balston
balston
Job submitted on Kathleen as _ccspapp_ to build the additional R packages and install Bioconductor: ``` job-ID prior name user state submit/start at queue slots ja-task-ID ----------------------------------------------------------------------------------------------------------------- 308885 2.70175 R-4.2.0-pa...
Additional R packages build job has started running.
Additional R packages build job has finished - took 4 hours. Checking the output for errors now ...
Possible problems: ``` (tbb) Building TBB using bundled sources ... make[1]: Entering directory `/lustre/scratch/ccspapp/R/work/RtmpyZ8lgc/R.INSTALL8751d16f4f4/RcppParallel/src/tbb/src' OS: linux arch=intel64 compiler=gcc runtime=cc10.2.0_libc2.17_kernel3.10.0 tbb_build_prefix=linux_intel64_gcc_cc10.2.0_libc2.17_kernel3.10.0 work_dir=/lustre/scratch/ccspapp/R/work/RtmpyZ8lgc/R.INSTALL8751d16f4f4/RcppParallel/src/build/linux_intel64_gcc_cc10.2.0_libc2.17_kernel3.10.0_release make[1]: Leaving directory `/lustre/scratch/ccspapp/R/work/RtmpyZ8lgc/R.INSTALL8751d16f4f4/RcppParallel/src/tbb/src' (tbb) TBB compilation finished successfully....
Everything seems to be OK. Installing R MPI support packages: ``` module -f unload compilers mpi gcc-libs module load beta-modules cd /shared/ucl/apps/build_scripts/ ./R-4.2.0_MPI_install ```
Done. Now to run some tests.
I've submitted a 2 node test job using the doMPI R package: ``` job-ID prior name user state submit/start at queue slots ja-task-ID ----------------------------------------------------------------------------------------------------------------- 309153 2.67273 doMPI-Ex1- ccaabaa qw 06/08/2022...
Test job failed because it couldn't load the Rmpi package. I need to check why this didn't install correctly in the previous step.
I've found the problem. The installer couldn't run a test MPI script so didn't install Rmpi. I'm now working out how to fix it.
I've now got Rmpi to install by setting OpenMPI parameters for single node MPI. I will now re-sbmit the 2 node test job using the doMPI R package.