Install Request: Upgrade R to 4.2.0 and Bioconductor to 3.15 [IN05264358]

[balston]

The latest R version currently on the clusters (R 4.1.1) cannot install the nlmixr package (Nonlinear Mixed Effects Models in Population PK/PD) as it depends on at least one other package (symengine) that requires at least R 4.2. This type of problem will become an increasing problem with older R versions.

• R 4.2.0 was released on 22nd April 2022 - https://cran.r-project.org/
• Bioconductor 3.15 was released on 27th April 2022 - http://bioconductor.org/

Note: This is the R version we should have as the default on RStudio from September 2022.

[balston]

Linked to Jira issue:

https://ucldata.atlassian.net/browse/RCE-877

[balston]

Building base R on Myriad first.

[balston]

Build script updated and uploaded to Myriad.

Building base R and recommended packages using:

cd /shared/ucl/apps/build_scripts
module unload -f compilers mpi gcc-libs
module load beta-modules
module load gcc-libs/10.2.0
module load compilers/gnu/10.2.0
module load openblas/0.3.13-serial/gnu-10.2.0
module load java/1.8.0_92
module load fftw/3.3.9/gnu-10.2.0
module load ghostscript/9.19/gnu-4.9.2
module load texinfo/6.6/gnu-4.9.2
module load texlive/2019
module load gsl/2.7/gnu-10.2.0
module load hdf/5-1.10.6/gnu-10.2.0
module load udunits/2.2.28/gnu-10.2.0
module load netcdf/4.8.1/gnu-10.2.0
module load pcre2/10.37/gnu-10.2.0
./R-4.2.0_install 2>&1 | tee ~/Software/R/R-4.2.0_install.log-25052022

[balston]

Build has completed. Looks OK so will make a module ready for the next stage of the build.

[balston]

Building additional packages using:

./R-4.2.0_packages_install 2>&1 | tee ~/Software//R//R-4.2.0_packages_install.log-25052022

Note: this will probably need running more than once.

[balston]

Myriad is now running the extra R packages build after a couple of minor issues - I had forgotten that Myriad needs extra modules for OpenMPI 4.0.5 and I had to remove the old adapt package as it fails to compile now (it is no longer on CRAN anyway).

[balston]

It has failed at attempting to build another old package not on CRAN (Design). Will remove and rerun tomorrow.

[balston]

Additional R and Bioconductor packages build completed. Now checking the log for problems.

[balston]

Possible problems:

readelf: Error: /lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel/lib/libtbb.so: Failed to read file header
readelf: Error: /lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel/lib/libtbbmalloc.so: Failed to read file header
readelf: Error: /lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel/lib/libtbbmalloc_proxy.so: Failed to read file header
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppParallel)

Install RcppParallel again to check.

* installing *source* package ‘protolite’ ...
** package ‘protolite’ successfully unpacked and MD5 sums checked
** using staged installation
Package protobuf was not found in the pkg-config search path.
Perhaps you should add the directory containing `protobuf.pc'
to the PKG_CONFIG_PATH environment variable
No package 'protobuf' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lprotobuf
<stdin>:1:10: fatal error: google/protobuf/message.h: No such file or directory
compilation terminated.
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because protobuf was not found. Try installing:
 * deb: libprotobuf-dev (Debian, Ubuntu, etc)
 * rpm: protobuf-devel (Fedora, EPEL)
 * csw: protobuf_dev (Solaris)
 * brew: protobuf (OSX)
If protobuf is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a protobuf.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘protolite’

This one needs fixing because:

ERROR: dependency ‘protolite’ is not available for package ‘geojson’
* removing ‘/lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/geojson’

[balston]

I've reinstalled RcppParallel using:

./R-4.2.0_single_package_install RcppParallel

and it has installed correctly as far as I can tell.

[balston]

Protobuf protobuf/3.17.3/gnu-10.2.0 wasn't installed on Myriad. Installing with:

module -f unload compilers mpi gcc-libs
module load beta-modules
module load gcc-libs/10.2.0
module load compilers/gnu/10.2.0
module load python3/3.9-gnu-10.2.0
./protobuf-3.17.3_install

[balston]

Redone geojsonio using:

./R-4.2.0_single_package_install geojsonio

[balston]

Installing R MPI support packages:

./R-4.2.0_MPI_install

[balston]

Module bundle updated and uploaded to Myriad.

Now ready to run some test jobs.

[balston]

Basic R tests work and parallel run using the doMPI package works.

Modules required are:

module -f unload compilers mpi gcc-libs
module load beta-modules
module load r/r-4.2.0_bc-3.15

[balston]

Ready to deploy on the other clusters.

[balston]

Deploying on Kathleen next. there is a Jira story here:

https://ucldata.atlassian.net/browse/RCE-946

for this.

[balston]

Basic R plus recommended packages built on Kathleen.

[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 ccspapp      qw    06/07/2022 12:37:46                                   80

[balston]

Additional R packages build job has started running.

[balston]

Additional R packages build job has finished - took 4 hours. Checking the output for errors now ...

[balston]

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.
g++ -std=gnu++14 -I"/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include  -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic  -g -O2  -c init.cpp -o init.o
g++ -std=gnu++14 -I"/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include  -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic  -g -O2  -c options.cpp -o options.o
g++ -std=gnu++14 -shared -L/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/lib -L/usr/local/lib64 -o RcppParallel.so init.o options.o -L/shared/ucl/apps/curl/7.47.1/gnu-4.9.2/lib -L/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/lib -lR
installing via 'install.libs.R' to /lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
readelf: /lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel/lib/libtbb.so: Error: /lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel/lib/libtbb.so: Failed to read file header
readelf: /lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel/lib/libtbbmalloc.so: Error: /lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel/lib/libtbbmalloc.so: Failed to read file header
readelf: /lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel/lib/libtbbmalloc_proxy.so: Error: /lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel/lib/libtbbmalloc_proxy.so: Failed to read file header
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppParallel)

but RcppParallel appears to have installed. I may do a single package install again to confirm.

[balston]

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

[balston]

Done. Now to run some tests.

[balston]

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 18:31:42                                   80

[balston]

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.

[balston]

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.

[balston]

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.

[balston]

The doMPI test job has worked.

I'm now trying a snow test job again over 2 nodes.

[balston]

The snow test job has failed:

GERun:  mpirun RMPISNOW
Loading required package: utils
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------

Attaching package: ‘rlecuyer’

The following object is masked from ‘package:Rmpi’:

    .onUnload

--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[39576,1],46]
  Exit code:    1
--------------------------------------------------------------------------

Investigating ...