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Revert "sage: preload openblasCompat"

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This reverts commit 4900bbee17.

The issue that was supposed to fix is now fixed by lazy-loading rpy2 and
makign sure scipy is loaded before that.
That is not quite as nice, but preloading is now causing its own issues
with openblas 0.3.4:
https://github.com/xianyi/OpenBLAS/issues/1936
This commit is contained in:
Timo Kaufmann 2018-12-28 22:46:10 +01:00
parent 360eddd3a3
commit 95909d4fb6
2 changed files with 18 additions and 15 deletions
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22
pkgs/applications/science/math/sage/default.nix
View File

@ -32,9 +32,8 @@ let
# `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
sagelib = self.callPackage ./sagelib.nix {
inherit ecl;
inherit sage-src;
pynac = pkgs.pynac; # *not* python.pkgs.pynac
inherit flint ecl arb;
inherit sage-src pynac singular;
linbox = pkgs.linbox.override { withSage = true; };
};
};
@ -60,6 +59,7 @@ let
# the files its looking fore are located. Also see `sage-env`.
env-locations = callPackage ./env-locations.nix {
inherit pari_data ecl;
inherit singular;
cysignals = python.pkgs.cysignals;
three = nodePackages.three;
mathjax = nodePackages.mathjax;
@ -70,7 +70,7 @@ let
sage-env = callPackage ./sage-env.nix {
sagelib = python.pkgs.sagelib;
inherit env-locations;
inherit python ecl palp pythonEnv;
inherit python ecl singular palp flint pynac pythonEnv;
pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
};
@ -84,6 +84,7 @@ let
sage-with-env = callPackage ./sage-with-env.nix {
inherit pythonEnv;
inherit sage-env;
inherit pynac singular;
pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
three = nodePackages.three;
};
@ -123,6 +124,19 @@ let
ignoreCollisions = true;
} // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
arb = pkgs.arb.override { inherit flint; };
singular = pkgs.singular.override { inherit flint; };
# *not* to confuse with the python package "pynac"
pynac = pkgs.pynac.override { inherit singular flint; };
# With openblas (64 bit), the tests fail the same way as when sage is build with
# openblas instead of openblasCompat. Apparently other packages somehow use flints
# blas when it is available. Alternative would be to override flint to use
# openblasCompat.
flint = pkgs.flint.override { withBlas = false; };
# Multiple palp dimensions need to be available and sage expects them all to be
# in the same folder.
palp = symlinkJoin {

11
pkgs/applications/science/math/sage/sage-env.nix
View File

@ -163,17 +163,6 @@ writeTextFile rec {
# for find_library
export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular]}:$DYLD_LIBRARY_PATH"
# Make sure the correct openblas library is picked up. Without this, sage
# can either end up using flints openblas (which is not openblasCopmat, thus
# leading to the issues described in https://trac.sagemath.org/ticket/26000)
# or R's blas, leading to the issues described in
# https://bitbucket.org/rpy2/rpy2/issues/491.
# The first issue could alternatively be solved by overriding flint's
# openblas dependency and the second one is effectively solved by loading
# rpy2 lazily in sage. Preloading explicitly makes all the headaches go
# away much easier and more future proof though.
export LD_PRELOAD="${openblasCompat}/lib/libopenblas.so:$LD_PRELOAD"
'';
} // {
lib = sagelib; # equivalent of `passthru`, which `writeTextFile` doesn't support