| Summary: | sci-chemistry/avogadro segmentation fault with icc-built openbabel | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | urcindalo <urcindalo> |
| Component: | Current packages | Assignee: | Gentoo Chemistry-Related Packages <sci-chemistry> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | ||
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Bug Depends on: | |||
| Bug Blocks: | 444348 | ||
After some trials I found the culprit: openbabel-2.3.2 When the latter is compiled with icc, avogadro fails with a segmentation fault at launch time. But, if I recompile openbabel with gcc, even though the rest of the dependencies and avogadro itself are compiled with icc, avogadro launches well. I also tried to recompile openbabel dependencies with icc, one at a step, but inchi fails this way: === >>> Emerging (1 of 1) sci-libs/inchi-1.04 * inchi-1.04.zip SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] >>> cfg-update-1.8.2-r1: Creating checksum index... >>> Unpacking source... >>> Unpacking inchi-1.04.zip to /var/tmp/portage/sci-libs/inchi-1.04/work >>> Source unpacked in /var/tmp/portage/sci-libs/inchi-1.04/work >>> Preparing source in /var/tmp/portage/sci-libs/inchi-1.04/work/INCHI-1-API ... * Applying inchi-1.03-shared.patch ... [ ok ] * Applying inchi-1.04-static.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/inchi-1.04/work/INCHI-1-API ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-libs/inchi-1.04/work/INCHI-1-API ... make -j5 C_COMPILER=icc CPP_COMPILER=icpc 'LINKER=icpc -Wl,-O1 -Wl,--as-needed' 'SHARED_LINK=icc -Wl,-O1 -Wl,--as-needed -shared' 'C_COMPILER_OPTIONS=${P_INCL} -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ' 'CPP_COMPILER_OPTIONS=${P_INCL} -D_LIB -ansi -O2 -gcc -ip -frtti -c ' 'C_OPTIONS=-O2 -gcc -ip -fPIC -c ' 'LINKER_OPTIONS=-Wl,-O1 -Wl,--as-needed' CREATE_MAIN= ISLINUX=1 icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichican2.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichiprt1.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichicano.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichiprt2.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichicans.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichiprt3.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichiisot.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichiqueu.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichiring.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichimak2.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichisort.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichimake.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichister.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichimap1.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichitaut.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichimap2.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichi_bns.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/runichi.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichi_io.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichimap4.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/strutil.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichinorm.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/util.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichiparm.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichiread.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichirvr1.c icc -I../../main -I../../common -ansi -DCOMPILE_ANSI_ONLY -O2 -gcc -ip -c ../../common/ichirvr2.c ../../common/ichiread.c(4535) (col. 19): internal error: 0_1451 compilation aborted for ../../common/ichiread.c (code 4) make: *** [ichiread.o] Error 4 === I don't know if this info is relevant and I imagine it deserves a bug by itself, but I just say it here for completeness purposes. Thanks for the report. Although we are trying to officially provide compilers other then gcc, the priority of fixing incompatibilities is quite low. Could you please attach a icc build build.log of openbabel? The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=eb9a93f86bfb9c892d99268f6812e7b13660f851 commit eb9a93f86bfb9c892d99268f6812e7b13660f851 Author: Mikle Kolyada <zlogene@gentoo.org> AuthorDate: 2018-05-07 22:24:59 +0000 Commit: Mikle Kolyada <zlogene@gentoo.org> CommitDate: 2018-05-07 22:24:59 +0000 sci-chemistry/avogadro: remove last rited package Closes: https://bugs.gentoo.org/645030 Closes: https://bugs.gentoo.org/447532 Closes: https://bugs.gentoo.org/649500 sci-chemistry/avogadro/Manifest | 1 - .../avogadro/avogadro-1.2.0_p20170207.ebuild | 90 ---------------------- .../files/avogadro-1.1.1-boost-join-moc.patch | 78 ------------------- .../files/avogadro-1.1.1-mkspecs-dir.patch | 12 --- .../avogadro/files/avogadro-1.1.1-no-strip.patch | 12 --- .../avogadro/files/avogadro-1.1.1-openbabel.patch | 16 ---- .../files/avogadro-1.1.1-pkgconfig_eigen.patch | 8 -- .../avogadro/files/avogadro-1.2.0-numpy.patch | 13 ---- sci-chemistry/avogadro/metadata.xml | 20 ----- 9 files changed, 250 deletions(-) |
I'm in the process of recompiling my scientific software with icc. So far so good, except avogadro. After recompiling many packages, including *every* dependency for avogadro v1.0.3-r1 or v1.1.0 (according to the ebuilds), avogadro recompiles well but I can no longer launch it, even if it is compiled back with gcc instead of icc. Here is the error I'm seeing: === $ avogadro "Avogadro version: 1.1.0 Git: LibAvogadro version: 1.1.0 Git: " Locale: "C" Libavogadro translations not found. System has OpenGL support. About to test OpenGL capabilities. OpenGL capabilities found: Double Buffering. Direct Rendering. Antialiasing. Loading plugins: "/usr/bin/../lib64/avogadro/1_1" Searching for plugins in "/usr/lib64/avogadro/1_1" Searching for plugins in "/usr/lib64/avogadro/1_1/colors" Searching for plugins in "/usr/lib64/avogadro/1_1/engines" Searching for plugins in "/usr/lib64/avogadro/1_1/extensions" Searching for plugins in "/usr/lib64/avogadro/1_1/tools" Loading plugins: "/home/user/.avogadro/1_1/plugins" Segmentation fault === I know this info is not very helpful, so I will be happy to provide you with as much info as you may need. I just don't know where to begin. Thanks in advance.