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
