Launching

PyMOL Refuses to Launch on CentOS 5+ or any SELinux System

If PyMOL refuses to start and you get a message like:

$ ./pymol
/home/vertrees/pymol/pymol.exe: error while loading shared libraries: /home/vertrees/pymol/ext/lib/libmkl_def.so: cannot restore segment prot after reloc: Permission denied

then your SELinux security level is set too high. This happens to _anyone_ using the Intel fortran libraries that we ship (this also pesters companies likes Wolfram that sells Mathematica)! The work around is easy. You can reduce the enforcement with:

sudo /usr/sbin/setenforce 0

or

Replace “enforcing” by “permissive” in /etc/selinux/config, then restart.

# This file controls the state of SELinux on the system.
# SELINUX= can take one of these three values:
#	enforcing - SELinux security policy is enforced.
#	permissive - SELinux prints warnings instead of enforcing.
#	disabled - No SELinux policy is loaded.
SELINUX=enforcing
# SELINUXTYPE= can take one of these two values: 
#	targeted - Targeted processes are protected,
#	mls - Multi Level Security protection.
SELINUXTYPE=targeted 
 
troubleshooting/linux.txt
 
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