Can't install in macOS Mojave with OpenMP support

[alazarolop]

Hi,

I'm running macOS Mojave 10.14.5 and R 3.6.0 and I was able to install ClusterR without any issue, but when I tried to run any of the functions with multi-threads, it didn't work.

So I tried to fix it following indications in this link (https://stackoverflow.com/questions/40904488/openmp-r-and-macos). I had libomp installed using homebrew, so I just created ~.R/Makevars file with:

SHLIB_OPENMP_CFLAGS=-Xpreprocessor -fopenmp
SHLIB_OPENMP_CXXFLAGS=-Xpreprocessor -fopenmp

After that and while trying to install ClusterR again, I get this error:

** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘ClusterR’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/local/lib/R/3.6/site-library/00LOCK-ClusterR/00new/ClusterR/libs/ClusterR.so':
  dlopen(/usr/local/lib/R/3.6/site-library/00LOCK-ClusterR/00new/ClusterR/libs/ClusterR.so, 6): Symbol not found: ___kmpc_for_static_fini
  Referenced from: /usr/local/lib/R/3.6/site-library/00LOCK-ClusterR/00new/ClusterR/libs/ClusterR.so
  Expected in: flat namespace
 in /usr/local/lib/R/3.6/site-library/00LOCK-ClusterR/00new/ClusterR/libs/ClusterR.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/3.6/site-library/ClusterR’
Warning in install.packages :
  installation of package ‘ClusterR’ had non-zero exit status

I also tried to follow the guide mention at the beginning of the link, but it didn't work too.

Is there anything I am missing? How could I fix it?
Thank you very much in advance.

[mlampros]

hi @alazarolop,

there was a similar issue regarding the installation of ClusterR on Macintosh with OpenMP enabled.
In the past I managed to use OpenMP on my Macintosh computer by following this tutorial, which was updated at 06/18/2017 ( highly probable there are more recent tutorials available on the web ) and is also mentioned in your web-link. I use an older version of Macintosh than Mojave and I'm not sure if currently OpenMP is enabled by default. I assume you want to avoid reconfiguring your personal computer and just enable OpenMP by adding the OPENMP flags in your ~.R/Makevars file.

[alazarolop]

Hi @mlampros, thanks for writing and sorry for the delay.

I've tried these days different indications, I'm getting the same outcome though .

Exactly, that's the point. I didn't want to install any other "clang" package manually and outside Homebrew as it's said in the guide. I reckon I will tray it step by step in a clean VM, so I can rule out and then I will write back.

[mlampros]

Hi @alazarolop,

if your intention is to find out if the ClusterR package fits your needs and you are familiar with docker, I can upload a dockerfile with Rstudio pre-installed so that you can build and run it on a linux instance where OpenMP is installed by default.

[alazarolop]

Hi @mlampros , excuse me for my late answer. I didn't know about OpenMP where running in Linux by default, maybe I can give it a try then. The dockerfile would be very helpful.

Thank you for your concern.

[mlampros]

Hi @alazarolop,

I uploaded the Dockerfile and added details on how to build / run the docker image at the end of the README.md file. I tested it on Ubuntu 18.04.
Let me know if it works for you too.

[stale]

This is Robo-lampros because the Human-lampros is lazy. This issue has been automatically marked as stale because it has not had recent activity. It will be closed after 7 days if no further activity occurs. Feel free to re-open a closed issue and the Human-lampros will respond.

[alazarolop]

@mlampros Sorry for my late response. I've finally got running ClusterR with OpenMP capability by using this guide. They key point was the gcc version I was using, so apparently one needs to manually create symlinks to Home-brew gcc in order to get it in working. Thank you for your help with the Dockerfile too.