Summary: | sci-biology/t-coffee: util_dp_sim.c:1016: internal compiler error | ||
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Product: | Gentoo Linux | Reporter: | Martin Mokrejš <mmokrejs> |
Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
Status: | RESOLVED UPSTREAM | ||
Severity: | normal | CC: | ribosome, toolchain |
Priority: | High | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
URL: | http://gcc.gnu.org/bugzilla/show_bug.cgi?id=16876 | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Attachments: | ccFN9EEB.out |
Description
Martin Mokrejš
2005-12-07 06:37:48 UTC
Created attachment 74230 [details]
ccFN9EEB.out
Thanks for reporting. Using -O2 will not solve the problem, but -O0 actually will. (I have not benchmarked how slow t-coffee actually is when not optimised at all, but it might be a problem when extracting the aligned sequences and iterating the alignment multiple times.) Since this is a reproducable GCC 3.4 specific compiler error, I am CCing the toolchain team. It is not specific to version 3.18. (The latest version, 3.27, is also affected.) I have added a warning message to the ebuild for version 3.27. I checked different CFLAGS combinations, and it seems users of the stable version (2.66) are not affected at all. Unfortunately, this version is now masked since the archive may no longer be downloaded. Curse restricting downloading for grant purposes. :\ Yeah, I had to use CFLAGS="" emerge -u t-coffee :( This bug should be really filed to gcc guys. The preprocessed file should make them able to fix it in a moment. (In reply to comment #2) > Thanks for reporting. Using -O2 will not solve the problem, but -O0 actually > will. Please note that "-O1" also works fine. "-O1 -funit-at-a-time" fails however. This is a problem in gcc-3.4 all the way up to mainline. Putting to reso->upstream until we get a patch. ribosome, can you make it strip all -O[123] flags in the meanwhile? It's a bit annoying to just have the compile be broken. Anything new on this? I am still getting this problem with gcc-3.4.5 but not with gcc-3.3.6. Maybe running temporarily gcc-config(1) would be a better temporary fix for this. ribosome - I suggest adding -fno-unit-at-a-time with gcc-3.4.x; e.g. adding: [[ $(gcc-version) == "3.4" ]] && append-flags -fno-unit-at-a-time in src_compile() prior to the make. This gets it to compile at -O2 for me; you may also want to try -O3 and -Os as they're popular. Since I'm not a biologist I have no idea what the application does so can't check that it actually works 8-) (In reply to comment #9) > ribosome - I suggest adding -fno-unit-at-a-time with gcc-3.4.x; e.g. adding: > > [[ $(gcc-version) == "3.4" ]] && append-flags -fno-unit-at-a-time > > in src_compile() prior to the make. This gets it to compile at -O2 for me; you > may also want to try -O3 and -Os as they're popular. Since I'm not a biologist > I have no idea what the application does so can't check that it actually works > 8-) > Added to the ebuild. Thanks for the suggestion. |