[R-sig-ME] testing OpenMP-enabled glmmTMB on various configurations
Edgar J Gonzalez
edg@rjgonz@|ez @end|ng |rom c|enc|@@@un@m@mx
Tue Jan 14 02:33:13 CET 2020
Hi. This is what I got:
> library(remotes)
> remotes::install_github("glmmTMB/glmmTMB/glmmTMB using conditional_openmp")
Downloading GitHub repo glmmTMB/glmmTMB using 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 using gmail.com <mailto:bbolker using 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 using 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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