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smithlabcode / dnmtools

Tools for analyzing DNA methylation data
https://dnmtools.readthedocs.io
GNU General Public License v3.0
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unknown vectorizer cost model ‘very-cheap’ #209

Closed shaohuaihan closed 2 months ago

shaohuaihan commented 5 months ago

When I install the software I got the error below:

../../../src/abismal/src/abismal.cpp:2208:36: error：unknown vectorizer cost model ‘very-cheap’

andrewdavidsmith commented 5 months ago

Please give full information or I can't help.

cb4github commented 3 months ago

See my mention here for details, but per @andrewdavidsmith's request, I've copied from there my result including the same error as @shaohuaihan.

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'?

I hope this helps.

Best, CB

andrewdavidsmith commented 3 months ago

@cb4github Thanks for the details on this. I think it should be fixed as of commit #217 . Let me know if you are able to test it. You might also directly try the same thing in the abismal repo. That's where I made the change initially and then updated them in dnmtools.

cb4github commented 2 months ago

@andrewdavidsmith I tried building the new master - still using gcc/8.5.0 - and still received errors indicating c++17 is insufficient such as the following.

../../../src/abismal/src/AbismalIndex.cpp:41:12: error: 'std::inclusive_scan' has not been declared
 using std::inclusive_scan;
            ^~~~~~~~~~~~~~

module load gcc/8.5.0 htslib/1.19 autoconf/2.71 htslib/1.20 gsl/2.6

Here's the resulting (warning: entire) log of my attempted make. Thanks again.

Command follows...
make
Output follows...
make  all-recursive
make[1]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build'
Making all in src/smithlab_cpp
make[2]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build/src/smithlab_cpp'
make  all-am
make[3]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build/src/smithlab_cpp'
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT GenomicRegion.o -MD -MP -MF .deps/GenomicRegion.Tpo -c -o GenomicRegion.o ../../../src/smithlab_cpp/GenomicRegion.cpp
In file included from ../../../src/smithlab_cpp/GenomicRegion.hpp:27,
                 from ../../../src/smithlab_cpp/GenomicRegion.cpp:23:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
 };
  ^
mv -f .deps/GenomicRegion.Tpo .deps/GenomicRegion.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT MappedRead.o -MD -MP -MF .deps/MappedRead.Tpo -c -o MappedRead.o ../../../src/smithlab_cpp/MappedRead.cpp
In file included from ../../../src/smithlab_cpp/GenomicRegion.hpp:27,
                 from ../../../src/smithlab_cpp/MappedRead.hpp:26,
                 from ../../../src/smithlab_cpp/MappedRead.cpp:23:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
 };
  ^
mv -f .deps/MappedRead.Tpo .deps/MappedRead.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT OptionParser.o -MD -MP -MF .deps/OptionParser.Tpo -c -o OptionParser.o ../../../src/smithlab_cpp/OptionParser.cpp
In file included from ../../../src/smithlab_cpp/OptionParser.cpp:37:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
 };
  ^
mv -f .deps/OptionParser.Tpo .deps/OptionParser.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT QualityScore.o -MD -MP -MF .deps/QualityScore.Tpo -c -o QualityScore.o ../../../src/smithlab_cpp/QualityScore.cpp
In file included from ../../../src/smithlab_cpp/QualityScore.cpp:26:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
 };
  ^
mv -f .deps/QualityScore.Tpo .deps/QualityScore.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT chromosome_utils.o -MD -MP -MF .deps/chromosome_utils.Tpo -c -o chromosome_utils.o ../../../src/smithlab_cpp/chromosome_utils.cpp
In file included from ../../../src/smithlab_cpp/GenomicRegion.hpp:27,
                 from ../../../src/smithlab_cpp/chromosome_utils.hpp:37,
                 from ../../../src/smithlab_cpp/chromosome_utils.cpp:23:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
 };
  ^
mv -f .deps/chromosome_utils.Tpo .deps/chromosome_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT bisulfite_utils.o -MD -MP -MF .deps/bisulfite_utils.Tpo -c -o bisulfite_utils.o ../../../src/smithlab_cpp/bisulfite_utils.cpp
mv -f .deps/bisulfite_utils.Tpo .deps/bisulfite_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT smithlab_os.o -MD -MP -MF .deps/smithlab_os.Tpo -c -o smithlab_os.o ../../../src/smithlab_cpp/smithlab_os.cpp
In file included from ../../../src/smithlab_cpp/smithlab_os.cpp:30:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
 };
  ^
mv -f .deps/smithlab_os.Tpo .deps/smithlab_os.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT smithlab_utils.o -MD -MP -MF .deps/smithlab_utils.Tpo -c -o smithlab_utils.o ../../../src/smithlab_cpp/smithlab_utils.cpp
In file included from ../../../src/smithlab_cpp/smithlab_utils.cpp:23:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
 };
  ^
mv -f .deps/smithlab_utils.Tpo .deps/smithlab_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT zlib_wrapper.o -MD -MP -MF .deps/zlib_wrapper.Tpo -c -o zlib_wrapper.o ../../../src/smithlab_cpp/zlib_wrapper.cpp
mv -f .deps/zlib_wrapper.Tpo .deps/zlib_wrapper.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT dna_four_bit.o -MD -MP -MF .deps/dna_four_bit.Tpo -c -o dna_four_bit.o ../../../src/smithlab_cpp/dna_four_bit.cpp
mv -f .deps/dna_four_bit.Tpo .deps/dna_four_bit.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT cigar_utils.o -MD -MP -MF .deps/cigar_utils.Tpo -c -o cigar_utils.o ../../../src/smithlab_cpp/cigar_utils.cpp
mv -f .deps/cigar_utils.Tpo .deps/cigar_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -Wextra -Wpedantic -O3 -DNDEBUG -MT sam_record.o -MD -MP -MF .deps/sam_record.Tpo -c -o sam_record.o ../../../src/smithlab_cpp/sam_record.cpp
In file included from ../../../src/smithlab_cpp/sam_record.cpp:26:
../../../src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
 };
  ^
mv -f .deps/sam_record.Tpo .deps/sam_record.Po
rm -f libsmithlab_cpp.a
ar cru libsmithlab_cpp.a GenomicRegion.o MappedRead.o OptionParser.o QualityScore.o chromosome_utils.o bisulfite_utils.o smithlab_os.o smithlab_utils.o zlib_wrapper.o dna_four_bit.o cigar_utils.o sam_record.o
ranlib libsmithlab_cpp.a
make[3]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build/src/smithlab_cpp'
make[2]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build/src/smithlab_cpp'
Making all in src/abismal
make[2]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal'
make  all-recursive
make[3]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal'
Making all in src/smithlab_cpp
make[4]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal/src/smithlab_cpp'
make  all-am
make[5]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal/src/smithlab_cpp'
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -O3 -MT GenomicRegion.o -MD -MP -MF .deps/GenomicRegion.Tpo -c -o GenomicRegion.o ../../../../../src/abismal/src/smithlab_cpp/GenomicRegion.cpp
mv -f .deps/GenomicRegion.Tpo .deps/GenomicRegion.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -O3 -MT MappedRead.o -MD -MP -MF .deps/MappedRead.Tpo -c -o MappedRead.o ../../../../../src/abismal/src/smithlab_cpp/MappedRead.cpp
mv -f .deps/MappedRead.Tpo .deps/MappedRead.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -O3 -MT OptionParser.o -MD -MP -MF .deps/OptionParser.Tpo -c -o OptionParser.o ../../../../../src/abismal/src/smithlab_cpp/OptionParser.cpp
mv -f .deps/OptionParser.Tpo .deps/OptionParser.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -O3 -MT QualityScore.o -MD -MP -MF .deps/QualityScore.Tpo -c -o QualityScore.o ../../../../../src/abismal/src/smithlab_cpp/QualityScore.cpp
mv -f .deps/QualityScore.Tpo .deps/QualityScore.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -O3 -MT chromosome_utils.o -MD -MP -MF .deps/chromosome_utils.Tpo -c -o chromosome_utils.o ../../../../../src/abismal/src/smithlab_cpp/chromosome_utils.cpp
mv -f .deps/chromosome_utils.Tpo .deps/chromosome_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -O3 -MT bisulfite_utils.o -MD -MP -MF .deps/bisulfite_utils.Tpo -c -o bisulfite_utils.o ../../../../../src/abismal/src/smithlab_cpp/bisulfite_utils.cpp
mv -f .deps/bisulfite_utils.Tpo .deps/bisulfite_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -O3 -MT smithlab_os.o -MD -MP -MF .deps/smithlab_os.Tpo -c -o smithlab_os.o ../../../../../src/abismal/src/smithlab_cpp/smithlab_os.cpp
mv -f .deps/smithlab_os.Tpo .deps/smithlab_os.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -O3 -MT smithlab_utils.o -MD -MP -MF .deps/smithlab_utils.Tpo -c -o smithlab_utils.o ../../../../../src/abismal/src/smithlab_cpp/smithlab_utils.cpp
mv -f .deps/smithlab_utils.Tpo .deps/smithlab_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -O3 -MT zlib_wrapper.o -MD -MP -MF .deps/zlib_wrapper.Tpo -c -o zlib_wrapper.o ../../../../../src/abismal/src/smithlab_cpp/zlib_wrapper.cpp
mv -f .deps/zlib_wrapper.Tpo .deps/zlib_wrapper.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -O3 -MT dna_four_bit.o -MD -MP -MF .deps/dna_four_bit.Tpo -c -o dna_four_bit.o ../../../../../src/abismal/src/smithlab_cpp/dna_four_bit.cpp
mv -f .deps/dna_four_bit.Tpo .deps/dna_four_bit.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -O3 -MT cigar_utils.o -MD -MP -MF .deps/cigar_utils.Tpo -c -o cigar_utils.o ../../../../../src/abismal/src/smithlab_cpp/cigar_utils.cpp
mv -f .deps/cigar_utils.Tpo .deps/cigar_utils.Po
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../../../src/abismal/src/smithlab_cpp   -I/lustre/project/PI/apps/htslib/1.20/include  -Wall -O3 -MT sam_record.o -MD -MP -MF .deps/sam_record.Tpo -c -o sam_record.o ../../../../../src/abismal/src/smithlab_cpp/sam_record.cpp
mv -f .deps/sam_record.Tpo .deps/sam_record.Po
rm -f libsmithlab_cpp.a
ar cru libsmithlab_cpp.a GenomicRegion.o MappedRead.o OptionParser.o QualityScore.o chromosome_utils.o bisulfite_utils.o smithlab_os.o smithlab_utils.o zlib_wrapper.o dna_four_bit.o cigar_utils.o sam_record.o
ranlib libsmithlab_cpp.a
make[5]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal/src/smithlab_cpp'
make[4]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal/src/smithlab_cpp'
make[4]: Entering directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal'
depbase=`echo src/abismal.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/abismal  -I ../../../src/abismal/src/smithlab_cpp -I ../../../src/abismal/src/bamxx -I/lustre/project/PI/apps/htslib/1.20/include -fopenmp -Wall -Wextra -Wpedantic -Wno-unknown-attributes  -O3 -DNDEBUG  -MT src/abismal.o -MD -MP -MF $depbase.Tpo -c -o src/abismal.o ../../../src/abismal/src/abismal.cpp &&\
mv -f $depbase.Tpo $depbase.Po
In file included from ../../../src/abismal/src/abismal.cpp:34:
../../../src/abismal/src/AbismalAlign.hpp:100:2: warning: extra ';' [-Wpedantic]
 };  // namespace simple_aln
  ^
In file included from ../../../src/abismal/src/AbismalIndex.hpp:33,
                 from ../../../src/abismal/src/abismal.cpp:35:
../../../src/abismal/src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
 };
  ^
In file included from ../../../src/abismal/src/abismal.cpp:35:
../../../src/abismal/src/AbismalIndex.hpp:93:2: warning: extra ';' [-Wpedantic]
 };
  ^
In file included from ../../../src/abismal/src/abismal.cpp:37:
../../../src/abismal/src/bamxx/bamxx.hpp:194:2: warning: extra ';' [-Wpedantic]
 };  // namespace bamxx
  ^
cc1plus: warning: unrecognized command line option '-Wno-unknown-attributes'
depbase=`echo src/abismalidx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/abismal  -I ../../../src/abismal/src/smithlab_cpp -I ../../../src/abismal/src/bamxx -I/lustre/project/PI/apps/htslib/1.20/include -fopenmp -Wall -Wextra -Wpedantic -Wno-unknown-attributes  -O3 -DNDEBUG  -MT src/abismalidx.o -MD -MP -MF $depbase.Tpo -c -o src/abismalidx.o ../../../src/abismal/src/abismalidx.cpp &&\
mv -f $depbase.Tpo $depbase.Po
In file included from ../../../src/abismal/src/abismalidx.cpp:19:
../../../src/abismal/src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
 };
  ^
In file included from ../../../src/abismal/src/abismalidx.cpp:24:
../../../src/abismal/src/AbismalIndex.hpp:93:2: warning: extra ';' [-Wpedantic]
 };
  ^
cc1plus: warning: unrecognized command line option '-Wno-unknown-attributes'
depbase=`echo src/AbismalIndex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -std=c++17 -DHAVE_CONFIG_H -I. -I../../../src/abismal  -I ../../../src/abismal/src/smithlab_cpp -I ../../../src/abismal/src/bamxx -I/lustre/project/PI/apps/htslib/1.20/include -fopenmp -Wall -Wextra -Wpedantic -Wno-unknown-attributes  -O3 -DNDEBUG  -MT src/AbismalIndex.o -MD -MP -MF $depbase.Tpo -c -o src/AbismalIndex.o ../../../src/abismal/src/AbismalIndex.cpp &&\
mv -f $depbase.Tpo $depbase.Po
In file included from ../../../src/abismal/src/AbismalIndex.hpp:33,
                 from ../../../src/abismal/src/AbismalIndex.cpp:18:
../../../src/abismal/src/smithlab_cpp/smithlab_utils.hpp:52:2: warning: extra ';' [-Wpedantic]
 };
  ^
In file included from ../../../src/abismal/src/AbismalIndex.cpp:18:
../../../src/abismal/src/AbismalIndex.hpp:93:2: warning: extra ';' [-Wpedantic]
 };
  ^
In file included from ../../../src/abismal/src/AbismalIndex.cpp:32:
../../../src/abismal/src/bamxx/bamxx.hpp:194:2: warning: extra ';' [-Wpedantic]
 };  // namespace bamxx
  ^
../../../src/abismal/src/AbismalIndex.cpp:41:12: error: 'std::inclusive_scan' has not been declared
 using std::inclusive_scan;
            ^~~~~~~~~~~~~~
../../../src/abismal/src/AbismalIndex.cpp: In member function 'void AbismalIndex::select_two_letter_positions()':
../../../src/abismal/src/AbismalIndex.cpp:460:20: error: found ':' in nested-name-specifier, expected '::'
   for (auto &block : blocks) {
                    ^
                    ::
../../../src/abismal/src/AbismalIndex.cpp:460:14: error: 'block' has not been declared
   for (auto &block : blocks) {
              ^~~~~
../../../src/abismal/src/AbismalIndex.cpp:460:28: error: qualified-id in declaration before ')' token
   for (auto &block : blocks) {
                            ^
../../../src/abismal/src/AbismalIndex.cpp:493:4: error: expected ';' before 'if'
   }
    ^
    ;
   if (VERBOSE) clog << delta_seconds(s_time) << endl;
   ~~
../../../src/abismal/src/AbismalIndex.cpp:494:3: error: expected primary-expression before 'if'
   if (VERBOSE) clog << delta_seconds(s_time) << endl;
   ^~
../../../src/abismal/src/AbismalIndex.cpp:495:1: error: expected primary-expression before '}' token
 }
 ^
../../../src/abismal/src/AbismalIndex.cpp:494:54: error: expected ')' before '}' token
   if (VERBOSE) clog << delta_seconds(s_time) << endl;
                                                      ^
                                                      )
 }
 ~
../../../src/abismal/src/AbismalIndex.cpp:460:7: note: to match this '('
   for (auto &block : blocks) {
       ^
../../../src/abismal/src/AbismalIndex.cpp:495:1: error: expected primary-expression before '}' token
 }
 ^
../../../src/abismal/src/AbismalIndex.cpp:460:3: error: expected iteration declaration or initialization
   for (auto &block : blocks) {
   ^~~
../../../src/abismal/src/AbismalIndex.cpp: In member function 'void AbismalIndex::hash_genome()':
../../../src/abismal/src/AbismalIndex.cpp:505:3: error: 'inclusive_scan' was not declared in this scope
   inclusive_scan(begin(counter), end(counter), begin(counter));
   ^~~~~~~~~~~~~~
../../../src/abismal/src/AbismalIndex.cpp:507:3: error: 'inclusive_scan' was not declared in this scope
   inclusive_scan(begin(counter_t), end(counter_t), begin(counter_t));
   ^~~~~~~~~~~~~~
../../../src/abismal/src/AbismalIndex.cpp:509:3: error: 'inclusive_scan' was not declared in this scope
   inclusive_scan(begin(counter_a), end(counter_a), begin(counter_a));
   ^~~~~~~~~~~~~~
../../../src/abismal/src/AbismalIndex.cpp: In member function 'void AbismalIndex::compress_dp()':
../../../src/abismal/src/AbismalIndex.cpp:665:20: error: found ':' in nested-name-specifier, expected '::'
   for (auto &block : blocks) {
                    ^
                    ::
../../../src/abismal/src/AbismalIndex.cpp:665:14: error: 'block' has not been declared
   for (auto &block : blocks) {
              ^~~~~
../../../src/abismal/src/AbismalIndex.cpp:665:28: error: qualified-id in declaration before ')' token
   for (auto &block : blocks) {
                            ^
../../../src/abismal/src/AbismalIndex.cpp:757:4: error: expected ';' before 'max_candidates'
   }
    ^
    ;
../../../src/abismal/src/AbismalIndex.cpp:759:3:
   max_candidates = 100u;  // GS: this is a heuristic
   ~~~~~~~~~~~~~~
../../../src/abismal/src/AbismalIndex.cpp:760:3: error: expected primary-expression before 'if'
   if (VERBOSE) clog << delta_seconds(s_time) << endl;
   ^~
../../../src/abismal/src/AbismalIndex.cpp:759:25: error: expected ')' before 'if'
   max_candidates = 100u;  // GS: this is a heuristic
                         ^
                         )
   if (VERBOSE) clog << delta_seconds(s_time) << endl;
   ~~
../../../src/abismal/src/AbismalIndex.cpp:665:7: note: to match this '('
   for (auto &block : blocks) {
       ^
../../../src/abismal/src/AbismalIndex.cpp:665:3: error: expected iteration declaration or initialization
   for (auto &block : blocks) {
   ^~~
At global scope:
cc1plus: warning: unrecognized command line option '-Wno-unknown-attributes'
make[4]: *** [src/AbismalIndex.o] Error 1
make[4]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build/src/abismal'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/lustre/project/PI/build/centos7/dnmtools/build'
make: *** [all] Error 2
andrewdavidsmith commented 2 months ago

@cb4github Thanks. I can check it out some more. There are some potential problems that might not be addressable, but we can figure out if these are relevant. It's possible gcc 8.5 doesn't fully support c++17. They always have a list of which parts of the standard they support in each version, and it's rarely 100% until much later. There's also a chance that the "module" is an issue. I don't trust those myself; they are almost as bad as conda for pollution. And what's most likely, but we can fix, is that somewhere I forgot I had to just use c++17, since I've been using c++20 for some time now. If that were the case, my compiler, and the one on github runners, should have complained. Thinking out loud here, but I could use github runners to determine which compilers and versions are supported. Anyway, thanks again and I'll check it out asap.

andrewdavidsmith commented 2 months ago

Locking this issues and asking to open a new issue for different problems.