correctly configure R for BLAS/LAPACK & check configure output #1292
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
boegel
commented
Nov 21, 2017
|
|
||
| # make sure correct config script is used for Tcl/Tk | ||
| for dep in ['Tcl', 'Tk']: | ||
| root = get_software_root(dep) | ||
| 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)) |
There was a problem hiding this comment.
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')) |
There was a problem hiding this comment.
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
approved these changes
Nov 21, 2017
This was referenced Nov 21, 2017
This was referenced Dec 4, 2017
Closed
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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...