text mmseqs_20190131.log

Posted 2021-04-30
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ubuntu@bibigrid-master-64y44t0ith2ejcj:/vol/attached/data/opt/test/MMseqs2/build$ cmake -DHAVE_MPI=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..
-- The CXX compiler identification is GNU 5.4.0
-- The C compiler identification is GNU 5.4.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Source Directory: /vol/attached/data/opt/test/MMseqs2
-- Project Directory: /vol/attached/data/opt/test/MMseqs2
-- Compiler is GNU
-- ZSTD VERSION 1.3.8
-- ShellCheck disabled
-- Performing Test HAVE_POSIX_FADVISE
-- Performing Test HAVE_POSIX_FADVISE - Success
-- Using CPU native flags for SSE optimization:  -march=native
-- Performing Test HAVE_MM_MALLOC
-- Performing Test HAVE_MM_MALLOC - Success
-- Performing Test HAVE_POSIX_MEMALIGN
-- Performing Test HAVE_POSIX_MEMALIGN - Success
-- Performing Test HAVE_AVX2_EXTENSIONS
-- Performing Test HAVE_AVX2_EXTENSIONS - Success
-- Performing Test HAVE_AVX_EXTENSIONS
-- Performing Test HAVE_AVX_EXTENSIONS - Success
-- Performing Test HAVE_SSE4_2_EXTENSIONS
-- Performing Test HAVE_SSE4_2_EXTENSIONS - Success
-- Performing Test HAVE_SSE4_1_EXTENSIONS
-- Performing Test HAVE_SSE4_1_EXTENSIONS - Success
-- Performing Test HAVE_SSE3_EXTENSIONS
-- Performing Test HAVE_SSE3_EXTENSIONS - Success
-- Performing Test HAVE_SSE2_EXTENSIONS
-- Performing Test HAVE_SSE2_EXTENSIONS - Success
-- Performing Test HAVE_SSE_EXTENSIONS
-- Performing Test HAVE_SSE_EXTENSIONS - Success
-- Found AVX2 extensions, using flags:  -march=native -mavx2 -mfpmath=sse -Wa,-q
-- Found ZLIB
-- Performing Test HAVE_ZLIB_CHECK
-- Performing Test HAVE_ZLIB_CHECK - Success
-- ZLIB works
-- Found BZLIB
-- Performing Test HAVE_BZLIB_CHECK
-- Performing Test HAVE_BZLIB_CHECK - Success
-- BZLIB works
-- Found MPI_C: /usr/lib/openmpi/lib/libmpi.so
-- Found MPI_CXX: /usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so
-- Found MPI
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Found OpenMP
-- Configuring done
-- Generating done
-- Build files have been written to: /vol/attached/data/opt/test/MMseqs2/build
ubuntu@bibigrid-master-64y44t0ith2ejcj:/vol/attached/data/opt/test/MMseqs2/build$ make
Scanning dependencies of target cacode
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[  7%] Building CXX object lib/ksw2/CMakeFiles/ksw2.dir/ksw2_extz2_sse.cpp.o
[  7%] Built target ksw2
Scanning dependencies of target generated
[  7%] Generating ../generated/easysearch.sh.h
[  8%] Generating ../generated/easycluster.sh.h
[  8%] Generating ../generated/blastp.sh.h
[  8%] Generating ../generated/blastpgp.sh.h
[  9%] Generating ../generated/map.sh.h
[  9%] Generating ../generated/linclust.sh.h
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[ 11%] Generating ../generated/createindex.sh.h
[ 11%] Generating ../generated/createtaxdb.sh.h
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[ 13%] Generating ../generated/search2m.sh.h
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[ 14%] Generating ../generated/blastn.sh.h
[ 14%] Generating ../generated/nucleotide.out.h
[ 15%] Generating ../generated/blosum62.out.h
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[ 15%] Generating ../generated/CovSeqidQscPercMinDiagTargetCov.out.h
[ 16%] Generating ../generated/ExpOpt3_8_polished.cs32.lib.h
[ 16%] Generating ../generated/Library255_may17.lib.h
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[ 17%] Generating ../generated/libPolished_8.lib.h
[ 18%] Generating ../generated/searchslicedtargetprofile.sh.h
[ 18%] Generating ../generated/cs219.lib.h
[ 18%] Generating ../generated/linsearch.sh.h
[ 18%] Built target generated
Scanning dependencies of target mmseqs-framework
[ 18%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o
[ 18%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o
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[ 20%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o
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[ 21%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/alignment/BandedNucleotideAligner.cpp.o
[ 21%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/alignment/rescorediagonal.cpp.o
[ 21%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/clustering/Main.cpp.o
[ 22%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/clustering/AlignmentSymmetry.cpp.o
[ 22%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/clustering/Clustering.cpp.o
[ 23%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/clustering/ClusteringAlgorithms.cpp.o
[ 23%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/A3MReader.cpp.o
[ 23%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/Application.cpp.o
[ 24%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/BaseMatrix.cpp.o
[ 24%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/Command.cpp.o
[ 24%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/CommandCaller.cpp.o
[ 25%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/DBConcat.cpp.o
[ 25%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/DBReader.cpp.o
[ 25%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/DBWriter.cpp.o
[ 26%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/Debug.cpp.o
[ 26%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/FileUtil.cpp.o
/vol/attached/data/opt/test/MMseqs2/src/commons/FileUtil.cpp: In static member function ‘static void FileUtil::copyFile(const char*, const char*)’:
/vol/attached/data/opt/test/MMseqs2/src/commons/FileUtil.cpp:256:31: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
         write(dest, buf, size);
                               ^
[ 26%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/HeaderSummarizer.cpp.o
[ 27%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/KSeqWrapper.cpp.o
[ 27%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/MemoryMapped.cpp.o
[ 27%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/MMseqsMPI.cpp.o
[ 28%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/NucleotideMatrix.cpp.o
[ 28%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/Orf.cpp.o
[ 28%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/Parameters.cpp.o
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[ 29%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/Sequence.cpp.o
[ 30%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/SubstitutionMatrix.cpp.o
/vol/attached/data/opt/test/MMseqs2/src/commons/SubstitutionMatrix.cpp: In constructor ‘SubstitutionMatrix::SubstitutionMatrix(const char*, float, float)’:
/vol/attached/data/opt/test/MMseqs2/src/commons/SubstitutionMatrix.cpp:60:9: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
         if (alphabetSize < this->alphabetSize - 1) {
         ^
/vol/attached/data/opt/test/MMseqs2/src/commons/SubstitutionMatrix.cpp:74:9: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]
         if (alphabetSize < this->alphabetSize - 1) {
         ^
[ 30%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/commons/tantan.cpp.o
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[ 32%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/prefiltering/Indexer.cpp.o
[ 32%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/prefiltering/IndexBuilder.cpp.o
[ 33%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/prefiltering/KmerGenerator.cpp.o
[ 33%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/prefiltering/Main.cpp.o
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[ 36%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/multihit/besthitperset.cpp.o
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[ 38%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/multihit/SummarizeResultsBySet.cpp.o
[ 38%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/taxonomy/lca.cpp.o
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/vol/attached/data/opt/test/MMseqs2/src/linclust/kmermatcher.cpp: In instantiation of ‘size_t assignGroup(KmerPosition*, size_t, bool, int, float) [with int TYPE = 1; size_t = long unsigned int]’:
/vol/attached/data/opt/test/MMseqs2/src/linclust/kmermatcher.cpp:418:143:   required from here
/vol/attached/data/opt/test/MMseqs2/src/linclust/kmermatcher.cpp:520:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     bool canBeExtended = diagonal < 0 || (diagonal > (queryLen - hashSeqPair[i].seqLen));
                                                                    ^
/vol/attached/data/opt/test/MMseqs2/src/linclust/kmermatcher.cpp: In instantiation of ‘size_t assignGroup(KmerPosition*, size_t, bool, int, float) [with int TYPE = 0; size_t = long unsigned int]’:
/vol/attached/data/opt/test/MMseqs2/src/linclust/kmermatcher.cpp:420:143:   required from here
/vol/attached/data/opt/test/MMseqs2/src/linclust/kmermatcher.cpp:520:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
[ 40%] Building CXX object src/CMakeFiles/mmseqs-framework.dir/linclust/kmerindexdb.cpp.o
/vol/attached/data/opt/test/MMseqs2/src/linclust/kmerindexdb.cpp: In function ‘int kmerindexdb(int, const char**, const Command&)’:
/vol/attached/data/opt/test/MMseqs2/src/linclust/kmerindexdb.cpp:103:53: error: expected primary-expression before ‘=’ token
         std::pair<size_t, KmerPosition *> kmerRet = = KmerSearch::extractKmerAndSort(splitKmerCount, split, splits, seqDbr, par, subMat, KMER_SIZE, chooseTopKmer);
                                                     ^
/vol/attached/data/opt/test/MMseqs2/src/linclust/kmerindexdb.cpp:103:162: error: no matching function for call to ‘KmerSearch::extractKmerAndSort(size_t&, size_t&, size_t&, DBReader<unsigned int>&, Parameters&, BaseMatrix*&, const size_t&, size_t&)’
         std::pair<size_t, KmerPosition *> kmerRet = = KmerSearch::extractKmerAndSort(splitKmerCount, split, splits, seqDbr, par, subMat, KMER_SIZE, chooseTopKmer);
                                                                                                                                                                  ^
In file included from /vol/attached/data/opt/test/MMseqs2/src/linclust/kmerindexdb.cpp:10:0:
/vol/attached/data/opt/test/MMseqs2/src/linclust/kmersearch.h:20:46: note: candidate: static std::pair<long unsigned int, KmerPosition*> KmerSearch::extractKmerAndSort(size_t, size_t, size_t, DBReader<unsigned int>&, Parameters&, BaseMatrix*, size_t, size_t, size_t)
     static std::pair<size_t, KmerPosition *> extractKmerAndSort(size_t splitKmerCount, size_t split, size_t splits,
                                              ^
/vol/attached/data/opt/test/MMseqs2/src/linclust/kmersearch.h:20:46: note:   candidate expects 9 arguments, 8 provided
/vol/attached/data/opt/test/MMseqs2/src/linclust/kmerindexdb.cpp:181:100: error: ‘writePos’ was not declared in this scope
                 LinsearchIndexReader::writeIndex<Parameters::DBTYPE_NUCLEOTIDES>(dbw, hashSeqPair, writePos, par.alphabetSize, KMER_SIZE);
                                                                                                    ^
/vol/attached/data/opt/test/MMseqs2/src/linclust/kmerindexdb.cpp:183:100: error: ‘writePos’ was not declared in this scope
                 LinsearchIndexReader::writeIndex<Parameters::DBTYPE_AMINO_ACIDS>(dbw, hashSeqPair, writePos, par.alphabetSize, KMER_SIZE);
                                                                                                    ^
src/CMakeFiles/mmseqs-framework.dir/build.make:1598: recipe for target 'src/CMakeFiles/mmseqs-framework.dir/linclust/kmerindexdb.cpp.o' failed
make[2]: *** [src/CMakeFiles/mmseqs-framework.dir/linclust/kmerindexdb.cpp.o] Error 1
CMakeFiles/Makefile2:459: recipe for target 'src/CMakeFiles/mmseqs-framework.dir/all' failed
make[1]: *** [src/CMakeFiles/mmseqs-framework.dir/all] Error 2
Makefile:127: recipe for
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