| Summary: | sci-libs/cholmod-3.0.13: emake failed: nvcc fatal: Unknown option '-fPIC' | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Constantin Runge <c.runge> |
| Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | agrigo2001, alex, bugzilla, chn, dan, fatzer2, fordfrog, frp.bissey, ivan, jstein, kkrizka, leonchik1976, pacho, peter.gustafson, phobosk, poncho, sam, stefantalpalaru, waebbl-gentoo |
| Priority: | Normal | Keywords: | PATCH, PullRequest |
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| See Also: | https://github.com/gentoo/gentoo/pull/34020 | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: |
build.log
emerge --info libtool file from 3.0.14 cholmod_gpu.h cholmod-3.0.14-fix-CUDA.patch |
||
Thank you for the report. We need to have all information at hand before ticket assignment. That is why I ask you to * attach the logs and * paste the emerge info as described on https://wiki.gentoo.org/wiki/Attach_the_logs_to_the_bug_ticket Created attachment 628474 [details]
emerge --info
Added output of `emerge --info` as well. I've already attached the build.log when creating the ticket. Please tell, if something went wrong there.
It looks like this is a libtool problem. In theory, the build system should prepend the `lt_prog_compiler_pic` with `-Xcompiler` for the nvcc compiler. But I'm not really sure, why this rule is not applied. Could generate a new log (3.0.13 or 3.0.14) at -j1. Just to make things clearer. I think you have identified the most likely cause of trouble in any case. (In reply to François Bissey from comment #4) > Could generate a new log (3.0.13 or 3.0.14) at -j1. Just to make things > clearer. I think you have identified the most likely cause of trouble in any > case. No need for that now that I have looked more closely. Trying to identify what is going wrong in libtool. Can you attach the generated libtool file? Created attachment 663847 [details]
libtool file from 3.0.14
Thanks. That libtool doesn't contain any bits for nvcc, which explains why things fail. Either there is something to fix in configure.ac/Makefile.am to get the bits included or I use an alternative approach. I have ideas to test. I can put some ebuild in the sage-on-gentoo overlay or attach some files here for you to try. Which works better for you? (In reply to François Bissey from comment #9) > I have ideas to test. I can put some ebuild in the sage-on-gentoo overlay or > attach some files here for you to try. Which works better for you? you can attach it here, thank you :-) Sorry for the silence I am completely overloaded left and right. Created attachment 700836 [details]
cholmod_gpu.h
Bump. I've tried and failed to debug this.
Note also that the current tar.bz2 file for 3.0.14 doesn't include the headers for GPU.
cholmod-3.0.14/Include/cholmod_gpu.h
I'm attaching it here.
I also tried sage-on-gentoo overlay (3.0.13-r3) and no luck.
(In reply to Peter Gustafson from comment #12) > Created attachment 700836 [details] > cholmod_gpu.h > > Bump. I've tried and failed to debug this. > > Note also that the current tar.bz2 file for 3.0.14 doesn't include the > headers for GPU. > > cholmod-3.0.14/Include/cholmod_gpu.h > > I'm attaching it here. > > I also tried sage-on-gentoo overlay (3.0.13-r3) and no luck. Yes, I am sorry. I am completely overwhelmed with various things and that one has taken the back seat. I know precisely why this is failing. Fixing it is another story, I have some leads from a few other packages though. But at the end of the day, it looks like doing C+nvcc is easier with cmake than autoconf. Any news or further actions or possible fixes/workarounds on this issue? Note that this failure is caused by USE="cuda". It builds fine without it. Created attachment 749631 [details, diff]
cholmod-3.0.14-fix-CUDA.patch
A proposed patch: it's a bit hacky, but it should do the trick.
Also I'd suggest to inherit cuda.eclass to avoid problems with some other cuda-related stuff.
Worked for me! (In reply to Fat-Zer from comment #16) > Created attachment 749631 [details, diff] [details, diff] > cholmod-3.0.14-fix-CUDA.patch > > A proposed patch: it's a bit hacky, but it should do the trick. > > Also I'd suggest to inherit cuda.eclass to avoid problems with some other > cuda-related stuff. Works for me! thx for your patch! This should probably be upstreamed: https://github.com/DrTimothyAldenDavis/SuiteSparse/issues I see they have plenty of cuda bugs and commits in their repo and, then, this is likely to break again soon I also wonder if maybe we should move everything to a sci-libs/suitesparse ebuild to follow more easily upstream bumps and use their tarballs :/ (In reply to Pacho Ramos from comment #19) > This should probably be upstreamed: > https://github.com/DrTimothyAldenDavis/SuiteSparse/issues > > I see they have plenty of cuda bugs and commits in their repo and, then, > this is likely to break again soon > > I also wonder if maybe we should move everything to a sci-libs/suitesparse > ebuild to follow more easily upstream bumps and use their tarballs :/ That would make some things easier and some things more complicated. There wouldn't really be a configuration phase. Who wants to deal with a superbuild which is directed by a big Makefile? I did some very hackish monolithic build in sagemath and that's not pretty. That being said, getting more stuff upstream would be a great thing. (In reply to Pacho Ramos from comment #19) > This should probably be upstreamed: > https://github.com/DrTimothyAldenDavis/SuiteSparse/issues > That's a build-system-related issue, they don't use autotools upstream. It looks like a purely gentoo thing, so IMHO there is no reason to bother upstream with that. I suppose, the patch should be applied to what-ever repository where gentoo tarballs are maintained, but I got no idea where it is. same issue with sci-libs/cholmod-3.0.14 *** Bug 870583 has been marked as a duplicate of this bug. *** A working cholmod-3.0.14-r1 ebuild is available in my overlay: https://github.com/stefantalpalaru/gentoo-overlay I had to copy and fix "cuda.eclass" because of https://bugs.gentoo.org/880675 cholmod 4.0.0 is coming and it comes with a cmake build system that will solve the cuda issue once for all (cross fingers). This is still an issue in Gentoo, when is this being updated to fix it? In sage-on-gentoo (https://github.com/cschwan/sage-on-gentoo) I have the latest suitesparse software suite. The build system has been changed to cmake and that move alone should take care of the issue. If you want to try cholmod 4.0.3 from the overlay and report if cuda now behaves, I'd be quite happy. I am still pondering on the best way to migrate the new suitesparse to the main tree and whether or not I should write a small eclass for it. The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6c0474cc8a08172cdc244af680edba8be5ada95b commit 6c0474cc8a08172cdc244af680edba8be5ada95b Author: Paul Zander <negril.nx+gentoo@gmail.com> AuthorDate: 2023-11-27 19:58:40 +0000 Commit: Pacho Ramos <pacho@gentoo.org> CommitDate: 2023-12-16 09:20:20 +0000 sci-libs/cholmod: fix cuda build - include cuda patch from https://bugs.gentoo.org/715610#c16 - make use of cuda.eclass for nvcc Closes: https://bugs.gentoo.org/913921 Closes: https://bugs.gentoo.org/904973 Closes: https://bugs.gentoo.org/715610 Signed-off-by: Paul Zander <negril.nx+gentoo@gmail.com> Closes: https://github.com/gentoo/gentoo/pull/34020 Signed-off-by: Pacho Ramos <pacho@gentoo.org> sci-libs/cholmod/cholmod-3.0.13.ebuild | 14 ++- sci-libs/cholmod/cholmod-3.0.14.ebuild | 14 ++- .../cholmod/files/cholmod-3.0.14-fix-CUDA.patch | 109 +++++++++++++++++++++ 3 files changed, 133 insertions(+), 4 deletions(-) |
Created attachment 627938 [details] build.log Building the GPU target for cholmod fails with the message `nvcc fatal: Unknown option '-fPIC''. AFAIK, nvcc wants the '-fPIC' option with either '--compiler-options' or '-Xcompiler' prepended.