I think in your case it would be enough to use
preinstallopts = 'export PKG_CXXFLAGS="$CXXFLAGS -DSTAN_THREADS" &&'
(be warned though, I don't use R, this is just an mildly educated guess based
on that issue you mentioned).
On Wed, 27 Nov 2019 at 14:17, Loris Bennett <[email protected]> wrote:
Alan O'Cais <[email protected]> writes:
> I took a quick look at
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-Makevars and it
looks like you need to use PKG_CXXFLAGS
Yes, I just found a reference to PKG_CXXFLAGS here:
https://github.com/easybuilders/easybuild-easyconfigs/issues/8930
where the following construction is given:
toolchainopts = {'cstd': 'c99'}
preinstallopts = 'export PKG_CFLAGS="$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]>
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]> writes:
> >
> >> What does your hooks look like?
> >
> > def pre_configure_hook(self, *args, **kwargs):
> >
> > """Pre-configure hook"""
> >
> > # Build RStan with threading
> > ##################################################
> > if self.name == 'RStan':
> > self.cfg['buildopts'] = self.cfg['buildopts'] \
> > + 'CXX14FLAGS="$CXX14FLAGS -DSTAN_THREADS"'
> > self.log.info("[pre-build hook] Added -DSTAN_THREADS to CXX14FLAGS
to buildopts")
> > return
> >
> > def pre_extensions_hook(self, *args, **kwargs):
> >
> > """Pre-extensions hook"""
> >
> > # Build RStan with threading
> > ##################################################
> > if self.name == 'RStan':
> > self.cfg['buildopts'] = self.cfg['buildopts'] \
> > + 'CXX14FLAGS="$CXX14FLAGS -DSTAN_THREADS"'
> > 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]> 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]> 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 == 'RStan':
> >>>>>> self.cfg['buildopts'] = self.cfg['buildopts'] \
> >>>>>> + 'CXXFLAGS="$CXXFLAGS -DSTAN_THREADS"'
> >>>>>> 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]
> >>>>>
>
> --
> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> Internet: [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]
