other configuration commands.
Configuration of TOPSPIN • Continue with edsolv INDEX DONE INDEX Check the list of lock solvents and click Save if it is correct → Click Close • Continue with edhead Select the current probe, click the button Define as current probe → Click Exit • A window ’Edit Spectrometer Parameter’ will appear:
Configuration of TOPSPIN 71 INDEX INDEX DONE Check if the connections between preamplifier and probe are set correctly → click Save if it is correct → Click Close • Continue with edprosol Check the parameters for your favorite nuclei, change them and calculate them, if necessary → Click Save to store to disk → Click Exit
Configuration of TOPSPIN • Continue with edlock INDEX DONE INDEX Check the lock table values (field, lock phase, ...), change them and click Save if necessary, otherwise click Abort • Continue with edscon Check the spectrometer constants, change it and click Save if necessary, otherwise click Cancel After cf, expinstall,... have finished, insert a sample and make sure that you can lock on the lock solvent.
Configuration of TOPSPIN 73 6.2.2 If you want to configure a processing-PC like your spectrometer-PC: If the PC does not control a spectrometer but is used in connection with a particuINDEX lar spectrometer, e.g. for setting up experiments, processing and or plotting, you should configure it as that spectrometer. INDEX DONE For example the spectrometer is a AV300 configured with the name 'av300'. Do the following.
Configuration of TOPSPIN Pulse-programs that have different names to the original Bruker BioSpin files will not be destroyed during the installation INDEX DONE INDEX g) In the appearing window → Edit Spectrometer Parameter, check if the connections between preamplifier and probe are set correctly → click Save if it is correct → Click Close h) In the appearing window → Check Installation for Datastation (Customize) → Click Next
Configuration of TOPSPIN 75 INDEX INDEX DONE i) In the window that appears → Check the boxes of the NMR categories you are interested in1 → Click Next j) In the appearing dialog box → Select the spectrometer configuration name → Click Next 1. This selection defines which parametersets and pulse programs are available for usage after configuration is finished.
Configuration of TOPSPIN k) In the appearing dialog box → Check the items you want to install or, accept the default selection → Click Next INDEX DONE INDEX l) In the appearing dialog box → Select the default printer and plotter and the desired paper format → Click Next
Configuration of TOPSPIN 77 m) In the appearing window → Enter the desired spectrometer frequency, acquisition mode and pre-scan-delay or, accept the default values → Click Next INDEX INDEX DONE n) In the appearing information box → Check the configuration selection and, if it is correct → Click Finish The installation of the selected items, will start now. Wait until this process has finished.
Configuration of TOPSPIN mand in the Acquisition Reference manual. 6.2.3 If you want to use a default configuration on a datastation INDEX A default configuration can be used on a datastation. It is automatically performed DONE INDEX (no cf required) during the installation of TOPSPIN on a new computer, a new disk or in a new TOPSPIN installation directory. There are two default configuration available Bruker_default_av500 and Bruker_default_avi300 which correspond to two different Avance spectrometer.
Configuration of TOPSPIN 79 6.3.1 Firmware Update for boards without ethernet connection This chapter describes how to update the firmware for boards without ethernet INDEX connection on the example LCB board.
Configuration of TOPSPIN • A dialog comes up in the shell INDEX DONE INDEX 4. To check and eventually download a new firmware (from TOPSPIN) • type 2→ ENTER The check starts and ends for example as shown in the following picture A if there is a problem with a component you get an information to contact your service office if you need a firmware update you will get a message (A) with the length of time for the download (B). It is recommended to do the download as soon as possible. 5.
Configuration of TOPSPIN 81 • If you have done a download of newer firmware, you have to do cf again! • If you do not need any downloads, you can follow the instructions in the commandINDEX prompt to exit this tool. INDEX DONE 6.3.2 Firmware Update for boards with ethernet connection This chapter describes how to update the firmware for boards with ethernet connection on the example ELCB board.
Configuration of TOPSPIN 2. A window BSMS Service Web - Main appears. Click on Device Setup. INDEX DONE INDEX 3. The BSMS Service Web - Setup page appears. Click on the button Browse to select the BsmsCheckDownload.txt file. In a default installation this file is stored in the directory: C:\Bruker\TOPSPIN\conf\instr\servtool\bsmscnf\ Note: Selecting Get File BsmsCheckDownload.txt from Bruker ftp server is only necessary if a Bruker Service Engineer recommends to do this. 4.
Configuration of TOPSPIN 83 6. The BSMS Service Web - ELCB Firmware Download page appears. INDEX INDEX DONE Click on the button Browse to select the firmware version which is mentioned in the line Select the file.... In a default installation the file is stored in the directory: C:\Bruker\TOPSPIN\conf\instr\servtool\bsmscnf\ 7. Click on the button install firmware. Note: Selecting Get File elcb_firmware_XXXXXX.
Configuration of TOPSPIN 1. Please open the BSMS Service Web page. Click on Service. INDEX DONE INDEX 2. The ELCB Service Web page appears. Click under Active User Configuration / Parameters on Save to Disc. 3. The BsmsSaveUsrNvm.txt page appears. Click in the browser window on File → Save as... and choose the directory where the file BsmsSaveUsrNvm.
Configuration of TOPSPIN 85 should be stored. INDEX INDEX DONE 6.3.2.2 ELCB board: Restore user configuration 1. Please open the BSMS Service Web page. Click on Service. 2. The ELCB Service Web page appears.
Configuration of TOPSPIN Parameters on Save to Disc. INDEX DONE INDEX 3. The ELCB Service Web page appears. Under User Level you have to enter the User and Password and click on Login. Note: To get these two information please get in contact with your local Bruker BioSpin office. Addresses of several offices can be found in chapter 17, for contact information about all Bruker BioSpin office please go to our web server: http://www.bruker-biospin.de/NMR/about/offices 4.
Configuration of TOPSPIN 87 download. Click on Submit Query. INDEX INDEX DONE 6. The BSMS Service Web - Load User Configuration Status appears. Please check if the Status of User Configuration File Load is New User Settings successfully loaded. 6.4 A log of the entire system configuration The showconf command provides you with various information about your hardware and software, both of the PC and of the spectrometer.
Disks and to store the acquired datasets. ! It is strictly recommended to create a frequently backup of the ’VIFs’ - the ’Very Important Files’ - of the configuration of TOPSPIN, in order to make sure to get the information saved and to restore in special cases. There are many reasons like e.g. head crash or theft of the hard disk that makes it important that a weekly or monthly backup is made of important data, so that you would be able to restore the spectrometer configuration in a very short time.
should always use the nmr_save command from the highest software version. If your previous TOPSPIN/XWIN-NMR installation is not located on the same PC, you can even mount the respective network path on your local PC and tell nmr_save to take over the necessary information over the network. 6.5.
Configuration of TOPSPIN 2. Enter the location of the Installation to be saved (default is: ). INDEX 3. nmr_save will then offer a list of all available spectrometer configurations which are located in this respective installation. Select the correct configuration DONE INDEX in the field Spectrometer connfiguration (e.g. spect). In a typical setup your spectrometer configuration is called spect.
Configuration of TOPSPIN 91 ing. Clicking OK will accept the default values an execute nmr_save once in a month. INDEX INDEX DONE This Automatic Backup functionality is offered by the TopSpin command cron described below. 4. Now you can click on Save. This will create an archive file of all necessary information from the selected installation/spectrometer configuration. This file is called nmr_backup_-
Configuration of TOPSPIN can be defined user-specifically or by default. It offers full flexibility in time definition, off-schedule execution and user control. Here you can specify the command to be scheduled, some scheduling options and the starting time and date. The folINDEX lowing fields are available: DONE 1. Command: The command to be executed. INDEX 2. Description: A description of the command. 3. Execution scope: The scope of the command execution, User of TOPSPIN.
The following directories are saved completely (hidden files are ignored!): /conf/instr/autoshim/refmaps/ /conf/instr/probeheads/ /conf/instr//prosol/ /conf/instr//cortab/ /conf/instr//inmrusers/ /conf/instr/topshim/parameters/user /conf/instr/topshim/solvents/user /data/final/nmr/protocolfiles/ /exp/stan/nmr/lists/best-nmr/user/subset/fi /exp/stan/
Configuration of TOPSPIN /plot/layouts/ /prog/tcl/xwish3_scripts/ Additionally, the following files are also saved: INDEX /conf/instr/selpulse.* DONE INDEX /conf/instr/probehead /conf/instr//2Hlock /conf/instr//19Flock /conf/instr//best-nmr/CurrPushSolvent /conf/instr//best-nmr/hardware.par /conf/instr//best-nmr/hardware.
Configuration of TOPSPIN 95 time.tar. This file contains date and time of saving, so that overwriting the tar-file is not possible easily and the data are always available. Please note that Overwriting existing backup file is only possible by saving data twice in the same minute. INDEX It is recommended that all data are backuped on a different Server or CD to prevent INDEX DONE for a motherboard-crash. 6.5.
Configuration of TOPSPIN Please enter the NMR administration password and click OK. 4. Execute the TOPSPIN command cf INDEX DONE 6.5.6 How to use user_save and user_restore INDEX Similar to the function nmr_save and nmr_restore that saves and restores installation specific files, the commands user_save and user_restore save and restore user-specific data in a TAR-file.
to reuse the restored files you can find them in the restore destination you have chosen, in the subdirectory conf/instr with the extension .backup All other files are restored in their original places.
Chapter 7 Plotting and Printing with TopSpin 7.1 Printing / plotting data 7.1.1 Plotting and printing Under RED HAT ENTERPRISE LINUX WS 4, all common printer drivers can be used for plotting and printing. When a printer is installed under RED HAT ENTERPRISE LINUX WS 4, it can be used for plotting from TOPSPIN and TOPSPIN PLOT EDITOR. 7.1.2 Print/Plot from the Menu The current data window can be printed as follows: 1.
Plotting and Printing with TopSpin All these actions are equivalent; they open the Print dialog box. INDEX DONE INDEX 2. In the Print dialog box: • Select Print active window [prnt] • Click OK Before printing starts, the operating system print dialog box will appear to select e.g. the printer and printer properties. The Print dialog box contains two further options: • Print with layout - start Plot Editor [plot] If you select this option and click OK, the Plot Editor will be started.
Plotting and Printing with TopSpin 101 in TOPSPIN are used • from Plot Editor Reset Actions INDEX The plot limits and maximum intensity are set according to the TOPSPIN PLOT INDEX EDITOR Reset Actions DONE(right-click inside the TOPSPIN PLOT EDITOR data field and choose Automation to set the Reset Actions).
Plotting and Printing with TopSpin 7.1.5 Store (Export) a Data Window as Graphics File The clipboard and metafile formats are resizable vector formats. In addition to this, INDEX window in a graphics file of TOPSPIN allows you to save the contents of a data selectable type, e.g. .png, .tif, .wmf etc. To do that: DONE INDEX 1. Click Edit → Export 2. Navigate to the storage folder 3. Enter the destination filename and extension 4.
User Management 103 Chapter 8 INDEX INDEX DONE User Management 8.1 Adding a new user account If you want to add a new user1 and this new user already exists on other hosts in the network, make sure that you use the same User ID and User Name on all hosts in the network. It is also useful to use the same Group ID and Group Name, especially, if you want to mount directories via NFS between IRIX and Linux systems. Perform the following steps: 1. Click → System Settings → User and Groups 2.
User Management 3. A window KDE User Manager will appear: INDEX DONE INDEX • Click Add User 4. A window Create New User will appear • Enter the new User Name • Enter Full Name of the new user • Enter and confirm the password • Make sure that Create home directory is enabled and that a legal path is entered in the field Home directory.
User Management 105 /home/ • The field Create a private group of this user: INDEX a) enabled (default): INDEX This configuration in DONE conjunction with the default umask (002) will lead to the situation, that only the user is able to write in those files he created with the TOPSPIN. That means no other user could work with his spectroscopic data.
User Management 4. A window User Properties will appear: INDEX DONE INDEX • Click on Groups You will see in the appearing window the field Primary Group that shows the original group of the user.
User Management 107 Part II INDEX INDEX DONE RED-HAT Enterprise Linux WS 4 Installation-Tips and Configuration
User Management INDEX DONE INDEX
RED HAT Enterprise Linux WS 4 109 Chapter 9 INDEX INDEX DONE RED HAT Enterprise Linux WS 4 9.1 Hints for installation of Red Hat A Linux NMR workstation purchased from Bruker BioSpin comes with a preinstalled Linux distribution, currently RED HAT ENTERPRISE LINUX WS 4. If you want to install Red Hat by yourself, Bruker BioSpin recommends to use the installation guide of the Red Hat Documentation CD. This offers, in different languages, a very easy and detailed description of all necessary steps.
RED HAT Enterprise Linux WS 4 select Microsoft Intellimouse if you have a wheel mouse, otherwise the middle button will not work correctly) INDEX 3. In the window Disk Partitioning Setup choose Manually partition with Disk Druid 4. In the window Partitioning: DONE INDEX Bruker BioSpin recommends to create the following partitions on a 80GB harddisk.
RED HAT Enterprise Linux WS 4 ! 111 Note: Bruker BioSpin does not support SElinux at the moment. Therefor it is required to choose Disable in the section Enable SELinux! INDEX 8. In the window Timezone Selection: it is necessary to configure DONE the Location, but do not enable System clock uses INDEX UTC 9.
RED HAT Enterprise Linux WS 4 asked to reboot now or later. In case you want to install further CDs it is recommended to click on reboot later, because otherwise this process is stopped. INDEX 18. After finishing this installation you can start T OPSPIN installation (see chapter 2.2 for a brief description or chapter 4.3 for a detailed description) DONE INDEX 9.
If you are not connected to the internet you can install the respective rpms with the browser nautilus. To do this open a shell, enter the command nautilus, click on Places → Computer → CD drive → RedHat → RPMS and double click the respective filename. You have to enter the root password and then the installation process starts. The installation of each of the packages listed above is described in an individual chapter.
RED HAT Enterprise Linux WS 4 Hat Network user name and password.1 INDEX DONE INDEX You will now enter your individual Red Hat network area 1. For details about the registration at Red Hat Network see chapter 15.8.
RED HAT Enterprise Linux WS 4 115 4. Click on Systems INDEX INDEX DONE The list of systems which are registered for your individual Red Hat network account appears 5. Click on the name of the system you want to install the acroread package The summary of this system appears 6. Click on Alter Channel Subscriptions The page switches to the defined Base Software Channel and possible Software Channel Subscriptions. 7. Make sure that Red Hat Enterprise Linux WS (v. 4 for x86) Extra is checked. 8.
RED HAT Enterprise Linux WS 4 9. Click on Packages INDEX DONE INDEX 10. Click on Install New Packages 11. Select all packages which starts with acroread. In case you do not want to install any plugins select the main program acroread- only. 12. Scroll down to the end of the page and click on Install Selected packages 13. You get a summary of all selected packages, click Confirm to start installation. Installation will need a few seconds.
RED HAT Enterprise Linux WS 4 117 up2date --install acroread INDEX INDEX DONE Acrobat reader has now been installed, you can start it from a shell with the command acroread or create a icon on the desktop to start the program (for details see chapter 15.7). It will automatically opened when you open a manual from within TOPSPIN. 9.3.2 nfs-utils The software package nfs-utils is necessary if the PC controls a spectrometer. 1.
RED HAT Enterprise Linux WS 4 You will now enter your individual Red Hat network area 4. Click on Systems INDEX The list of systems which are registered for your individual Red Hat network account appears DONE INDEX 5. Click on the name of the system you want to install the acroread package The summary of this system appears 6. Click on Alter Channel Subscriptions The page switches to the defined Base Software Channel and possible Software Channel Subscriptions. 7.
RED HAT Enterprise Linux WS 4 119 1. Check if glibc-kernheaders and glibc-devel are installed so far • rpm -q glibc-kernheaders INDEX • rpm -q glibc-devel INDEX • is the output like this DONE glibc-kernheaders- glibc-devel- • Yes? You can skip this chapter • No? Go to step 2. 2. Open a web browser and go to: https://rhn.redhat.com/network 3. A web page appears which asks you to login as registered user. Enter your Red Hat Network user name and password.
RED HAT Enterprise Linux WS 4 14. You get a summary of all selected packages, click Confirm to start installation. Installation will need a few seconds. After it is finished you can see the word Done in the lower left corner of the window. INDEX 15. Go to a shell and login as root DONE with the command INDEX su enter your root password 16. Enter the commands up2date --install glibc-kernheaders up2date --install glibc-devel The packages glibc-kernheaders and glibc-devel have now been installed. 9.3.
RED HAT Enterprise Linux WS 4 121 5. Click on the name of the system you want to install the acroread package The summary of this system appears INDEX 6. Click on Alter Channel Subscriptions INDEX DONE The page switches to the defined Base Software Channel and possible Software Channel Subscriptions. 7. Make sure that Red Hat Enterprise Linux WS (v. 4 for x86) Extra is checked. 8. If you have checked this field for the first time you have to click on: Change Subscription 9. Click on Packages 10.
RED HAT Enterprise Linux WS 4 If an entry is off, you can activate it in general: /sbin/chkconfig on DONE INDEX INDEX If an entry is off, you can activate it for a specific runlevel: /sbin/chkconfig --level on for example to start bootparamd at runlevel 5: /sbin/chkconfig --level 5 bootparamd on With chkconfig command you define (permanently) which service will be started/not started on which runlevel after the next reboot.
Network configuration 123 Chapter 10 INDEX INDEX DONE Network configuration 10.1 Configuring the laboratory network The easiest way to add a Linux PC to a laboratory network is using DHCP (Dynamic Host Configuration Protocol). It allows you to go online just by defining the hostname. The IP address, name- and mailserver will be created dynamically.
Network configuration 10.2 Changing the hostname of the PC The hostname of the PC is defined within the INDEX network configuration. Because there are different possibilities how to set up a network correctly (DHCP, fix IP DONE INDEX address or no network connection) there is no general description on how to change the hostname. If you want to change the hostname just follow the instructions given in the chapters 10.4 - 10.6. Changing the hostname may has an effect on programs.
Network configuration 125 The output of this command shows a list of all ethernet cards and gives the information if the connection is working properly or not. INDEX If a ethernet card is not able to be activated in the graphical tool, you can use the following commands (in this example INDEX DONEfor ‚eth0‘): service network restart ifdown eth0 ifup eth0 10.4 Configuring the laboratory network by DHCP 1.
Network configuration 3.
Network configuration 127 e) In the window Network Configuration click on the tab pane Hosts1 INDEX INDEX DONE • Either this entry is correct and was visible in previous Linux versions, you will not see here an entry 127.0.0.1 / Name: localhost.localdomain / Nickname: localhost The operating system controls this entry and does not show it here in this interface. Nevertheless you can check the file /etc/hosts to get the information if this entry is there or not.
Network configuration f) Click on the tab pane DNS 1 INDEX DONE INDEX • enter the hostname without the domainname into the field Hostname 2 • click File → Save • click File → Quit Note that the information given here are very important. In case wrong names/addresses are entered here network calls might end in long time-outs which can cause e.g. acquisition problems. 10.5 Configuring the laboratory network by using a fixed TCP/IP address 1.
Network configuration 129 2. A window Network Configuration will appear INDEX INDEX DONE • On the tab pane Devices click on eth0 and click Edit . Note that it is necessary to use eth0 for your internet connection, because eth1 is required for your spectrometer network connection. 3.
Network configuration Activate device when computer starts • select the field: INDEX Statically set IP addresses and type in the DONE INDEX IP address, Subnet mask and Default Gateway Address that should be used from this PC (if you do not know them, contact your network administrator) • click OK g) In the window Network Configuration click on the tab pane Hosts1 • click Add and create an entry for the IP address of this PC. The Name has to be the full qualified domain name like this: nmrpc.
Network configuration 131 • The two entries ASP_ST2 and spect that can be seen in the picture are necessary for the spectrometer connection. If this PC does not control a spectrometer they INDEX are not necessary. h) Click on the tab pane DNS 1 INDEX DONE • enter the hostname without the domainname into the field Hostname 2 • enter the domain name in the field DNS Search Path • click File → Save • click File → Quit Note that the information given here are very important.
Network configuration 10.6 Spectrometer PC that should not be connected to the laboratory network INDEX In case the spectrometer PC should not be connected to the laboratory network, it DONE INDEX is nevertheless necessary to configure a kind of ’virtual network’. 1. Click → System Settings → Network 1 a window Query will appear and asks for the root password • enter root password 2. A window Network Configuration will appear • On the tab pane Devices click on eth0 and click Edit .
Network configuration 133 3. A window Ethernet Device will appear INDEX INDEX DONE • select the field: Activate device when computer starts • select the field: Statically set IP addresses and enter in the field: Address: 192.168.1.1 and in the field: Subnet Mask: 255.255.255.
i) In the window Network Configuration click on the tab pane Hosts1 • Either this entry is correct and was visible in previous Linux versions, you will not see here an entry 127.0.0.1 / Name: localhost.localdomain / Nickname: localhost The operating system controls this entry and does not show it here in this interface. Nevertheless you can check the file /etc/hosts to get the information if this entry is there or not. • click Add and create an entry for the IP address of this PC.
j) Click on the tab pane DNS 1 • enter the hostname without the domainname into the field Hostname 2 • enter the domain name in the field DNS Search Path • leave the DNS fields empty • click File → Save • click File → Quit Note that the information given here are very important. In case wrong names/addresses are entered here network calls might end in long time-outs which can cause e.g. acquisition problems. 10.
Network configuration lowing chapter can be used for checking the configuration. 10.7.1 Configuration of the spectrometer networkINDEX 1 1. Click → System Settings DONE→ Network INDEX a window Query will appear and asks for the root password • enter root password 2. A window Network Configuration will appear • click on eth1 which is the ethernet card you have to use for the spectrometer network connection and click Edit 1.
Network configuration 137 3. A window Ethernet Device will appear INDEX INDEX DONE • be sure that the field Activate Interface at boot time is checked1 • be sure that the field Allow any user to (de)activate interface is not checked • select the field: Statically set IP address and enter in the field: Address: 149.236.99.1 and in the field: Subnet Mask: 255.255.255.0 • click OK k) In the window Network Configuration click on the tab pane Hosts2 1.
Network configuration • be sure that there are the following entries: IP Name 149.236.99.1 DONE ASP_ST2 149.236.99.99 spect INDEX Nickname INDEX If one of them is missing click New → Add and create it • click File → Save • click File → Quit 10.8 Nameserver configuration In case there are some problems with the network, e.g. the name server is not available, everything on the desktop seems not to react anymore. In fact any activity takes a very long time.
Network configuration 139 the file /etc/nscd.conf and search for the line: positive-time-to-life hosts 3600 INDEX Change the value to: INDEX DONE positive-time-to-life hosts 260000 This will remember the name for about three days (~a weekend). This information is also available form the Bruker Knowledge Base item 5762: http://www.bruker-biospin.de/shell/bkb/show_bug.cgi?id=5762 10.
Network configuration 10.10 Accessing remote files and directories INDEX 10.10.1 Necessary Samba packages and configurations DONE INDEX To use samba it is necessary to install at the package smb and for the graphical configuration the package smb-swat. To allow access and configuration both packages must be enabled.
Network configuration 141 You will be asked for username and password. For configuration of SWAT it is necessary to login as root. Other users are neither able to see the whole information nor can change INDEX it! INDEX DONE There you have to define: • the password and the user for configuration in the Password section • the workgroup in the GLOBALS section • the directories you want to share in the SHARES section After configuration reboot the PC 10.10.
Network configuration Administrator the command looks like this: smbclient -L nmrpc.chemistry.university.com -U Administrator You will be asked to enter the users password.INDEX The answer of the command is a list of all shared directories on DONE the Windows PC, e.g.: INDEX Sharename Type Coment ---------- ----- ------- E$ Disk Default share tmp Disk now you have four information available a) b) c) d) 2.
Network configuration 143 /// / smbfs rw,gid=nmruser,dmask=775,credentials=,user 1 2 This is one INDEX line between smbfs and rw is a space. The option gid=nmruser,dmask=775 gives full control to the user and the group, others get read and INDEX DONE execute. 10.10.4 Mounting Windows 2000/XP partitions from a Linux host using NFS This requires that the NFS server is installed on the Windows PC.
Network configuration INDEX DONE INDEX
Installing a Printer 145 Chapter 11 INDEX INDEX DONE Installing a Printer 11.1 Introduction In the following you can found the description of the print system ‚CUPS‘. In RED HAT ENTERPRISE LINUX WS 4 CUPS is the only print system, the older ‚LPRng‘ is not available anymore. 11.2 Print system ‚CUPS‘ 1 11.2.1 Installation of a Local printer In order to install a Local printer on a Linux PC, you have to take the following steps: 1.
Installing a Printer • enter root password 2. The window Printer configuration will appear INDEX DONE INDEX • Click New 3.
Installing a Printer 147 4. The window changes to Queue name INDEX INDEX DONE Enter name and short description of the printer (in this example printer-nmr3 and HP printer on NMR-3) • Click Forward 5.
Installing a Printer 6. The window changes to Printer model INDEX DONE INDEX Select the manufacturer and the model of the printer in this example HP Laser Jet 1220) • Click Forward 7.
Installing a Printer 149 8. The new window Question appears INDEX INDEX DONE In case the printer is already connected it is recommended to print a test page • Click Yes If it is not connected so far, click on No and back in the window Printer configuration on Apply 9.
Installing a Printer 10. The new window Edit a print queue appears INDEX DONE INDEX 11. To change the driver click on the tab pane Printer driver If there are several printer drivers, ‚Postscript‘ is always a good choice, and the old ‚ljet4‘ works also in most cases very well) 12. Click OK and back in the window Printer configuration on Apply 13.
Installing a Printer 151 11.2.2 Installation of a Unix network printer In order to install a Unix network printer on a Linux PC, you have to take the following steps: INDEX INDEX 1. Click → System DONE Settings → Printing A window Query will appear and asks for the root password • enter root password 2. The window Printer configuration will appear • Click New 3.
Installing a Printer 4. The window changes to Queue name INDEX DONE INDEX Enter name and short description of the printer (in this example printer-nmr3 and HP printer on NMR-3) • Click Forward 5. The window changes to Queue type Select Networked UNIX (LPD) and enter the hostname/IP address1 and the queue of the printer (in this example viola.software.bruker.de and laserjet1200) • Click Forward 1. You can enter either a name or a IP address of the printer.
Installing a Printer 153 6. The window changes to Printer model INDEX INDEX DONE Select the manufacturer and the model of the printer in this example HP Laser Jet 1220) • Click Forward 7.
Installing a Printer 8. The new window Question appears INDEX DONE INDEX In case the printer is already connected it is recommended to print a test page • Click Yes If it is not connected so far, click on No and back in the window Printer configuration on Apply 9.
Installing a Printer 155 10. The new window Edit a print queue appears INDEX INDEX DONE 11. To change the driver click on the tab pane Printer driver If there are several printer drivers, ‚Postscript‘ is always a good choice, and the old ‚ljet4‘ works also in most cases very well) 12. Click OK and back in the window Printer configuration on Apply 13.
Installing a Printer 11.2.3 Installation of a Windows network printer In order to install a Windows network printer on a Linux PC, you have to take the INDEX following steps: DONE→ Printing INDEX 1. Click → System Settings A window Query will appear and asks for the root password • enter root password 2. The window Printer configuration will appear • Click New 3.
4. The window changes to Queue name Enter name and short description of the printer (in this example printer-nmr3 and HP printer on NMR-3) • Click Forward 5. The window changes to Queue type Select Networked Windows (SMB) and the required shared printer from the list. You will see all printers that are reachable without username and password. If the required printer is not in the list, ...
The window Authentication appears, enter all entries manually .. if it is on the list, click on the entry and the window Authentication will appear with those information that are available. Fill in the missing information about the user name and password. • Click Forward 6. The window changes to Printer model Select the manufacturer and the model of the printer • Click Forward 7.
8. The new window Question appears In case the printer is already connected it is recommended to print a test page • Click Yes If it is not connected so far, click on No and back in the window Printer configuration on Apply 9.
Installing a Printer 10. The new window Edit a print queue appears INDEX DONE INDEX 11. To change the driver click on the tab pane Printer driver If there are several printer drivers, ‚Postscript‘ is always a good choice, and the old ‚ljet4‘ works also in most cases very well) 12. Click OK and back in the window Printer configuration on Apply 13.
Installing a Printer 161 11.2.4 Installation of a Jet Direct printer In order to install a Jet Direct printer on a Linux PC, you have to take the following INDEX steps: INDEX 1. Click → System DONE Settings → Printing A window Query will appear and asks for the root password • enter root password 2. The window Printer configuration will appear • Click New 3.
Installing a Printer 4. The window changes to Queue name INDEX DONE INDEX Enter name and short description of the printer (in this example printer-nmr3 and HP printer on NMR-3) • Click Forward 5.
Installing a Printer 163 6. The window changes to Printer model Select the manufacturer and the model of the printer in this example HP Laser Jet 1220) INDEX INDEX DONE • Click Forward 7.
Installing a Printer 8. The new window Question appears INDEX DONE INDEX In case the printer is already connected it is recommended to print a test page • Click Yes If it is not connected so far, click on No and back in the window Printer configuration on Apply 9.
Installing a Printer 165 10. The new window Edit a print queue appears INDEX INDEX DONE 11. To change the driver click on the tab pane Printer driver If there are several printer drivers, ‚Postscript‘ is always a good choice, and the old ‚ljet4‘ works also in most cases very well) 12. Click OK and back in the window Printer configuration on Apply 13.
Installing a Printer INDEX DONE INDEX
Installing a Printer 167 Part III INDEX INDEX DONE Tips, Tricks and Troubleshooting
Installing a Printer INDEX DONE INDEX
Troubleshooting TopSpin 169 Chapter 12 INDEX INDEX DONE Troubleshooting TopSpin 12.1 TopSpin does not start If TOPSPIN does not start, you should first look for an error message in the window where the TOPSPIN startup messages appear. Then check if you have one of the following problems: • A window Choose Server or File appears: The file license.dat was not found. You might have one of the following problems: license.dat has been deleted or renamed → Setup the file license.dat as described in chapter 5.
Troubleshooting TopSpin • The file license.dat contains additional characters at the end of the FEATURE line (after ““) INDEX see chapter 5.2. • For some more information about license problems • If you do not get the licenseDONE to run: INDEX Open a shell and execute: /bin/sh flexlm_diagnostic /tmp/flexlm_diagnostic-out.txt The scripts may require 1 minute to execute. Please send the whole output of the TOPSPIN start window using copy&paste and the file /tmp/flexlm_diagnostic-out.
Troubleshooting TopSpin 171 Although you can now work with TopSpin you should restart the program as soon as possible. Typically wait until the current acquisition is finished, then exit and restart TopSpin. INDEX • No? go ahead with next step INDEX DONE 3. To kill the current TOPSPIN session completely, execute the shell command: killtopspin Note, that this will stop your TOPSPIN session and therefore also a running acquisition. 4. Start TOPSPIN and go on working. 12.2.
Troubleshooting TopSpin this is /opt/topspin The nedit window will appear and you will be asked if you want to create a new INDEX file. Select New File and in the main nedit window: • click on File → Paste DONE INDEX • click on File → Save • click on File → Exit Now it is necessary to pack all available information which Bruker needs to analyze your problem. For this open a shell and execute the following two commands: cd /prog/curdir/ tar cvzf /tmp/bug.tar.gz * ~/.
Troubleshooting TopSpin 173 ing boards are present in your spectrometer. name specific boards Troubleshooting information AVANCE (AV) CCU-RCU chapter 12.3.1 INDEX INDEX AVANVCE-II DONE CCU-DRU AVANCE-III IPSO-DRU chapter 12.3.1 chapter 12.3.2 For a convenient classification the respective boards are shown below. Note, the pictures are just an example, e.g. the EC level can be different. ? For troubleshooting information go to chapter 12.3.
Troubleshooting TopSpin ? Do I have an AV-II type spectrometer? Yes, if you have the two boards: CCU DONE INDEX andINDEX DRU For troubleshooting information go to chapter 12.3.1 ? Do I have an AV-III type spectrometer? Yes, if you have the two boards: IPSO and For troubleshooting information go to chapter 12.3.
Troubleshooting TopSpin 175 Note that CCU, RCU and DRU have an upright orientation while the Ipso board is typically horizontally orientated. In all cases the INDEX first step of troubleshooting should be to check if the spectrometer is on power andINDEX there is a physical network connection between the Linux PC and DONE the spectrometer. 12.3.1 Troubleshooting for AV and AV-II type of spectrometer First of all it is necessary to check the communication between the PC and the CCU.
Troubleshooting TopSpin Every entry in this file must be correct, otherwise there will be time-outs in network traffic which interfere with the connection to the spectrometer. INDEX 3.
Troubleshooting TopSpin 177 1. Open a Linux shell and become superuser; type su 2.
Troubleshooting TopSpin c) Switch on the acquisition rack after the PC has rebooted 4. Check the nameserver configuration: INDEX a) Type grep hosts /etc/nsswitch.conf What is the output of thisDONE command? INDEX Nothing? No problem, go to step 5. • Cannot open nsswitch.conf ? No problem, no nameserver; go to step 5. • hosts: files dns nisplus? No problem, this entry is correct; go to step 5 • hosts dns.... or hosts nisplus....? You found the problem: go to step b. b) Edit the file /etc/nsswitch.
Troubleshooting TopSpin 179 service nfs restart c) Type /sbin/chkconfig nfs on INDEX d) Type reviveccu DONE e) Run step INDEX 5a again and if NFS is still not running continue with step 7 7. Check if NFS is installed: a) Type rpm -q nfs-utils Does the output of this command show you the package nfs-utils? YES? Then NFS is installed, go to step 8 NO? Then you found the problem, install the package nfs-utils. For a installation description please refer to chapter 9.3.2 8.
Troubleshooting TopSpin e) Check the output of the command hostname -f Is the output of this command: INDEX a hostname.domainname? No problem, continue with step 9. a plain hostname? You DONE found the problem. Change the hostname as deINDEX scribed in chapter 10.3. Then continue with step 7h. f) Check the file /etc/hosts1 - at least the following entries have to exist for spectrometer control: 127.0.0.1 localhost.localdomain 149.236.99.1 ASP_ST2 localhost 149.236.99.
Troubleshooting TopSpin 181 the nameserver and DHCP server. h) Type reviveccu INDEX 9.
Troubleshooting TopSpin 1. Check if the ethernet cable between PC and CCU is properly connected. → Remove and re-connect the ethernet cable and the transceiver or minihub. 2. Check if the ethernet interface is broken. INDEX INDEX a) Physically connect the CCUDONE to the first ethernet interface (eth0) 1 b) Become superuser; type su c) Change the configurations between eth0 and eth1 as described in chapter 10.5 and 10.7.1.
Troubleshooting TopSpin 183 GATEWAYDEV= GATEWAY= INDEX • /etc/sysconfig/network-scripts/ifcfg-lo DEVICE=loINDEX DONE IPADDR=127.0.0.1 NETMASK=255.0.0.0 NETWORK=127.0.0.0 # If you're having problems with gated making 127.0.0.0/8 # a martian, you can change this to something else # (255.255.255.255, for example) BROADCAST=127.255.255.255 ONBOOT=yes NAME=loopback BOOTPROTO=none • /etc/sysconfig/network-scripts/ifcfg-eth1 BROADCAST=149.236.99.255 NETWORK=149.236.99.0 NETMASK=255.255.255.0 IPADDR=149.236.
Troubleshooting TopSpin socket_type= dgram user= root server= /usr/sbin/rpc.bootparamd INDEX wait= yes INDEX protocol= udp DONE rpc_version= 1 disable= no instances= 1 log_type= FILE /usr/diskless/bootparamd.log } 12.3.1.4 Files created for the spectrometer network • /usr/diskless/clients/spect/swapfile This file can also be created manually with the command: dd if=/dev/zero of=/usr/diskless/clients/spect/swapfile bs=8000000 count=1 • /etc/rc2.
Troubleshooting TopSpin 185 CCU visible in a shell on the PC. Check if cu is installed: INDEX rpm -q uucp INDEX DONE if it is installed and active the answer should be: uucp- If it is not installed yet, please refer to the installation description in chapter 9.3.2 In case of any problems with this package check the permissions of the program. 1.
Troubleshooting TopSpin • Click on Groups INDEX DONE INDEX You will see in the appearing window the field Primary Group that shows the original group of the user. Leave this entry unchanged, it is not necessary to modify the primary group, it is enough to define the uucp-group membership additionally. • In the field Select the groups that the user will be a member of you can now scroll to the group uucp and selecting the respective field • Click OK 2.
Troubleshooting TopSpin 187 12.3.1.6 View/change the prom parameters 1. Open a shell and become root INDEX 2. Type cu -lttyS1 DONE → You will INDEX get the prompt connected and you can see the CCU output messages: a) Push the reset button of the CCU b) Press Control-C to interrupt the boot process The CCU will be in Monitor Mode now, the prompt will change to >>, type: >> printenv You will get a list of environment variables, the most important are: netaddr=149.236.99.
Troubleshooting TopSpin 1. Open a shell and become root 2. Type cu -lttyS1 INDEX → you will get the prompt connected and after typing Enter you can see the CCU output DONE INDEX 3. Push the reset button of the CCU The CCU will try to boot now. The output of the boot process is listed below. The marks ‘---?---’ indicate positions where the boot process possibly hangs or goes into an endless loop: Autoboot: Waiting to load bfs()/usr/diskless/clients/spect/root/unix.
Troubleshooting TopSpin 189 Internet daemons: portmap inetd. NFS daemons: nfsd biod lockd statd. The systemINDEX is ready. Booting might hang, stop (and print an error message) or go into an endless loop DONE at one of theINDEX positions 1 through 5. This might be caused by one of the problems mentioned below. Check the indicated files and correct them if necessary or perform the indicated steps.
Troubleshooting TopSpin as specified by the entry files as specified above. • the network is not set up correctly; check /etc/hosts, /etc/bootINDEX params • the swapfile does not exist; check the file DONE INDEX /usr/diskless/clients/spect/swapfile If the file does not exist please refer to chapter 12.3.1.4 • start of bootparam fails; check if bootparamd is active right now1: ps -ef | grep bootparamd Does the answer show the two processes rpc.
Troubleshooting TopSpin 191 failed, rpc status 15 PANIC: vfs_mountroot: cannot mount root’ INDEX you had to check the file (see chapter 12.3.1.3) /etc/xinetd.d/bootparamd INDEX DONE f) If booting is very slow or hangs at an arbitrary point you might have a hardware problem (see chapter ). 4. To exit the cu program type: >> ~.Enter (press the keys: tilde, dot, Enter) 12.3.1.8 Running CCU diagnostic tests 1. Open a shell and become root 2.
Troubleshooting TopSpin To find out what are the IP addresses of the different (via ethernet connected) hardware units there are two different possibilities: INDEX • the TOPSPIN command ha (for hardware addresses) • the shell command ethernet-service-tools DONE INDEX Both commands offer a list of available (via ethernet connected) hardware units and their IP addresses. A mouse click on the name of a module opens the start page of the respective module in a web browser.
Troubleshooting TopSpin 193 A window appears that shows several hardware modules. Does the window offers an entry ‚IPSO‘? INDEX INDEX DONE Yes? The AV-III is booted correctly, go on with the TOPSPIN command cf No? Go to step 2 2.
c) Check the file /etc/hosts1 - at least the following entries have to exist for spectrometer control: 127.0.0.1 localhost.localdomain 149.236.99.1 ASP_ST2 localhost 149.236.99.99 spect If the ethernet card for the laboratory network is not configured as DHCP, also the name of the own PC has to be listed xyz.xyz.xyz.xyz name_of_own_pc.domain name_of_own_pc Does this entry exists? Yes? No problem, continue with the next step. No? You found the problem.
which is the answer of the above command hostname -fv Yes? No problem, continue with the next step. No? You found the problem. Contact your network administrator to correct the nameserver settings. 3. The firewall may prevent the spectrometer booting.
Troubleshooting TopSpin /sbin/service dhcpd status Is the answer like this: dhcpd (pid ) is running INDEX Yes? The DHCP service is running, go to the next step DONE INDEX No? You may have found the problem, the DHCP is not running, start it with the command service dhcpd start To make sure that it will automatically started with the next boot, enter the command chkconfig --level 2345 dhcpd on Now you have to reboot the spectrometer. 6.
Troubleshooting TopSpin 197 • execute /sbin/ifconfig -a • check what is the name of the network adapter which has the IP address INDEX 149.236.99.1 • Edit the file /etc/sysconfig/dhcpd and replace the line: INDEX DONE DHCPDARGS=eth1 with DHCPDARGS= • Save and exit the file • Start the DHCP server /sbin/service dhcpd start Does the spectrometer is able to boot now? Yes? You have fixed the problem, the DHCP service is now working correctly.
Troubleshooting TopSpin xinetd (pid ) is running ... No? You may have found the problem, the xinetd is not running, start it with the INDEX command service xinetd start DONE INDEX To make sure that it will automatically started with the next boot, enter the command chkconfig --level 345 xinetd on Now you have to reboot the spectrometer.
Troubleshooting TopSpin 199 For some pages you need an account to enter them. If you do not have one, go to www.bruker.de and click on Register Now. Fill out the form to get a free account. INDEX 12.4.2 RED HAT help INDEX DONE • Click → Documentation • Type man , e.g. man find 12.4.3 Checking the history of TOPSPIN The history function keeps track of all the commands you have entered in TOPSPIN and of all error messages.
Troubleshooting TopSpin 1. Check who is logged in; type who → warn all users who are logged in that you are going to shutdown the system INDEX 2. Become superuser: type su 3. Type reviveccu DONE INDEX → follow the instructions: a) You will be asked to switch off the acquisition rack b) reviveccu will automatically reboot the PC c) Switch on the acquisition rack after the PC has rebooted 12.5 Various problems in Linux 12.5.
Troubleshooting TopSpin 201 12.5.2 Programs like killtopspin, reviveccu and touser are not found These programs are delivered with TOPSPIN and are executed by the superuser INDEX if you become superuser with the command su, the profrom a shell. However, grams may not be found. You can solve this problem in two different ways: INDEX DONE 1. Become superuser with the command ‘su -’ or 2. Log out and log in as root Now the programs shmrm, reviveccu, touser etc.
Troubleshooting TopSpin 12.6 Useful configuration hints INDEX In this chapter you can find some useful configurations of the xorg.conf file. 12.6.1 Definition of the font path DONE INDEX In the file /etc/X11/xorg.conf you can add an information about the location of the fontpath, which make it easier for programs to find the necessary fonts. E.g. if you have fonts available in /usr/X11R6/lib/X11/rgb ... Section "Files" RgbPath"/usr/X11R6/lib/X11/rgb" FontPath "unix/:7100" EndSection ... 12.6.
Troubleshooting TopSpin /swapfile 203 file 2048726 0 -2 7. To activate the swap file during boot time enter the command: INDEX nedit /etc/fstab and duplicateINDEX the line that describes DONE the original swap entry. Change the second column from swap into /swapfile. Save and close this file. 8. Enter the command: reboot 12.7 Spectrometer hardware tests The TOPSPIN DVD contains various programs to test the spectrometer hardware components. 12.7.
Troubleshooting TopSpin INDEX DONE INDEX
Important Linux features 205 Chapter 13 INDEX INDEX DONE Important Linux features 13.1 Important Commands 13.1.1 rpm calls the Red Hat package manager which manage the installation of software packages. • rpm -q ABC → list version of installed package ABC • rpm --help → list options and their description for the rpm command • rpm -qa → list all installed programs • rpm -Uvh abc → install or upgrade the rpm package abc.
Important Linux features 13.1.2 cd INDEX cd: "change directory" DONE INDEX • cd → change to your home directory • cd dira → change to directory dira • cd /u/data/guest/nmr → change to directory /u/data/guest/nmr • cd dataseta → change to directory /u/data/guest/nmr/dataseta • cd .. → change to directory /u/data/guest/nmr • cd ../../usera/nmr → change to directory /u/data/usera/nmr 13.1.
Important Linux features 207 make fila writable for all users -rw-rw-rw- user group 102 Apr 10 12.20 fila INDEX INDEXfila • chmod ug+x DONE make fila executable for the owner and the group -rwxrwxrw- user group 102 Apr 10 12.20 fila • chmod o-w fila make fila not writable for others -rwxrwxr-- user group 102 Apr 10 12.20 fila • chmod -R +w dira make the directory tree dira, including all files and sub directories, writable for all users 2.
Important Linux features make fila read/write/execute for the owner, read/execute for the group and execute for others -rwxr-x--x user group 102 AprINDEX 10 12.20 fila DONE INDEX • chmod -R 222 dira make the directory tree dira, including all files and sub directories, writable for all users 13.1.5 chown / chgrp chown /chgrp: change the owner/group of a file or directory. The output of: ls -l filea or ls -ld dira shows the result.
Important Linux features 209 • set the owner and group of the directory tree dira to usera and grpa INDEX chown usera.grpa dira INDEX DONE -rwxr-xr-x usera grpa 102 Apr 10 12.20 dira 13.1.
Important Linux features • search for stringa in the output of a command, e.g. ps -ef ps -efw| grep stringa 13.1.
Important Linux features 13.1.
Important Linux features • kill directly processes with PID 1149, 1151 and 1143 kill -9 1149 1151 1143 DONE INDEX INDEX Use kill -9 PID only if kill PID does not kill the process! 13.1.10 compress, gzip compress, gzip, bzip: compression to reduce the size of a file File compression can be used to: • save disk space on rarely used files • reduce network traffic (e.g. rcp, ftp, E-mail) • compress a file, fila is replaced by fila.Z compress fila • uncompress a file, fila.
Important Linux features 213 bunzip2 fila Some remarks: INDEX INDEXdoes not DONE • Uncompression require the suffix .Z or .gz • compression factor depends on the file type (20-70%) • gzip gives a better reduction in size than compress 13.1.11 tar tar: This command allows to convert a directory (tree) into a file. This is a convenient tool for attaching many files to an email or transferring them via ftp • copy the directory-tree dira into the file dira.tar tar cvf dira.
Important Linux features • append filb to the end of the archive tar rvf dira.tar filb INDEX INDEX • append if fila does not exist in DONE fila.tar or if it exists but has been modified tar uvf dira.tar fila • you can copy with relative pathnames e.g. cd /u/data/guest/nmr tar cvf dataseta • or with absolute pathnames e.g. tar cvf /u/data/guest/nmr/dataseta 13.2 Important Files 13.2.
Important Linux features 215 mail:*:11432:0:99999:7::: news:*:11432:0:99999:7::: INDEX uucp:*:11432:0:99999:7::: operator:*:11432:0:99999:7::: INDEX DONE games:*:11432:0:99999:7::: gopher:*:11432:0:99999:7::: ftp:*:11432:0:99999:7::: nobody:*:11432:0:99999:7::: nscd:!!:11432:0:99999:7::: mailnull:!!:11432:0:99999:7::: ident:!!:11432:0:99999:7::: rpc:!!:11432:0:99999:7::: rpcuser:!!:11432:0:99999:7::: xfs:!!:11432:0:99999:7::: gdm:!!:11432:0:99999:7::: apache:!!:11535:0:99999:7::: testuser:oaHKvUemEH3
Important Linux features - contains the complete login account information - has one line for each user (account) on the system, each line contains 7 fields sepINDEX arated by colons DONE INDEX example root:x:0:0:root:/root:/bin/bash bin:x:1:1:bin:/bin: daemon:x:2:2:daemon:/sbin: adm:x:3:4:adm:/var/adm: lp:x:4:7:lp:/var/spool/lpd: sync:x:5:0:sync:/sbin:/bin/sync shutdown:x:6:0:shutdown:/sbin:/sbin/shutdown halt:x:7:0:halt:/sbin:/sbin/halt mail:x:8:12:mail:/var/spool/mail: news:x:9:13:news:/var/spool
testuser:x:1001:1003:testuser:/home/testuser:/bin/bash meaning of the fields: 1: Login name 2: password 3: User Id; must be a unique number for each user 4: Group Id; must be a unique number for each group 5: Full Name; the users full name, may contain blanks 6: home directory; usually /home/"user", but can be different 7: shell; must contain full pathname e.g.
Important Linux features • has one line for each group on the system Each line contains 4 fields separated by colons: DONE INDEX INDEX example root::0:root users::100:guest,jim meaning of the fields: 1. the Group Name 2. encrypted group password; usually empty 3. group Id; must be unique for a group and the same on each host 4.
Important Linux features 219 • PATH=$PATH:/home/guest • NMR=/opt/topspin/data/guest/nmr INDEX • export PATH NMR DONE • 1r() { findINDEX $@ -name 1r -ls } • alias ts=topspin Now open a new shell: • umask will be set to 002 • guests home directory is part of the Linux search path • you can type cd $NMR instead of cd /opt/topspin/data/guest/nmr • you can type 1r for searching all files called 1r in the in the directory trees dirA and dirB • you can type ts instead of topspin Note the differ
• each user can set his own umask, e.g in his .profile or .bashrc 1. For this it is necessary to add a line like this: umask 0002 The 4-digit number must start with zero. The following three digits describe the permissions for the user, group and others. examples 1. create a file fila, e.g. with vi, for different values of umask 2.
• offers the user a way to communicate with the OS. • is selected upon installation of a new user Type echo $SHELL to find out which shell you use! different Linux shells and the files executed during login: • .profile sh and bash (also executes .bashrc if it exists) • .cshrc csh and tcsh Important differences between shells 1: • How do you set environment variables sh and bash: 1. export variable=value csh and tcsh: 1.
Important Linux features • How to repeat and change a previously entered command 1. use the arrow keys to get a command back INDEX 2. use the arrow keys to move around in the line use Control-a to move DONE to the beginningINDEX of the line use Control-e to move to the end of the line 3. change the command according to your needs 4.
Important Linux features 223 PS1=’\W’ e) certain characters, e.g.: INDEX PS1=hello or PS1=% or PS1=’>’ 1 INDEX of the DONE f) a combinations items above, e.g.: PS1=’\h:\w>’ in case of the last example the prompt will look like: : /u/data/guest > 3. save the file and leave the editor 4. log out and log in again to see the effect of the change The second prompt can be set be defining the variable PS2. If you want to read the manual pages for the bash, type: man bash 13.
Important Linux features this line can be defined in your file .bashrc Open a new shell and type data to execute the function. INDEX 3. use copy and paste DONE INDEX mark text by holding the left mouse button down paste this text somewhere by clicking the middle mouse button 4. use the Linux shells bash or tcsh • use the arrow keys up/down to repeat and/or modify previously entered commands • use the Tab key to complete commands and paths 5.
Important Linux features 225 When executing scripta a possible output is: Wed Jan 3 03:51:07 PST 1996 /home/guest scripta INDEX INDEX DONE fila Note: the first line of the script should be: #! /bin/sh 2.
Important Linux features 13.4.3 cron - crontab Any Linux command or program can be executed automatically on a regular basis.
File and directory handling 227 Chapter 14 INDEX INDEX DONE File and directory handling 14.1 Permissions and Type of Access 14.1.1 Permissions of a file The permissions of a file: • determine what each user can do with the file • are represented : • by a set of characters -, r, w and x or • by a set of numbers between 0 and 7 1 = x = file is executable 2 = w= file is writable 4 = r = file is readable The numbers 3, 5, 6 and 7 are combinations of 1,2 and 4: e.g.
File and directory handling 14.1.2 Permissions of a directory The permissions of a directory are represented as follows: 1 = x = search 2 = w= write INDEX DONE INDEX 4 = r = read 14.1.3 Types of Access Each file has 3 sets of permissions for 3 categories of users: • the actual owner (shortened ’u’ like user) • users who have the same group ID as the owner 1 (shortened ’g’ like group) • users who have a different group ID than the owner (shortened ’o’ like other) 14.1.
File and directory handling 229 The permissions of the directory dira are 754: INDEX • everybody can read (= see) the directory dira, e.g. use ls on dira DONE of the group sys can read and search e.g. • only the INDEX owner jim and members use cd, pwd, ls, cat, more, du, file on or in dira • only the owner jim can also write or remove files in dira, e.g. use rm, cp, mv, touch on files in dira • In the following example the directories dira, dirb and dirc are assumed to be readable and searchable.
File and directory handling INDEX DONE INDEX
Useful tools for Red Hat Enterprise Linux WS 4 231 Chapter 15 INDEX UsefulINDEX tools DONE for Red Hat Enterprise Linux WS 4 This chapter contains a description of some tools we found useful. We realize that many other tools are available for various purposes and we are very interested in your experiences. Just send your comments to: nmr-software-support@bruker.de 15.1 How to use a memory stick under Linux In previous Red Hat versions it was not easy to use a USB-memory stick.
Useful tools for Red Hat Enterprise Linux WS 4 Add → Panel → Child Panel 2. Click right on the main panel and select Configure Panel INDEX DONE INDEX 3. In the window Configure Panel go to the tab Arrangement and select Child Panel in the field Settings For 4. Define as Position the lower rectangle on the right side, set Length to 5% and Size to 37 pixels (see picture) 5. Select Main Panel in the field Settings For 6.
Useful tools for Red Hat Enterprise Linux WS 4 233 8. Enable: Allow other windows to cover the panel and INDEX Raise when the pointers touches the screen‘s: Bottom Edge DONE 9. Select ChildINDEX Panel in the field Settings For 10. Enable: Allow other windows to cover the panel and Raise when the pointers touches the screen‘s: Bottom Right Corner 11. Click OK 12. Click right on the top of the new panel and select: Add → Applet → Devices 13.
Useful tools for Red Hat Enterprise Linux WS 4 15.2 Firewall configuration ! RED HAT ENTERPRISE LINUX WS 4 has a firewallINDEX package inside. You can activate and configure it during installation (see chapter 9.1) or in the running system.
Useful tools for Red Hat Enterprise Linux WS 4 a window Security Level Configuration will appear INDEX INDEX DONE 4. Select under Security level the entry Enable firewall 5. Select under Trusted Services the entry SSH 6. Select under Trusted devices the entry eth1 7. The window now looks like this, click on OK 8.
Useful tools for Red Hat Enterprise Linux WS 4 Now the configuration of the Firewall is finished and your system is protected right now. INDEX Note that this tool described here allows not a very specific configuration, but it is useful for a quick and secure setting.
Useful tools for Red Hat Enterprise Linux WS 4 237 15.3.1 Installation description of an additional package: xinetd1 Other packages are installed similarly INDEX 1. Check if xinetd is installed so far INDEX • rpm -q xinetd DONE • is the output like this xinetd- • Yes? You can skip this chapter • No? Go to step 2. 2. Insert RED HAT ENTERPRISE LINUX WS 4 Operating System CD 2 of 4 3. Click → System Tools → More System Tools → File Manager Super User Mode 4.
Useful tools for Red Hat Enterprise Linux WS 4 xinetd smb xinetd 0:off 1:off 2:off 3:on 4:on 5:on 6:off INDEX 0:off 1:off 2:off 3:on 4:on 5:on 6:off based services: DONE INDEX rexec: on rlogin: on rsh: on telnet: on vsftpd: on swat: on 15.4 Configure a second monitor The NVidia graphics cards which are part of the PC equipment delivered by Bruker BioSpin Germany have two ports (DVI and VGA). Because of this it is possible to add a second monitor to the system.
Useful tools for Red Hat Enterprise Linux WS 4 239 would be only one with a double width. You can either • stretch the TOPSPIN window over the two monitors simply by clicking on the border of theINDEX TOPSPIN window and move the mouse until the window has the desired size or INDEX DONE • work with e.g. TOPSPIN on one Monitor and e.g. ICON-NMR on the second one. Just open the respective windows and move them with mouse to the desired position. 15.
Useful tools for Red Hat Enterprise Linux WS 4 In both examples sunflower is the hostname and netx.lab.com is the domainname of the remote host. To allow rcp, rsh and rlogin network wideINDEX in all directions, you must setup the file /etc/hosts.allow orDONE .rhosts onINDEX each host. 15.6 Creating a screenshot of the desktop There are several programs that offer the possibility for creating a screenshot of the desktop or of individual windows.
Useful tools for Red Hat Enterprise Linux WS 4 241 • type in the command for opening the manual in a shell: acroread /opt/topspin/prog/docu/english/xwinproc/pdf/install_guide_linux.pdf INDEX (if case you have installed TOPSPIN in the default directory /opt/topspin) INDEX DONE 15.8 Register your Linux system with Red Hat The license agreement of RED HAT ENTERPRISE LINUX WS 4 demanded to register the PC to the Red Hat Network service.
Useful tools for Red Hat Enterprise Linux WS 4 • New Log In 4. The window changes to INDEX DONE INDEX Enter all required information (fields marked with a small red asterisk). At the bottom of the window click on • Create Login 5.
Useful tools for Red Hat Enterprise Linux WS 4 243 6. In the field Product ID Number enter your license key for RED HAT ENTERPRISE LINUX WS 4 7. The windowINDEX changes to INDEX DONE 8. you have successfully activated your license code, you can now go to next chapter and register the PC to the Red Hat Network 15.8.2 Register the PC to the Red Hat Network 1. Log in as root 2. Open a Linux shell and enter up2date 3.
Useful tools for Red Hat Enterprise Linux WS 4 4. The window Red Hat Network Configuration will appear INDEX DONE INDEX • Click on the tab pane Retrieval / Installation 5. The window changes to Retrieval / Installation • Disable the entry Do not upgrade packages when local configuration file has been modified • Click on the tab pane Package Exceptions 6.
Useful tools for Red Hat Enterprise Linux WS 4 • Click on the entry kernel and click on Remove INDEX INDEX DONE • Click OK 7. The window Question will appear • Click Yes 8.
Useful tools for Red Hat Enterprise Linux WS 4 9. The window will change to Review the Red Hat Privacy Statement INDEX DONE INDEX • Click Forward 10. The window will change to Login Enable Use Existing Account and enter the username and password that you have specified in chapter 15.8.
11. The window will change to Register a System Profile - Hardware • Click Forward 12. The window will change to Register a System Profile - Packages • Click Forward 13.
Useful tools for Red Hat Enterprise Linux WS 4 If you have already activeted your license code as it is described in chapter 15.8.1, the process will go on with updating your system. Just follow the instructions given. If you have not done the activation so far,INDEX the following information window would appear. DONE INDEX 15.8.
Useful tools for Red Hat Enterprise Linux WS 4 1. Log in as root 2. Click on the Icon at the lower right side of the desktop INDEX INDEX DONE 3. The window Red Hat Network Alert Notification Tool will appear • Click Forward 4.
Useful tools for Red Hat Enterprise Linux WS 4 5. The window Proxy Configuration will appear INDEX DONE INDEX If you use a proxy server enter the required information, if not just leave the fields empty • Click Forward 6. The window Configuration Complete will appear • Click Apply 15.9 The Emergency Recovery DVD Each PC which is delivered from Bruker BioSpin Germany comes with a Emergency Recovery DVD. This DVD contains an image of the PC and can be used for restoring the PC.
Useful tools for Red Hat Enterprise Linux WS 4 251 More information about nmr_backup and the TOPSPIN command nmr_save file are available in chapter 6.5 INDEX 15.9.1 Using the Emergency Recovery CD INDEX DONE ! Note: This should be done by experienced people only! All data currently on the disk will be destroyed! If in doubt please contact your system administrator, maybe it is still possible to get data from the old disk.
10. In the window Restore Partitions Resize you now have the possibility to change the size of individual partitions. This is only necessary e.g. if you use a smaller hard disk that on which the image was created. So if you use the same disk size you can check No, I do not want to resize partitions. → Click on Next 11. In case the hard disk which you have selected contains already partitions you must select Yes, I want to delete all the partitions on the destination hard disk drive before restoring.
15.10.1 Creating an image You need a boot-CD to start Acronis True Image, if there is no such CD, you can install Acronis True Image on a Windows system and create the Bootable Rescue Media from there. The original Acronis True Image installation CD is usually bootable. 1. Insert a bootable Acronis True Image CD and boot the PC. The window Acronis True Image appears. → Click on Create Image 2. The window Create Image Wizard - Welcome to the Create Image Wizard appears. → Click on Next 3.
Useful tools for Red Hat Enterprise Linux WS 4 8. The window Create Image Wizard - Compression Level appears, select Maximum. → Click on Next INDEX 9. The window Create Image Wizard - Image Archive Protection appears. You can DONE INDEX enter a password to protect your image. If in doubt do not choose a password, this makes it more save for the restoring of the image. → Click on Next 10. The window Create Image Wizard - Image Archive Comments appears.
Useful tools for Red Hat Enterprise Linux WS 4 255 5. When the burning process is finished an information window will appear. 15.12 Add a new INDEX harddisk ! INDEX DONE NOTE: Using the command fdisk is recommended only for seasoned persons, because formatting the old harddisk will destroy all data on this disk! To buy a new harddisk on the Linux PC is quite easy because you can buy a usual harddisk in a PC store. After installing the new disk you have to do the following: 1. Start the PC 2.
Useful tools for Red Hat Enterprise Linux WS 4 In case you need help just type m and choose the possibility you want 8. After partitioning is done you have to create the filesystem on the new partitions. This can be done with the command INDEX mkfs /dev/sdbx DONE INDEX where x is the partition you want to configure 9.
Appendix 257 Chapter 16 INDEX INDEX Appendix DONE 16.1 Some notes for the helium handling In the TOPSPIN home directory (default is /opt/topspin) in the directory prog/logfiles are two files named heliumlog and heliumlog.err. The heliumlog saves the current helium level in a new line every night at 3.00 am. The heliumlog.err documents possible errors during detection of the helium level. 16.1.
Appendix 4. Click File → Save as 5. Save the file as heliumlimit in the installation directory of TOPSPIN INDEX (default is /opt/topspin) in the subdirectory conf/instr/ DONE INDEX 16.1.1.2 Create shell script ’heliumwarn’ for email notification In this chapter you find an example for the shell script that will be execute the email notification in case the helium level is less than the entry (in %) in the file heliumlimit 1. Click → Editors → Text Editor 2.
Appendix 259 user=`whoami` #--------------------------# prepare the email message: INDEX #--------------------------MSG="\n\ INDEX DONE Caution:\n\ The magnet of the spectrometer $INSTRUMENT \n\ has an helium level of $LEVEL % \n\ which is less than the limit of $LIMIT %: \n\ Please order liquid helium and refill this magnet.
Appendix 16.2 Script for saving important files TOPSPIN offers a script (xwinnmr.save) for savingINDEX important files that are not delivered by Bruker BioSpin. This script can save and extract user specific data from DONE INDEX the TOPSPIN_HOME directory and puts them into a tar-file. Files that start with an "." are ignored. The script can be started as follows: • Open a Linux shell and enter /prog/bin/scripts/ xwinnmr.
Appendix 261 • -spect spectrometer name (e.g. spect; default is the current name) INDEX • -verbose print more information while backing up For safety reasons the tar-fileDONE will not be replaced by executing the xwinINDEX nmr.save script once again. So if you like to use the script several times, you have to move the xwin_backup.tar file from the directory /xwin_backup on a backup medium (floppy, CD, DVD ...
Appendix INDEX DONE INDEX
Bruker BioSpin addresses Chapter 17 INDEX DONE BrukerINDEX BioSpin addresses Germany Bruker BioSpin GmbH Silberstreifen D-76287 Rheinstetten Tel: (++49) (721) 51 61 0 Fax: (++49) (721) 51 71 01 Bruker BioSpin Software Department Silberstreifen D-76287 Rheinstetten Tel: (++49) (721) 5161 455 Fax: (++49) (721) 5161 943 http://www.bruker-biospin.de ftp server: ftp.bruker.de Email: nmr@bruker-biospin.de (sales) mbu@bruker.de (service) applik@bruker.de (application) nmr-software-support@bruker.
Bruker BioSpin addresses USA Bruker BioSpin Corporation 15 Fortune Drive Manning Road Billerica, MA. 01821-3991DONE Tel: (++1)(978) (++1)(978) Fax: (++1)(978) (++1)(978) 667 667 667 667 9580 9580 6168 2955 INDEX INDEX 5195 (center) 5444 (application) (center) (application) http://www.bruker-biospin.com ftp server: ftp.bruker.com Email: applab@bruker.com center@bruker.com software@bruker.
Bruker BioSpin addresses Banner lane Coventry CV4 9GH Tel: (++44)(2476) INDEX 855200 Fax: (++44)(2476) 465317 DONE web server: INDEX www.bruker.co.uk Email:service@bruker.co.uk apps@bruker.co.uk Our webpage http://www.bruker-biospin.
Bruker BioSpin addresses INDEX DONE INDEX
Index Symbols .bashrc 218 .cshrc 219 .profile 220, 223, 224 .rhosts 239, 240 /etc/bootparams 182, 190 /etc/exports 181, 182 /etc/hosts 176, 178, 182, 189, 190 /etc/hosts.allow 240 /etc/init.d/bfsd 184 /etc/nsswitch.conf 178 /etc/rc2.d/S95bfsd 184 /etc/shadow 214 /etc/startd 175 /etc/sysconfig/network 178, 182 /etc/sysconfig/network-scripts/ifcfgeth1 183 /etc/xinetd.
I-268 command cf 35, 78 configuration 35 expinstall 35 compress 212 configuration 59 datastation 25, 78 default 25, 78 directory 73 name 28, 67, 75 confout 87 conventions 10 copy and paste 224 CPU 12 cron 226 cron check 28 crontab 226 csh 219, 221 cu 187 CUPS 145 curinst 176 INDEX INDEX D DAEMON line 54, 55 datastation configuration 78 dd 184 debug information 171 default printer 28, 68, 76 selection in expinstall 28, 68, 76 Demo license 52, 54, 55, 56, 57 desktop manager 17 Developer license 52 DHCP 123,
I-269 FLEXLM 38, 42 Flexlm license manager 53, 55, 56, 57 Floating license 53, 54, 55INDEX fstab file 183 INDEX ftp 212, 236 ftp server 172 Full license 52, 56, 57 full name 217 G Ghost 252 Gimp 240 glibc-devel 112 glibc-kernheaders 112 GLP 38, 42, 51 Good Laboratory Practice 38, 42 graphics card 12 graphics file export 102 import 102 png 102 tif 102 wmf 102 grep 209, 226 group 206, 217, 218, 220, 228 group id 228 gs 172 gzip 212 H ha 192 Hardware requirements 12 hardware tests 203 headcrash 78 helium 257 h
I-270 LINUX function 223 LINUX shell 224 lists 225 lmgr 53 lmreread 57 lmutil 53 loop structure 225 LPRng 145 ls 206, 220, 225, 228 INDEX INDEX NMR-SIM 37, 41, 51, 55 nmr-software-support 231 nmrsu 22, 35 Node address 56 DONE Node Locked license 54 Notification Tool 248 nsswitch.
I-271 RED HAT 199 spectrometer 135 Red Hat Documentation 109 spectrometer-PC 25, 62 INDEX Red Hat Enterprise Linux WS 4.
I-272 U umask 219 INDEX UNIX host 143 up2date 243 INDEX User Manager 103, 105, 185 uucp 112, 120, 121, 185 V Very Important Files 87 VIF 87 W who 199, 200 Windows 2000 141, 143 Windows XP 11 wmf 102 wobb 172 Word 102 X xinetd 197 xinetd.
