Compiling

Step 3: Get and setup AFNI

export BASE_DIR=/nfsscratch/PREDICT/hjohnson/20121205_src/
mkdir -p ${BASE_DIR}
 
cd ${BASE_DIR}
curl http://afni.nimh.nih.gov/pub/dist/tgz/afni_src.tgz -o afni_src.tgz
tar xfz afni_src.tgz
# Optional: rm /nfsscratch/PREDICT/hjohnson/20121121_src/afni_src.tgz

## NOTE:  Suma won't build  SUMA because of missing GL library, and wont build parallel because it is stupid


cd afni_src
ls Makefile*
sed 's#/usr/bin/gcc#/usr/bin/gcc44#g' Makefile.linux_gcc33_64 | \
sed 's#/usr/X11R6/include#/usr/include#g' | \
sed 's#/usr/X11R6/lib64#/usr/lib64#g' | \
sed 's#LLIBS *= \(.*\)#LLIBS = \1 -lpng -ljpeg -lXm#g' | \
sed 's%^ *INSTALL_PREREQ%#%g' |
sed 's%INSTALLDIR = ./linux_gcc33_64%INSTALLDIR = ./linux_RHEL5%g' >  Makefile
 
make -j1 totality

NOTE: EVERYTHING BELOW HERE IS NOT RELEVANT OR NEEDED FOR AFNI BUILD THEY ARE NOTES THAT MAY HELP WITH OTHER BUILDS.

cd /nfsscratch/PREDICT/hjohnson/20121121_src/
# Install f2c executable
rsync -avz netlib.org::netlib/f2c/src f2c
cd f2c
mkdir -p bin share/man/man1
cd src 
make -f makefile.u
cp f2c ../bin
cp f2c.1t ../share/man/man1
 
# Install f2c library
cd .. # PWD == /nfsscratch/PREDICT/hjohnson/20121121_src/f2c
curl http://www.netlib.org/f2c/libf2c.zip>libf2c.zip
mkdir libf2c lib
cd libf2c
unzip ../libf2c.zip
make -f makefile.u
make -f makefile.u install LIBDIR=../lib
 
# Create the module file for f2c
echo -e "#%Module\n\
proc ModuleHelp { } {\n\
       puts stderr " This module loads the Fortran-to-C" \n\
       puts stderr " compiler f2c into your local environment."\n\
	puts stderr " Creation date: 2012-12-05"\n\
}\n\
set env_base 	/nfsscratch/PREDICT/hjohnson/20121121_src/f2c\n\
module-whatis   "module for Fortran-to-C compiler f2c "\n\
set curMod [module-info name]\n\
prepend-path     PATH                    $env_base/bin\n\
prepend-path     LD_LIBRARY_PATH         $env_base/lib\n\
prepend-path     MANPATH                 $env_base/share/man" > ~/privatemodules/f2c

# Possible solution:
sudo yum --installroot=/nfsscratch/PREDICT/hjohnson/20121121_src/X11 install xorg-x11-drivers.x86_64
####################### IGNORE #################################
cd /nfsscratch/PREDICT/hjohnson/20121121_src/
mkdir X11
cd X11
wget -A tar.gz -r http://www.x.org/releases/X11R7.7/src/
mv www.x.org/releases/X11R7.7 ./
rm -rf www.x.org
cd X11R7.7/proto
for FILE in `ls`; do tar xvf $FILE; done
 
tar xvf libX11-1.5.0.tar.gz
cd libX11-1.5.0
 
 
 
# Create the module file for X11R7.7
mkdir ~/privatemodules/X11
echo -e "#%Module\n\
proc ModuleHelp { } {\n\
       puts stderr " This module loads X11" \n\
       puts stderr " into your local environment."\n\
	puts stderr " Creation date: 2012-12-05"\n\
}\n\
set env_base 	/nfsscratch/PREDICT/hjohnson/20121121_src/X11\n\
module-whatis   "module for full X11 "\n\
set curMod [module-info name]\n\
setenv			 X11_DEFAULT			 R7.7
prepend-path     PATH                    $env_base/bin\n\
prepend-path     LD_LIBRARY_PATH         $env_base/lib\n\
prepend-path     MANPATH                 $env_base/share/man" > ~/privatemodules/X11/R7.7
 
# Specify the module version for X11
echo -e "#%Module\n\
\n\
if [info exists env(X11_DEFAULT)] {\n\
	set 	 	ModulesVersion 				 $env(X11_DEFAULT)\n\
} else {\n\
	set			ModulesVersion				 "R7.7"\n\
}" > ~/privatemodules/X11/.version
####################### IGNORE #################################

cd /nfsscratch/PREDICT/hjohnson/20121121_src/afni_src
make totality suma

mv -f ../afni/linux_gcc44_64/afni/* ../afni/linux_gcc44_64/abin  # TODO: verify paths once build succedes

AFNI

Compiling

Step 3: Get and setup AFNI

Running