Offer openblas's lapack to programs run under Sage

[EmmanuelCharpentier]

Rationale : Openblas offers LAPACK, but there is no lapack.so file available in the current installation. Programs called by (something in) Sage can't use it.

Case in point : jags (an MCMC sampler of some use to Bayesian users of R) doesn't install under the Sage shell ; however, this is necessary : a system installation called from Sage (i. e. from Sage's R) will detect a conflict between system's LAPACK and Sage's Openblas.

The simple expedient of linking libopenblas.so to liblapack.so in $SAGE_ROOT is suffocient for installing and using JAGS.

Plan : patch Openblas' spkg-install to create this link.

Timetable : whenever I can recreate a distinct Sage installation for creation of a "clean" patch (i. e. not on the next few days...).

CC: @kiwifb @dimpase

Component: numerical

Branch/Commit: u/charpent/offer_openblas_s_lapack_to_programs_run_under_sage @ cb5df83

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/21736

[EmmanuelCharpentier]

Branch: u/charpent/offer_openblas_s_lapack_to_programs_run_under_sage

[EmmanuelCharpentier]

Commit: cb5df83

[EmmanuelCharpentier]

comment:2

Builds OK. Passes ptestlong with two transient failures (both tests pass when run standalone) :

----------------------------------------------------------------------
sage -t --long --warn-long 97.7 src/sage/homology/simplicial_complex.py  # 1 doctest failed
sage -t --long --warn-long 97.7 src/sage/matrix/matrix_integer_dense.pyx  # Timed out (and interrupt failed)
----------------------------------------------------------------------
Total time for all tests: 3819.2 seconds
    cpu time: 17189.6 seconds
    cumulative wall time: 20998.4 seconds
Makefile:112 : la recette pour la cible « ptestlong » a échouée
make: *** [ptestlong] Erreur 5

real	128m40,205s
user	683m11,124s
sys	76m18,572s
charpent@asus16-ec:/usr/local/sage-exp$ sage -t --long --warn-long 97.7 src/sage/homology/simplicial_complex.py  # 1 doctest failed
Running doctests with ID 2016-10-21-09-52-12-a6e288e2.
Git branch: mabranche
Using --optional=database_gap,mpir,python2,sage
Doctesting 1 file.
sage -t --long --warn-long 97.7 src/sage/homology/simplicial_complex.py
    [588 tests, 5.88 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 6.1 seconds
    cpu time: 3.1 seconds
    cumulative wall time: 5.9 seconds
charpent@asus16-ec:/usr/local/sage-exp$ sage -t --long --warn-long 97.7 src/sage/matrix/matrix_integer_dense.pyx  # Timed out (and interrupt failed)
Running doctests with ID 2016-10-21-09-52-35-de03d437.
Git branch: mabranche
Using --optional=database_gap,mpir,python2,sage
Doctesting 1 file.
sage -t --long --warn-long 97.7 src/sage/matrix/matrix_integer_dense.pyx
    [573 tests, 13.34 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 13.5 seconds
    cpu time: 23.3 seconds
    cumulative wall time: 13.3 seconds

Forgot to add : the same patch in another private branch allows the normal use of LAPACK : jags buils and runs fine.

==> needs_review

---

New commits:

cb5df83

Trivially symlink liblapack.so to libopenblas.so.

[mkoeppe]

comment:3

Is this ticket still relevant?

[dimpase]

comment:4

I guess not, our (or system) lapack.pc should take care of this.

[dimpase]

Reviewer: Dima Pasechnik