Closed cb4github closed 4 months ago
@cb4github Thanks for this! I know the source of the problem and will prioritize fixing it.
Fixed with commit #214 and a release will happen soon to propagate this fix. Thank again @cb4github this really helps!
@andrewdavidsmith Many thanks for fixing this. I'm currently unable to install from the resulting master without an updated tar ball or Dockerfile or working configure script. Thanks. Best, CB
Update: I was able to reproduce issue #209 using gcc/8.5.0, which supports C++17 as mentioned in the README.
Yet, as I understand it, this appears to be inconsistent with the very-cheap
optimization not being available until gcc 12.1.
Here, I believe, is a relevant quote from the RH developers' website here.
Only relatively recently in GCC 12.1 was the auto-vectorizer enabled when -O2 is specified.
Here is sample output from that attempted make.
make[4]: Entering directory `/lustre/project/<PI>/build/centos7/dnmtools/src/abismal'
depbase=`echo src/abismal.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I ./src/smithlab_cpp -I ./src/bamxx -fopenmp -O3 -MT src/abismal.o -MD -MP -MF $depbase.Tpo -c -o src/abismal.o src/abismal.cpp &&\
mv -f $depbase.Tpo $depbase.Po
In file included from src/abismal.cpp:34:
src/AbismalAlign.hpp:215:50: error: unknown vectorizer cost model 'very-cheap'
#pragma GCC optimize("vect-cost-model=very-cheap")
^
src/AbismalAlign.hpp:215:50: note: valid arguments to '-fvect-cost-model=' are: cheap dynamic unlimited; did you mean 'cheap'?
Please advise. Thanks.
@cb4github Would you be able to move that to the #209 or open a new issue? I've got a reply, but want to keep things separate if that's ok.
Describe the bug See subject.
To Reproduce Steps to reproduce the behavior (steps 1-8 for data preparation):
Expected behavior Resulting hmr file non-empty.
Screenshots N/A
Desktop (please complete the following information):
module show dnmtools/1.4.2
/lustre/project/PI/apps/centos7/modulefiles/dnmtools/1.4.2:
module-whatis DNMTools is a set of tools for analyzing DNA methylation data from high-throughput sequencing experiments, especially whole genome bisulfite sequencing (WGBS), but also reduced representation bisulfite sequencing (RRBS). module load anaconda3/2023.07 singularity/3.9.0 prepend-path PATH /lustre/project/PI/apps/dnmtools/1.4.2/bin prepend-path PATH /lustre/project/PI/apps/dnmtools/1.4.2/bin/utils setenv DNMTOOLS_IMAGE /lustre/project/PI/singularity_images/dnmtools_latest_plus_bash.sif
%post apk update apk add bash apk add bash-doc apk add bash-completion
%test bash
Smartphone (please complete the following information):
Additional context Please let me know if you need any more information. Thanks.
Best, CB