Open marcc-hpc opened 6 years ago
Thank you Kevin! Extremely helpful, @ch4rr0 and I will take a look. Hopefully we can close that older issue you referenced (#38) as well.
We've been able to build Bowtie 1.2.1.1 with the Intel compilers (2017 update 4), see https://github.com/easybuilders/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.1.1-intel-2017b.eb .
This required two patches:
typedef
mentioned here as well, see https://github.com/easybuilders/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/b/Bowtie/int64typedef.patchcpuid
issue via https://github.com/easybuilders/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2_void2int.patchWith Bowtie 1.2.2 however, I'm now running into a new problem when compiling hit.cpp
:
/xxx/software/GCCcore/6.4.0/bin/../include/c++/6.4.0/bits/stl_algobase.h(343): error: no operator "=" matches these operands
operand types are: HitSink::batch = HitSink::batch
*__result = std::move(*__first);
(+ other very similar errors)
The full error log is available at https://gist.github.com/boegel/d5449745047fa9180ece95f4adf3337d .
Any ideas on this?
With some help from @wpoely86, I've been able to compile Bowtie 1.2.2, the required additional patch to fix the compilation errors mentioned above is available at https://github.com/easybuilders/easybuild-easyconfigs/pull/5717/files#diff-1e411412b51a5818cc46e8432ae0ef73 .
@BenLangmead Would you please make a new bowtie1 release with the above patches?
Ill look into the patch today and will try to have a beta build up by this evening. In the coming weeks I will be working towards an official release for bowtie which will include fixes for this issue.
I have committed the necessary changes to support the Intel Compiler Collection. The changes were committed to the bug_fixes
branch and will get merged to master
as we approach a release.
Here's a build I created using ICC and the changes mentioned (can't guarantee it's portability). bowtie-1.2.2.1-INTEL-linux-x86_64.zip
Hi @ch4rr0 , thank you for your efforts. I see https://github.com/gentoo/sci/blob/master/sci-biology/bowtie/files/bowtie-1.2.2-fix-Intel-compilation.patch is now obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b on the bug_fixes
branch but unfortunately I cannot compile with even gcc-8.2.0 -std=c++03
. But I will better open a new issue.
I was able to without issue. What compilation errors are you getting?
Disregard -- I see you opened an issue.
Hi @BenLangmead and rest of Bowtie team, Kevin here from MARCC.
We are trying to more closely follow releases. Issue #38 covered issues with compilation.
I was comparing the two commits, and it appears the primary issues are
SeqAn-1.1/seqan/platform.h
: Intel compiler guards (or not) were used for branch v1.2.1processor_support.h
):Currently:
Previously:
I went back to what worked for v1.2.1 (re-inserting guard)
Compilation command:
If you want to test on MARCC with Intel 17: