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Segmentation fault in easy-cluster starting in dc7f8ad #916

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kalekundert opened this issue Dec 5, 2024 · 2 comments
Closed

Segmentation fault in easy-cluster starting in dc7f8ad #916

kalekundert opened this issue Dec 5, 2024 · 2 comments

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@kalekundert
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kalekundert commented Dec 5, 2024 •
edited
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The following easy-cluster command fails with a segmentation fault:

$ mmseqs easy-cluster mmc_pdb_dna.fasta mmc_pdb_dna_id_80_align_80_cov_0_clust_0 /tmp --min-seq-id 0.8 -c 0.8 --cov-mode 0 --cluster-mode 0 --cluster-reassign
Command output and error message 
easy-cluster mmc_pdb_dna.fasta mmc_pdb_dna_id_80_align_80_cov_0_clust_0 /tmp --min-seq-id 0.8 -c 0.8 --cov-mode 0 --cluster-mode 0 --cluster-reassign

MMseqs Version:                     	dc7f8adb258dcb38dcad966f0c67ee407b8da61b
Substitution matrix                 	aa:blosum62.out,nucl:nucleotide.out
Seed substitution matrix            	aa:VTML80.out,nucl:nucleotide.out
Sensitivity                         	4
k-mer length                        	0
Target search mode                  	0
k-score                             	seq:2147483647,prof:2147483647
Alphabet size                       	aa:21,nucl:5
Max sequence length                 	65535
Max results per query               	20
Split database                      	0
Split mode                          	2
Split memory limit                  	0
Coverage threshold                  	0.8
Coverage mode                       	0
Compositional bias                  	1
Compositional bias                  	1
Diagonal scoring                    	true
Exact k-mer matching                	0
Mask residues                       	1
Mask residues probability           	0.9
Mask lower case residues            	0
Minimum diagonal score              	15
Selected taxa                       	
Include identical seq. id.          	false
Spaced k-mers                       	1
Preload mode                        	0
Pseudo count a                      	substitution:1.100,context:1.400
Pseudo count b                      	substitution:4.100,context:5.800
Spaced k-mer pattern                	
Local temporary path                	
Threads                             	24
Compressed                          	0
Verbosity                           	3
Add backtrace                       	false
Alignment mode                      	3
Alignment mode                      	0
Allow wrapped scoring               	false
E-value threshold                   	0.001
Seq. id. threshold                  	0.8
Min alignment length                	0
Seq. id. mode                       	0
Alternative alignments              	0
Max reject                          	2147483647
Max accept                          	2147483647
Score bias                          	0
Realign hits                        	false
Realign score bias                  	-0.2
Realign max seqs                    	2147483647
Correlation score weight            	0
Gap open cost                       	aa:11,nucl:5
Gap extension cost                  	aa:1,nucl:2
Zdrop                               	40
Rescore mode                        	0
Remove hits by seq. id. and coverage	false
Sort results                        	0
Cluster mode                        	0
Max connected component depth       	1000
Similarity type                     	2
Weight file name                    	
Cluster Weight threshold            	0.9
Single step clustering              	false
Cascaded clustering steps           	3
Cluster reassign                    	true
Remove temporary files              	true
Force restart with latest tmp       	false
MPI runner                          	
k-mers per sequence                 	21
Scale k-mers per sequence           	aa:0.000,nucl:0.200
Adjust k-mer length                 	false
Shift hash                          	67
Include only extendable             	false
Skip repeating k-mers               	false
Database type                       	0
Shuffle input database              	true
Createdb mode                       	1
Write lookup file                   	0
Offset of numeric ids               	0

cluster /tmp/4370635669764546076/input /tmp/4370635669764546076/clu /tmp/4370635669764546076/clu_tmp --max-seqs 20 -c 0.8 --cov-mode 0 --spaced-kmer-mode 1 --alignment-mode 3 -e 0.001 --min-seq-id 0.8 --cluster-mode 0 --cluster-reassign 1 --remove-tmp-files 1

Set cluster sensitivity to -s 1.000000
Set cluster iterations to 1
prefilter /tmp/4370635669764546076/clu_tmp/123078550843082693/query_seqs /tmp/4370635669764546076/clu_tmp/123078550843082693/input_step_redundancy /tmp/4370635669764546076/clu_tmp/123078550843082693/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -s 1 -k 15 --target-search-mode 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 10000 --max-seqs 20 --split 0 --split-mode 2 --split-memory-limit 0 -c 0.8 --cov-mode 0 --comp-bias-corr 0 --comp-bias-corr-scale 1 --diag-score 0 --exact-kmer-matching 1 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --min-ungapped-score 60 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --threads 24 --compressed 0 -v 3

Query database size: 66 type: Nucleotide
Estimated memory consumption: 8G
Target database size: 33 type: Nucleotide
Index table k-mer threshold: 0 at k-mer size 15
Index table: counting k-mers
[=================================================================] 100.00% 33 0s 0ms
Index table: Masked residues: 0
Index table: fill
[=================================================================] 100.00% 33 0s 0ms
Index statistics
Entries:          9
DB size:          8192 MB
Avg k-mer size:   0.000000
Top 10 k-mers
    TCCCTTTTTAGATTT	1
    CTCTTTTTGGATTTT	1
    CCTCTTTTAGGTTTT	1
    CTTTTAGGGGTTTGT	1
    TTTAGAGGTTTGTGT	1
    TCCTTTTAGATTTTG	1
    TTTTAGGAGATTGTG	1
    CCTTTTAGAGTTTGG	1
    TTTTGGAGATTGGGG	1
    AAAAAAAAAAAAAAA	0
Time for index table init: 0h 0m 2s 704ms
Process prefiltering step 1 of 1

k-mer similarity threshold: 0
Starting prefiltering scores calculation (step 1 of 1)
Query db start 1 to 66
Target db start 1 to 33
/tmp/4370635669764546076/clu_tmp/123078550843082693/nucleotide_clustering.sh: line 48: 28837 Segmentation fault      (core dumped) $RUNNER "$MMSEQS" prefilter "$QUERY" "$INPUT" "${TMP_PATH}/pref" ${PREFILTER_PAR}
Error: Prefilter step died
Error: Search died

Here's the input file I used: mmc_pdb_dna.fasta

In case it's relevant, these are sequences taken from the PDB. My "real" input is all of the DNA sequences in the PDB, but the file I linked above is a pared down version with only the first 50 sequences. However, this is still enough to produce the segfault.

I performed a git bisect, and found that this error started in dc7f8ad. Here's a diff showing the change introduced by this commit:

$ git diff dc7f8adb~1 dc7f8adb
diff --git a/src/prefiltering/CacheFriendlyOperations.cpp b/src/prefiltering/CacheFriendlyOperations.cpp
index 61abc40f..5d2316d4 100644
--- a/src/prefiltering/CacheFriendlyOperations.cpp
+++ b/src/prefiltering/CacheFriendlyOperations.cpp
@@ -40,7 +40,7 @@ size_t CacheFriendlyOperations<BINSIZE>::findDuplicates(IndexEntryLocal **input,
     do {
         setupBinPointer();
         CounterResult *lastPosition = (binDataFrame + BINCOUNT * binSize) - 1;
-        for (unsigned int i = indexFrom; i < indexTo; ++i) {
+        for (unsigned int i = indexFrom; i <= indexTo; ++i) {
             const size_t N = input[i + 1] - input[i];
             hashIndexEntry(i, input[i], N, lastPosition);
         }

I don't understand what this code is doing, by my guess is that the i <= indexTo condition allows an out-of-bounds access.

Environment Details

  • MMseqs version: self-compiled
  • Build commands: 
    mkdir build
cd build

cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. ..
make
make install
  • CMake version: 3.31.2
  • Compiler: GCC 14.2.1
  • Server specifications:
    • RAM: 64GB
    • AVX2/SSE supported
  • Operating system: Linux 6.12.1-arch1-1 x86_64
Git bisect log 
git bisect start
# status: waiting for both good and bad commits
# good: [78ae2c5b8dba889079745e8013deeb30c3ac8a1a] Update result2msa to support clustered dbs
git bisect good 78ae2c5b8dba889079745e8013deeb30c3ac8a1a
# status: waiting for bad commit, 1 good commit known
# bad: [ddc19be546230aceb027bb0f9ef16a81a5b36fe6] Remove libgcc_s as a dependency when trying to compile static binaries
git bisect bad ddc19be546230aceb027bb0f9ef16a81a5b36fe6
# good: [a66ad0c27f80457ce18602cda7fc0925894cbdc8] Allow easy-search to work with --gpu 1
git bisect good a66ad0c27f80457ce18602cda7fc0925894cbdc8
# good: [0889c78b502c5380616cd60f1b197ed62f35af52] Error out in various search modes without GPU support
git bisect good 0889c78b502c5380616cd60f1b197ed62f35af52
# bad: [0310e6b578e110370600a811e57744fd8f648885] Merge branch 'skip_orf'
git bisect bad 0310e6b578e110370600a811e57744fd8f648885
# good: [2c1f500c3915c7b7f8690ac71a488c586072ce49] make sure translated_search with skip_orf option (extractorfs->extractframes & translatenucs) works
git bisect good 2c1f500c3915c7b7f8690ac71a488c586072ce49
# good: [964bfaa2d46231dd19533271820fb0bf3a74c9f8] change extracframes to have same output with extractframes+tranlatenucs
git bisect good 964bfaa2d46231dd19533271820fb0bf3a74c9f8
# bad: [266c894c117a9bd650450974747424ce51124bf5] Update regression for prev commit bug fix
git bisect bad 266c894c117a9bd650450974747424ce51124bf5
# bad: [dc7f8adb258dcb38dcad966f0c67ee407b8da61b] Reapply "Make sure last position is properly evaluated in Prefilter"
git bisect bad dc7f8adb258dcb38dcad966f0c67ee407b8da61b
# first bad commit: [dc7f8adb258dcb38dcad966f0c67ee407b8da61b] Reapply "Make sure last position is properly evaluated in Prefilter"
Build output 
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.10 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
  to tell CMake that the project requires at least <min> but has been updated
  to work with policies introduced by <max> or earlier.


-- The CXX compiler identification is GNU 14.2.1
-- The C compiler identification is GNU 14.2.1
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Source Directory: /home/kale/research/software/forks/MMseqs2
-- Project Directory: /home/kale/research/software/forks/MMseqs2
-- 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
CMake Deprecation Warning at lib/tinyexpr/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.10 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
  to tell CMake that the project requires at least <min> but has been updated
  to work with policies introduced by <max> or earlier.


-- 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_NATIVE
-- Performing Test ATOMIC_NATIVE - Failed
-- Performing Test ATOMIC_WITH_LIB
-- Performing Test ATOMIC_WITH_LIB - Success
-- Found Atomic: /usr/lib/libatomic.so
-- 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
-- Configuring done (1.8s)
-- Generating done (0.0s)
-- Build files have been written to: /home/kale/research/software/forks/MMseqs2/build
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/home/kale/research/software/forks/MMseqs2/lib/tinyexpr/tinyexpr.c: In function ‘base’:
/home/kale/research/software/forks/MMseqs2/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/kale/research/software/forks/MMseqs2/lib/tinyexpr/tinyexpr.c:372:19:
/home/kale/research/software/forks/MMseqs2/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/kale/research/software/forks/MMseqs2/lib/tinyexpr/tinyexpr.c:366:19:
/home/kale/research/software/forks/MMseqs2/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/kale/research/software/forks/MMseqs2/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by ‘malloc’
   88 |     te_expr *ret = malloc(size);
      |                    ^~~~~~~~~~~~
/home/kale/research/software/forks/MMseqs2/lib/tinyexpr/tinyexpr.c: In function ‘base’:
/home/kale/research/software/forks/MMseqs2/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/kale/research/software/forks/MMseqs2/lib/tinyexpr/tinyexpr.c:366:19:
/home/kale/research/software/forks/MMseqs2/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by ‘malloc’
   88 |     te_expr *ret = malloc(size);
      |                    ^~~~~~~~~~~~
/home/kale/research/software/forks/MMseqs2/lib/tinyexpr/tinyexpr.c: In function ‘base’:
/home/kale/research/software/forks/MMseqs2/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/kale/research/software/forks/MMseqs2/lib/tinyexpr/tinyexpr.c:444:19:
/home/kale/research/software/forks/MMseqs2/lib/tinyexpr/tinyexpr.c:88:20: note: object of size 16 allocated by ‘malloc’
   88 |     te_expr *ret = malloc(size);
      |                    ^~~~~~~~~~~~
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In file included from /usr/include/c++/14.2.1/algorithm:60,
                 from /home/kale/research/software/forks/MMseqs2/lib/simd/simd.h:9,
                 from /home/kale/research/software/forks/MMseqs2/src/commons/CSProfile.h:9,
                 from /home/kale/research/software/forks/MMseqs2/src/commons/CSProfile.cpp:5:
In function ‘typename __gnu_cxx::__enable_if<std::__is_scalar<_Tp>::__value, void>::__type std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = float*; _Tp = double]’,
    inlined from ‘void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = float*; _Tp = double]’ at /usr/include/c++/14.2.1/bits/stl_algobase.h:998:21,
    inlined from ‘void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = float*; _Tp = double]’ at /usr/include/c++/14.2.1/bits/stl_algobase.h:1029:20,
    inlined from ‘float* CSProfile::computeProfile(unsigned char*, int, float*, float*, float, float, float) [with int type = 2]’ at /home/kale/research/software/forks/MMseqs2/src/commons/CSProfile.cpp:383:14,
    inlined from ‘float* CSProfile::computeProfileCs(int, float*, float*, float, float)’ at /home/kale/research/software/forks/MMseqs2/src/commons/CSProfile.cpp:350:58:
/usr/include/c++/14.2.1/bits/stl_algobase.h:952:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
  952 |         *__first = __tmp;
      |         ~~~~~~~~~^~~~~~~
In function ‘typename __gnu_cxx::__enable_if<std::__is_scalar<_Tp>::__value, void>::__type std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = float*; _Tp = double]’,
    inlined from ‘void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = float*; _Tp = double]’ at /usr/include/c++/14.2.1/bits/stl_algobase.h:998:21,
    inlined from ‘void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = float*; _Tp = double]’ at /usr/include/c++/14.2.1/bits/stl_algobase.h:1029:20,
    inlined from ‘float* CSProfile::computeProfile(unsigned char*, int, float*, float*, float, float, float) [with int type = 2]’ at /home/kale/research/software/forks/MMseqs2/src/commons/CSProfile.cpp:418:14,
    inlined from ‘float* CSProfile::computeProfileCs(int, float*, float*, float, float)’ at /home/kale/research/software/forks/MMseqs2/src/commons/CSProfile.cpp:350:58:
/usr/include/c++/14.2.1/bits/stl_algobase.h:952:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified size between 18446743867551121408 and 18446744073709551520 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
  952 |         *__first = __tmp;
      |         ~~~~~~~~~^~~~~~~
In member function ‘float* CSProfile::computeProfile(unsigned char*, int, float*, float*, float, float, float) [with int type = 2]’,
    inlined from ‘float* CSProfile::computeProfileCs(int, float*, float*, float, float)’ at /home/kale/research/software/forks/MMseqs2/src/commons/CSProfile.cpp:350:58:
/home/kale/research/software/forks/MMseqs2/src/commons/CSProfile.cpp:418:24: note: destination object allocated here
  418 |     std::fill(profile, profile + (seqLen * (Sequence::PROFILE_AA_SIZE + 4)), 0.0);
      |                        ^~~~~~~
In function ‘typename __gnu_cxx::__enable_if<std::__is_scalar<_Tp>::__value, void>::__type std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = float*; _Tp = double]’,
    inlined from ‘void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = float*; _Tp = double]’ at /usr/include/c++/14.2.1/bits/stl_algobase.h:998:21,
    inlined from ‘void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = float*; _Tp = double]’ at /usr/include/c++/14.2.1/bits/stl_algobase.h:1029:20,
    inlined from ‘float* CSProfile::computeProfile(unsigned char*, int, float*, float*, float, float, float) [with int type = 0]’ at /home/kale/research/software/forks/MMseqs2/src/commons/CSProfile.cpp:383:14,
    inlined from ‘float* CSProfile::computeSequenceCs(unsigned char*, int, float)’ at /home/kale/research/software/forks/MMseqs2/src/commons/CSProfile.cpp:354:58:
/usr/include/c++/14.2.1/bits/stl_algobase.h:952:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
  952 |         *__first = __tmp;
      |         ~~~~~~~~~^~~~~~~
In function ‘typename __gnu_cxx::__enable_if<std::__is_scalar<_Tp>::__value, void>::__type std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = float*; _Tp = double]’,
    inlined from ‘void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = float*; _Tp = double]’ at /usr/include/c++/14.2.1/bits/stl_algobase.h:998:21,
    inlined from ‘void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = float*; _Tp = double]’ at /usr/include/c++/14.2.1/bits/stl_algobase.h:1029:20,
    inlined from ‘float* CSProfile::computeProfile(unsigned char*, int, float*, float*, float, float, float) [with int type = 0]’ at /home/kale/research/software/forks/MMseqs2/src/commons/CSProfile.cpp:418:14,
    inlined from ‘float* CSProfile::computeSequenceCs(unsigned char*, int, float)’ at /home/kale/research/software/forks/MMseqs2/src/commons/CSProfile.cpp:354:58:
/usr/include/c++/14.2.1/bits/stl_algobase.h:952:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified size between 18446743867551121408 and 18446744073709551520 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
  952 |         *__first = __tmp;
      |         ~~~~~~~~~^~~~~~~
In member function ‘float* CSProfile::computeProfile(unsigned char*, int, float*, float*, float, float, float) [with int type = 0]’,
    inlined from ‘float* CSProfile::computeSequenceCs(unsigned char*, int, float)’ at /home/kale/research/software/forks/MMseqs2/src/commons/CSProfile.cpp:354:58:
/home/kale/research/software/forks/MMseqs2/src/commons/CSProfile.cpp:418:24: note: destination object allocated here
  418 |     std::fill(profile, profile + (seqLen * (Sequence::PROFILE_AA_SIZE + 4)), 0.0);
      |                        ^~~~~~~
[100%] Linking CXX static library libmmseqs-framework.a
[100%] Built target mmseqs-framework
[100%] Building CXX object src/CMakeFiles/mmseqs.dir/mmseqs.cpp.o
[100%] Linking CXX executable mmseqs
[100%] Built target mmseqs
[  1%] Built target microtar
[ 17%] Built target generated
[ 18%] Built target ksw2
[ 18%] Built target tinyexpr
[ 19%] Built target version
[ 20%] Built target tantan
[ 25%] Built target alp
[ 36%] Built target libzstd_static
[100%] Built target mmseqs-framework
[100%] Built target mmseqs
Install the project...
-- Install configuration: "RELEASE"
-- Installing: /home/kale/research/software/forks/MMseqs2/build/bin/mmseqs
-- Installing: /home/kale/research/software/forks/MMseqs2/build/util/bash-completion.sh
martin-steinegger added a commit that referenced this issue Dec 6, 2024
@martin-steinegger
Fix issue #916
e3b16fa
@martin-steinegger
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Thank you for the detailed bug report. This helped a lot.
I pushed a fix.

@kalekundert
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Thanks for getting to this so quickly! I can confirm the new commit resolves the segfault for me.

sooyoung-cha added a commit to rachelse/foldseek that referenced this issue Dec 9, 2024
@sooyoung-cha
Squashed 'lib/mmseqs/' changes from ddc19be5..7f5c0003
53079be 
7f5c0003 Fix memory issue
b80ce103 Fix issues in masksequence
a2d01d01 Rework masking and add N repeat masking
e3b16faf Fix issue soedinglab/MMseqs2#916

git-subtree-dir: lib/mmseqs
git-subtree-split: 7f5c0003a9135add5a2b6f14ab822e527b3df547
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@kalekundert @martin-steinegger