I think in your case it would be enough to use preinstallopts = 'export PKG_CXXFLAGS="$CXXFLAGS -DSTAN_THREADS" &&' (be warned though, I don't use R, this is just an mildly educated guess based on that issue you mentioned).
On Wed, 27 Nov 2019 at 14:17, Loris Bennett <[email protected]<mailto:[email protected]>> wrote: Alan O'Cais <[email protected]<mailto:[email protected]>> writes: > I took a quick look at > https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-Makevars > and it looks like you need to use PKG_CXXFLAGS Yes, I just found a reference to PKG_CXXFLAGS here: https://github.com/easybuilders/easybuild-easyconfigs/issues/8930 where the following construction is given: toolchainopts = {'cstd': 'c99'} preinstallopts = 'export PKG_CFLAGS="$CFLAGS" && ' How would this look in my case? Does the macro STAN_THREADS need to be set as a toolchain option? If so, what is the correct dictionary key? Cheers, Loris > 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. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email [email protected]<mailto:[email protected]> -- 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. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
