SPM/Installation on 64bit Linux

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All versions of SPM are supported under Linux 64 bit and the installation should be fairly the same with any version. You might have to recompile SPM MEX files (*.mexa64) if those provided with the SPM distribution do not appear to be compatible with your system.

Contents 1 SPM8 1.1 Installation 1.2 Compilation 2 SPM5 2.1 Installation 2.2 Compilation 3 SPM2 3.1 Installation 3.2 Compilation 4 General comments 4.1 Prerequisites 4.1.1 Hardware 4.1.2 Software 4.2 Compilation Troubleshooting 4.2.1 lstdc++ not Required 4.2.2 MEX Required 4.2.3 Missing files 4.3 Compilation notes for SPM2: 4.3.1 Updates for Makefile 4.3.2 Updates for spm_platform.m

[edit] SPM8

[edit] Installation

Download spm8.zip and its updates spm8_updates_rxxxx.zip in your home directory then type the following in a Terminal:

cd /home/login
unzip spm8.zip
unzip -o spm8_updates_rxxxx.zip -d spm8

Start MATLAB and add SPM into your path, either using File > Set Path > Add Folder... or typing

addpath /home/login/spm8

in MATLAB's workspace.

[edit] Compilation

In a Terminal, from the src folder of your SPM8 installation, type:

cd /home/login/spm8/src
make distclean
make && make install
make toolbox-distclean
make toolbox && make toolbox-install
make external-distclean
make external && make external-install

[edit] SPM5

[edit] Installation

Download spm5.tar.gz, its updates Updates_xxxx.tar.gz in your home directory then type the following in a Terminal:

cd /home/login
tar xvfz spm5.tar.gz
tar xvfz Updates_xxxx.tar.gz -C spm5

Start MATLAB and add SPM into your path, either using File > Set Path > Add Folder... or typing

addpath /home/login/spm5

in MATLAB's workspace.

[edit] Compilation

In a Terminal, from the src folder of your SPM5 installation, type:

cd /home/login/spm5/src
make distclean
make && make install

[edit] SPM2

[edit] Installation

Download spm2.tar.gz and its updated MEX files SPM2_LINUX64_MEX.tar.gz in your home directory then type the following in a Terminal:

cd /home/login
tar xvfz spm2.tar.gz
tar xvfz SPM2_LINUX64_MEX.tar.gz -C spm2

Start MATLAB and add SPM into your path, either using File > Set Path > Add Folder... or typing

addpath /Users/login/spm2

in MATLAB's workspace.

[edit] Compilation

In a Terminal, type:

cd /home/login/spm2
make clean.Linux.A64
make Linux.A64

[edit] General comments

The error "bad image handle dimensions" when trying to load files is an indication that you need to (re)compile the SPM MEX files.

[edit] Prerequisites

[edit] Hardware

A cpu that supports the x86-64 architecture.

[edit] Software

Operating system

A 64bit Linux distribution for the x86-64 architecture.

Compiler & Libraries

GCC version 3.4.0 or later. This is the first GCC release with proper x86-64 support. Glibc version 2.3.0 or later

Matlab

Matlab R14 SP1 or newer, as this is the first Matlab release that supports the x86-64 architecture.

[edit] Compilation Troubleshooting

[edit] lstdc++ not Required

If you get the error message "cannot find -lstdc++", you can edit your mexopts.sh config file and delete or disable the -lstdc++ compiler flags. It will compile properly without these flags.

Another solution is to install the libstdc++5 package using your package manager.

With the install of libtdc++5, the lstdc++ error persist, just do a symbolic link like

ln -s /usr/lib64/libstdc++.so.6 /usr/lib64/libstdc++.so 

and it should work fine

[edit] MEX Required

If you get the error "mex: command not found" check that mex is in your path. Either add the matlab binary directory (usually /usr/local/matlab/bin) to your path or create a link to mex somewhere already in the path (usually /usr/local/bin).

• Adding the path:
  • Type: PATH=/usr/local/matlab/bin:$PATH
• Creating a Link:
  • Enter your local binary direcotry: cd /usr/local/bin
  • Create the link: ln -s /usr/local/matlab/bin/mex
  • (Note: Creating a link in /usr/local/bin requires root privileges).

[edit] Missing files

If you get build errors such as math.h does not exist when trying to execute the command "make && make install", then you probably need to install the build-essentials package. At the command line type: "sudo aptitude install build-essential" (for Ubuntu). if you have sudo privileges or simply log in as root or obtain superuser status and type: "aptitude install build-essential". After the package is downloaded and installed retry "make && make install" in the spm5/src directory and you should be good to go.

[edit] Compilation notes for SPM2:

[edit] Updates for Makefile

In order to make the recompilation process work, the Makefile provided in the spm2.tar.gz package needs to be patched. Also the file spm_platform.m needs an update.

The updated Makefile adds a new architecture, Linux.a64:

Linux.a64:
  make all SUF=mexa64  CC="gcc -O3 -funroll-loops -fPIC -march=x86-64" \
  MEX="mex COPTIMFLAGS='-O3 -funroll-loops -fPIC -march=x86-64'"

Plus an appropriate section for clean and verb.mexa64.

The -fPIC option is necessary to allow linking on 64bit Linux.
-march=x86-64 provides generic optimisations for both Opteron and 64bit Xeon. If the code is running on a 64bit Xeon you can change it to -march=nocona (the first revision of the Xeon processor supporting EM64T had codename nocona), if you have an Opteron or Athlon64, change it to -march=opteron. This might give you an extra performance boost.

[edit] Updates for spm_platform.m

Matlab for 64bit Linux identifies itself as GLNXA64 as opposed to GLNX86 when running 32bit Matlab. Endian-ness doesn't change, so I added this to the PDefs cell list:

                'GLNXA64',      'unx',  0;...

and added GLNXA64 to the list of other unix platforms at the font configuration.