Red Hat ENTERPRISE LINUX WS 2.1 - Guida di Installazione

Installation GuideTopSpin 2.1 Red Hat Enterprise Linux WS 4Version 2.1.0

10 IntroductionDONEINDEXINDEXThe first part shows how to install and configure TOPSPIN and some essential addi-tional software packages. It is recomme

100 Plotting and Printing with TopSpinDONEINDEXINDEXAll these actions are equivalent; they open the Print dialog box.2. In the Print dialog box:•Selec

Plotting and Printing with TopSpin 101DONEINDEXINDEXin TOPSPIN are used • from Plot Editor Reset ActionsThe plot limits and maximum intensity are set

102 Plotting and Printing with TopSpinDONEINDEXINDEX7.1.5 Store (Export) a Data Window as Graphics FileThe clipboard and metafile formats are resizabl

User Management 103DONEINDEXINDEXChapter 8User Management8.1 Adding a new user account If you want to add a new user1 and this new user already exists

104 User ManagementDONEINDEXINDEX3. A window KDE User Manager will appear: • Click Add User4. A window Create New User will appear • Enter the new Use

User Management 105DONEINDEXINDEX/home/<USER_NAME>•The field Create a private group of this user:a) enabled (default):This configuration in conj

106 User ManagementDONEINDEXINDEX4. A window User Properties will appear:• Click on Groups You will see in the appearing window the field Primary Grou

User Management 107DONEINDEXINDEXPart IIRED-HAT Enterprise Linux WS 4 Installation-Tips and Configuration

108 User ManagementDONEINDEXINDEX

RED HAT Enterprise Linux WS 4 109DONEINDEXINDEXChapter 9RED HAT Enterprise Linux WS 49.1 Hints for installation of Red HatA Linux NMR workstation purc

Introduction 11DONEINDEXINDEX1.3 Safety RegulationsIn order to work safety in laboratories with NMR-spectrometers all users have tofollow the safety r

110 RED HAT Enterprise Linux WS 4DONEINDEXINDEXselect Microsoft Intellimouse if you have a wheel mouse, otherwise the middlebutton will not work corre

RED HAT Enterprise Linux WS 4 111DONEINDEXINDEXNote: Bruker BioSpin does not support SElinux at the moment. Therefor it isrequired to choose Disable i

112 RED HAT Enterprise Linux WS 4DONEINDEXINDEXasked to reboot now or later. In case you want to install further CDs it is recom-mended to click on re

113If you are not connected to the internet you can install the respective rpms with thebrowser nautilus. To do this open a shell, enter the command n

114 RED HAT Enterprise Linux WS 4DONEINDEXINDEXHat Network user name and password.1You will now enter your individual Red Hat network area1. For deta

RED HAT Enterprise Linux WS 4 115DONEINDEXINDEX4. Click on Systems The list of systems which are registered for your individual Red Hat network ac-cou

116 RED HAT Enterprise Linux WS 4DONEINDEXINDEX9. Click on Packages 10. Click on Install New Packages11. Select all packages which starts with acrorea

RED HAT Enterprise Linux WS 4 117DONEINDEXINDEXup2date --install acroread Acrobat reader has now been installed, you can start it from a shell with th

118 RED HAT Enterprise Linux WS 4DONEINDEXINDEXYou will now enter your individual Red Hat network area4. Click on Systems The list of systems which ar

RED HAT Enterprise Linux WS 4 119DONEINDEXINDEX1. Check if glibc-kernheaders and glibc-devel are installed so far • rpm -q glibc-kernheaders • rpm -q

12 IntroductionDONEINDEXINDEXthat Bruker cannot support the use of above-named systems. For detailed informa-tion please look up the software support

120 RED HAT Enterprise Linux WS 4DONEINDEXINDEX14. You get a summary of all selected packages, click Confirm to start installation.Installation will n

RED HAT Enterprise Linux WS 4 121DONEINDEXINDEX5. Click on the name of the system you want to install the acroread packageThe summary of this system a

122 RED HAT Enterprise Linux WS 4DONEINDEXINDEXIf an entry is off, you can activate it in general:/sbin/chkconfig <service> onIf an entry is off

Network configuration 123DONEINDEXINDEXChapter 10Network configuration10.1 Configuring the laboratory networkThe easiest way to add a Linux PC to a la

124 Network configurationDONEINDEXINDEX10.2 Changing the hostname of the PCThe hostname of the PC is defined within the network configuration. Because

Network configuration 125DONEINDEXINDEXThe output of this command shows a list of all ethernet cards and gives the in-formation if the connection is w

126 Network configurationDONEINDEXINDEX3. A window Ethernet Device will appear • select the field:Activate device when computer starts • select the fi

Network configuration 127DONEINDEXINDEXe) In the window Network Configuration click on the tab pane Hosts1 • Either this entry is correct and was visi

128 Network configurationDONEINDEXINDEXf) Click on the tab pane DNS 1• enter the hostname without the domainname into the field Hostname 2•click File

Network configuration 129DONEINDEXINDEX2. A window Network Configuration will appear • On the tab pane Devices click on eth0 and click Edit . Note tha

Introduction 13DONEINDEXINDEXHardware components that are TOPSPIN version or operating system dependent arelisted below. Components that are not liste

130 Network configurationDONEINDEXINDEXActivate device when computer starts • select the field:Statically set IP addressesand type in the IP address,

Network configuration 131DONEINDEXINDEX• The two entries ASP_ST2 and spect that can be seen in the picture are neces-sary for the spectrometer connect

132 Network configurationDONEINDEXINDEX10.6 Spectrometer PC that should not be connected to the laboratory networkIn case the spectrometer PC should n

Network configuration 133DONEINDEXINDEX3. A window Ethernet Device will appear • select the field:Activate device when computer starts • select the fi

i) In the window Network Configuration click on the tab pane Hosts1 • Either this entry is correct and was visible in previous Linux versions, youwill

135j) 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

136 Network configurationDONEINDEXINDEXlowing chapter can be used for checking the configuration.10.7.1 Configuration of the spectrometer network1. Cl

Network configuration 137DONEINDEXINDEX3. A window Ethernet Device will appear • be sure that the field Activate Interface at boot time is checked1 •

138 Network configurationDONEINDEXINDEX• be sure that there are the following entries:If one of them is missing click New → Add and create it •click F

Network configuration 139DONEINDEXINDEXthe file /etc/nscd.conf and search for the line:positive-time-to-life hosts 3600Change the value to:positiv

14 IntroductionDONEINDEXINDEX• FCU 4:• RCU: • Multiple Receiver RCU:FCU 4 required minimum EC Levelpart # H9727 anypart # H9773 anyRCUaa. AVANCE-sp

140 Network configurationDONEINDEXINDEX10.10 Accessing remote files and directories 10.10.1 Necessary Samba packages and configurationsTo use samba it

Network configuration 141DONEINDEXINDEXYou will be asked for username and password. For configuration of SWAT it isnecessary to login as root. Other u

142 Network configurationDONEINDEXINDEXAdministrator the command looks like this:smbclient -L nmrpc.chemistry.university.com -U AdministratorYou will

Network configuration 143DONEINDEXINDEX//<WIN_PC_NAME>/<WIN_PC_SHARE> /<WIN_PC_DATA_DIR> smbfsrw,gid=nmruser,dmask=775,credentials=&

144 Network configurationDONEINDEXINDEX

Installing a Printer 145DONEINDEXINDEXChapter 11Installing a Printer11.1 IntroductionIn the following you can found the description of the print syste

146 Installing a PrinterDONEINDEXINDEX• enter root password2. The window Printer configuration will appear • Click New3. A window Add a new Print Queu

Installing a Printer 147DONEINDEXINDEX4. The window changes to Queue name Enter name and short description of the printer (in this example printer-nmr

148 Installing a PrinterDONEINDEXINDEX6. The window changes to Printer model Select the manufacturer and the model of the printer in this example HP L

Installing a Printer 149DONEINDEXINDEX8. The new window Question appears In case the printer is already connected it is recommended to print a test pa

15• TCU 3:• RX22:1.4.3.2 AVANCE III-spectrometers• IPSO 19’’ H9987TCU 3 required minimum EC Levelpart # H5813, EC level 00 to 19 09 (recommended 12)

150 Installing a PrinterDONEINDEXINDEX10. The new window Edit a print queue appears 11. To change the driver click on the tab pane Printer driver If t

Installing a Printer 151DONEINDEXINDEX11.2.2 Installation of a Unix network printerIn order to install a Unix network printer on a Linux PC, you have

152 Installing a PrinterDONEINDEXINDEX4. The window changes to Queue name Enter name and short description of the printer (in this example printer-nmr

Installing a Printer 153DONEINDEXINDEX6. The window changes to Printer model Select the manufacturer and the model of the printer in this example HP L

154 Installing a PrinterDONEINDEXINDEX8. The new window Question appears In case the printer is already connected it is recommended to print a test pa

Installing a Printer 155DONEINDEXINDEX10. The new window Edit a print queue appears 11. To change the driver click on the tab pane Printer driver If t

156 Installing a PrinterDONEINDEXINDEX11.2.3 Installation of a Windows network printerIn order to install a Windows network printer on a Linux PC, you

1574. The window changes to Queue name Enter name and short description of the printer (in this example printer-nmr3and HP printer on NMR-3)• Click Fo

The window Authentication appears, enter all entries manually.. if it is on the list, click on the entry and the window Authentication will appearwith

1598. The new window Question appears In case the printer is already connected it is recommended to print a test page• Click Ye sIf it is not connecte

16 IntroductionDONEINDEXINDEX• IPSO-AQSS H9984• DPP1:1.4.4 Software requirementsBecause of the variety of Linux systems and their possible problems wi

160 Installing a PrinterDONEINDEXINDEX10. The new window Edit a print queue appears 11. To change the driver click on the tab pane Printer driver If t

Installing a Printer 161DONEINDEXINDEX11.2.4 Installation of a Jet Direct printerIn order to install a Jet Direct printer on a Linux PC, you have to t

162 Installing a PrinterDONEINDEXINDEX4. The window changes to Queue name Enter name and short description of the printer (in this example printer-nmr

Installing a Printer 163DONEINDEXINDEX6. The window changes to Printer modelSelect the manufacturer and the model of the printer in this example HP La

164 Installing a PrinterDONEINDEXINDEX8. The new window Question appears In case the printer is already connected it is recommended to print a test pa

Installing a Printer 165DONEINDEXINDEX10. The new window Edit a print queue appears 11. To change the driver click on the tab pane Printer driver If t

166 Installing a PrinterDONEINDEXINDEX

Installing a Printer 167DONEINDEXINDEXPart IIITips, Tricks and Troubleshooting

168 Installing a PrinterDONEINDEXINDEX

Troubleshooting TopSpin 169DONEINDEXINDEXChapter 12Troubleshooting TopSpin 12.1 TopSpin does not startIf TOPSPIN does not start, you should first look

1.5 Important Red Hat Linux Enterprise WS 4 configurations1.5.1 KDE - desktop manager: recommended by Bruker BioSpinAll information described in this

170 Troubleshooting TopSpinDONEINDEXINDEX• The file license.dat contains additional characters at the end of theFEATURE line (after ““)• For some more

Troubleshooting TopSpin 171DONEINDEXINDEXAlthough you can now work with TopSpin you should restart the pro-gram as soon as possible. Typically wait un

172 Troubleshooting TopSpinDONEINDEXINDEXthis is /opt/topspinThe nedit window will appear and you will be asked if you want to create a newfile. Selec

Troubleshooting TopSpin 173DONEINDEXINDEXing boards are present in your spectrometer. For a convenient classification the respective boards are shown

174 Troubleshooting TopSpinDONEINDEXINDEX?Do I have an AV- I I type spectrometer? Yes, if you have the two boards:CCU and DRUFor troubleshooting info

Troubleshooting TopSpin 175DONEINDEXINDEXNote that CCU, RCU and DRU have an upright orientation while the Ipso board istypically horizontally orientat

176 Troubleshooting TopSpinDONEINDEXINDEXEvery entry in this file must be correct, otherwise there will be time-outs in net-work traffic which interfe

Troubleshooting TopSpin 177DONEINDEXINDEX1. Open a Linux shell and become superuser; type su -2. Check if there are firewall rules that prohibit to co

178 Troubleshooting TopSpinDONEINDEXINDEXc) Switch on the acquisition rack after the PC has rebooted4. Check the nameserver configuration: a) Type gre

Troubleshooting TopSpin 179DONEINDEXINDEXservice nfs restartc) Type /sbin/chkconfig nfs on d) Type reviveccue) Run step 5a again and if NFS is still n

18 IntroductionDONEINDEXINDEX

180 Troubleshooting TopSpinDONEINDEXINDEXe) Check the output of the command hostname -fIs the output of this command: a hostname.domainname? No proble

Troubleshooting TopSpin 181DONEINDEXINDEXthe nameserver and DHCP server. h) Type reviveccu9. Check if the /usr/diskless partitions are exported:a) T

182 Troubleshooting TopSpinDONEINDEXINDEX1. Check if the ethernet cable between PC and CCU is properly connected. → Remove and re-connect the ethernet

Troubleshooting TopSpin 183DONEINDEXINDEXGATEWAYDEV=GATEWAY=• /etc/sysconfig/network-scripts/ifcfg-loDEVICE=loIPADDR=127.0.0.1NETMASK=255.0.0.0NETWORK

184 Troubleshooting TopSpinDONEINDEXINDEXsocket_type= dgramuser= rootserver= /usr/sbin/rpc.bootparamdwait= yesprotocol= udprpc_version= 1disable= noin

Troubleshooting TopSpin 185DONEINDEXINDEXCCU visible in a shell on the PC. Check if cu is installed:rpm -q uucpif it is installed and active the answe

186 Troubleshooting TopSpinDONEINDEXINDEX• Click on Groups You will see in the appearing window the field Primary Group that shows theoriginal group o

Troubleshooting TopSpin 187DONEINDEXINDEX12.3.1.6 View/change the prom parameters1. Open a shell and become root2. Type cu -lttyS1→ You will get the p

188 Troubleshooting TopSpinDONEINDEXINDEX1. Open a shell and become root2. Type cu -lttyS1→ you will get the prompt connected and after typing Enter y

Troubleshooting TopSpin 189DONEINDEXINDEXInternet daemons: portmap inetd.NFS daemons: nfsd biod lockd statd.The system is ready.Booting might hang, st

Express Installation and Configuration of TOPSPIN 19DONEINDEXINDEXChapter 2Express Installation and Configuration of TOPSPIN2.1 About this chapterThis

190 Troubleshooting TopSpinDONEINDEXINDEXas specified by the entry files as specified above.• the network is not set up correctly; check /etc/hosts, /

Troubleshooting TopSpin 191DONEINDEXINDEXfailed, rpc status 15PANIC: vfs_mountroot: cannot mount root’you had to check the file (see chapter 12.3.1.3)

192 Troubleshooting TopSpinDONEINDEXINDEXTo find out what are the IP addresses of the different (via ethernet connected) hard-ware units there are two

Troubleshooting TopSpin 193DONEINDEXINDEXA window appears that shows several hardware modules. Does the windowoffers an entry ‚IPSO‘? Yes? The AV-III

c) Check the file /etc/hosts1 - at least the following entries have to exist for spectrometer control: 127.0.0.1 localhost.localdomain localhost149.23

195which is the answer of the above command hostname -fvYes? No problem, continue with the next step. No? You found the problem. Contact your network

196 Troubleshooting TopSpinDONEINDEXINDEX/sbin/service dhcpd statusIs the answer like this:dhcpd (pid <xxxx>) is runningYes? The DHCP service is

Troubleshooting TopSpin 197DONEINDEXINDEX• execute /sbin/ifconfig -a • check what is the name of the network adapter which has the IP address149.236.9

198 Troubleshooting TopSpinDONEINDEXINDEXxinetd (pid <xxxx>) is running ...No? You may have found the problem, the xinetd is not running, start

Troubleshooting TopSpin 199DONEINDEXINDEXFor some pages you need an account to enter them. If you do not have one, go towww.bruker.de and click on Reg

DONEINDEXINDEXCopyright (C) 2007 by Bruker BioSpin GmbHPart-No: H9556SL2/10revision state: 19/10/2007 (Version 2.1.0)The information in this manual ma

20 Express Installation and Configuration of TOPSPINDONEINDEXINDEX2.2 Installing TOPSPINThe main decision you have to make during installation is wher

200 Troubleshooting TopSpinDONEINDEXINDEX1. Check who is logged in; type who→ warn all users who are logged in that you are going to shutdown the syst

Troubleshooting TopSpin 201DONEINDEXINDEX12.5.2 Programs like killtopspin, reviveccu and touser are not foundThese programs are delivered with TOPSPIN

202 Troubleshooting TopSpinDONEINDEXINDEX12.6 Useful configuration hintsIn this chapter you can find some useful configurations of the xorg.conf file.

Troubleshooting TopSpin 203DONEINDEXINDEX/swapfile file 2048726 0 -27. To activate the swap file during boot time enter the command:nedit /etc/fstaban

204 Troubleshooting TopSpinDONEINDEXINDEX

Important Linux features 205DONEINDEXINDEXChapter 13Important Linux features13.1 Important Commands13.1.1 rpmcalls the Red Hat package manager which m

206 Important Linux featuresDONEINDEXINDEX13.1.2 cdcd: "change directory"• cd → change to your home directory• cd dira → change to directory

Important Linux features 207DONEINDEXINDEXmake fila writable for all users-rw-rw-rw- user group 102 Apr 10 12.20 fila• chmod ug+x filamake fila execut

208 Important Linux featuresDONEINDEXINDEXmake fila read/write/execute for the owner, read/execute for the group andexecute for others-rwxr-x--x user

Important Linux features 209DONEINDEXINDEX• set the owner and group of the directory tree dira to usera and grpachown usera.grpa dira-rwxr-xr-x usera

Express Installation and Configuration of TOPSPIN 21DONEINDEXINDEX5. The window TOPSPIN Installation Manager appears.6. The window Welcome! appear.• C

210 Important Linux featuresDONEINDEXINDEX• search for stringa in the output of a command, e.g. ps -efps -efw| grep stringa 13.1.7 findfind: search fo

Important Linux features 211DONEINDEXINDEX13.1.8 psps: show the Linux process table• show all processesps -efwUID PID PPID C STIME TTY TIME COMDroot 0

212 Important Linux featuresDONEINDEXINDEX• kill directly processes with PID 1149, 1151 and 1143kill -9 1149 1151 1143Use kill -9 PID only if kill PID

Important Linux features 213DONEINDEXINDEXbunzip2 filaSome remarks:• Uncompression does not require the suffix .Z or .gz• compression factor depends o

214 Important Linux featuresDONEINDEXINDEX• append filb to the end of the archivetar rvf dira.tar filb• append if fila does not exist in fila.tar or i

Important Linux features 215DONEINDEXINDEXmail:*:11432:0:99999:7:::news:*:11432:0:99999:7:::uucp:*:11432:0:99999:7:::operator:*:11432:0:99999:7:::game

216 Important Linux featuresDONEINDEXINDEX- contains the complete login account information- has one line for each user (account) on the system, each

217testuser:x:1001:1003:testuser:/home/testuser:/bin/bashmeaning of the fields:1: Login name 2: password3: User Id; must be a unique number for each u

218 Important Linux featuresDONEINDEXINDEX• has one line for each group on the systemEach line contains 4 fields separated by colons:example root::0:r

Important Linux features 219DONEINDEXINDEX• PAT H = $ PA T H : / h o m e / g u e s t• NMR=/opt/topspin/data/guest/nmr• export PATH NMR• 1r() { find $@

22 Express Installation and Configuration of TOPSPINDONEINDEXINDEXdow.112. If a previous TOPSPIN installation is available in the global environment v

• each user can set his own umask, e.g in his .profile or .bashrc 1. For thisit is necessary to add a line like this:umask 0002The 4-digit number must

221• offers the user a way to communicate with the OS.• is selected upon installation of a new userType echo $SHELL to find out which shell you use!di

222 Important Linux featuresDONEINDEXINDEX• How to repeat and change a previously entered command1. use the arrow keys to get a command back2. use th

Important Linux features 223DONEINDEXINDEXPS1=’\W’ e) certain characters, e.g.: PS1=hello or PS1=% or PS1=’>’ 1f) a combinations of the items above

224 Important Linux featuresDONEINDEXINDEXthis line can be defined in your file .bashrcOpen a new shell and type data to execute the function.3. use c

Important Linux features 225DONEINDEXINDEXWhen executing scripta a possible output is:Wed Jan 3 03:51:07 PST 1996/home/guestscriptafilaNote: the first

226 Important Linux featuresDONEINDEXINDEX13.4.3 cron - crontabAny Linux command or program can be executed automatically on a regular basis.check if

File and directory handling 227DONEINDEXINDEXChapter 14File and directory handling14.1 Permissions and Type of Access14.1.1 Permissions of a file The

228 File and directory handlingDONEINDEXINDEX14.1.2 Permissions of a directory The permissions of a directory are represented as follows: 1 = x = sea

File and directory handling 229DONEINDEXINDEXThe permissions of the directory dira are 754: • everybody can read (= see) the directory dira, e.g. use

Express Installation and Configuration of TOPSPIN 23DONEINDEXINDEXa) Type in the NMR ADMINISTRATION PASSWORDb) Re-enter the NMR ADMINISTRATION PASSWOR

230 File and directory handlingDONEINDEXINDEX

Useful tools for Red Hat Enterprise Linux WS 4 231DONEINDEXINDEXChapter 15Useful tools for Red Hat Enterprise Linux WS 4This chapter contains a descri

232 Useful tools for Red Hat Enterprise Linux WS 4DONEINDEXINDEXAdd → Panel → Child Panel2. Click right on the main panel and select Configure Panel3.

Useful tools for Red Hat Enterprise Linux WS 4 233DONEINDEXINDEX8. Enable: Allow other windows to cover the panel and Raise when the pointers touches

234 Useful tools for Red Hat Enterprise Linux WS 4DONEINDEXINDEX15.2 Firewall configurationRED HAT ENTERPRISE LINUX WS 4 has a firewall package inside

Useful tools for Red Hat Enterprise Linux WS 4 235DONEINDEXINDEXa window Security Level Configuration will appear 4. Select under Security level the e

236 Useful tools for Red Hat Enterprise Linux WS 4DONEINDEXINDEXNow the configuration of the Firewall is finished and your system is protectedright no

Useful tools for Red Hat Enterprise Linux WS 4 237DONEINDEXINDEX15.3.1 Installation description of an additional package: xinetd1Other packages are in

238 Useful tools for Red Hat Enterprise Linux WS 4DONEINDEXINDEXxinetd 0:off 1:off 2:off 3:on 4:on 5:on 6:offsmb 0:off 1:off 2:off 3:on 4:on 5:on 6:of

Useful tools for Red Hat Enterprise Linux WS 4 239DONEINDEXINDEXwould be only one with a double width. You can either• stretch the TOPSPIN window over

24 Express Installation and Configuration of TOPSPINDONEINDEXINDEXwindows (e.g. an editor window) and check if no other users are logged ininto this P

240 Useful tools for Red Hat Enterprise Linux WS 4DONEINDEXINDEXIn both examples sunflower is the hostname and netx.lab.com is the domainnameof the re

Useful tools for Red Hat Enterprise Linux WS 4 241DONEINDEXINDEX• type in the command for opening the manual in a shell:acroread /opt/topspin/prog/doc

242 Useful tools for Red Hat Enterprise Linux WS 4DONEINDEXINDEX• New Log In4. The window changes toEnter all required information (fields marked with

Useful tools for Red Hat Enterprise Linux WS 4 243DONEINDEXINDEX6. In the field Product ID Number enter your license key for RED HAT ENTER-PRISE LINUX

244 Useful tools for Red Hat Enterprise Linux WS 4DONEINDEXINDEX4. The window Red Hat Network Configuration will appear • Click on the tab pane Retrie

Useful tools for Red Hat Enterprise Linux WS 4 245DONEINDEXINDEX• Click on the entry kernel and click on Remove• Click OK7. The window Question will a

246 Useful tools for Red Hat Enterprise Linux WS 4DONEINDEXINDEX9. The window will change to Review the Red Hat Privacy Statement• Click Forward10. Th

24711. The window will change to Register a System Profile - Hardware• Click Forward12. The window will change to Register a System Profile - Packages

248 Useful tools for Red Hat Enterprise Linux WS 4DONEINDEXINDEXIf you have already activeted your license code as it is described in chapter 15.8.1,t

Useful tools for Red Hat Enterprise Linux WS 4 249DONEINDEXINDEX1. Log in as root 2. Click on the Icon at the lower right side of the desktop 3. The w

Express Installation and Configuration of TOPSPIN 25DONEINDEXINDEXWhen a user starts a new TOPSPIN version for the first time, a window LICENSEwill ap

250 Useful tools for Red Hat Enterprise Linux WS 4DONEINDEXINDEX5. The window Proxy Configuration will appear If you use a proxy server enter the requ

Useful tools for Red Hat Enterprise Linux WS 4 251DONEINDEXINDEXMore information about nmr_backup and the TOPSPIN command nmr_savefile are available i

10. In the window Restore Partitions Resize you now have the possibility to changethe size of individual partitions. This is only necessary e.g. if yo

25315.10.1 Creating an imageYou need a boot-CD to start Acronis True Image, if there is no such CD, you caninstall Acronis True Image on a Windows sys

254 Useful tools for Red Hat Enterprise Linux WS 4DONEINDEXINDEX8. The window Create Image Wizard - Compression Level appears, select Maxi-mum.→ Click

Useful tools for Red Hat Enterprise Linux WS 4 255DONEINDEXINDEX5. When the burning process is finished an information window will appear.15.12 Add a

256 Useful tools for Red Hat Enterprise Linux WS 4DONEINDEXINDEXIn case you need help just type m and choose the possibility you want8. After partitio

Appendix 257DONEINDEXINDEXChapter 16Appendix16.1 Some notes for the helium handlingIn the TOPSPIN home directory (default is /opt/topspin) in the dire

258 AppendixDONEINDEXINDEX4. Click File → Save as5. Save the file as heliumlimit in the installation directory of TOPSPIN(default is /opt/topspin) in

Appendix 259DONEINDEXINDEXuser=`whoami`#---------------------------# prepare the email message:#---------------------------MSG="\n\Caution:\n\The

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 cr

260 AppendixDONEINDEXINDEX16.2 Script for saving important filesTOPSPIN offers a script (xwinnmr.save) for saving important files that are not deliv-e

Appendix 261DONEINDEXINDEX• -spect <x> spectrometer name (e.g. spect; default is the cur-rent name)• -verbose print more information while bac

262 AppendixDONEINDEXINDEX

Bruker BioSpin addresses 263DONEINDEXINDEXChapter 17Bruker BioSpin addressesGermanyBruker BioSpin GmbHSilberstreifenD-76287 RheinstettenTel: (++49) (7

264 Bruker BioSpin addressesDONEINDEXINDEXUSABruker BioSpin Corporation15 Fortune Drive Manning RoadBillerica, MA. 01821-3991Tel: (++1)(978) 667 9580

Bruker BioSpin addresses 265DONEINDEXINDEXBanner laneCoventry CV4 9GHTel: (++44)(2476) 855200Fax: (++44)(2476) 465317web server: www.bruker.co.ukEmail

266 Bruker BioSpin addressesDONEINDEXINDEX

I-267IndexSymbols.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

I-268DONEINDEXINDEXcommandcf 35, 78configuration 35expinstall 35compress 212configuration 59datastation 25, 78default 25, 78directory 73name 28, 67, 7

I-269DONEINDEXINDEXFLEXLM 38, 42Flexlm license manager 53, 55, 56, 57Floating license 53, 54, 55fstab file 183ftp 212, 236ftp server 172Full license 5

27f) A window will appear:Additional configuration. Security check. Enable peakpower check (POWCHK). Enable puls power check (PULCHK).Choose the optio

I-270DONEINDEXINDEXLINUX function 223LINUX shell 224lists 225lmgr 53lmreread 57lmutil 53loop structure 225LPRng 145ls 206, 220, 225, 228MMac address 5

I-271DONEINDEXINDEXRED HAT 199Red Hat Documentation 109Red Hat Enterprise Linux WS 4.0 109Register 243Release Letter 9, 21, 39remote files 140requirem

I-272DONEINDEXINDEXUumask 219UNIX host 143up2date 243User Manager 103, 105, 185uucp 112, 120, 121, 185VVery Important Files 87VIF 87Wwho 199, 200Windo

d) In the appearing window: Check the required system → Click Nexte) In the appearing dialog box: Select the spectrometer configuration name →Click Ne

29After cf, expinstall,... have finished insert a sample and make sure that youcan lock on the lock solvent. Type ii and read with rpar a standard Bru

3ContentsChapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91.1 Abou

30 Express Installation and Configuration of TOPSPINDONEINDEXINDEX

Express Installation and Configuration of TOPSPIN 31DONEINDEXINDEXPart ITopSpin Installation and Configuration

32 Express Installation and Configuration of TOPSPINDONEINDEXINDEX

General Installation Information 33DONEINDEXINDEXChapter 3General Installation Information3.1 Installation orderA complete new installation on a PC co

34 General Installation InformationDONEINDEXINDEX

Installing TOPSPIN 35DONEINDEXINDEXChapter 4Installing TOPSPIN4.1 NMR SUPERUSER and NMR ADMINISTRATION PASSWORDTOPSPIN offers a complete new password

36 Installing TOPSPINDONEINDEXINDEXthem does not affect the other.With the information about the NMR ADMINISTRATION PASSWORD and NMRSUPERUSER TOPSPIN

Installing TOPSPIN 37DONEINDEXINDEX4.1.2 How to define a new NMR ADMINSTRATION PASSWORDTo define a new NMR ADMINISTRATION PASSWORD, for example becaus

38 Installing TOPSPINDONEINDEXINDEX3. NMR-GLP: Program for ’Good Laboratory Practice’ tests 4. FLEXLM: License manager required for starting TOPSPIN p

Installing TOPSPIN 39DONEINDEXINDEX• If the shell of the next step does not appear automatically you have click onthe DVD icon on your desktop and cli

4DONEINDEXINDEX4.3 Installing TOPSPIN. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

40 Installing TOPSPINDONEINDEXINDEX7. A window Please select a target directory for TOPSPIN will appear: Enter an installation path which does not exi

Installing TOPSPIN 41DONEINDEXINDEX9.1. If Customized was selected in step 9 ... a window Please select products to install will appear: • Select t

42 Installing TOPSPINDONEINDEXINDEX• FLEXlm: License manager required for starting TOPSPIN pro-grams. • NMR-GLP: Program for’Good Laboratory Practice’

Installing TOPSPIN 43DONEINDEXINDEXrecommended to accept the default path! 1• Click Next13. A window appear that displays the programs which will be i

44 Installing TOPSPINDONEINDEXINDEX• Enter any other userIf the user does not exists, installation will create it. For further details seechapter 4.1

45b) 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 shellb) enter the comman

46 Installing TOPSPINDONEINDEXINDEXwindows (e.g. an editor window) and check if no other users are logged ininto this PC) then click on Yes• If you ha

Installing TOPSPIN 47DONEINDEXINDEX4.4 Perl and GCCThe packages Perl and GCC are automatically installed in the directory<TOPSPIN_HOME>/gnu and

48 Installing TOPSPINDONEINDEXINDEXWe will then send you the information by email. 4.6 The usage of the NMR-GUIDENMR-GUIDE 4.0 that comes with TOPSPIN

Installing TOPSPIN 49DONEINDEXINDEX4.6.2 Java Requirements for NMR-GUIDE 4.0For using NMR-GUIDE 4.0 that comes with the TOPSPIN 2.1 version it is not

5DONEINDEXINDEX7.1.1 Plotting and printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

50 Installing TOPSPINDONEINDEXINDEXhttp://localhost:6600/guide/index.htmlYou can now use the functionality of NMR-GUIDE4.6.3.2 Using the NMR-GUIDE sea

The TOPSPIN license 51DONEINDEXINDEXChapter 5The TOPSPIN license5.1 Questions and answers about the TOPSPIN license 1. Which programs need a license?

https://www.bruker-biospin.de/NMR/nmrsoftw/licensesor contact your local Bruker BioSpin representative. 3. What kind of licenses do I need?If you want

53If more than one license is available, as many copies of the program as are cov-ered by the license can be started simultaneously.4. Which licensing

54 The TOPSPIN licenseDONEINDEXINDEX• The operating system on the three computers can be the same or can be dif-ferent (Linux, Windows).8. What is a N

The TOPSPIN license 55DONEINDEXINDEXNo, a Demo license is Node Locked uncounted and therefore only requires FEA-TURE lines. If SERVER and/or DAEMON li

56 The TOPSPIN licenseDONEINDEXINDEX• the number of licenses and your order number (not necessary for demolicense)Licenses can be ordered from the Ger

The TOPSPIN license 57DONEINDEXINDEXDAEMON bruker_ls /usr/local/flexlm/Bruker/bruker_lsFEATURE TOPSPIN1 bruker_ls 0.0 6-aug-2018 3 0B0E4011FF0CD32FBFF

58 The TOPSPIN licenseDONEINDEXINDEX

Configuration of TOPSPIN 59DONEINDEXINDEXChapter 6Configuration of TOPSPINThe idea of this chapter is to give you some guidelines to full spectrometer

6DONEINDEXINDEX11.2.2 Installation of a Unix network printer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

60 Configuration of TOPSPINDONEINDEXINDEX6.1.1 You have a TopSpin/XWIN-NMR configuration that you like to use for TopSpin (on the same PC)You can take

Configuration of TOPSPIN 61DONEINDEXINDEX6.1.2 You have a TopSpin/XWIN-NMR configuration that you like to use for TOPSPIN (on another PC)Before you st

62 Configuration of TOPSPINDONEINDEXINDEXsoftware. If you have to click on Cf or Expinstall depends on what you want to dowith TOPSPIN. You are mainly

Configuration of TOPSPIN 63DONEINDEXINDEXb) A window Cf will appear:Most likely you will select an existing configuration and press Edit toconfirm thi

64 Configuration of TOPSPINDONEINDEXINDEXof trouble-shooting.d) In case the information window mod hconfserver appears:• your spectrometer has not a B

Configuration of TOPSPIN 65DONEINDEXINDEXnected. The RS232/485 channel for external devices-Table appears.Check if the tty-numbers of the hardware com

66 Configuration of TOPSPINDONEINDEXINDEXthe NMR ADMINISTRATION PASSWORD a couple of times): • Continue with expinstall a) Type in the NMR ADMINISTRAT

Configuration of TOPSPIN 67DONEINDEXINDEXAU-programs and Pulse-programs (If you have some, you have to archivethem in a different directory before exe

68 Configuration of TOPSPINDONEINDEXINDEXIn the dialog box that appears → Check the items you want to install or,accept the default selection → Click

Configuration of TOPSPIN 69DONEINDEXINDEX→ Click Nexth) In the information box that appears → Check the configuration selectionand, if it is correct

7DONEINDEXINDEX13.1.7 find . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

70 Configuration of TOPSPINDONEINDEXINDEX• Continue with edsolvCheck the list of lock solvents and click Save if it is correct → Click Close• Continue

Configuration of TOPSPIN 71DONEINDEXINDEXCheck if the connections between preamplifier and probe are set correctly →click Save if it is correct → Clic

72 Configuration of TOPSPINDONEINDEXINDEX• Continue with edlockCheck the lock table values (field, lock phase, ...), change them and clickSave if nece

Configuration of TOPSPIN 73DONEINDEXINDEX6.2.2 If you want to configure a processing-PC like your spectrometer-PC: If the PC does not control a spectr

74 Configuration of TOPSPINDONEINDEXINDEXPulse-programs that have different names to the original Bruker BioSpinfiles will not be destroyed during the

Configuration of TOPSPIN 75DONEINDEXINDEXi) In the window that appears → Check the boxes of the NMR categories youare interested in1 → Click Nextj) In

76 Configuration of TOPSPINDONEINDEXINDEXk) In the appearing dialog box → Check the items you want to install or, acceptthe default selection → Click

Configuration of TOPSPIN 77DONEINDEXINDEXm) In the appearing window → Enter the desired spectrometer frequency,acquisition mode and pre-scan-delay or

78 Configuration of TOPSPINDONEINDEXINDEXmand in the Acquisition Reference manual. 6.2.3 If you want to use a default configuration on a datastationA

Configuration of TOPSPIN 79DONEINDEXINDEX6.3.1 Firmware Update for boards without ethernet connectionThis chapter describes how to update the firmware

8DONEINDEXINDEX16.1.1 Automatic notification for helium refill . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

80 Configuration of TOPSPINDONEINDEXINDEX• A dialog comes up in the shell4. To check and eventually download a new firmware (from TOPSPIN)•type 2→ ENT

Configuration of TOPSPIN 81DONEINDEXINDEX• If you have done a download of newer firmware, you have to do cf again!• If you do not need any downloads,

82 Configuration of TOPSPINDONEINDEXINDEX2. A window BSMS Service Web - Main appears. Click on Device Setup.3. The BSMS Service Web - Setup page appea

Configuration of TOPSPIN 83DONEINDEXINDEX6. The BSMS Service Web - ELCB Firmware Download page appears.Click on the button Browse to select the firmwa

84 Configuration of TOPSPINDONEINDEXINDEX1. Please open the BSMS Service Web page. Click on Service.2. The ELCB Service Web page appears. Click under

Configuration of TOPSPIN 85DONEINDEXINDEXshould be stored.6.3.2.2 ELCB board: Restore user configuration1. Please open the BSMS Service Web page. Clic

86 Configuration of TOPSPINDONEINDEXINDEXParameters on Save to Disc.3. The ELCB Service Web page appears. Under User Level you have to enter theUser a

Configuration of TOPSPIN 87DONEINDEXINDEXdownload. Click on Submit Query.6. The BSMS Service Web - Load User Configuration Status appears. Please chec

Disks and to store the acquired datasets.It is strictly recommended to create a frequently backup of the ’VIFs’ - the ’VeryImportant Files’ - of the c

89should always use the nmr_save command from the highest software version.If your previous TOPSPIN/XWIN-NMR installation is not located on the same P

9Chapter 1Introduction1.1 About this manualThis manual describes the installation of the TOPSPIN 2.1 under RED HAT ENTER-PRISE LINUX WS 4.It is availa

90 Configuration of TOPSPINDONEINDEXINDEX2. Enter the location of the Installation to be saved (default is: <TOPSPIN_HOME>).3. nmr_save will the

Configuration of TOPSPIN 91DONEINDEXINDEXing. Clicking OK will accept the default values an execute nmr_save once in amonth.This Automatic Backup func

92 Configuration of TOPSPINDONEINDEXINDEXcan be defined user-specifically or by default. It offers full flexibility in time defi-nition, off-schedule

93The following directories are saved completely (hidden files are ignored!):<TOPSPIN_HOME>/conf/instr/autoshim/refmaps/<TOPSPIN_HOME>/con

94 Configuration of TOPSPINDONEINDEXINDEX<TOPSPIN_HOME>/plot/layouts/<TOPSPIN_HOME>/prog/tcl/xwish3_scripts/Additionally, the following fi

Configuration of TOPSPIN 95DONEINDEXINDEXtime.tar. This file contains date and time of saving, so that overwriting the tar-fileis not possible easily

96 Configuration of TOPSPINDONEINDEXINDEXPlease enter the NMR administration password and click OK.4. Execute the TOPSPIN command cf6.5.6 How to use u

97to reuse the restored files you can find them in the restore destination you havechosen, in the subdirectory conf/instr with the extension .backupAl

99Chapter 7Plotting and Printing with TopSpin7.1 Printing / plotting data7.1.1 Plotting and printing Under RED HAT ENTERPRISE LINUX WS 4, all common p