Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)
Hi,
I tried to narrow down what broke clustalo on mipsel.
The test from 1.2.4-5 passes with the binary in buster,
but not when rebuilding it in buster.
gcc versions:
7: works
8: broken
9: broken
10: broken
clustalo in buster was built with gcc 7, a rebuild with the gcc 8 now in
buster would result in a broken binary.
Rebuilding with gcc 8 with -O0 does not work around the problem,
this is unlikely to be the the common case of optimization changes
breaking buggy code.
What does fix the problem is disabling OpenMP.
I suspect OpenMP is somehow broken in gcc >= 8 on mipsel.
Below is a workaround patch (lower performance of clustalo on mipsel
shouldn't be a major problem).
cu
Adrian
--- clustalo-1.2.4/debian/rules 2020-04-14 12:19:44.000000000 +0300
+++ clustalo-1.2.4/debian/rules 2020-04-14 12:19:44.000000000 +0300
@@ -9,6 +9,11 @@
%:
dh $@
+ifneq (,$(filter $(DEB_HOST_ARCH), mipsel))
+override_dh_auto_configure:
+ dh_auto_configure -- --without-openmp
+endif
+
override_dh_auto_build-indep:
# nothing to do here
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