[3dem] Suprim 5.7 installation

[slaton]

Jools,

This is my workflow for building Suprim on debian (5.0/lenny). Should be 
fairly similar on Ubuntu.

If you install to a location other than /usr/local, adjust as needed.

If you're not on a 64-bit box you'll have to change SUPRIM_TARGET.

If you don't use environment modules you can ignore that bit, but do make 
sure you define all of the SUPRIM environment stuff as described in the 
readme.


1 - Building tkImgDip

Edit Makefile and change these lines:

 INSTALL_DIR=/usr/local/tkImgDip
 INCLUDES = -I/sw/include -I/usr/local/include -I/usr/include/tcl8.4
 LINKDIRS = -L/sw/lib -L/usr/local/lib -L/usr/lib

*Important: Be sure the INCLUDES and LINKDIRS lines you are editing are in 
the "Normal version" block of code.

make; make install


2 - Building Suprim

Verify that gfortran and libg2c0 packages are installed. If not already 
there, add symlink:

 # cd /usr/lib
 # ln -s /usr/lib/libg2c.so.0 /usr/lib/libg2c.so

Create suprim environment module and load it. Make sure SUPRIM_PATH is
defined.

Edit Makefile.linux64 and change these lines:

 CFLAGS=$(S_CFLAGS) -g -I$(INCDIR) -I/usr/include/tcl8.4 -O3 -DLINUX -fPIC 
$(BUGGY_MRC)
 FC=gfortran

*Important: If you forgot the libg2c symlink you will see this error when 
building with gfortran:

 Tklatlib.c:588: warning: cast from pointer to integer of different size
 /usr/bin/ld: cannot find -lg2c
 collect2: ld returned 1 exit status
 make[1]: *** [Tklat.so] Error 1

export SUPRIM_TARGET=linux64
make; make install

*Note that there may be an issue trying to run make install with sudo, as 
depending on your shell/config, sudo may not inherit the environment (such 
as SUPRIM_TARGET).


good luck
slaton

Slaton Lipscomb
Nogales Lab, Howard Hughes Medical Institute
http://cryoem.berkeley.edu

On Wed, 4 Mar 2009, Hodgkinson.Julie at mh-hannover.de wrote:

> 
> Hi all,
> 
> This is an image analysis question rather than an EM question but I am 
> hoping someone here will be able help. Anyone have any experience with 
> installing Suprim in Ubuntu? Can it be done? We are installing Suprim 
> 5.7 in Ubuntu (Kubuntu) distro below. We managed to install the 
> libtkImgDip-1.7.4, after chasing down a number of missing libraries, but 
> compiling Suprim 5.7 falls over. More sepcifics if someone thinks they 
> might be able to help.
> 
> 2.6.24-23-generic #1 SMP 
> DISTRIB_ID=Ubuntu
> DISTRIB_RELEASE=8.04
> DISTRIB_CODENAME=hardy
> DISTRIB_DESCRIPTION="Ubuntu 8.04.2"
> 
> cheers,
> 
> Jools