Personal tools
You are here: Home → CDAT → Download and Install → In Depth Installation Guide → Install Environment and Platform Specific Notes
Navigation
 
Document Actions

Install Environment and Platform Specific Notes

  Table of Contents Previous Next
Contents Previous Next

Software installation is divided into three parts: PYSRC, EXSRC, and CDAT. The PYSRC distribution contains everything needed to make a Tcl/Tk Python executable that is current enough to run CDAT. (Note: if you already have a suitable Python installation, the PYSRC installation can be skipped. See details below in section 7.) The EXSRC distribution contains required external packages necessary to support CDAT. The CDAT distribution contains Python modules and subsystems that are explicitly designed to for the analysis of climate simulation and climate observed data.

GNU Make - GNU Project - Free Software Foundation (FSF)

Before installing CDAT, you must have GNU Make installed on your system. GNU Make is a tool which controls the generation of executables and other non-source files of a program from the program's source files. To obtain the latest version of GNU Make, please visit the web site: http://directory.fsf.org/make.html

.

 

Where Should I Install CDAT?

The notation <CDAT_INSTALL_DIRECTORY> indicates the full path name of the directory into which CDAT is to be installed.

The notation <CDAT_SRC_DIRECTORY> indicates the full path name of the directory where you uncompressed and un-tarred the CDAT source code.

It is required that the parent directory <CDAT_INSTALL_DIRECTORY> exists, and that you have write permission in it. For distributions that will be used by others, for example /usr/local/cdat-4.0 would be an appropriate name for the <CDAT_INSTALL_DIRECTORY>.

However, /usr/local is a poor choice, as chances of collisions with other installations and associated unintended consequences are too high and uninstalling becomes difficult. The <CDAT_INSTALL_DIRECTORY> will be created if necessary, with the following subdirectories: bin, DODS, lib, include, info, man, sample_data.


BUG WITH SCIPY 0.8.0

 

Please see for a patch that will allow scipy to compile

: http://projects.scipy.org/scipy/attachment/ticket/1180/0001-FIX-define-macro-to-access-C99-extensions-from-C.patch

 


Platform Compiler Options

Most platforms will build CDAT, as-is with the GNU Compiler Collection (GCC) compiler, but on some platforms the environment variable "CC" may need to be set before building CDAT. See the table below for details.

Platform Set CC environment variable Notes
AIX cc_r  
Cygwin gcc Use default gcc
HP-UX 11 cc +z  
IRIX 6.5 cc Use configuration option "-c irix" to get n32 X11
Linux flavors gcc Use default gcc
Mac OS X gcc Use default gcc
OSF1 cc  
Solaris 8 cc -mt  
Solaris 9 gcc Use default gcc

The way to set the environment variable CC depends on the shell used. For example:

csh or tcsh: 
setenv CC value
bash or sh: 
set CC=value; export CC

If the value is more than one word, double quotes must surround it. For example:

setenv CC "cc –mt"

 

Special Macintosh OS X 10.6.x (Snow Leopard) Installation Instructions

Snow Leopard is 64bit, CDAT builds everything to be 64bit. Therefore if you are getting external libraries via .dmg make sure they have support for x86_64

 

In particular Qt by default comes as a 32bit build.

 

But you can obtain the "cocoa" (64Bit) version form Nokia at:

ftp://ftp.qt.nokia.com/qt/sources

look for the file:

ftp://ftp.qt.nokia.com/qt/source/qt-mac-cocoa-opensource-4.6.3.dmg

Or whatever version you wish to install. The important point here to make sure you get the "cocoa" version.

These will install and work with CDAT (--with-qt-bin=/usr --with-qt-lib=/Library/Frameworks --enable-qt-framework )

 

Special Macintosh OS X 10.3.x, 10.4.x and  10.5.x Installation Instructions

Optional changing the shell mode (i.e., bash, tcsh, csh, etc.): Change your shell preference environment by typing: chsh at the prompt. Then edit the file that appears. (Follow instructions in the file for editing.) You then must reboot your machine for the change to take effect.

Setting 'root': To become the "su" root user in an xterm window, you must first set one menu item. To start, you will need to select the "Finder" icon on your desktop. In the "Finder" window, select the following icons: "Applications", then "Utilities", then "NetInfo Manager". In the main menu of the "NetInfo Manager" window and under the "Security" menu, select the "Authenticate" menu item and follow the instructions. If you are operating under the 10.5 OS, then to enable the root user, type: "sudo passwd root" and give the desired password. This command is issued in the Terminal window. If you don't want to set a root password, then you can issue the "sudo -s" command.

Note: If you don't remember the root password, you can put in the 1st Mac OS X install disk and change the password when the prompt message states that you should do so.

Note 2: Before that, or if you don't have the disk you can try to do the following:
select the "Finder" icon on your desktop. In the "Finder" window, select the following icons: "Applications", then "Utilities", then "NetInfo Manager". In the main menu of the "NetInfo Manager" window and under the "Security" menu, select the "Authenticate" menu item, "Disable Root", then try to "Enable Root" again it should complain about root password being empty, you can now reset it to your choice.

Xcode Tools Installation: If the -lcrt1.o or bundle1.o errors occur on compilation, then you need to reinstall the Xcode Tools! This is an unfortunate bug resulting from conflicting installers. The correct way to fix this problem is to install the full Xcode Tools 1.1 CD, which you can download from http://connect.apple.com/. (For testing the Mac OS X 10.3.x CDAT installation, we installed the latest Xcode Tools (version 1.5).)

Tiger Note: On Tiger you can also obtain Xcode Tools from http://connect.apple.com , we tested with version 2.1

You will also need the X11 libraries. You can only get this from the Xcode Tools 1.0 CD. From the CD, go to "Packages", then install "X11SDK.pkg". This will place the following libraries in your /usr/X11R6/lib directory:

libFS.a libXTrap.a libXi.a libXt.a libfntstubs.a
libGL.a libXau.a libXinerama.a libXtst.a libfontconfig.a
libGLU.a libXaw.a libXmu.a libXv.a libfontenc.a
libGLw.a libXcursor.a libXmuu.a libXvMC.a libfreetype.a
libICE.a libXdmcp.a libXp.a libXxf86misc.a liboldX.a
libOSMesa.a libXext.a libXpm.a libXxf86vm.a libpsres.a
libSM.a libXfont.a libXrandr.a libdps.a libxkbfile.a
libX11.a libXfontcache.a libXrender.a libdpstk.a libxkbui.a
libXRes.a libXft.a libXss.a libexpat.a

Fortran installation: See: http://r.research.att.com/tools/

 This will put the binaries in /usr/local/bin. (The gfortran installation is only needed for some "contrib" modules and is not necessary for CDAT building.)

CDAT installation: Make sure your xterm window has gfortran by typing:

which gfortran
If not found, then follow appropriate the steps above.

Finally, follow the standard Express Installation instructions above.

 

Mac OS X 10.5.6 (SnowLeopard)

 

CDAT will not build out of the box on SnowLeopard. You will need a few prelimanry steps to build tcl/tk correctly. Otherwise vcdat will crash.

If you do not plan on using tcl/tk (i.e VCDAT) then go ahead and build CDAT out of the box.

Otherwise follow these instruction

get the sources at:

http://opensource.apple.com/tarballs/tcl/tcl-87.tar.gz

tar xzvf tcl-87.tar.gz

cd tcl-87

sudo make

sudo make install

.... VERY LONG WAIT ...

mkdir -p /opt/cdat/Externals

cp -pfr /tmp/tcl/Release/usr/* /opt/cdat/Externals

 

Replace "/opt/cdat/Externals" with the location of your externals

i.e if you're going to build cdat with

./configure --prefix=/usr/local/cdat

Then replace /opt/cdat/Externals with /usr/local/cdat/Externals

BUT if you're going to build CDAT with:

./configure --prefix=/usr/local/cdat --with-externals=/usr/local/Externals

THEN replace /opt/cdat/Externals with /usr/local/Externals

 

Then simply build CDAT as you would on any othe rplatform. It will pick the right tcl/tk

 

Mac OS X 10.5.x (Leopard)

 

Thanks to Stephane Raynaud and Jerry Potter for patiently helping us port CDAT ot 10.5.x

 

  • On some system freetype will fail to build, leading to bad cairo and vcs, You need to make your system aware of where perl is, for example:
    • setenv PERL5LIB "/sw/lib/perl5"
  • Also some system will fail to pick up PKG_CONFIG correct path:
    • setenv PKG_CONFIG_PATH "/ypu/path/Externals/lib/pkgconfig"

 


Problem with "readline" module on  Mac OS X 10.4.x

 

On Tiger you might not be able to build python with readline, since Python seems to systematically pick the system readline which is not complete.

To solve this issue, simply remove readline from your /usr/lib and build the system again. You may want to relink from /usr/lib to your readline.

 

Problem with "head" module on  Mac OS X

 

On some MAC CDAT may fail building vcs because it failed because building cairo went wrong because the build of fontconfig went wrong, because the "/usr/bin/head" program is corrupted! This happens when you install the Perl libwww library on an HFS+ system volume. It tries to create a new command /usr/bin/HEAD, which overwrites the existing head command because the file system is case-insensitive. head is a standard command used in many shell scripts and Makefiles. You need to get the original head executable back. See Q6.4 at the following link: http://finkproject.org/faq/comp-general.php

 

Fink CDAT Installation on Mac OS X 10.3.x

From the Fink website,"Fink is defined as a project that wants to bring the full world of Unix Open Source software to Darwin and Mac OS X. It has two main goals:

  • First, to modify existing Open Source software so that it will compile and run on Mac OS X.
  • Second, to make the results available to casual users as a coherent, comfortable distribution that matches what Linux users are used to."

The project offers precompiled binary packages as well as a fully automated build-from-source system.

To install "fink", follow the instructions located at the following website:

By the courtesy of Jeff Whitaker, CDAT can be installed with the Fink application by typing:

fink install cdat

Other useful Linux/Unix applications can be installed by using Fink. For a full listing of applications, type:

fink list

Fink CDAT Installation on Mac OS X 10.4.x (Tiger)

Special thansk to Kevin Marsh for these

 

1) (re)install fink (using 0.8)

2) "sudo gcc_select 4.0"

3) "fink install cdat"
-complains about missing c++-filt in /usr/bin/ when trying to build
gcc-3.4.3

4) reinstall bsd.pkg from the Tiger DVD (in
"/System/Installation/Packages" folder, not "Xcode Tools") to get
/usr/bin/c++filt. Actually locating and installing the pesky missing
c++-filt was eventually done with Jeff's help and hunting through a few
newsgroup postings (see
http://comments.gmane.org/gmane.os.apple.fink.general/17670). It looks
like c++filt is not always reinstalled after the Tiger upgrade.

5) "fink install cdat"
-finishes, but complains "can't build cdms"; cdat & vcdat are created in
/sw/bin/ 

6)sudo gcc_select 3.3

7) "fink install cdat"
-reports "unpacking cdat-4.0", but still no cdms. Tried
removing/reinstalling cdat several times, but no cdms built.

8) "fink purge cdat"

9) rebuild cdat (under fink commander)

10) "fink install cdat" (still using gcc3.3) 
-this completes ok; I can now get a vcdat gui and plot some test Netcdf
data.

 


Special Cygwin (Windows XP) installation instructions (did not succeed in a while)

Install Cygwin from http://cygwin.com. When selecting the Packages for the Cygwin installation, it is important to select "Install" for "Base" and "X11". This will ensure that all the appropriate libraries needed for CDAT builds properly. In general, it is not a bad idea to select "Install" for "All" packages if you have the disk space.

Note: The "Cygwin Setup" can be a little confusing for first time users. When the package selection window appears, you will see the package name, a cycle icon, and the text "Default". If you select the text "Default" it will change to "Install". At the very top of this window you will see the "All" line. For the "All" line, we recommend that you toggle the selection from "Default" to "Install". This toggle from "Default" to "Install" will also change all subsequent package preinstall indications from "Default" to "Install" and will insure that the packages needed for CDAT will be installed accordingly.

Once you’ve installed Cygwin, select the Cygwin icon (located on your desktop) or from the "Start Menu" select "All Programs" then "Cygwin Bash Shell". In the window that appears, type:

rebaseall

If your TMP or TEMP environment variables are not set properly, you may need to issue the following command:

TMP=/tmp rebaseall

After issuing the rebaseall command, type:

startx

Note: It is extremely important to issue the rebaseall command; otherwise threading for Python and CDAT will not work properly.

Note: If your $HOME path has a space (or spaces) in it, then you will need to remove the space(s) by editing the /etc/passwd file. Make sure your account has "Computer Administrator" privileges. If not, then you will need to log on with an account that does. In the /etc/passwd file, find your user account and change your home directory path to remove all spaces. For example, if your path has:

  • /home/firstname lastname:/bin/bash

change it to:

  • /home/lastname:/bin/tcsh

When you have finished making your changes, you are required to reboot your machine for the changes to occur.

 

 

Special (Ubuntu) Linux installation instructions

Special thansk to Johnny Lin, Alexis Zubrow , Jerry Potter and everyone else for this contribution.

 

Introduction

 

Explicitly set the default compiler

If you don't explicitly set the environment variables specifying which compilers to use, you may end up compiling different libraries with different compilers. Thus, in csh or tcsh, make sure you execute:

setenv CC gcc
setenv FC gfortran
setenv CXX g++

or in Bash:

export CC=gcc
export FC=gfortran
export CXX=g++

Do this before you run the express install.

But I want OpenDAP!

If you want OpenDAP then enable it with the --with-opendap keyword in the above configure call. However, installation with OpenDAP often fails, and since I didn't need OpenDAP, I decided to try the install with it disabled. It seems that adding libcurl4-dev and curl fixes the problem (see packages belloow)

If at first you don't succeed ...

Throughout the install process, different problems might come up (packages aren't found, things don't build, etc.). In general, if that happens, my advice is to just delete everything in the target directory and the source directory, unpack the tar file again, and reinstall. (The recommended way is to just clean up the build directory, but I like the brute force approach to cleaning.) Sometimes this is enough to fix the problem.

If reinstalling doesn't work, then you'll have to look at the log files. (Btw, the logs are in logs and are named <package-name>.LOG. You might also be interested in the config.log files which are located in the package sub-directories.

Ubuntu packages needed

If you have only the minimal Ubuntu install, there is a good chance that you won't be able to do a successful install of CDAT, since additional packages are needed. Here's the list of what I added (you can add them using Synaptic, Ubuntu's GUI-based package manager):

  • bison *
  • byacc *
  • flex *
  • gawk *
  • g++
  • gfortran (for contrib packages)
  • libxt-dev
  • libx11-dev
  • tcsh (just highly recomended)
  • xorg-dev (also called xserver-xorg-dev)
  • *: doesn't seem to be needed anymore

Of these packages, xorg-dev is the really key one (see, for instance, Alexis Zubrow's experience with installing on Debian, which is very similar to Ubuntu). You may be able to do a successful build without adding all of the others, but because I didn't have the time to try reinstalling by adding one package at a time, I don't know if all the above is necessary. But with them all, it works.

 

 

 


 		 Table of Contents Previous Next
Contents Previous Next
Powered by Plone