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steineggerlab / foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.
https://foldseek.com
GNU General Public License v3.0
825 stars 101 forks source link

build from src fails: header file missing #62

Closed gitozi closed 2 years ago

gitozi commented 2 years ago

Expected Behavior

Should compile on linux without errors

Current Behavior

Throws error about missing header file encoder_weights_3di.kerasify.h during make

Steps to Reproduce (for bugs)

normal build procedure: clone git repo, untar, create build dir, cmake, make

Foldssek Output (for bugs)

Please make sure to also post the complete output of Spacepharer. You can use gist.github.com for large output.

[ 87%] Building CXX object lib/3di/CMakeFiles/3di.dir/structureto3di.cpp.o
/home/user/packages/foldseek/foldseek/lib/3di/structureto3di.cpp:7:10: fatal error: encoder_weights_3di.kerasify.h: No such file or directory
    7 | #include "encoder_weights_3di.kerasify.h"
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [lib/3di/CMakeFiles/3di.dir/build.make:76: lib/3di/CMakeFiles/3di.dir/structureto3di.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:880: lib/3di/CMakeFiles/3di.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

Environment

self-compiled from git source commit 90b254585d398393cbca9c3515feb4ec4a1e7a9f RebornOS (ArchLinux)

milot-mirdita commented 2 years ago

You need to have either xxd (usually from a vim or vim-common package) or perl installed to generate the header during build. Can you post the whole cmake output?

gitozi commented 2 years ago

I could not see any hints regarding the dependencies you are mentioning, neither from the install instructions nor from the cmake output:

[user@server build]$ cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. ..
-- The C compiler identification is GNU 12.2.0
-- The CXX compiler identification is GNU 12.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Source Directory: /home/user/packages/foldseek/foldseek/lib/mmseqs
-- Project Directory: /home/user/packages/foldseek/foldseek/lib/mmseqs
-- Compiler is GNU 
-- 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
-- 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
-- Performing Test ATOMIC_LIBRARY_NATIVE
-- Performing Test ATOMIC_LIBRARY_NATIVE - Failed
-- Performing Test ATOMIC_LIBRARY_LIB
-- Performing Test ATOMIC_LIBRARY_LIB - Success
-- Found Atomic: atomic  
-- IPS4O sorting works
-- 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 OpenMP
-- ShellCheck not found
-- Configuring done
-- Generating done
-- Build files have been written to: /home/user/packages/foldseek/foldseek/build
milot-mirdita commented 2 years ago

Can you post the make output please too

gitozi commented 2 years ago 
[user@server build]$ make -j1
[  0%] Generating ../generated/VTML80.out.h
[  1%] Generating ../generated/VTML40.out.h
[  2%] Generating ../generated/nucleotide.out.h
[  2%] Generating ../generated/blosum62.out.h
[  2%] Generating ../generated/PAM30.out.h
[  3%] Generating ../generated/CovSeqidQscPercMinDiag.lib.h
[  3%] Generating ../generated/CovSeqidQscPercMinDiagTargetCov.lib.h
[  3%] Generating ../generated/ExpOpt3_8_polished.cs32.lib.h
[  3%] Generating ../generated/Library255_may17.lib.h
[  4%] Generating ../generated/libPolished_8.lib.h
[  4%] Generating ../generated/cs219.lib.h
[  4%] Generating ../generated/krona_prelude.html.h
[  5%] Generating ../generated/result_viz_prelude.html.zst.h
[  6%] Generating ../generated/K4000.crf.h
[  6%] Generating ../generated/easysearch.sh.h
[  7%] Generating ../generated/easycluster.sh.h
[  8%] Generating ../generated/easytaxonomy.sh.h
[  8%] Generating ../generated/easyrbh.sh.h
[  9%] Generating ../generated/blastp.sh.h
[  9%] Generating ../generated/blastpgp.sh.h
[ 10%] Generating ../generated/map.sh.h
[ 10%] Generating ../generated/rbh.sh.h
[ 10%] Generating ../generated/linclust.sh.h
[ 10%] Generating ../generated/clustering.sh.h
[ 11%] Generating ../generated/cascaded_clustering.sh.h
[ 11%] Generating ../generated/update_clustering.sh.h
[ 11%] Generating ../generated/searchtargetprofile.sh.h
[ 11%] Generating ../generated/createindex.sh.h
[ 12%] Generating ../generated/createtaxdb.sh.h
[ 12%] Generating ../generated/translated_search.sh.h
[ 12%] Generating ../generated/taxpercontig.sh.h
[ 12%] Generating ../generated/multihitdb.sh.h
[ 12%] Generating ../generated/multihitsearch.sh.h
[ 12%] Generating ../generated/enrich.sh.h
[ 12%] Generating ../generated/blastn.sh.h
[ 12%] Generating ../generated/searchslicedtargetprofile.sh.h
[ 13%] Generating ../generated/taxonomy.sh.h
[ 13%] Generating ../generated/linsearch.sh.h
[ 13%] Generating ../generated/databases.sh.h
[ 13%] Generating ../generated/nucleotide_clustering.sh.h
[ 13%] Generating ../generated/iterativepp.sh.h
[ 14%] Generating ../generated/tsv2exprofiledb.sh.h
[ 14%] Built target generated
[ 15%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/entropy_common.c.o
[ 15%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/fse_decompress.c.o
[ 15%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/threading.c.o
[ 16%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/pool.c.o
[ 16%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/zstd_common.c.o
[ 16%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/error_private.c.o
[ 17%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/xxhash.c.o
[ 17%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/hist.c.o
[ 17%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/fse_compress.c.o
[ 18%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/huf_compress.c.o
[ 18%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_compress.c.o
[ 18%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstdmt_compress.c.o
[ 18%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_fast.c.o
[ 19%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_double_fast.c.o
[ 19%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_lazy.c.o
[ 19%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_opt.c.o
[ 20%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_ldm.c.o
[ 20%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/huf_decompress.c.o
[ 20%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress.c.o
[ 21%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress_block.c.o
[ 21%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_ddict.c.o
[ 21%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o
[ 22%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o
[ 22%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o
[ 22%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o
[ 23%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o
[ 23%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o
[ 23%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o
[ 24%] Linking C static library libzstd.a
[ 24%] Built target libzstd_static
[ 25%] Building C object lib/mmseqs/lib/tinyexpr/CMakeFiles/tinyexpr.dir/tinyexpr.c.o
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base':
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:373:16: warning: array subscript 'te_expr[0]' is partly outside array bounds of 'unsigned char[16]' [-Warray-bounds]
  373 |             ret->bound = s->bound;
      |                ^~
In function 'new_expr',
    inlined from 'base' at /home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:372:19:
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'
   88 |     te_expr *ret = malloc(size);
      |                    ^~~~~~~~~~~~
In function 'new_expr',
    inlined from 'base' at /home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:366:19:
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:93:15: warning: array subscript 'te_expr[0]' is partly outside array bounds of 'unsigned char[16]' [-Warray-bounds]
   93 |     ret->type = type;
      |     ~~~~~~~~~~^~~~~~
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'
   88 |     te_expr *ret = malloc(size);
      |                    ^~~~~~~~~~~~
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base':
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:367:16: warning: array subscript 'te_expr[0]' is partly outside array bounds of 'unsigned char[16]' [-Warray-bounds]
  367 |             ret->value = s->value;
      |                ^~
In function 'new_expr',
    inlined from 'base' at /home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:366:19:
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'
   88 |     te_expr *ret = malloc(size);
      |                    ^~~~~~~~~~~~
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c: In function 'base':
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:446:16: warning: array subscript 'te_expr[0]' is partly outside array bounds of 'unsigned char[16]' [-Warray-bounds]
  446 |             ret->value = NAN;
      |                ^~
In function 'new_expr',
    inlined from 'base' at /home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:444:19:
/home/user/packages/foldseek/foldseek/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by 'malloc'
   88 |     te_expr *ret = malloc(size);
      |                    ^~~~~~~~~~~~
[ 25%] Linking C static library libtinyexpr.a
[ 25%] Built target tinyexpr
[ 26%] Building C object lib/mmseqs/lib/microtar/CMakeFiles/microtar.dir/microtar.c.o
[ 26%] Linking C static library libmicrotar.a
[ 26%] Built target microtar
[ 27%] Building CXX object lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/lambda_calculator.cpp.o
[ 27%] Building CXX object lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/lubksb.cpp.o
[ 27%] Building CXX object lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/ludcmp.cpp.o
[ 28%] Building CXX object lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/nrutil.cpp.o
[ 28%] Built target cacode
[ 29%] Building CXX object lib/mmseqs/lib/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o
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[ 33%] Built target alp
[ 33%] Building CXX object lib/mmseqs/lib/ksw2/CMakeFiles/ksw2.dir/ksw2_extz2_sse.cpp.o
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/home/user/packages/foldseek/foldseek/lib/3di/structureto3di.cpp:7:10: fatal error: encoder_weights_3di.kerasify.h: No such file or directory
    7 | #include "encoder_weights_3di.kerasify.h"
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [lib/3di/CMakeFiles/3di.dir/build.make:76: lib/3di/CMakeFiles/3di.dir/structureto3di.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:880: lib/3di/CMakeFiles/3di.dir/all] Error 2
make: *** [Makefile:136: all] Error 2
milot-mirdita commented 2 years ago

Can you try as a workaround to call:

make local-generated
make

Not sure why the dependency resolution is going wrong. I saw this before but have no idea what’s causing it.

gitozi commented 2 years ago

Thanks a lot! The workaround worked!

FYI: I suspected that it might be because shellcheck was not installed on my system. But even after having shellcheck installed it failed at the same point.

gitozi commented 2 years ago

PS: I am using cmake version 3.24.3

milot-mirdita commented 2 years ago

I pushed a fix that should fix the issue without the workaround.

gitozi commented 2 years ago

I can confirm that I can now build without the workaround. Thanks again!