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Compilation error: zlib found but not working #15

Open
FranckLejzerowicz opened this issue Jul 26, 2019 · 4 comments
Open

Compilation error: zlib found but not working #15

FranckLejzerowicz opened this issue Jul 26, 2019 · 4 comments

Comments

@FranckLejzerowicz
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FranckLejzerowicz commented Jul 26, 2019 •
edited

Expected Behavior

Compiling the code using cmake

Current Behavior

Not compiling successfully

stdin:

$ cmake -DCMAKE_BUILD_TYPE=RELEASE -DZLIB_LIBRARY=/home/flejzerowicz/softs/zlib-1.2.11/lib -DZLIB_INCLUDE_DIR=/home/flejzerowicz/softs/zlib-1.2.11/include -DCMAKE_INSTALL_PREFIX=. ..

stdout:

-- Source Directory: /home/flejzerowicz/softs/plass/lib/mmseqs
-- Project Directory: /home/flejzerowicz/softs/plass/lib/mmseqs
-- Compiler is GNU 
-- ZSTD VERSION 1.3.8
-- ShellCheck not found
-- Using CPU native flags for SSE optimization:  -march=native
-- Found AVX2 extensions, using flags:  -march=native -mavx2 -mfpmath=sse -Wa,-q
-- Found ZLIB
-- ZLIB does not work
-- Found BZLIB
-- BZLIB does not work
-- Found OpenMP
-- ShellCheck not found
-- Configuring done
-- Generating done
-- Build files have been written to: /home/flejzerowicz/softs/plass/build
flejzerowicz@barnacle:~/softs/plass/build$ make -j 4
[  1%] Built target ksw2
[  2%] Built target cacode
[  7%] Built target alp
[ 20%] Built target tinyexpr
[ 21%] Built target generated
[ 24%] Built target local-generated
[ 25%] Built target version
[ 36%] Built target libzstd_static
[ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertmsa.cpp.o
[ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/view.cpp.o
[ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/createtsv.cpp.o
[ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/createsubdb.cpp.o
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/util/convertmsa.cpp:5:0:
/home/flejzerowicz/softs/plass/lib/mmseqs/lib/gzstream/gzstream.h:31:10: fatal error: zlib.h: No such file or directory
 #include <zlib.h>
          ^~~~~~~~
compilation terminated.
make[2]: *** [lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertmsa.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/all] Error 2
make: *** [all] Error 2

Context

Providing context helps us come up with a solution and improve our documentation for the future.

zlib is installed in non standard location but it is found anyways, as well as running cmake without the flags
-DZLIB_LIBRARY=/home/flejzerowicz/softs/zlib-1.2.11/lib -DZLIB_INCLUDE_DIR=/home/flejzerowicz/softs/zlib-1.2.11/include

Your Environment

Include as many relevant details about the environment you experienced the bug in.

  • Git commit used: NA (because not installed successfully)
    git clone https://github.com/soedinglab/plass.git
    was run on July 25th 2019

  • For self-compiled and Homebrew: Cmake versions used: cmake 3.7.2
    availble on the server through:
    module load cmake_3.7.2

  • Operating system and version:

uname -a

Linux barnacle.ucsd.edu 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
@milot-mirdita
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milot-mirdita commented Jul 27, 2019 •
edited

You could try to execute:
CXXFLAGS="-L/home/flejzerowicz/softs/zlib-1.2.11/lib -I/home/flejzerowicz/softs/zlib-1.2.11/include" cmake ...

That should get cmake to recognize the right paths. However it would make more sense if you used something like Linuxbrew instead to manage dependencies manually (works without having admin rights).

However we should not try to include gzstream if we could not find zlib. We'll fix that issue for the next release. (See soedinglab/MMseqs2@8199cca).

@FranckLejzerowicz
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I have created a conda environment and from there, installed zlib with linuxbrew.
Then I have erased the build folder, and restarted the installation procedure, but the problem persisted...

So I have erased the entire plass folder, re-cloned, and restarted the installation procedure, and now it is OpenMP that make an error:

(plass) flejzerowicz@barnacle:~/softs/plass$ git submodule update --init
Submodule 'lib/mmseqs' (https://github.com/soedinglab/MMseqs2.git) registered for path 'lib/mmseqs'
Initialized empty Git repository in /home/flejzerowicz/softs/plass/lib/mmseqs/.git/
remote: Enumerating objects: 5, done.
remote: Counting objects: 100% (5/5), done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 30295 (delta 0), reused 1 (delta 0), pack-reused 30290
Receiving objects: 100% (30295/30295), 25.98 MiB | 25.56 MiB/s, done.
Resolving deltas: 100% (23360/23360), done.
Submodule path 'lib/mmseqs': checked out 'fd1c34dae218b20d16bcaf35d7bbca0b8f8ef844'

(plass) flejzerowicz@barnacle:~/softs/plass$ mkdir build && cd build

(plass) flejzerowicz@barnacle:~/softs/plass/build$ cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. ..
-- The CXX compiler identification is GNU 7.2.0
-- Check for working CXX compiler: /home/flejzerowicz/usr/miniconda3/bin/c++
-- Check for working CXX compiler: /home/flejzerowicz/usr/miniconda3/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- The C compiler identification is GNU 7.2.0
-- Check for working C compiler: /home/flejzerowicz/usr/miniconda3/bin/cc
-- Check for working C compiler: /home/flejzerowicz/usr/miniconda3/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: /home/flejzerowicz/softs/plass/lib/mmseqs
-- Project Directory: /home/flejzerowicz/softs/plass/lib/mmseqs
-- Compiler is GNU 
-- ZSTD VERSION 1.3.8
-- ShellCheck disabled
-- Performing Test HAVE_POSIX_FADVISE
-- Performing Test HAVE_POSIX_FADVISE - Success
-- Performing Test HAVE_POSIX_MADVISE
-- Performing Test HAVE_POSIX_MADVISE - 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 - Failed
-- ZLIB does not work
-- Found BZLIB
-- Performing Test HAVE_BZLIB_CHECK
-- Performing Test HAVE_BZLIB_CHECK - Failed
-- BZLIB does not work
CMake Error at lib/mmseqs/src/CMakeLists.txt:233 (message):
  -- Could not find OpenMP.  Skip check with -DREQUIRE_OPENMP=0.


-- Configuring incomplete, errors occurred!

@FranckLejzerowicz
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Hi @milot-mirdita and thanks for the quick answer.

I could work it out using the conda install, but for optimized performance, I would have preferred compiling, but in the process couldn't be found zlib.h or more precisley work with it (see other attempt below).

Note that I can't use the pre-compiled executable, although I think I use a system on which that should be working:

$ uname -a | grep x86_64
Linux barnacle.ucsd.edu 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

$ ./plass/bin/plass -h
FATAL: kernel too old
Aborted (core dumped)

For compiling, I have also tried with the flag -DREQUIRE_OPENMP=0 but this still throw an error.

flejzerowicz@barnacle:~/softs/plass/build$ cmake -DREQUIRE_OPENMP=0 -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. ..
-- Source Directory: /home/flejzerowicz/softs/plass/lib/mmseqs
-- Project Directory: /home/flejzerowicz/softs/plass/lib/mmseqs
-- Compiler is GNU 
-- ZSTD VERSION 1.3.8
-- ShellCheck not found
-- Using CPU native flags for SSE optimization:  -march=native
-- Found AVX2 extensions, using flags:  -march=native -mavx2 -mfpmath=sse -Wa,-q
-- Found ZLIB
-- ZLIB does not work
-- Found BZLIB
-- BZLIB does not work
-- ShellCheck not found
-- Configuring done
-- Generating done
-- Build files have been written to: /home/flejzerowicz/softs/plass/build
flejzerowicz@barnacle:~/softs/plass/build$ make -j 4 && install
Scanning dependencies of target ksw2
Scanning dependencies of target cacode
Scanning dependencies of target generated
Scanning dependencies of target alp
[  0%] Generating ../generated/easysearch.sh.h
[  0%] Building CXX object lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/lambda_calculator.cpp.o
[  0%] Building CXX object lib/mmseqs/lib/ksw2/CMakeFiles/ksw2.dir/ksw2_extz2_sse.cpp.o
[  1%] Generating ../generated/easycluster.sh.h
[  1%] Generating ../generated/easytaxonomy.sh.h
[  2%] Generating ../generated/blastp.sh.h
[  2%] Generating ../generated/blastpgp.sh.h
[  2%] Generating ../generated/map.sh.h
[  2%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o
[  3%] Generating ../generated/rbh.sh.h
[  3%] Generating ../generated/linclust.sh.h
[  3%] Generating ../generated/clustering.sh.h
[  4%] Generating ../generated/cascaded_clustering.sh.h
[  4%] Generating ../generated/update_clustering.sh.h
[  5%] Generating ../generated/searchtargetprofile.sh.h
[  5%] Generating ../generated/createindex.sh.h
[  5%] Generating ../generated/createtaxdb.sh.h
[  5%] Built target ksw2
[  6%] Generating ../generated/translated_search.sh.h
[  6%] Generating ../generated/taxonomy.sh.h
[  7%] Building CXX object lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/lubksb.cpp.o
[  7%] Generating ../generated/multihitdb.sh.h
[  7%] Building CXX object lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/ludcmp.cpp.o
[  8%] Generating ../generated/multihitsearch.sh.h
[  8%] Generating ../generated/summarizeresultsbyset.sh.h
Scanning dependencies of target tinyexpr
[  9%] Generating ../generated/enrich.sh.h
[  9%] Building C object lib/mmseqs/lib/tinyexpr/CMakeFiles/tinyexpr.dir/tinyexpr.c.o
[  9%] Generating ../generated/blastn.sh.h
[  9%] Generating ../generated/VTML80.out.h
[ 10%] Building CXX object lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/nrutil.cpp.o
[ 11%] Generating ../generated/nucleotide.out.h
[ 11%] Generating ../generated/blosum62.out.h
[ 11%] Generating ../generated/PAM30.out.h
[ 11%] Built target cacode
[ 11%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_random.cpp.o
[ 12%] Generating ../generated/CovSeqidQscPercMinDiag.lib.h
[ 13%] Linking C static library libtinyexpr.a
[ 13%] Generating ../generated/CovSeqidQscPercMinDiagTargetCov.lib.h
[ 14%] Generating ../generated/ExpOpt3_8_polished.cs32.lib.h
[ 15%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o
[ 15%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o
[ 15%] Generating ../generated/Library255_may17.lib.h
[ 15%] Built target tinyexpr
[ 15%] Generating ../generated/libPure_blosum62_255.lib.h
[ 15%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o
[ 16%] Generating ../generated/libPure_blosum62_32.lib.h
[ 16%] Generating ../generated/libPolished_8.lib.h
[ 16%] Generating ../generated/searchslicedtargetprofile.sh.h
Scanning dependencies of target local-generated
[ 17%] Generating ../generated/cs219.lib.h
[ 17%] Generating ../generated/assembler.sh.h
[ 17%] Generating ../generated/linsearch.sh.h
[ 17%] Generating ../generated/hybridassembler.sh.h
[ 18%] Generating ../generated/nuclassembler.sh.h
[ 18%] Built target generated
[ 18%] Generating ../generated/predict_coding_acc9260_56x96.model.h
Scanning dependencies of target libzstd_static
[ 18%] Generating ../generated/predict_coding_acc9623_57x32x64.model.h
[ 19%] Generating ../generated/predict_coding_acc9540_57x32x64.model.h
[ 19%] Generating ../generated/predict_coding_acc9642_57x32x64.model.h
[ 20%] Generating ../generated/predict_coding_acc9598_57x32x64.model.h
[ 20%] Generating ../generated/predict_coding_acc9743_57x32x64.model.h
[ 20%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/entropy_common.c.o
[ 20%] Built target local-generated
[ 21%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o
Scanning dependencies of target version
[ 21%] Building CXX object src/version/CMakeFiles/version.dir/Version.cpp.o
[ 21%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o
[ 21%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/fse_decompress.c.o
[ 22%] Linking CXX static library libversion.a
[ 22%] Built target version
[ 23%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/threading.c.o
[ 23%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o
[ 23%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/pool.c.o
[ 24%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/zstd_common.c.o
[ 24%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/error_private.c.o
[ 24%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/xxhash.c.o
[ 25%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/hist.c.o
[ 26%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o
[ 26%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/fse_compress.c.o
[ 26%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o
[ 26%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/huf_compress.c.o
[ 27%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_compress.c.o
[ 27%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstdmt_compress.c.o
[ 28%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_fast.c.o
[ 29%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alp.cpp.o
[ 29%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o
[ 29%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_basic.cpp.o
[ 29%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_double_fast.c.o
[ 29%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_lazy.c.o
[ 30%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_opt.c.o
[ 31%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o
[ 31%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o
[ 31%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_ldm.c.o
[ 31%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/huf_decompress.c.o
[ 31%] Built target alp
[ 32%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress.c.o
[ 32%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress_block.c.o
Scanning dependencies of target mmseqs-framework
[ 33%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_ddict.c.o
[ 33%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o
[ 33%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o
[ 34%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o
[ 34%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o
[ 34%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o
[ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o
[ 35%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o
[ 36%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o
[ 36%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o
[ 36%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o
[ 37%] Linking C static library libzstd.a
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.h:7:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/QueryMatcher.h:11,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/Alignment.cpp:2:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/Alignment.cpp:272:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel num_threads(threads)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/Alignment.cpp:288:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 5) reduction(+: alignmentsNum, totalPassedNum)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/Alignment.cpp:414:0: warning: ignoring #pragma omp barrier [-Wunknown-pragmas]
 #pragma omp barrier
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/Alignment.cpp:418:0: warning: ignoring #pragma omp barrier [-Wunknown-pragmas]
 #pragma omp barrier
 
[ 37%] Built target libzstd_static
[ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.h:5:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/IndexReader.h:6,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/Alignment.h:6,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/Main.cpp:1:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
[ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o
[ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o
[ 39%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o
[ 39%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/StripedSmithWaterman.cpp.o
[ 39%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/BandedNucleotideAligner.cpp.o
[ 40%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/rescorediagonal.cpp.o
[ 40%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/Main.cpp.o
[ 40%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/AlignmentSymmetry.cpp.o
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.h:7:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/QueryMatcher.h:11,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/rescorediagonal.cpp:8:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
[ 41%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/Clustering.cpp.o
/home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/rescorediagonal.cpp:116:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/rescorediagonal.cpp:136:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 1)
 
[ 41%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/clustering/ClusteringAlgorithms.cpp.o
/home/flejzerowicz/softs/plass/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:30:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:36:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 100)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:95:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:101:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 1000)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:186:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for schedule(dynamic, 1000)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:49:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel reduction (+:elementCount)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:55:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 10)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:284:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:290:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 1000)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:329:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:335:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 1000)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:402:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:408:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 1000)
 
[ 42%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/A3MReader.cpp.o
[ 42%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Application.cpp.o
[ 42%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/BaseMatrix.cpp.o
[ 43%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Command.cpp.o
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/rescorediagonal.cpp:1:0:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/DistanceCalculator.h: In function 'int doRescorediagonal(Parameters&, DBWriter&, DBReader<unsigned int>&, size_t, size_t)':
/home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/DistanceCalculator.h:272:95: warning: 'globalAliStat.DistanceCalculator::globalAliSigma' may be used uninitialized in this function [-Wmaybe-uninitialized]
         return 0.5 - 0.5 * erf((score / len - globalAliMu) / (sqrt(2.0 / sqrt((float) len)) * globalAliSigma));
                                                                                               ^~~~~~~~~~~~~~
/home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/rescorediagonal.cpp:99:24: note: 'globalAliStat.DistanceCalculator::globalAliSigma' was declared here
     DistanceCalculator globalAliStat;
                        ^~~~~~~~~~~~~
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/rescorediagonal.cpp:1:0:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/DistanceCalculator.h:272:45: warning: 'globalAliStat.DistanceCalculator::globalAliMu' may be used uninitialized in this function [-Wmaybe-uninitialized]
         return 0.5 - 0.5 * erf((score / len - globalAliMu) / (sqrt(2.0 / sqrt((float) len)) * globalAliSigma));
                                ~~~~~~~~~~~~~^~~~~~~~~~~~~~
/home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/rescorediagonal.cpp:99:24: note: 'globalAliStat.DistanceCalculator::globalAliMu' was declared here
     DistanceCalculator globalAliStat;
                        ^~~~~~~~~~~~~
[ 43%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/CommandCaller.cpp.o
[ 43%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/DBConcat.cpp.o
[ 44%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/DBReader.cpp.o
/home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/DBConcat.cpp:58:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel num_threads(threads)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/DBConcat.cpp:64:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 10) reduction(max:maxKeyA)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/DBConcat.cpp:96:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel num_threads(threads)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/DBConcat.cpp:102:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 10)
 
[ 44%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/DBWriter.cpp.o
[ 45%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Debug.cpp.o
/home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/DBReader.cpp:695:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel num_threads(localThreads)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/DBReader.cpp:701:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 10) reduction(max:max)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/DBWriter.cpp:98:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/DBWriter.cpp:105:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(static)
 
[ 45%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/ExpressionParser.cpp.o
[ 45%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/FileUtil.cpp.o
[ 46%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/HeaderSummarizer.cpp.o
[ 46%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/KSeqWrapper.cpp.o
[ 46%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/MemoryMapped.cpp.o
[ 47%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/MMseqsMPI.cpp.o
[ 47%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/NucleotideMatrix.cpp.o
[ 48%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Orf.cpp.o
[ 48%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Parameters.cpp.o
[ 48%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/ProfileStates.cpp.o
[ 49%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/LibraryReader.cpp.o
[ 49%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/ScoreMatrixFile.cpp.o
[ 49%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Sequence.cpp.o
[ 50%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/SubstitutionMatrix.cpp.o
[ 50%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/tantan.cpp.o
[ 51%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/UniprotKB.cpp.o
[ 51%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/commons/Util.cpp.o
[ 51%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/CacheFriendlyOperations.cpp.o
[ 52%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/ExtendedSubstitutionMatrix.cpp.o
/home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/Util.cpp:463:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel num_threads(threadCnt)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/Util.cpp:470:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic,10)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/Util.cpp:501:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel num_threads(threadCnt)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/Util.cpp:505:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 1) reduction (+: cnt)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/Util.cpp:617:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel reduction(+:n)
 
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.h:7:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:1:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/ExtendedSubstitutionMatrix.cpp:40:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/ExtendedSubstitutionMatrix.cpp:45:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(static)
 
[ 52%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/Indexer.cpp.o
[ 52%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/IndexBuilder.cpp.o
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexBuilder.h:4:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:1:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:103:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:122:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
         #pragma omp for schedule(dynamic, 100) reduction(+:totalKmerCount, maskedResidues)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:227:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:243:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
         #pragma omp for schedule(dynamic, 100)
 
[ 53%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/KmerGenerator.cpp.o
[ 53%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/Main.cpp.o
[ 54%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/Prefiltering.cpp.o
[ 54%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/PrefilteringIndexReader.cpp.o
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/Prefiltering.h:7:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/Main.cpp:2:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/Prefiltering.h:7:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/Prefiltering.cpp:1:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/Prefiltering.cpp:411:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/Prefiltering.cpp:422:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(static)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/Prefiltering.cpp:770:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel num_threads(localThreads)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/Prefiltering.cpp:788:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 2) reduction (+: kmersPerPos, resSize, dbMatches, doubleMatches, querySeqLenSum, diagonalOverflow)
 
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.h:5:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:1:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
[ 54%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/QueryMatcher.cpp.o
[ 55%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/ReducedMatrix.cpp.o
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.h:7:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/QueryMatcher.h:11,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:8:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
[ 55%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/SequenceLookup.cpp.o
[ 55%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/UngappedAlignment.cpp.o
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.h:7:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/UngappedAlignment.h:10,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:4:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
[ 56%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/prefiltering/ungappedprefilter.cpp.o
[ 56%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/besthitperset.cpp.o
[ 57%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/combinepvalperset.cpp.o
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.h:7:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/QueryMatcher.h:11,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp:12:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp:79:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp:94:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 1)
 
[ 57%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/resultsbyset.cpp.o
[ 57%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/Aggregation.cpp.o
[ 58%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/MultiHitDb.cpp.o
/home/flejzerowicz/softs/plass/lib/mmseqs/src/multihit/Aggregation.cpp:57:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/multihit/Aggregation.cpp:67:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for
 
[ 58%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/MultiHitSearch.cpp.o
[ 58%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/multihit/SummarizeResultsBySet.cpp.o
[ 59%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/lca.cpp.o
[ 59%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/addtaxonomy.cpp.o
/home/flejzerowicz/softs/plass/lib/mmseqs/src/taxonomy/lca.cpp:71:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/taxonomy/lca.cpp:83:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
         #pragma omp for schedule(dynamic, 10) reduction (+:taxonNotFound, found)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/taxonomy/addtaxonomy.cpp:63:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/taxonomy/addtaxonomy.cpp:73:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
         #pragma omp for schedule(dynamic, 10) reduction (+: deletedNodes, taxonNotFound)
 
[ 60%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/NcbiTaxonomy.cpp.o
[ 60%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/filtertaxdb.cpp.o
/home/flejzerowicz/softs/plass/lib/mmseqs/src/taxonomy/filtertaxdb.cpp:58:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/taxonomy/filtertaxdb.cpp:67:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
         #pragma omp for schedule(dynamic, 10)
 
[ 60%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/createtaxdb.cpp.o
[ 61%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/taxonomy/taxonomyreport.cpp.o
[ 61%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/linclust/kmermatcher.cpp.o
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.h:7:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/QueryMatcher.h:11,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/linclust/kmermatcher.cpp:15:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/linclust/kmermatcher.cpp:69:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/linclust/kmermatcher.cpp:71:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 1)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/linclust/kmermatcher.cpp:134:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/linclust/kmermatcher.cpp:169:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 100)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/linclust/kmermatcher.cpp:364:0: warning: ignoring #pragma omp barrier [-Wunknown-pragmas]
 #pragma omp barrier
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/linclust/kmermatcher.cpp:372:0: warning: ignoring #pragma omp barrier [-Wunknown-pragmas]
 #pragma omp barrier
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/linclust/kmermatcher.cpp:752:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel num_threads(1)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/linclust/kmermatcher.cpp:758:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/linclust/kmermatcher.cpp:811:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for schedule(dynamic, 1) num_threads(threads)
 
[ 61%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/linclust/kmerindexdb.cpp.o
[ 62%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/linclust/kmersearch.cpp.o
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.h:7:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/QueryMatcher.h:11,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/linclust/kmersearch.cpp:5:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.h:5:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/linclust/kmerindexdb.cpp:3:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
[ 62%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/linclust/LinsearchIndexReader.cpp.o
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.h:5:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:6:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
[ 63%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/alignall.cpp.o
[ 63%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/alignbykmer.cpp.o
[ 63%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/apply.cpp.o
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.h:5:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/IndexReader.h:6,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/alignment/Alignment.h:6,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/util/alignall.cpp:9:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/alignall.cpp:49:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/alignall.cpp:66:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 1)
 
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.h:7:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/QueryMatcher.h:11,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/util/alignbykmer.cpp:8:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/alignbykmer.cpp:167:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/alignbykmer.cpp:190:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 1)
 
[ 64%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/clusthash.cpp.o
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/clusthash.cpp:48:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/clusthash.cpp:55:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 10000)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/clusthash.cpp:91:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/clusthash.cpp:96:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 2)
 
[ 64%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/compress.cpp.o
[ 64%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convert2fasta.cpp.o
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/compress.cpp:32:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/compress.cpp:39:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 1)
 
[ 65%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertalignments.cpp.o
[ 65%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertca3m.cpp.o
[ 66%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertkb.cpp.o
[ 66%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertmsa.cpp.o
In file included from /home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.h:5:0,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/IndexReader.h:6,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/util/convertalignments.cpp:7:
/home/flejzerowicz/softs/plass/lib/mmseqs/src/prefiltering/IndexTable.h:187:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
         #pragma omp parallel for
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/convertalignments.cpp:222:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel num_threads(localThreads)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/convertalignments.cpp:249:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp  for schedule(dynamic, 10)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/convertca3m.cpp:30:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/convertca3m.cpp:42:0: warning: ignoring #pragma omp for [-Wunknown-pragmas]
 #pragma omp for schedule(dynamic, 10)
 
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/convertmsa.cpp: In function 'int convertmsa(int, const char**, const Command&)':
/home/flejzerowicz/softs/plass/lib/mmseqs/src/util/convertmsa.cpp:25:39: error: invalid use of incomplete type 'std::ifstream {aka class std::basic_ifstream<char>}'
         in = new std::ifstream(par.db1);
                                       ^
In file included from /home/flejzerowicz/usr/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.2.0/bits/localefwd.h:41:0,
                 from /home/flejzerowicz/usr/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.2.0/string:43,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/commons/Parameters.h:7,
                 from /home/flejzerowicz/softs/plass/lib/mmseqs/src/util/convertmsa.cpp:1:
/home/flejzerowicz/usr/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.2.0/iosfwd:116:11: note: declaration of 'std::ifstream {aka class std::basic_ifstream<char>}'
     class basic_ifstream;
           ^~~~~~~~~~~~~~
make[2]: *** [lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/util/convertmsa.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/all] Error 2
make: *** [all] Error 2

Thanks

@milot-mirdita milot-mirdita reopened this Jul 31, 2019
@milot-mirdita
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I fixed the broken include in the latest git commit. You have to also install a newer compiler to use Plass. Please also do that with linuxbrew (brew install gcc).

Then you should be able to compile Plass with the following commands:

mkdir build && cd build
CC=gcc-5 CXX=g++-5 cmake ..
make -j8

I also tried to reproduce the problem with a fresh linuxbrew installation, but I couldn't get zlib and libbz2 to work there either. So you might not be able to load compressed files.

The easier path would probably be to ask whoever has an admin account on the system to install those two packages as system packages. I would still use the newer compiler provided by linuxbrew however.

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@milot-mirdita @FranckLejzerowicz