I took a quick look at https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-Makevars and it looks like you need to use PKG_CXXFLAGS
On Wed, 27 Nov 2019 at 13:41, Åke Sandgren <[email protected]<mailto:[email protected]>> wrote: Ahhh R package.... no I think that's a lot harder. Not sure how R packages are built so can't currently help there. Anyway, you should use this way of changing things like buildopts self.cfg.update('buildopts', "BIGNUMA=1 ") And in pre_configure_hook you should only change opts related to configure step. build step opts should be done in pre_build_hook On 11/27/19 1:29 PM, Loris Bennett wrote: > Åke Sandgren <[email protected]<mailto:[email protected]>> > writes: > >> What does your hooks look like? > > def pre_configure_hook(self, *args, **kwargs): > > """Pre-configure hook""" > > # Build RStan with threading > ################################################## > if self.name<http://self.name> == 'RStan': > self.cfg['buildopts'] = self.cfg['buildopts'] \ > + 'CXX14FLAGS="$CXX14FLAGS -DSTAN_THREADS"' > self.log.info<http://self.log.info>("[pre-build hook] Added > -DSTAN_THREADS to CXX14FLAGS to buildopts") > return > > def pre_extensions_hook(self, *args, **kwargs): > > """Pre-extensions hook""" > > # Build RStan with threading > ################################################## > if self.name<http://self.name> == 'RStan': > self.cfg['buildopts'] = self.cfg['buildopts'] \ > + 'CXX14FLAGS="$CXX14FLAGS -DSTAN_THREADS"' > self.log.info<http://self.log.info>("[pre-extensions hook] Added > -DSTAN_THREADS to CXX14FLAGS to buildopts") > return > > I have also tried this with CXXFLAGS. > > In my own copy of the EC I have tried various things: > > #preconfigopts = "-DSTAN_THREADS" > #buildopts = "-DSTAN_THREADS" > #preconfigopts = 'CXXFLAGS="$CXXFLAGS -DSTAN_THREADS" ' > #buildopts = 'CXXFLAGS="$CXXFLAGS -DSTAN_THREADS" ' > buildopts = ' -DSTAN_THREADS CC="$CC" FC="$F77"' > > My impression is that none of these things affect the way the R packages > are build. > > Cheers, > > Loris > >> And in what hook are you trying to do this? (Which i'll see when you >> show me the hook ...) >> >> On 11/27/19 10:19 AM, Loris Bennett wrote: >>> Hi Åke, >>> >>> Åke Sandgren <[email protected]<mailto:[email protected]>> >>> writes: >>> >>>> You might need to add it to the configopts (preconfigopts). Not sure >>>> which steps that easyconfig/block is going through. >>> >>> I have tried tweaking the EC directly with >>> >>> preconfigopts = 'CXXFLAGS="$CXXFLAGS -DSTAN_THREADS" ' >>> >>> but this doesn't help. In the log I see >>> >>> == 2019-11-27 10:01:00,566 easyconfig.py:583 INFO setting easyconfig >>> parameter preconfigopts: value CXXFLAGS="$CXXFLAGS -DSTAN_THREADS" >>> (type: <type 'str'>) >>> >>> but subsequently >>> >>> == 2019-11-27 10:01:01,750 environment.py:97 INFO Environment variable >>> CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno >>> (previously undefined) >>> >>> A heavy-handed approach would seem to be redefining the default value of >>> CXXFLAGS global. Is that possible? >>> >>> Otherwise it looks like I'll have to patch the Makefiles in the sources. >>> >>> Cheers, >>> >>> Loris >>> >>>> On 11/21/19 10:05 AM, Loris Bennett wrote: >>>>> Loris Bennett >>>>> <[email protected]<mailto:[email protected]>> writes: >>>>> >>>>>> Hi, >>>>>> >>>>>> I am trying to install >>>>>> >>>>>> RStan-2.18.2-foss-2018b-R-3.5.1.eb >>>>>> >>>>>> with the additional compiler flag: >>>>>> >>>>>> -DSTAN_THREADS >>>>>> >>>>>> I want to us a hook and tried >>>>>> >>>>>> def pre_configure_hook(self, *args, **kwargs): >>>>>> >>>>>> """Pre-build hook""" >>>>>> >>>>>> # Build RStan with threading >>>>>> ################################################## >>>>>> if self.name<http://self.name> == 'RStan': >>>>>> self.cfg['buildopts'] = self.cfg['buildopts'] \ >>>>>> + 'CXXFLAGS="$CXXFLAGS -DSTAN_THREADS"' >>>>>> self.log.info<http://self.log.info>("[pre-build hook] Added >>>>>> -DSTAN_THREADS to CXXFLAGS to buildopts") >>>>>> return >>>>>> >>>>>> In the log file I can see that the hooks is called, but the flag >>>>>> doesn't seem to be used. >>>>>> >>>>>> What am I doing wrong? >>>>> >>>>> I have also tried adding >>>>> >>>>> buildopts = "-DSTAN_THREADS" >>>>> >>>>> to my own copy of the easyconfig. This does appear in >>>>> the log file has having been set: >>>>> >>>>> == 2019-11-21 09:20:23,543 easyconfig.py:583 INFO setting easyconfig >>>>> parameter buildopts: value -DSTAN_THREADS (type: <type 'str'>) >>>>> >>>>> but it is not passed to the compiler. The compile lines do contain >>>>> other macros, but these are obviously coming from elsewhere: >>>>> >>>>> g++ -std=gnu++14 >>>>> -I"/trinity/shared/easybuild/software/R/3.5.1-foss-2018b/lib64/R/include" >>>>> -DNDEBUG -I"../inst/include" >>>>> >>>>> -I"`"/trinity/shared/easybuild/software/R/3.5.1-foss-2018b/lib64/R/bin/Rscript" >>>>> --vanilla -e "cat(system.file('include', 'src', package = >>>>> 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS >>>>> -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION ... >>>>> >>>>> Any ideas how I could insert "-DSTAN_THREADS"? Or can this kind of >>>>> thing only be done by patching the Makefile? >>>>> >>>>> Cheers, >>>>> >>>>> Loris >>>>> >>>>> -- >>>>> Dr. Loris Bennett (Mr.) >>>>> ZEDAT, Freie Universität Berlin Email >>>>> [email protected]<mailto:[email protected]> >>>>> -- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: [email protected]<mailto:[email protected]> Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se -- Dr. Alan O'Cais E-CAM Software Manager Juelich Supercomputing Centre Forschungszentrum Juelich GmbH 52425 Juelich, Germany Phone: +49 2461 61 5213 Fax: +49 2461 61 6656 E-mail: [email protected]<mailto:[email protected]> WWW: http://www.fz-juelich.de/ias/jsc/EN ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. 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