Cluster: Various GCC, how important is consistency?
Dear Jeroen Did you rebuild R-3.3.1 and all of the packages with GCC-5.3 in order to make this work? The part that worries me is that the shared libraries won't be consistent, with various versions of GCC in play.
On Tue, Oct 18, 2016 at 5:55 AM, Jeroen Ooms <jeroen.ooms at stat.ucla.edu> wrote:
On Tue, Oct 18, 2016 at 1:44 AM, Paul Johnson <pauljohn32 at gmail.com> wrote:
Administrator suggested I try to build with the GCC that is provided with the nodes, which is gcc-4.4.7.
Redhat provides an alternative compiler (gcc 5.3 based) in one of it's opt-in repositories called "redhat developer toolkit" (RDT). In CentOS you install it as follows: yum install -y centos-release-scl yum install -y devtoolset-4-gcc-c++ This compiler is specifically designed to be used alongside the EL6 stock gcc 4.4.7. It includes a simple 'enable' script which will put RDT gcc and g++ in front of your PATH and LD_LIBRARY_PATH and so on. So what I do on CentOS is install R from EPEL (built with stock gcc 4.4.7) and whenever I need to install an R package that uses e.g. CXX11, simply start an R shell using the RDT compilers: source /opt/rh/devtoolset-4/enable R From what I have been able to test, this works pretty well (though I am not a regular EL user). But I was able to build R packages that use C++11 (such as feather) and once installed, these packages can be used even in a regular R session (without RDT enabled).
Paul E. Johnson http://pj.freefaculty.org Director, Center for Research Methods and Data Analysis http://crmda.ku.edu I only use this account for email list memberships. To write directly, address me at pauljohn at ku.edu.