commit: 74d3bc3916a6fefac6f5a1f810b855b7046696bb
Author: Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 3 05:32:25 2025 +0000
Commit: Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
CommitDate: Mon Sep 8 17:21:19 2025 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=74d3bc39
sci-physics/espresso: fix multitude of extremely severe runtime / test issues
At the heart of this issue is that tests were disabled, via a wholly
bogus and clearly unresearched claim that a dep isn't packaged. No such
dep exists -- the "dep" is a source code file inside the package
sources. It "does not exist" because cmake does not build tests when
running ctest. This is evidenced by loads of other C++ tests not running
at all because... they weren't built.
To fix this, patch the cmake files to expose a target for building
tests.
Next step: for absolutely unfathomable reasons, the package set up
-DCMAKE_SKIP_RPATH=YES, which exists solely to break the software into a
million pieces, as libraries are installed to site-packages and none of
the code can find the dependencies. This cmake option is seriously
advanced low-level debugging, using it at all is a huge red flag.
And the cherry on top is that using it also breaks running tests! Tests
cannot run if test programs cannot find the just-built libraries which
aren't in ld.so.conf. To work around *this*, the ebuild -- in the same
commit adding the bogus RESTRICT=test -- added an LD_PRELOAD of one out
of the four ${BUILD_DIR} libraries loaded by test code. This is *totally
insane*, as the correct solution is either rpath or LD_LIBRARY_PATH, and
LD_PRELOAD injects code into programs such as `mkdir -p "${BUILD_DIR}"`
which in case it wasn't completely obvious, DOES NOT WORK.
```
* environment, line 276: Called die
* The specific snippet of code:
*** The MPI_Type_free() function was called before MPI_INIT was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.
[localhost:00084] Local abort before MPI_INIT completed completed successfully,
but am not able to aggregate error messages, and not able to guarantee that all
other processes were killed!
*** The MPI_Type_free() function was called before MPI_INIT was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.
[localhost:00085] Local abort before MPI_INIT completed completed successfully,
but am not able to aggregate error messages, and not able to guarantee that all
other processes were killed!
* mkdir -p "${BUILD_DIR}" || die
```
Again, there was no reason to ever assume this could work, and the fact
that it was even possible to think it might be a good idea should have
been worrying: it implied that the installed software might not run
without injecting libraries. Indeed, it didn't run.
Since we are massively renovating the testsuite already, add a couple
needed bdeps, some backport patches fixing issues with the tests, and
skip the final remaining test failures. Additionally, it seems numpy
needs to be pinned to 1.* as indicated by some test fails.
Bug: https://github.com/espressomd/espresso/issues/5166
Bug: https://bugs.gentoo.org/811186
Signed-off-by: Eli Schwartz <eschwartz <AT> gentoo.org>
sci-physics/espresso/espresso-4.2.0.ebuild | 44 ++++++++++++++++++++++++++----
1 file changed, 38 insertions(+), 6 deletions(-)
diff --git a/sci-physics/espresso/espresso-4.2.0.ebuild
b/sci-physics/espresso/espresso-4.2.0.ebuild
index e5a5919f291c..9ccffbce0805 100644
--- a/sci-physics/espresso/espresso-4.2.0.ebuild
+++ b/sci-physics/espresso/espresso-4.2.0.ebuild
@@ -24,9 +24,6 @@ LICENSE="GPL-3"
SLOT="0"
IUSE="cuda doc examples +fftw +hdf5 test"
-# unittest_decorators not packaged
-RESTRICT="test"
-
REQUIRED_USE="
${PYTHON_REQUIRED_USE}"
@@ -34,7 +31,7 @@ RDEPEND="
${PYTHON_DEPS}
$(python_gen_cond_dep '
>=dev-python/cython-0.26.1[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
+ <dev-python/numpy-2[${PYTHON_USEDEP}]
')
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
fftw? ( sci-libs/fftw:3.0 )
@@ -48,6 +45,11 @@ DEPEND="${RDEPEND}
dev-texlive/texlive-latexextra
virtual/latex-base
)
+ test? (
+ $(python_gen_cond_dep '
+ dev-python/scipy[${PYTHON_USEDEP}]
+ ')
+ )
"
DOCS=( AUTHORS NEWS Readme.md ChangeLog )
@@ -57,11 +59,19 @@ PATCHES=(
# https://github.com/espressomd/espresso/pull/4655
# boost 1.81
"${FILESDIR}"/${P}-boost1.81.patch
+
"${FILESDIR}"/0001-allow-building-test-deps-without-running-ctest-indir.patch
+ "${FILESDIR}"/${P}-test-deprecations.patch
+ "${FILESDIR}"/${P}-test-rounding.patch
)
src_prepare() {
use cuda && cuda_src_prepare
cmake_src_prepare
+
+ # These produce tests that aren't run by "make check", but ctest picks
+ # them up by default, against upstream's intention.
+ cd testsuite || die
+ cmake_comment_add_subdirectory cmake scripts
}
src_configure() {
@@ -73,7 +83,6 @@ src_configure() {
-DCMAKE_DISABLE_FIND_PACKAGE_FFTW3=$(usex !fftw)
-DWITH_HDF5=$(usex hdf5)
-DCMAKE_DISABLE_FIND_PACKAGE_HDF5=$(usex !hdf5)
- -DCMAKE_SKIP_RPATH=YES
)
cmake_src_configure
}
@@ -85,7 +94,30 @@ src_compile() {
}
src_test() {
- LD_PRELOAD="${BUILD_DIR}/src/core/Espresso_core.so" cmake_src_test
+ CMAKE_SKIP_TESTS=(
+ # These 13 tests fail with
+ # "The MPI_Type_free() function was called before MPI_INIT was
invoked."
+ #
+ # I do not know why. But, we didn't used to run any tests at
all,
+ # so, baby steps.
+ SingleReaction_test
+ reaction_methods_utils_test
+ rotation_test
+ grid_test
+ Lattice_test
+ lb_exceptions
+ thermostats_test
+ bonded_interactions_map_test
+ ObjectHandle_test
+ AutoParameters_test
+ Accumulators_test
+ Constraints_test
+ Actors_test
+ )
+
+ # testsuite uses exclude_from_all, and lists all targets as deps for
their custom rule
+ cmake_build check
+ cmake_src_test
}
src_install() {
