testing OpenMP-enabled glmmTMB on various configurations
Hi. This is what I got:
library(remotes)
remotes::install_github("glmmTMB/glmmTMB/glmmTMB at conditional_openmp")
Downloading GitHub repo glmmTMB/glmmTMB at conditional_openmp These packages have more recent versions available. Which would you like to update? 1: All 2: CRAN packages only 3: None 4: RcppEigen (0.3.3.5.0 -> 0.3.3.7.0) [CRAN] 5: Rcpp (1.0.1 -> 1.0.3 ) [CRAN] Enter one or more numbers, or an empty line to skip updates: 1 RcppEigen (0.3.3.5.0 -> 0.3.3.7.0) [CRAN] Rcpp (1.0.1 -> 1.0.3 ) [CRAN] Installing 2 packages: RcppEigen, Rcpp probando la URL 'https://cran.itam.mx/bin/macosx/el-capitan/contrib/3.6/RcppEigen_0.3.3.7.0.tgz <https://cran.itam.mx/bin/macosx/el-capitan/contrib/3.6/RcppEigen_0.3.3.7.0.tgz>' Content type 'application/x-gzip' length 4842361 bytes (4.6 MB) ================================================== downloaded 4.6 MB probando la URL 'https://cran.itam.mx/bin/macosx/el-capitan/contrib/3.6/Rcpp_1.0.3.tgz <https://cran.itam.mx/bin/macosx/el-capitan/contrib/3.6/Rcpp_1.0.3.tgz>' Content type 'application/x-gzip' length 3099696 bytes (3.0 MB) ================================================== downloaded 3.0 MB The downloaded binary packages are in /var/folders/bt/kwm2wvnn0m37kj9j7b4dxdch0000gn/T//RtmpYU7u2V/downloaded_packages checking for file ?/private/var/folders/bt/kwm2wvnn0m37kj9j7b4dxdch0000gn/T/R? checking for file ?/private/var/folders/bt/kwm2wvnn0m37kj9j7b4dxdch0000gn/T/RtmpYU7u2V/remotes486647c4e2db/glmmTMB-glmmTMB-42b0d9c/glmmTMB/DESCRIPTION? (404ms) ? preparing ?glmmTMB?: ? checking DESCRIPTION meta-information ... ? cleaning src ? checking for LF line-endings in source and make files and shell scripts ? checking for empty or unneeded directories Removed empty directory ?glmmTMB/inst/misc? ? looking to see if a ?data/datalist? file should be added ? building ?glmmTMB_1.0.0.tar.gz? * installing *source* package ?glmmTMB? ... ** using staged installation ** libs clang++ -arch x86_64 -ftemplate-depth-256 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -Wno-macro-redefined -Wno-unknown-pragmas -c glmmTMB.cpp -o glmmTMB.o clang: error: unsupported option '-fopenmp' make: *** [glmmTMB.o] Error 1 ERROR: compilation failed for package ?glmmTMB? * removing ?/Library/Frameworks/R.framework/Versions/3.6/Resources/library/glmmTMB? * restoring previous ?/Library/Frameworks/R.framework/Versions/3.6/Resources/library/glmmTMB? Error: Failed to install 'glmmTMB' from GitHub: (convertido del aviso) installation of package ?/var/folders/bt/kwm2wvnn0m37kj9j7b4dxdch0000gn/T//RtmpYU7u2V/file48666cf3703/glmmTMB_1.0.0.tar.gz? had non-zero exit status Hope it helps...
On Jan 13, 2020, at 4:04 PM, Ben Bolker <bbolker at gmail.com <mailto:bbolker at gmail.com>> wrote:
Hi folks,
We're trying to troubleshoot a version of glmmTMB that enables OpenMP
support, but we have a fairly limited set of test platforms and it would
be nice to know if many users are going to have installation difficulties.
If you have development tools (and the 'remotes' package) installed
and a few free minutes, it would be great if you could try
remotes::install_github("glmmTMB/glmmTMB/glmmTMB at conditional_openmp")
and let us know if you have any trouble installing (it should install
whether or not you have OpenMP enabled ...)
If you're feeling energetic or distractible, you could try the tests here:
https://github.com/glmmTMB/glmmTMB/issues/481#issuecomment-572767245 <https://github.com/glmmTMB/glmmTMB/issues/481#issuecomment-572767245>
the expected result is you should see *either* warnings that OpenMP is
not enabled *or* at least some speed-up for the parallel version over
the serial version.
Results (especially problematic ones!) welcome at
https://github.com/glmmTMB/glmmTMB/issues/481
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