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It’s not particularly easy to create a bootable USB flash drive so you can try running Linux on a PowerPC Mac. It took me a couple weeks of research, asking questions of our Linux on PowerPC Macs group on Facebook, and experimenting before I could finally boot into Linux 14.04 from a thumb drive. I learned some lessons. I’m going to make it a lot easier for you to install Linux on your old PPC Macs.

I’ve experimented with Linux and BSD Macs going back to the Mac IIci era, and I’ve never had much luck. Back in the olden days, Linux was a text-based operating system similar to MS-DOS. Everything was handled through the command line in the late 1990s. This time around I wanted to create a “live” flash drive so I could make sure it actually worked before committing to installing Linux on a hard drive.

If only I’d had a blank CD-R or DVD-R, it would have been a lot easier!

My original testbed was a Late 2005 2.3 GHz Power Mac G5 Dual with 3 GB of RAM and two hard drives, one with OS X 10.4 Tiger, the other with OS X 10.5 Leopard. It’s my most powerful PowerPC Mac, so I figured it would be a good way to take Linux for a spin.

Pick a Distro

Step one is to choose your distribution. After talking with others in our small-but-growing Linux PPC Facebook group, I settled on Lubuntu as a good starting point. Lubuntu is known for having a lighter-weight user interface, LXDE – similar to what Simon Royal used when he put LXLE on an old PC.

Ubuntu Linux has a simple numbering scheme for its versions. Version 14.04 was released in the 4th month of 2014, and 16.04 in the 4th month of 2016. That’s also the latest version available for PowerPC at present. You can download 14.04 and 16.04 from this page, earlier versions from this page, where you can also get version 12.04 for PowerPC, among many other architectures.

PowerPC distros prior to version 12.04 have separate 32-bit and 64-bit installers. The only PowerPC Macs that can use a 64-bit operating system are G5 iMacs and Power Macs. Anything before G5 can only use a 32-bit Linux. Starting with version 12.04 the 32-bit and 64-bit versions are part of the same package for Macs.

I suggest you start by downloading Mac (PowerPC) and IBM-PPC (POWER5) desktop CD, which is designed to be burnt to a CD-R and give you a fully bootable way to test out Linux before you commit to it. That’s fine if you have blank CD-R media or a CD-RW disc, but I haven’t burnt a CD in years and have no blanks at present.

That was also the biggest reason I had problems. Using a USB Flash Drive was an exercise in frustration.

The USB Flash Drive Problem

I do, however, have a few 8 GB and larger USB flash drives, and there are plenty of instructions online for properly formatting the flash drive and getting the bootable ISO installed. And none of them worked on my Power Mac G5. I would spend hours trying this, that, and the other thing. Formatting the flash drive was the easy part; installing the ISO and creating a bootable system stumped me.

The only method I found that worked for creating a bootable USB flash drive with Lubuntu on it required me to use Etcher, a freeware app that takes an ISO and creates a bootable flash drive from it. However, Etcher doesn’t run on PowerPC Macs. Nor does it run on my Intel Macs with OS X 10.6 Snow Leopard. I had to use one of my Macs with OS X 10.11 El Capitan installed, and that did the job.

In other words, you need a fairly modern Mac to create the bootable flash drive you need to launch Linux on PowerPC Macs.

I formatted the flash drive as FAT, exFAT, HFS+, Apple Partition Map, GUID Partition Map, and Master Boot Record. Etcher dutifully imaged the ISO file to the flash drive. But it wouldn’t boot.

The key is to format the flash drive using Master Boot Record and FAT. Those are not the default settings, so you’ll have to find them in your version of Disk Utility.

But It Won’t Boot

I’ve been a spoiled Mac user since 1986, and if I’d had a CD-R or DVD-R, this would have been easy. Start your Mac, hold down the C key, and it will boot from whatever is in your optical drive. That goes back to the first Macs with built-in CD-ROM drives. It’s easy, but there’s nothing nearly as easy for booting from a USB flash drive.

On most Macs, if you hold down the Option key (marked Opt on some Mac keyboards, Alt on Windows keyboard) at startup, your Mac will present you with all the bootable options on your computer. On my Power Mac G5, the options are OS X 10.4.11 Tiger, 10.4.11 Tiger Server, and 10.5.8 Leopard.

If I’d had an external USB or FireWire drive, it would have shown up as well. But no matter what I did, the USB thumb drive never showed up as an option. I couldn’t boot from it in the traditional way.

Open Firmware

Whatever the reason, my last generation Power Mac G5 will only boot from the flash drive if I startup in Open Firmware. Hold down Cmd, Opt, O, and F at startup and hold them down until text appears on the upper left corner of your display. Your modern Mac be in Open Firmware (OF, as in two of the keys you hold down to boot into it). OF is a low-level operating system with a command line interface, like the Apple II+ at work that was the first computer I used, the Commodore VIC-20 and 64 that I used at home because they fit my low-end budget, and that Zenith Z-151 PC running MS-DOS 3.3 circa 1987.

Launch OF. That can take a while, as OF tests all your system memory every time you launch it. Just hold those 4 keys down until OF tells you to let go of them.

As long as you only have one bootable USB device, such as the flash drive with Lubuntu or an external CD-ROM or DVD drive, you can type in the following to boot from that device on a dual-core Power Mac G5:

boot ud:,:tbxi

and then hit Return or Enter. That worked perfectly with my Late 2005 Power Mac G5, but it would not work with my older 2.0 GHz dual-processor Power Mac G5s no matter what I did, and I didn’t bother to try it on an iMac G5.

If you have more than one bootable device, type devalias at the prompt, hit Return, and you will see a lengthy list of devices like this.

That was a bit of a rabbit trail for me. In the end I found the command that let me boot from the front USB port on my older Power Mac G5 – these are all equivalent:

boot usb2/disk@1:2,yaboot
boot usb2/disk:2,yaboot
boot usb2/@1:2,yaboot

But that only worked on one of my Power Mac G5s. The other three I tried simply would not boot from the flash drive. This was an exercise in frustration!

Making a Bootable Linux Hard Drive

Once I saw that Lubuntu ran decently on my ancient Power Mac G5 Dual, I knew that I wanted to install it on a hard drive so it would boot more quickly and allow me to add more software. That would have been easy on the Dual, but I didn’t want to reformat either of its hard drives, so I went through my small collection of older Power Mac G5 models in search of one that would boot from the flash drive so I could easily reformat its hard drive and install Lubuntu.

When I finally got one up and running – the third one I tried (the first one wouldn’t even boot, the second wouldn’t boot from the flash drive) – I started the installer. I really appreciate the concise, thorough, helpful explanations of what each choice means. It’s the kind of polish we don’t see with the Mac OS; Apple knows that most of us just want it to run. Ubuntu knows that we are interested in making informed decisions and that it needs to educate us through the process. Nice!

Or so it seemed. Then it wanted to upgrade from 14.04 to 16.04, but every time I tried to do that, it nattered at me about removing certain files using sudo and compressing other files – neither of which I am able to do. How can I remove 35.6 M of files when I don’t even know what’s necessary?

Okay, I should have just started with the Lubuntu 16.04 ISO, but I didn’t know it at the time. If you want to try Linux on a PowerPC Mac, choose the 16.04 Long Term Release (LTR) version and be done with big upgrades until the next LTR version, probably in April 2018.

If you’re just experimenting, you might want to use Lubuntu 17.04. And if you’re patient, you might want to wait until April when Lubuntu 18.04 LTR is due.

Lesson Learned: Burn a Disc Instead!

I wanted you to understand the frustration of trying to do things with a USB flash drive before telling you to bite the bullet and burn a DVD-R disk with the distro of your choosing. You can burn a CD-R, but that usually means trimming the Linux distro to fit on a disc. With DVD-R you’ve got lots of room for distros approaching 1 GB in size.

And you don’t have to use Open Firmware at all.

Booting from the DVD-R was a breeze after all the frustration I had to deal with creating a bootable flash drive and then actually booting from it. I wiped the 80 GB drive in a 2.0 GHz dual-processor Power Mac G5 with 3 GB RAM and installed Lubuntu. I ended up with a very nice, friendly, functional Linux machine that lets me run the latest version of Firefox on a 2005 Power Mac that was left behind with Mac OS X 10.6 Snow Leopard shipped in August 2009.

Is It Practical?

There are two questions to address here: Is it practical to continue using PowerPC Macs in 2018? And is it practical to run Linux on PowerPC Macs instead of OS X 10.4 Tiger or 10.5 Leopard?

Hardware

For those who have a Power Mac G5 Quad, the last and most powerful PowerPC Mac ever, the answer is a resounding yes. With four cores running at 2.5 GHz, you’ve got comparable power to the earliest 4-core Mac Pro. This is lustworthy hardware, although not especially practical in terms of the current it draws.

Dual-processor and dual-core Power Mac G5s are competent performers, and the faster dual-processor Power Mac G4 machines are solid workhorses as well with decent amounts of power. I wouldn’t want to use a Power Mac below 800 MHz or so with Tiger or Leopard, but dual 733 MHz or faster CPUs work well enough.

There may be tasks where processing power isn’t an issue, perhaps a home file server or web server, and there even a 233 MHz iMac G3 may provide all the power you need. Using MAMP, Tiger and Leopard can be configured as Unix servers.

Operating System

If you’re wed to Mac software, Linux probably isn’t going to be on our daily driver Mac. There is a whole learning curve going to a different operating system and using primarily free open source software that may have the power of commercial apps – but you need to figure out how to access it.

But if you want to set up a machine with an up-to-date operating system and browser that can be used more like a Chromebook than a Mac, Linux could be for you. Firefox is a staple in the Linux world, and the latest version is fast with a reduced memory footprint. I can run it on my Power Mac G5 Dual nicely. Not as nicely as a 3 GHz Core i3 iMac, but nicely nonetheless.

Honestly, I would go the triple-boot route. Today I put separate Tiger and Leopard partitions on any G4 or G5 Mac I set up, usually with Leopard getting 2-3 times as much space as Tiger, depending on the size of the hard drive. To learn to live in the Linux world, I would go with two hard drives when possible – one just for Linux, which likes to partition its hard drive just so – and one with partitions for Tiger and Leopard.

Facebook: Ouch

Facebook is a remarkably bloated environment, and you’ve probably been spoiled with modern hardware or the mobile version. Even on my dual-core 2.3 GHz G5, Facebook is frustratingly slow. You can really speed it up by going to m.facebook.com instead of www.facebook.com. That puts you in the mobile version, which has its own drawbacks but runs a lot faster than the desktop version.

Conclusion

Don’t try to do it on your own. We’ve created a helpful Facebook group of people who have managed to get Linux running on PowerPC hardware and those who are learning how. Linux on PowerPC Macs was invaluable in helping me get this far.

keywords: #ppclinux #linuxonmac

short link: https://goo.gl/anff6h

NOTICE

NMRPipe is now distributed via a new site at the Institute of Bioscience and BiotechnologyResearch. This NIH website is no longer updated.

The new distribution site is here (www.nmrpipe.com redirects to the new site too):

www.ibbr.umd.edu/nmrpipe

LEGACY VERSION, NO LONGER UPDATED
NMRPipe Installation Guide, Install Files, and Sample Data
November 24 2015

NMRPipe is an extensive software system for processing, analyzing, and exploiting NMR spectroscopic data. This web page contains NMRPipe installation files, as well as demo data with example processing andanalysis schemes.The main web site for the software, with links to tutorials and documentation is:

http://spin.niddk.nih.gov/NMRPipe

In addition, there are several web-based applications for manipulatingchemical shifts, dipolar couplings, Small-Angle X-Ray Scatteringdata, and molecular structures. The applications include web-based servers for TALOS+, TALOS-N, and SPARTA+ chemical shift analysis. You can find the various servers here:

http://spin.niddk.nih.gov/bax/nmrserver
The NMRPipe system is officially unsupported by the NIHand without warranties or guarantees of any kind.There is an unofficial mailing list for information on use and features of NMRPipe ... you can join and post your ownquestions and comments by going to the following web page:
http://groups.yahoo.com/neo/groups/nmrpipe/info

Some previous versions of NMRPipe have an expiration date. To override the expiration date, try the following environment variable setting:

The following are GENERAL REQUIREMENTS for installing and using NMRPipe:

  • A working knowledge of UNIX, including use of a text editor, andcreation of shell scripts.
  • One of the required UNIX systems such as Linux (most all PC versions), Mac OS X, or SFU 3.5 for Windows XP Pro.
  • The system used for installation must be 32-bit compatible. This means that64-bit systems must have 32-bit compatibility libraries installed as needed.
  • A user account with C-shell (/bin/csh or /bin/tcsh) as the default shell.
  • X11 Graphics server and the xterm terminal window.
  • A three-button scroll-wheel mouse or its equivalent.

The installation of NMRPipe posted here provides the followingfeatures and versions:

  • Standard Options, including nmrPipe, nmrDraw, nmrWish, TALOS+, SPARTA+,DC, MFR, DYNAMO, ACME.
  • Conversion tools for Bruker, Varian, and other formats.
  • NMRPipe for Linux: version linux9(Fedora Core 9, glibc2.8, 32-bit) and version linux (Fedora Core 4, glibc2.3, 32-bit). These Linux versions of NMRPiperequire 32-bit compatibility libraries when used on64-bit systems. The install procedure will automaticallychoose the NMRPipe Linux version that is suitable, so NMRPipe can be installed on most versions of Linux currently in use.
  • A 64-bit version of NMRPipe: linux212_64(CentOS 6.5, glibc2.12, 64-bit). This 64-bit version will only be installedif you include the option +type linux212_64 for theinstall.com installation script.The version of the nmrDraw graphical interface included is still the 32-bit version,and no 64-bit version of nmrDraw will be produced. So wheninstalling 64-bit versions of NMRPipe, 32-bit compatibilitylibraries will still be required. Information on how to installrequired libraries for recent CentOS and Ubuntu systems is provided belowin the System-Specific Installation Notes for Linux.
  • NMRPipe for Mac OS X Intel/PPC (version mac, built on Mac OS X 10.5.8 gcc 4.0.1 XQuartz 2.6.3).
  • NMRPipe for Windows XP Pro running SFU 3.5 (version winxp).
  • NMRPipe for SGI Irix (version sgi6x, built on Irix 6.5 for mips2).
  • NMRPipe Sparc Solaris (version sol, built on SunOS 5.6).
  • C Source Code for programs which read, write, and interpret the NMRPipedata format (directory format in the installation).
  • C Source Code for Creating NMRPipe Plug-In Functions (directory nmruserin the installation).

NMRPipe Installation Files

When downloading software from this web site, you are agreeing toour Terms of Use, including the termsthat there is no right to privacy on this system, and that thethe software from this web site is not to be redistributed without permission from the author.

Use care when downloading; depending on settings, certain web browsers may try to unpack a given file, convert it to a different text format, or display it as a web page rather than saving it as a file. If you experience such problems, try different methods for downloading and saving thefiles, or use a different web browser if possible.

Note well that if the file contents or names are changed in any way during download, the install procedure will not work:

  • When downloading, be sure to retain the exact file name shown here,renaming if needed!
  • When downloading, check that the final file size matches the size shown here exactly!

Windows Internet Explorer: Right-Click, 'Save Target As'
Linux Mozilla: Right-Click, 'Save Link As' ...if a .com file is displayed as a web page, use 'File/Save As'.
Mac OS X Safari: Right-Click, 'Download Linked File (As)'

File NumberFile NameRequiredPost DateFile SizeContents
File 1NMRPipeX.tZYesNov 24, 2015 86,276,925 bytesNMRPipe executables and files for Linux and Mac (Version 8.7 Rev 2015.320.15.26)
File 2install.comYesNov 24, 2015 46,104 bytesInstall script
File 3binval.comYesNov 24, 2015 3,872 bytesUsed by install script
File 4plugin.smile.tZNoSep 1, 2016 53,267,711 bytesSMILE MD NUS Reconstruction
File 5talos.tZNoNov 24, 2015 192,502,073 bytesFiles required for TALOS-N, TALOS+, and SPARTA+
File 6dyn.tZNoNov 24, 2015 143,850,933 bytesOptional Ramachandran surfaces for TALOS+ graphics, PDB data and all files for DYNAMO and MFR
File 7NMRPipeL.tZNoNov 24, 2015 64,143,867 bytesNMRPipe legacy executables (SGI, Windows XP Pro, Sparc Solaris)

As an alternative to downloading via a web browser, on linux systems with the command wget available, you can download theinstall files as follows:

On Mac OS X systems, you can download the files with the curl command:

NMRPipe on a Virtual Machine

As an alternative to installing a hardware-specific version of NMRPipe from above,we now also provide a complex installation of NMRPipe on a CentOS 6.5 Linux Virtual Machine. The virtual machine can be run on most any recent Windows PC, Mac OS X system, or even on another version of Linux. The virtual installation requires either VMware Player software, or VirtualBox software.

File NumberFile NameRequiredPost DateFile SizeContents
File 1NMRPipe_CentOS6.5.ovaYesOct 6 2015 4,055,105,536 bytesNMRPipe on a CentOS 6.5 Virtual Machine

The NMRPipe virtual installation is pre-configured with the usernamenmruser and the passwordnmrpipe (all lower case). The root password is also nmrpipe.

As an alternative to downloading this very large file via a web browser, if you have access toa system with the command wget available (most linux systems), you can download thevirtual machine as follows:

On Mac systems, download the file using the curl command:

The installation details for the Virtual Machine NMRPipe are included below.

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NMRPipe Citation Information

F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Bax:NMRPipe: a multidimensional spectral processing system based onUNIX pipes. J. Biomol. NMR.6, 277-293 (1995).

Introduction to Installation of NMRPipe

The install procedure for NMRPipe automatically provides the following features and hardware versions:

  • Hardware and OS: software versions for the following systems:
    • linux: Linux Intel PC 32-bit (Built on Fedora 4, using glibc 2.3).
    • linux9: Linux Intel PC 32-bit (Built on Fedora 9, using glibc 2.8).
    • linux212_64: Linux Intel PC 64-bit (CentOS 6.5, glibc2.12, 64-bit).
    • winxp: Windows XP Pro (Requires Microsoft SFU 3.5 and X11 Server).
    • mac: Mac OS X PPC and Intel (Built on OS X 10.5.8 gcc 4.0.1 XQuartz 2.6.3).
    • sgi6x: SGI Irix (Built on IRIX 6.5)
    • sol: Sparc Solaris (Legacy Version 7.3 of NMRPipe, built on SunOS 5.6; ).
    *The 64-bit version linux212_64 will only be installed if you include the option+type linux212_64for theinstall.com installation script.
  • NMRPipe: comprehensive NMR conversion and processing, 1D-4D.
  • NMRDraw: interactive phasing, display, 1D-4D peak detection.
  • NMRWish: TCL/Tk scripting for custom display and analysis.
  • ACME: COSY proton-proton coupling measurement.
  • TALOS+: prediction of protein phi/psi from chemical shifts.
  • TALOS-N: prediction of protein phi/psi and chi from chemical shifts.
  • SPARTA+: prediction of protein chemical shifts from structure.
  • DC: Dipolar Coupling Calculations.
  • MFR: NMR Parameter Fragment Homology Search (Molecular Fragment Replacement).
  • DYNAMO: molecular structure analysis, including:
    • Simulated Annealing structure calculation.
    • Simulation of dipolar couplings and protein backbone chemical shifts,estimation of alignment tensor parameters from measured couplings.
    • List, manipulate, and display structure parameters such as backboneangles.

If there are any PROBLEMS installing NMRPipe, PLEASE review the install instructions carefully, including the section about INSTALLATION PROBLEMS below.

This text describes both the GENERAL and SYSTEM-SPECIFIC details for installation of NMRPipe. Please review BOTH the general and system-specific details carefully before installing the software -- this will help us to use our resources in the most effective way as we continue to develop and distribute NMRPipe.

NMRPipe is a UNIX-based system, and so it will require a familiarity of UNIX to install and use the software. This means that an NMRPipe user must be familiar with the UNIX command-line and environment, and know how to create and edit UNIX shell-scripts using a text editor. This is true for all versions of NMRPipe, including the Mac OS X and Windows XP versions.

Some web browsers, especially those used on Windows and Mac OS X, may change the extensions of downloaded files, or attempt to decompress any downloaded files which have been previously compressed. Therefore, when downloading NMRPipe files, take care to retain the exact original file names, and disable any automatic decompression or adjustment of downloaded files. The size of the downloaded files should exactly match the posted sizes.

The most common installation problems involve one of these issues:

  • The user's default shell must be set to the C-Shell (/bin/csh); this is often done with the UNIX 'chsh' command, or by system-specificmethods described below.
  • The user must have a .cshrc file in their home directory,which includes the appropriate commands for establishing the UNIX environment variables required by NMRPipe.
    The necessary initialization commands can be found in the file README_NMRPIPE_USERSwhich is created during installation. If these initialization commands are not executed properly, or if the initializationsettings are changed by settings for other software,error messages like the following will result:
    • nmrPipe: Command not found.
    • cannot find manpage for 'nmrPipe'
    • NMRTXT: Undefined variable
    • Error in startup script: can't read 'env(TCLPATH)': no such variable
    • Application initialization failed: Can't find a usable init.tcl
    • error while loading shared libraries:libxview.so
    • error while loading shared libraries:libtcl8.4.so
    • error while loading shared libraries:libtk8.4.so
    • error while loading shared libraries:libBLT24.so
    • 'Can't find a usable init.tcl
    • XView error: Cannot open connection to window server

    As noted elsewhere, it is important to LOG OUT and LOG IN AGAIN after changingthe '.cshrc' file in order for the NMRPipe initialization to become active.Since other configuration changes might require restarting the computer,it is best to perform a complete restart if possible.
    If the NMRPipe initialization is performed properly, several NMRPipe-relatedenvironment variables will be defined. Use the UNIX commandprintenv to list the current environment variables,in order to check that the NMRPipe-related ones are defined.for example:
  • Many NMRPipe applications make use of output from C-shell scripts, many of which may execute a user's .cshrcfile when invoked. So, it is important that the commands in .cshrcdo not produce anytext output when the .cshrc file is executed, or some NMRPipe applications may fail.You can test for this by counting the characters produced when the .cshrc file is executeddirectly, which should produce the output 0:
  • Many recent 64-bit versions of Linux do not install the 32-bit librariesrequired by NMRPipe. In this case, all of the programs of NMRPipe willfail to run. See the notes on Linux Platform installationbelow for more information.
  • In some cases, especially on SGI systems and many Linux environments, the fonts required by the nmrDraw application are not present or not loaded properly. If the required fonts are not available,the nmrDraw program may fail and generate an error message such as:The NMRPipe installation includes fonts suitable for most systems;in most cases, this kind of problem can be fixed by executing an NMRPipefont.com initialization script from within the user's .cshrcfile.In other cases, such as Linux Fedora Core 12, the fonts required bynmrDraw are not available by default, but canbe downloaded and installed with a command like the following:
  • Certain Linux environments, such as Ubuntu, don't have 'Helvetica' andsome other common fonts. This can affect the appearanceof NMRWish-based graphical applications, such as the varian and brukercommands. Installing the following font package might help:
  • Certain graphics environments may not be suitable, depending on thewindow manager (the program that manages the graphical desktop of thecomputer) and the color settings (such as 8-bit color or 24-bit color). For example, certain versions of the Linux Gnome Desktop graphics environment using 32-bit color might cause nmrDraw to run slowlyor not at all, or cause problems in other graphical applicationslike TALOS+. Such problems can be often be fixed by adjusting the color settings (24-bit color is recommended) or using a different window manager (such as Linux KDE instead of Gnome).
  • In order to run the nmrDraw program, Mac OS X users might have to install updated versions of Mac's X11 graphics server. They might also need to adjust X11 mouse focus settings. More details are given in the Mac OS X installation notes below.

How to Install a Hardware specific Version of NMRPipe: a Quick Overview

The specific steps needed to install NMRPipe will differ dependingon the hardware and operating system, and also on how a given computer or its network is configured. The installation will require that you are familiar with UNIX and the UNIX command line,and that you already know how to create and edit UNIX shell scripts.

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Some of the NMRPipe directories contain demo data and scriptswhich require read-write access. For this reason, it is oftenuseful to install 'personal' copies of NMRPipe rather than install the software via the 'root' account.

The specific details for installing NMRPipe on particular operatingsystems are given in the sections below.In general, the steps for installing NMRPipe will involve:

  1. Set up a system with UNIX, an X11 graphics server, a useraccount with the C-shell as the default shell, and with the 'xterm'terminal window available from the UNIX command-line.The system should have a three-button scroll-wheel mouse or its equivalent.
  2. Create a directory for the NMRPipe installation, where youhave complete permissions to create, read, write, and execute files.
  3. Put the NMRPipe install files into the selected install directory.The usual files are as follows, although you may be provided withadditional files for extra features or updates:
    • install.com (the install script)
    • binval.com (an auxiliary script which determines system type)
    • NMRPipeX.tZ (all versions of NMRPipe)
    • talos.tZ (optional, files required for TALOS+ and SPARTA+)
    • dyn.tZ (optional, files required for DYNAMO and MFR).

  4. Depending on how the NMRPipe install files are obtained, it will benecessary adjust the file permissions so that it is possibleto read all of the install files and to execute the install scripts.This will generally be performed via the UNIX command chmod,for example:
  5. From an 'xterm' terminal window, execute the install.com script; in most cases, no argumentswill be required; it will be sufficient to make the install scripts executable, then run the install.com script. Note: Use thecommand ./install.com +help to generate a listof install command-line options.
    If a specific version of NMRPipe is desired use the +typeoption. For example to use the 64-bit Linux version (linux212_64) insteadof the default linux9 version:
  6. During the install procedure, one or more initialization script files will be created. These initialization scripts must be executedfrom within the '.cshrc' file in the user's home directory.They will establish the environment variables and executablepath which are needed to run the components of NMRPipe.The details about the initialization scripts and how to usethem in '.cshrc' will be listed in the file README_NMRPIPE_USERS which is also created during installation:
    • com/nmrInit.*.com (where * is linux9, mac, winxp, etc.)
    • dynamo/com/dynInit.com (if DYNAMO is installed)
    • com/font.com (font initialization, only needed for some systems).

  7. Once NMRPipe is installed, and the user's '.cshrc' filehas been adjusted appropriately, log out and log in again.Note that it is important to LOG OUT and LOG IN AGAIN after changingthe '.cshrc' file in order for the NMRPipe initialization to become active.

    After logging in again,activate an 'xterm' terminal window; it should then be possible to use the components of NMRPipe from the 'xterm' command-line.

In summary, the NMRPipe install procedure will look something like thisexample, where the home directory is /Users/frank:

NOTE well that in some cases, the install procedure may generate informational warning message or error messages, but still complete correctly. So, after the installation procedure, you should try TESTING THE INSTALLATION as below. After testing, you may want to make OTHER ADJUSTMENTS, also below.

As a convenience, the install.com procedure above can be adjustedto read the installation files from some other source location, for example from a CD-rom. This is done by the install.com +src option.In such a case, only the files 'install.com' and 'binval.com'need to be in the current directory. For example, if all of the installfiles are stored together on the CD-rom mounted as /media/cdrom andthe home directory is /Users/frank:

The installation procedure performs several software andgraphics tests to check the status of the installation. In somecases, these tests might issue warning messages even though theinstallation completes properly. In some cases, these testsmay fail in a way which interrupts the installation. If thishappens, you can suppress the post-installation software testswith the +nopost option, for example:

How to Install the Virtual Version of NMRPipe

Spinny Cube (demo) Mac Os Catalina

  1. Get and Install VMware Player or VirtualBox. On PC hardware, the installation of these applications might require enabling virtualization options in the computer’s BIOS. Consult the application documentation for additional installation details.

    At the time of this writing, VMware Player and VirtualBox applications can be found here:

  2. Use the virtual application (VMWare Player or VirtualBox) to unpack the NMRPipe_CentOS6.5.ova file.The virtual machine is large (~ 5Gb) and will grow larger with use, so choose a suitable location, and keep in mind any automated backup procedures that might be in use on your computer.
  3. Run the NMRPipe Virtual Machine. Running the virtual machine is like turning on a PC – an operating system will start in the usual way, but in its own window.
  4. First Time Configuration. When you start the virtual machine for the first time, you might see a message that “long mode” for 64-bit systems will be disabled … this is expected, and not a problem. On PC hardware, you also might see a message asking that you first enable virtualization options (Intel VT-x) in your computer’s BIOS. And, you might see a message asking whether the Virtual Machine was moved or copied -- select the “Copied” option.
  5. Adjust BIOS Settings of the Computer. If needed, restart the computer, enter the BIOS setup during startup, and adjust the BIOS options to enable virtualization as needed.
  6. Log in to Virtual Linux. When the virtual machine starts, you can log in via the “nmruser” user account. The password for the 'nmruser' account is “nmrpipe” and the root password is also 'nmrpipe' (all lower case). Note also that the Virtual Machine can be configured so that it is possible to drag and drop files and folders between the Virtual Machine window and the Desktop of the host operating system.
  7. Use NMRPipe. Once you log in as “nmruser”, you can open a terminal window from the command panel at the top of the desk top. All the usual facilities of NMRPipe will be available.
  8. Configure the Virtual Machine environment and Linux. Consult the virtual application (VMWware or VirtualBox) documentation for details on configuring the virtual player for options such as use of removable devices, shared folders, printing, networking and software updates. You can configure the virtual Linux operating system as you would any other Linux installation. The root password for the virtual machine is “nmrpipe”.
  9. Exit the Virtual Machine. When you are done with a session, don’t exit the virtual machine by closing the window via the usual “X” icon – this is the equivalent of unplugging a PC while it is running, and might make the virtual machine unusable. We also recommend that you do not suspend the virtual machine. Instead, when exiting the virtual machine, be sure to shut it down via the system menus for “Shutdown”, just as you would for an actual PC.

What Users Should Do to Run NMRPipe

The tools and scripts of the NMRPipe system require use of the C-shell (/bin/csh) or the related T C-Shell (/bin/tcsh) as the user's default shell. Other shells, such as the Bourne Shell 'sh', or the 'bash' shell, will not be suitable. So, in order to use NMRPipe, users may have to reset their default shell accordingly. The UNIX command 'chsh' is commonly used to set the default shell; see the UNIX 'man chsh' help text for information on how to use this command on your system.

If the automated installation succeeded, users need only execute the initialization scripts that were created, by adding lines such as the following to their '.cshrc' file. These commands should preferably be added at the very end of the .cshrc file that the NMRPipe environment variables do not get reset accidentally by other application initialization commands. The details about these initialization scripts and how to usethem in '.cshrc' will be listed in the file README_NMRPIPE_USERSwhich is also created during installation.

As noted above,it is important to LOG OUT and LOG IN AGAIN after changingthe '.cshrc' file in order for the NMRPipe initialization to become active.

Also, regarding fonts: only use the 'font.com' script if the 'install.com' procedure orREADME_NMRPIPE_USERS file indicates thatit is needed for your system (mostly just SGI/IRIX systems, andsome versions of Linux):

Testing the Installation

In order to confirm that you can access the software correctly, try logging out first, then logging in and using these commands:

When using graphical programs in the NMRPipe system, note that all versions of the software expect use of a three-button scroll-wheel mouse or its equivalent.

Other Adjustments

NMRDRAW: after testing, you may wish to edit the script called 'nmrDraw'. The font size argument called '-scale' can be adjusted to suit user preferences for text in buttons, menus, etc. The font arguments '-type1' (regular font) and '-type2' (large font) will affect the size of text used for axes and labels, and for text editing windows. Possible values for '-scale', '-type1' and '-type2' include 'small', 'medium', 'large', and 'extraLarge'.

You can also adjust the nmrDraw window size to compensate for space on the screen used by window manager command panels, etc. Add the options '-xAdj' or '-yAdj' followed by a pixel count to reduce the nmrDraw window size by the given number of pixels (for example ' -xAdj 20').

Many NMRPipe applications are actually NMRWish TCL/TK scripts.These use a small number of common font definitions, which canbe adjusted by setting environment variables. Examples arelisted in the com/nmrInit.*.com file, and look like this:

Installation Problems

There are a few common difficulties with installation of NMRPipe, and these generally relate to the various environment variables required to use the software, or to the font settings used by the 'nmrDraw' program.

If there are install problems, besides reviewing the notes here, see also the next section for system-specific installation details.

Environment Variable Problems

The most common problem when first using the installation concerns the proper setting of environment variables. As described above, the environment variables needed by NMRPipe are established by the script 'com/nmrInit.*.com' created during the install procedure. This script sets environment variables and executable path for the C-Shell; it WILL NOT work for 'bash' or 'sh' shells.

The necessary initialization commands can be found in thefile README_NMRPIPE_USERS which is created during installation.

If the various NMRPipe environment variables are not defined properly, 'Undefined variable' or 'library' error messages will be generated, for example:

  • NMRTXT: Undefined variable
  • Error in startup script: can't read 'env(TCLPATH)': no such variable
  • can't find a usable init.tcl
  • error while loading shared libraries:libxview.so
  • error while loading shared libraries:libtcl8.4.so
  • error while loading shared libraries:libtk8.4.so
  • error while loading shared libraries:libBLT24.so
If there are problems running the software, look at the definitions in your version of 'com/nmrInit.*.com'. Then, use the 'printenv' command to see if the actual current environment is set up as required. In many cases, certain environment variables need by NMRPipe may get reset by other commands elsewhere in '.cshrc'. To avoid this problem, put the NMRPipe initialization commands at the end of the '.cshrc' file. As noted elsewhere, it is important to LOG OUT and LOG IN AGAIN after changingthe '.cshrc' file in order for the NMRPipe initialization to become active.

Font Problems in NMRDraw and NMRWish Applications

The 'nmrDraw' program uses certain 'lucida' and 'open look' fonts which are not available on all systems by default. The NMRPipe install procedure will attempt to test whether or not these fonts are available, and provide them if needed. The script 'com/font.com' is used to provide the fonts on systems which do not have them. This file is usually executed from a user's '.cshrc' file.

(demo)

If the fonts cannot be found, 'nmrDraw' will issue error messages like this one:

If this happens, check the definitions in file 'com/font.com', and adjust them if needed.

Alternatively, on some Linux systems, such as Fedora Core 12, fonts needed by NMRDraw are not available by default, but can be downloaded and installed with the following command:

Certain Linux environments, such as Ubuntu, don't have 'Helvetica' andsome other common fonts. This can affect the appearanceof NMRWish-based graphical applications, such as the varian and brukercommands. Installing the following font package might help:

NMRDraw XView Notifier Errors

In some cases, 'nmrDraw' may display 'XView Notifier Error' or similar messages; this will generally not cause a problem in the actual use of the software. However, in many cases, these error messages can be suppressed by editing the 'nmrDraw' script to add or remove a font specification '-fn', for example,

Use the unix command 'which nmrDraw' to find the script on your installation.

NMRDraw Runs Slowly, or Not At All
Graphics Applications Such as TALOS+ Have Distorted Displays

Certain graphics environments may be problematic for nmrDrawand other graphical applications, such as the TALOS+ Ranachandran display.This can sometimes depend on the window manager (the program that manages the graphical desktop of thecomputer) or the color settings (such as 8-bit color or 24-bit color).For example, certain versions of the Linux Gnome Desktop graphicsenvironment using 32-bit color might cause nmrDraw to run slowlyor not at all. Such problems can be often be fixed by adjusting thecolor settings (24-bit color is most common), by using a different windowmanager (such as Linux KDE instead of Gnome), or by updating the displaydrivers. In the most difficult cases, we have sometimes resortedto changing graphics hardware ... in the experience of NMRPipe's author,NVidia graphics hardware (rather than Radeon or Intel) seems to be thebest choice for NMRPipe.

Recently, some versions of Linux include special tools for enteringAsian language text, such as SCIM. Some of these 'Input Method' toolsmay cause problems with NMRDraw and other graphical programs.If you have problems on Linux systems entering text into graphicsprograms or using graphical menus, etc, find and disable any specialinput methods such as SCIM that might be running.

On Mac OS X, NMRDraw Will Not Run, or Freezes

See the Mac OS X installation notes below for details on configuringsoftware and settings for nmrDraw.

All of the NMRPipe Programs Fail to Run

A particular installation of NMRPipe might not be compatible with allversions of a given operating system. For example, the currentMac OS X version of NMRPipe will generally require a system with MacOS X version 10.4 or higher.In these cases, none of the programs in the NMRPipe system will workunless the operating system is upgraded appropriately.

In the case of current Linux versions, NMRPipe requires 32-bit compatibilitylibraries when run on 64-bit hardware. If these libraries are notinstalled, every NMRPipe program will issue an error messages such ascommand not found even though the program is availableon the executable path and the NMRPipe environment variables are set properly. In these cases, use the appropriate commands to install 32-bitlibraries etc. as needed -- the details will depend on your versionof Linux, and might be something like one of the following: