Opened 7 months ago

Last modified 7 weeks ago

#31456 needs_review enhancement

Add package regina (as a pip package)

Reported by: mkoeppe Owned by:
Priority: major Milestone: sage-9.5
Component: packages: optional Keywords:
Cc: slelievre, dunfield, mgoerner, culler, vdelecroix, dimpase Merged in:
Authors: Matthias Koeppe Reviewers: Dima Pasechnik
Report Upstream: N/A Work issues:
Branch: u/mkoeppe/add_package_regina__and_prerequisite_script_packages_ (Commits, GitHub, GitLab) Commit: 6b5a5e387be6911f3e27f869a9dc1a3333b97638
Dependencies: Stopgaps:

Status badges

Description (last modified by mkoeppe)

http://sageregina.unhyperbolic.org/ provides a pip-installable package that provides Regina with all prerequisites. We add it as a pip package.

Proper Sage packaging of Regina would require major work - Regina vendors various libraries (including normaliz and pybind11), see https://regina-normal.github.io/docs/license.html

Other install scripts (not used in this ticket):

Part of #31176 (Meta-ticket: Add packages from 3-manifolds / computop), #31164 (Meta-ticket: Add user packages from https://wiki.sagemath.org/SageMathExternalPackages as optional/experimental packages)

Change History (20)

comment:1 Changed 7 months ago by slelievre

  • Cc slelievre added

See also: #17077.

comment:2 Changed 7 months ago by mkoeppe

  • Description modified (diff)

comment:3 Changed 7 months ago by mkoeppe

  • Description modified (diff)

comment:4 Changed 7 months ago by mkoeppe

  • Branch set to u/mkoeppe/add_package_regina__and_prerequisite_script_packages_

comment:5 Changed 7 months ago by mkoeppe

  • Authors set to Matthias Koeppe
  • Cc dunfield mgoerner culler vdelecroix added
  • Commit set to a53aac87d3dea31ee029f6911567c51a89341357
  • Description modified (diff)
  • Status changed from new to needs_review
  • Summary changed from Add package regina (and prerequisite script packages) to Add package regina (as a pip package, using sageRegina)

New commits:

a53aac8build/pkgs/regina: New

comment:6 Changed 7 months ago by dunfield

The next release of Regina (6.1) will be somewhat easier to package since it will no longer depend on Boost; the current 6.0 requires both the Boost header files (IIRC more than is in the current "Boost cropped" required by Sage) and a couple binary Boost libraries.

comment:7 Changed 6 months ago by mkoeppe

  • Milestone changed from sage-9.3 to sage-9.4

Moving this ticket to 9.4, as it seems unlikely that it will be merged in 9.3, which is in the release candidate stage

comment:8 Changed 3 months ago by mkoeppe

  • Cc dimpase added

comment:9 Changed 3 months ago by dimpase

Would it be more natural to make it depend on fully built Sage, so that it can be tested with spkg-check, by the 1-liner

import regina.sageRegina; regina.sageRegina.runTests()

comment:10 follow-up: Changed 3 months ago by dimpase

build works on macOS, on Linux I get a weird no space left on device from the linker, even though I have 255Gb free on the volume I build. More space needed on /tmp (there is "only" 3.6Gb) ? I don't know.

[regina]     g++ -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-rpath-link,/home/scratch2/dimpase/sage/sage/local/lib -L/home/scratch2/dimpase/sage/sage/local/lib -Wl,-rpath,/home/scratch2/dimpase/sage/sage/local/lib build/temp.linux-x86_64-3.8/regina_2bbddde/engine/split/sigcensus.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/split/signature.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/split/sigisomorphism.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/l31pillow.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/txicore.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/standardtri.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/snappeacensustri.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/plugtrisolidtorus.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/trivialtri.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/snappedtwosphere.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/layeredlensspace.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/layeredtorusbundle.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/layeredloop.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/satblocktypes.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/layeredchainpair.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/spiralsolidtorus.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/satblock.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/satregion.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/trisolidtorus.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/satblockstarter.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/layering.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/snappedball.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/satannulus.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/blockedsfstriple.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/layeredchain.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/pillowtwosphere.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/layeredsolidtorus.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/pluggedtorusbundle.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/blockedsfsloop.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/blockedsfs.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/augtrisolidtorus.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/subcomplex/blockedsfspair.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/snappea/uimessages.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/snappea/xmlsnappeareader.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/snappea/snappeatriangulation.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/snappea/fundgroup.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/snappea/examplesnappea.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/snappea/homology.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/census/gluingpermsearcher3.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/census/census.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/census/hyperbolic.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/census/gluingpermsearcher4.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/census/gluingperms.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/census/gluingpermsearcher2.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/census/closedprimemin.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/census/compact.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/census/euler.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/manifold/sfs.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/manifold/graphtriple.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/manifold/sfsaltset.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/manifold/lensspace.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/manifold/graphloop.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/manifold/simplesurfacebundle.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/manifold/torusbundle.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/manifold/order.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/manifold/graphpair.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/manifold/manifold.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/manifold/handlebody.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/manifold/snappeacensusmfd.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/treewidth/treedecomposition.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/file/globaldirs.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/file/fileinfo.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/nsvectorquadclosed.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/disc.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/nsvectorquadoctclosed.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/disctype.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/components.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/normalsurface.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/csv.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/links.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/nsvectorquad.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/nsvectoranstandard.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/enumfilter.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/nsvectororientedquad.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/nsvectororiented.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/crushandcut.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/prism.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/surfacefilter.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/enumerator.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/nsvectorstandard.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/orientable.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/xmlsurfacereader.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/normalsurfaces.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/xmlfilterreader.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/boundaries.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/nsvectorquadoct.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/stdtoquad.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/surfaces/quadtostd.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/foreign/isosig.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/foreign/dehydration.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/foreign/orb.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/libnormaliz/linear_algebra.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/libnormaliz/other_algorithms.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/libnormaliz/output.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/libnormaliz/primal.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/libnormaliz/offload_handler.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/libnormaliz/enumeration.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/libnormaliz/cone_and_control.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/angle/anglestructure.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/angle/anglestructures.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/angle/xmlanglestructreader.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/utilities/xmlcallback.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/utilities/i18nutils.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/utilities/memstream.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/utilities/osutils.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/utilities/randutils.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/utilities/boolset.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/utilities/base64.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/utilities/xmlutils.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/utilities/stringutils.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/packet/script.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/packet/xmlpacketreaders.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/packet/xmlpacketreader.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/packet/pdf.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/packet/packet.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/packet/text.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/packet/open.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/flype.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/gauss.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/modellinkgraph.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/pass.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/reidemeister.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/jenkins.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/link.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/homfly.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/jones.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/tangle.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/xmllinkreader.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/reidemeister-tangle.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/complement.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/simplify.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/sig.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/dt.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/rewrite.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/algebra.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/link/examplelink.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/enumerate/treeconstraint.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/enumerate/treetraversal.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/enumerate/treelp.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/enumerate/typetrie.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/algebra/abeliangroup.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/algebra/xmlalgebrareader.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/algebra/homgrouppresentation.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/algebra/markedabeliangroup.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/algebra/grouppresentation.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/maths/binom.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/maths/ray.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/maths/rational.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/maths/primes.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/maths/matrixops.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/maths/integer.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/maths/approx.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/maths/numbertheory.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/maths/cyclotomic.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/maths/matrix2.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/maths/seedprimes.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/core/engine.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/hypersurface/xmlhypersurfacereader.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/hypersurface/hsvectorstandard.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/hypersurface/triangulate.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/hypersurface/links.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/hypersurface/enumerate.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/hypersurface/normalhypersurfaces.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/hypersurface/normalhypersurface.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/triangulation/xmltrireader4.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/triangulation/facetpairing3.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/triangulation/xmltrireader2.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/triangulation/example4.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/triangulation/homologicaldata.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/triangulation/example3.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/triangulation/facenumbering.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/triangulation/xmltrireader3.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/triangulation/facepair.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/triangulation/example2.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/snappea/snappy/snappy_get_gluing_equations.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/snappea/kernel/Moebius_transformations.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/snappea/kernel/cusp_cross_sections.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/snappea/kernel/change_peripheral_curves.o build/temp.linux-x86_64-3.8/regina_2bbddde/engine/snappea/kernel/cusps.o 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build/temp.linux-x86_64-3.8/regina_2bbddde/python/packet/pdf.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/packet/packetlistener.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/packet/packet.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/packet/packettype.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/packet/text.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/packet/pypacket.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/link/modellinkgraph.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/link/link.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/link/tangle.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/link/pylink.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/link/examplelink.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/sage/pysage.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/simplex6.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/isomorphism8.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/isomorphism7.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/isomorphism10.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/example9.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/pygeneric.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/example7.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/simplex13.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facetpairing6.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/boundarycomponent15.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/triangulation13.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/boundarycomponent11.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/boundarycomponent8.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facetpairing13.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/boundarycomponent12.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/boundarycomponent9.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facetpairing2.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/face12.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/isomorphism13.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/example15.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facetpairing14.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/triangulation14.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/simplex9.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/simplex5.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/boundarycomponent13.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/triangulation8.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/face7.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/isomorphism5.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/face14.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/isomorphism15.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/simplex7.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/triangulation10.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/component8.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/triangulation7.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facetpairing11.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/face8.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/example6.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/simplex12.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/example8.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/boundarycomponent5.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/component10.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/boundarycomponent10.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/triangulation12.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/isomorphism6.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/example10.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/isomorphism12.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facetpairing8.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/component14.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/component5.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facetpairing10.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facetpairing5.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/simplex10.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/isomorphism9.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/example5.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/example13.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/boundarycomponent14.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/face11.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/face6.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/component11.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/face5.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/simplex14.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/triangulation6.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facetpairing7.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facetpairing15.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facetspec.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/component13.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/simplex11.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/example11.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facehelper.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/boundarycomponent7.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/triangulation5.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/component9.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/triangulation15.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/face15.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facetpairing4.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/example14.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/simplex15.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/face9.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/face10.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/component12.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/isomorphism11.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/component15.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/triangulation9.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/isomorphism14.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/component6.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/triangulation11.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/component7.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facetpairing12.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/facetpairing9.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/face13.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/example12.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/simplex8.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/generic/boundarycomponent6.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/algebra/abeliangroup.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/algebra/homgrouppresentation.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/algebra/markedabeliangroup.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/algebra/pyalgebra.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/algebra/grouppresentation.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/progress/pyprogress.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/progress/progresstracker.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/perm2.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/binom.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/perm3.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/rational.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/primes.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/matrixops.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/integer.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/laurent.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/perm5.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/matrixint.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/largeinteger.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/perm4.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/pymaths.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/perm.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/numbertheory.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/cyclotomic.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/matrix2.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/laurent2.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/maths/polynomial.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/hypersurface/pyhypersurface.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/hypersurface/hyperflags.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/hypersurface/hypercoords.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/hypersurface/normalhypersurfaces.o build/temp.linux-x86_64-3.8/regina_2bbddde/python/hypersurface/normalhypersurface.o -L/usr/lib64 -Lbuild/temp.linux-x86_64-3.8 -lgmp -lgmpxx -lm -ltokyocabinet_regina -llibxml_regina -o build/lib.linux-x86_64-3.8/regina/engine.cpython-38-x86_64-linux-gnu.so -lbz2 -lz
[regina]     /usr/bin/ld: final link failed: No space left on device
[regina]     collect2: error: ld returned 1 exit status
[regina]     error: command 'g++' failed with exit status 1
[regina]     ----------------------------------------
[regina] ERROR: Command errored out with exit status 1: /home/scratch2/dimpase/sage/sage/local/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-fh__hucb/sageregina_b1eebb35c7804c5abb600ad32424aed7/setup.py'"'"'; __file__='"'"'/tmp/pip-install-fh__hucb/sageregina_b1eebb35c7804c5abb600ad32424aed7/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-tilo1oin/install-record.txt --single-version-externally-managed --compile --install-headers /home/scratch2/dimpase/sage/sage/local/include/site/python3.8/sageRegina Check the logs for full command output.
make[2]: *** [Makefile:2623: regina-no-deps] Error 1
make[1]: *** [Makefile:2623: regina] Error 2
make[1]: Leaving directory '/home/scratch2/dimpase/sage/sage/build/make'

real    84m47.022s
user    85m8.909s
sys     3m22.958s
***************************************************************
Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make regina'):

It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

make: *** [Makefile:39: regina] Error 1
clpc171[/home/scratch2/dimpase/sage/sage]$
clpc171[/home/scratch2/dimpase/sage/sage]$ df -h
Filesystem                                   Size  Used Avail Use% Mounted on
devtmpfs                                     7.8G     0  7.8G   0% /dev
tmpfs                                        7.8G  400K  7.8G   1% /dev/shm
tmpfs                                        7.8G  9.5M  7.8G   1% /run
/dev/sda1                                     52G   39G   10G  80% /
/dev/sda7                                    3.9G   15M  3.7G   1% /home
/dev/sda6                                    3.9G   42M  3.6G   2% /tmp
/dev/sda5                                     12G  3.9G  7.3G  35% /var
/dev/sda9                                     40G   30G  7.7G  80% /usr/local
/dev/sda8                                    120G   91G   24G  80% /home/scratch
/dev/sdb1                                    458G  180G  255G  42% /home/scratch2
/dev/sda3                                    3.9G   17M  3.7G   1% /var/tmp
tmpfs                                        1.6G   16K  1.6G   1% /run/user/42
fsnfs-data.cs.ox.ac.uk:/homes/staff/dimpase  3.8T  3.6T  195G  95% /auto/users/dimpase
tmpfs                                        1.6G     0  1.6G   0% /run/user/11462
clpc171[/home/scratch2/dimpase/sage/sage]$

comment:11 Changed 3 months ago by dimpase

On macOS engine.cpython-39-darwin.so is 52Mb - big, but nothing crazy.

comment:12 follow-up: Changed 3 months ago by dimpase

does not build on 32-bit

[regina]     gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iboost_1_75_0 -Iregina_2bbddde/engine -Iregina_2bbddde/python -Itokyocabinet-1.4.48 -Ilibxml2-2.9.3/include -I/home/dima/sage/dev/sage/local/include -I/usr/include/python3.8 -c regina_2bbddde/engine/angle/xmlanglestructreader.cpp -o build/temp.linux-i686-3.8/regina_2bbddde/engine/angle/xmlanglestructreader.o -fpermissive -std=c++14
[regina]     In file included from regina_2bbddde/engine/maths/integer.h:49:0,
[regina]                      from regina_2bbddde/engine/maths/rational.h:43,
[regina]                      from regina_2bbddde/engine/angle/anglestructure.h:44,
[regina]                      from regina_2bbddde/engine/angle/anglestructures.h:47,
[regina]                      from regina_2bbddde/engine/angle/xmlanglestructreader.h:44,
[regina]                      from regina_2bbddde/engine/angle/xmlanglestructreader.cpp:34:
[regina]     regina_2bbddde/engine/utilities/intutils.h:231:20: error: ‘int128_type’ in namespace ‘boost’ does not name a type
[regina]          typedef boost::int128_type type;
[regina]                         ^~~~~~~~~~~
[regina]     regina_2bbddde/engine/utilities/intutils.h:232:20: error: ‘uint128_type’ in namespace ‘boost’ does not name a type
[regina]          typedef boost::uint128_type utype;
[regina]                         ^~~~~~~~~~~~
[regina]     In file included from regina_2bbddde/engine/triangulation/facenumbering.h:43:0,
[regina]                      from regina_2bbddde/engine/triangulation/detail/face.h:45,
[regina]                      from regina_2bbddde/engine/triangulation/generic/face.h:45,
[regina]                      from regina_2bbddde/engine/triangulation/detail/triangulation.h:55,
[regina]                      from regina_2bbddde/engine/triangulation/generic/triangulation.h:207,
[regina]                      from regina_2bbddde/engine/triangulation/dim3/triangulation3.h:55,
[regina]                      from regina_2bbddde/engine/triangulation/dim3.h:45,
[regina]                      from regina_2bbddde/engine/angle/xmlanglestructreader.cpp:35:
[regina]     regina_2bbddde/engine/triangulation/detail/facenumbering.h: In static member function ‘static bool regina::detail::FaceNumberingImpl<3, 1, true>::containsVertex(unsigned int, unsigned int)’:
[regina]     regina_2bbddde/engine/triangulation/detail/facenumbering.h:625:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[regina]                  return (vertex == edgeVertex[face][0] ||
[regina]                          ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
[regina]     regina_2bbddde/engine/triangulation/detail/facenumbering.h:626:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[regina]                          vertex == edgeVertex[face][1]);
[regina]                          ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
[regina]     regina_2bbddde/engine/triangulation/detail/facenumbering.h: In static member function ‘static bool regina::detail::FaceNumberingImpl<4, 1, true>::containsVertex(unsigned int, unsigned int)’:
[regina]     regina_2bbddde/engine/triangulation/detail/facenumbering.h:743:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[regina]                  return (vertex == edgeVertex[face][0] ||
[regina]                          ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
[regina]     regina_2bbddde/engine/triangulation/detail/facenumbering.h:744:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[regina]                          vertex == edgeVertex[face][1]);
[regina]                          ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
[regina]     regina_2bbddde/engine/triangulation/detail/facenumbering.h: In static member function ‘static bool regina::detail::FaceNumberingImpl<4, 2, false>::containsVertex(unsigned int, unsigned int)’:
[regina]     regina_2bbddde/engine/triangulation/detail/facenumbering.h:809:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[regina]                  return (vertex == triangleVertex[face][0] ||
[regina]                          ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
[regina]     regina_2bbddde/engine/triangulation/detail/facenumbering.h:810:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[regina]                          vertex == triangleVertex[face][1] ||
[regina]                          ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
[regina]     regina_2bbddde/engine/triangulation/detail/facenumbering.h:811:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[regina]                          vertex == triangleVertex[face][2]);
[regina]                          ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
[regina]     error: command 'gcc' failed with exit status 1
[regina]     ----------------------------------------
[regina] ERROR: Command errored out with exit status 1: /home/dima/sage/dev/sage/local/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-wpwte5ec/sageregina_15b0fb0a8849472a82e6450833373eaf/setup.py'"'"'; __file__='"'"'/tmp/pip-install-wpwte5ec/sageregina_15b0fb0a8849472a82e6450833373eaf/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-dqft7148/install-record.txt --single-version-externally-managed --compile --install-headers /home/dima/sage/dev/sage/local/include/site/python3.8/sageRegina Check the logs for full command output.

Make it experimental rather than optional?

comment:13 Changed 3 months ago by dunfield

FYI, sageRegina is being superseded by https://github.com/3-manifolds/regina_wheels. As of yesterday, you can now do:

sage -pip install --pre regina

and it should install self-contained binary wheels on macOS and Linux, for 64bit Intel only. Test command is now:

sage -m regina.test

This is based the current development version of Regina, not the 6.0.1 release.

I've never seen the No space on device error when building Regina, except possibly if I was doing it in Docker on macOS and the Docker VM itself was running out of disk space.

Last edited 3 months ago by dunfield (previous) (diff)

comment:14 Changed 3 months ago by git

  • Commit changed from a53aac87d3dea31ee029f6911567c51a89341357 to 6b5a5e387be6911f3e27f869a9dc1a3333b97638

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

968af37build/pkgs/regina: New
6b5a5e3build/pkgs/regina: Switch from sageRegina to regina

comment:15 Changed 3 months ago by mkoeppe

  • Summary changed from Add package regina (as a pip package, using sageRegina) to Add package regina (as a pip package)

comment:16 Changed 3 months ago by dimpase

OK, this works, but can an optional package not be supported on 32-bit Linux (nor on FreeBSD, which is another platform Sage should work on)

And, how about arm64?

comment:17 Changed 3 months ago by dimpase

  • Reviewers set to Dima Pasechnik

comment:18 in reply to: ↑ 10 Changed 3 months ago by mgoerner

Replying to dimpase:

build works on macOS, on Linux I get a weird no space left on device from the linker, even though I have 255Gb free on the volume I build. More space needed on /tmp (there is "only" 3.6Gb) ? I don't know.

Unfortunately, the intermediate object files are really big. You can use: export TMPDIR=... if /tmp does not have enough space, see http://sageregina.unhyperbolic.org/troubleshoot.html

comment:19 in reply to: ↑ 12 Changed 3 months ago by mgoerner

Replying to dimpase:

does not build on 32-bit

[regina]     regina_2bbddde/engine/utilities/intutils.h:231:20: error: ‘int128_type’ in namespace ‘boost’ does not name a type
[regina]          typedef boost::int128_type type;
[regina]                         ^~~~~~~~~~~

The problem is with the boost configuration. The good news is that regina and sageRegina no longer use boost. Fixed automatically when regina 6.1(-alpha) is coming out.

comment:20 Changed 7 weeks ago by mkoeppe

  • Milestone changed from sage-9.4 to sage-9.5
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