correctly configure R for BLAS/LAPACK & check configure output#1292
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wpoely86 merged 2 commits intoeasybuilders:developfrom Nov 21, 2017
Merged
correctly configure R for BLAS/LAPACK & check configure output#1292wpoely86 merged 2 commits intoeasybuilders:developfrom
wpoely86 merged 2 commits intoeasybuilders:developfrom
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boegel
commented
Nov 21, 2017
| if root: | ||
| dep_config = os.path.join(root, 'lib', '%sConfig.sh' % dep.lower()) | ||
| self.cfg.update('configopts', '-with-%s-config=%s' % (dep.lower(), dep_config)) | ||
| self.cfg.update('configopts', '--with-%s-config=%s' % (dep.lower(), dep_config)) |
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Nasty typo here, this went undetected because the existing R easyconfigs already include --with-tcl-config and --with-tk-config in configopts...
boegel
commented
Nov 21, 2017
| # define $BLAS_LIBS to build R correctly against BLAS/LAPACK library | ||
| # $LAPACK_LIBS should *not* be specified since that may lead to using generic LAPACK | ||
| # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1435 | ||
| env.setvar('BLAS_LIBS', os.getenv('LIBBLAS_MT')) |
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I am using $LIBBLAS_MT here, while existing R easyconfigs use $LIBBLAS.
This matter mainly when using Intel MKL, i.e. multithreaded vs sequential, see also the discussion in #202.
We could/should make this configurable, and stick to linking with the sequential BLAS library by default?
wpoely86
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Nov 21, 2017
This was referenced Nov 21, 2017
This was referenced Dec 4, 2017
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R is currently not being configured correctly, see easybuilders/easybuild-easyconfigs#1435 and also easybuilders/easybuild-easyconfigs#4773.
If
LAPACK_LIBSis defined inpreconfigopts, R reports that LAPACK is being builtgeneric, which seems wrong (although it may be OK for LAPACK, since there are no tuned LAPACK libraries, all the tuning is done in the BLAS library afaik).This change only defines
$BLAS_LIBSin the environment, and checks the output of the configure command to make sure that BLAS/LAPACK is i) used, ii) correctly configured (i.e. nogeneric).The R easyconfigs (in particular the recent easybuilders/easybuild-easyconfigs#5090 and easybuilders/easybuild-easyconfigs#5360) will need to be modified as well, since they now hard set
LAPACK_LIBSviapreconfigopts, which leads toLAPACK(generic)being reported.That's a bit of a catch-22 situation though, since removing
preconfigptspart and not including--with-blas --with-lapackin the easyconfig files requires that this updated easyblock is used, otherwise R gets (sliently) built without BLAS/LAPACK...