On a cluster that is based on RedHat 6.2, we are updating to R-3.3.1. I have, from time to time, run into problems with various R packages and some older versions of GCC. I wish we had newer Linux in the cluster, but with 1000s of nodes running 1000s of jobs, well, they don't want a restart.
Administrator suggested I try to build with the GCC that is provided with the nodes, which is gcc-4.4.7. To my surprise, R-3.3.1 compiled with that. After that, I got quite far, many 100s of packages compiled, but then I hit a snag that RccArmadillo explicitly refuses to build with anything older than gcc-4.6. The OpenMx package and emplik packages also refuse to compile with old gcc The cluster uses a module system, it is easy enough to swap in various gcc versions to see what compiles. I did succeed compiling RcppArmadillo with gcc 4.9.2. But Rcpp is not picky, it compiled with gcc-4.4.7. I worry... 1) will reliance on various GCC make the packages incompatible with R, or each other? I logged out, logged back in, with R 3.3.1 I can run library(RcppArmadillo) library(Rcpp) with no errors so far. But I'm not stress testing it much. I should rebuild everything? I expect that if I were to use gcc-6 on one package, it would not be compatible with binaries built with 4.4.7. But is there a zone of tolerance allowing 4.4.7 and 4.9 packages to coexist? 2) If I build with non-default GCC, are all of the R users going to hit trouble if they don't have the same GCC I use? Unless I make some extraordinary effort, they are getting GCC 4.4.7. If they try to install a package, they are getting that GCC, not the one I use to build RcppArmadillo or the other trouble cases (or everything, if you say I need to go back and rebuild). >From an administrative point of view, should I tie R-3.3.1 to a particular version of GCC? I think I could learn how to do that. On the cluster, they use the module framework. There are about 50 versions of GCC. It is easy enough ask for a newer one: $ module load gcc/4.9.2 It puts the gcc 4.9.2 binaries and shared libraries at the front of the PATHs. pj -- Paul E. Johnson http://pj.freefaculty.org Director, Center for Research Methods and Data Analysis http://crmda.ku.edu To write me directly, address me at pauljohn at ku.edu. ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
