There are many issues with different gcc versions, but they can at least be minimized by using static linking, i.e. you should at the very least use -static-libstdc++ -static-libgcc to make sure you don't mix runtime versions. We run into the same problem since C++11 compilers are rare on production machines, but as long as you can isolate the packages away from the dynamically loaded code it often works since R only works at symbol level as long as you have a self-contained binary. The only other thing to worry about are ABI changes, but unless you use Fortran they tend to be compatible enough.
Cheers, Simon > On Oct 17, 2016, at 7:44 PM, Paul Johnson <pauljoh...@gmail.com> wrote: > > 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 > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
