Re: packages requiring Intel's libmkl_rt library

[Brook Milligan <brook%nmsu.edu@localhost>]

> On Feb 8, 2018, at 2:10 AM, Benny Siegert <bsiegert%gmail.com@localhost> wrote:
> 
> On Thu, Feb 8, 2018 at 8:26 AM Brook Milligan <brook%nmsu.edu@localhost> wrote:
> 
>> I am installing math/py-numpy on a system with Intel compilers.  It ends
> up requiring the libmkl_rt library, which is in /opt/intel/…, which is
> exactly where the path in the relevant numpy library points.  However, the
> checks in mk/check/check-shlibs.mk indicate that it is missing.
> 
>> How is this supposed to be handled so that libraries like this can be
> found?
> 
> Try adding the directory in question to BUILDLINK_PASSTHRU_DIRS in mk.conf.

This does not work, either in mk.conf or the package Makefile.

I note that math/py-numpy/Makefile has the following two blocks:

# XXX Avoid picking up other compilers when installed
.include "../../mk/compiler.mk”

# This package bypasses the wrappers and calls the compilers directly when
# linking, so ensure that we pass through requisite options.
LDFLAGS+=		${_COMPILER_ABI_FLAG.${ABI}}

The value of CC_VERSION in this case is gcc-4.4.7, yet it is clearly using an Intel compiler (how else would it require libmkl_rt?)  Thus, it seems that the second comment is correct and that including compiler.mk is not relevant (although it was originally included in revision 1.6 for the fortran compiler, which might be different I suppose.)

The solution I have currently is a bunch of lines in the Makefile like the following, one for each *.so in PLIST:

CHECK_SHLIBS_SKIP+=	${PYSITELIB}/numpy/core/multiarray.so

This avoids the problem, but should perhaps not be unconditional in the Makefile.

What make variables could be used in a condition surrounding these lines?

The current issue is on an XSEDE.org HPC system running linux.  I’m guessing this is unlikely to be a general linux issue, but rather one associated with using this Intel compiler.  Jason, with your HPC experience, do you have ideas?

Thanks for any help.

Cheers,
Brook