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Created September 12, 2022 16:47
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foldseek MPI error logs
Raw
stderr.log
*** Error in `foldseek': double free or corruption (out): 0x0000000002e9a050 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81679)[0x14eb84b52679]
foldseek(_ZN8DBReaderIjE5closeEv+0x16b)[0x5b45ab]
foldseek(_ZN8DBWriter10mergeIndexEPPKcjRKSt6vectorImSaImEE+0x6a)[0x61feba]
foldseek(_ZN8DBWriter12mergeResultsEPKcS1_PS1_S2_mbbb+0x35c)[0x6241dc]
foldseek(_ZN8DBWriter5closeEbb+0x12a)[0x62627a]
foldseek(_Z14structurealigniPPKcRK7Command+0xe70)[0x4e6560]
foldseek(_Z10runCommandP7CommandiPPKc+0x30)[0x5a1190]
foldseek(main+0x347)[0x477fb7]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x14eb84af3505]
foldseek[0x48bbef]
======= Memory map: ========
00400000-01265000 r-xp 00000000 00:35 627980610 /opt/area/shared/programs/x86_64/foldseek/3-915ef7d/bin/foldseek
01465000-01466000 r--p 00e65000 00:35 627980610 /opt/area/shared/programs/x86_64/foldseek/3-915ef7d/bin/foldseek
01466000-014ce000 rw-p 00e66000 00:35 627980610 /opt/area/shared/programs/x86_64/foldseek/3-915ef7d/bin/foldseek
014ce000-014d1000 rw-p 00000000 00:00 0
02e4b000-02f21000 rw-p 00000000 00:00 0 [heap]
14df68000000-14df68021000 rw-p 00000000 00:00 0
14df68021000-14df6c000000 ---p 00000000 00:00 0
14df6dffb000-14df78000000 rw-p 00000000 00:00 0
14df78000000-14df7b653000 rw-p 00000000 00:00 0
14df7b653000-14df7c000000 ---p 00000000 00:00 0
14df7dfff000-14df80000000 rw-p 00000000 00:00 0
14df80000000-14df83684000 rw-p 00000000 00:00 0
14df83684000-14df84000000 ---p 00000000 00:00 0
14df85fff000-14df88000000 rw-p 00000000 00:00 0
14df88000000-14df8b681000 rw-p 00000000 00:00 0
14df8b681000-14df8c000000 ---p 00000000 00:00 0
14df8dfff000-14df90000000 rw-p 00000000 00:00 0
14df90000000-14df937a6000 rw-p 00000000 00:00 0
14df937a6000-14df94000000 ---p 00000000 00:00 0
14df95fff000-14df98000000 rw-p 00000000 00:00 0
14df98000000-14df9b68f000 rw-p 00000000 00:00 0
14df9b68f000-14df9c000000 ---p 00000000 00:00 0
14df9dfff000-14dfa0000000 rw-p 00000000 00:00 0
14dfa0000000-14dfa3615000 rw-p 00000000 00:00 0
14dfa3615000-14dfa4000000 ---p 00000000 00:00 0
14dfa5fff000-14dfa8000000 rw-p 00000000 00:00 0
14dfa8000000-14dfab748000 rw-p 00000000 00:00 0
14dfab748000-14dfac000000 ---p 00000000 00:00 0
14dfadfff000-14dfb0000000 rw-p 00000000 00:00 0
14dfb0000000-14dfb3627000 rw-p 00000000 00:00 0
14dfb3627000-14dfb4000000 ---p 00000000 00:00 0
14dfb4000000-14dfb7665000 rw-p 00000000 00:00 0
14dfb7665000-14dfb8000000 ---p 00000000 00:00 0
14dfb8000000-14dfbb61f000 rw-p 00000000 00:00 0
14dfbb61f000-14dfbc000000 ---p 00000000 00:00 0
14dfbc000000-14dfbf546000 rw-p 00000000 00:00 0
14dfbf546000-14dfc0000000 ---p 00000000 00:00 0
14dfc0000000-14dfc365c000 rw-p 00000000 00:00 0
14dfc365c000-14dfc4000000 ---p 00000000 00:00 0
14dfc5fff000-14dfc8000000 rw-p 00000000 00:00 0
14dfc8000000-14dfcb641000 rw-p 00000000 00:00 0
14dfcb641000-14dfcc000000 ---p 00000000 00:00 0
14dfcdfff000-14dfd0000000 rw-p 00000000 00:00 0
14dfd0000000-14dfd3626000 rw-p 00000000 00:00 0
14dfd3626000-14dfd4000000 ---p 00000000 00:00 0
14dfd5fff000-14dfd8000000 rw-p 00000000 00:00 0
14dfd8000000-14dfdb656000 rw-p 00000000 00:00 0
14dfdb656000-14dfdc000000 ---p 00000000 00:00 0
14dfddfff000-14dfe0000000 rw-p 00000000 00:00 0
14dfe0000000-14dfe3760000 rw-p 00000000 00:00 0
14dfe3760000-14dfe4000000 ---p 00000000 00:00 0
14dfe5fff000-14dfe8000000 rw-p 00000000 00:00 0
14dfe8000000-14dfeb5fa000 rw-p 00000000 00:00 0
14dfeb5fa000-14dfec000000 ---p 00000000 00:00 0
14dfedfff000-14dff0000000 rw-p 00000000 00:00 0
14dff0000000-14dff37ce000 rw-p 00000000 00:00 0
14dff37ce000-14dff4000000 ---p 00000000 00:00 0
14dff5fff000-14dff8000000 rw-p 00000000 00:00 0
14dff8000000-14dffb6a5000 rw-p 00000000 00:00 0
14dffb6a5000-14dffc000000 ---p 00000000 00:00 0
14dffdfff000-14e000000000 rw-p 00000000 00:00 0
14e000000000-14e003621000 rw-p 00000000 00:00 0
14e003621000-14e004000000 ---p 00000000 00:00 0
14e005fff000-14e008000000 rw-p 00000000 00:00 0
14e008000000-14e00b62e000 rw-p 00000000 00:00 0
14e00b62e000-14e00c000000 ---p 00000000 00:00 0
14e00dfff000-14e010000000 rw-p 00000000 00:00 0
14e010000000-14e013637000 rw-p 00000000 00:00 0
14e013637000-14e014000000 ---p 00000000 00:00 0
14e015fff000-14e018000000 rw-p 00000000 00:00 0
14e018000000-14e01b5d0000 rw-p 00000000 00:00 0
14e01b5d0000-14e01c000000 ---p 00000000 00:00 0
14e01d106000-14e01d107000 ---p 00000000 00:00 0
14e01d107000-14e01d307000 rw-p 00000000 00:00 0
14e01d307000-14e01d308000 ---p 00000000 00:00 0
14e01d308000-14e01d508000 rw-p 00000000 00:00 0
14e01d508000-14e01d509000 ---p 00000000 00:00 0
14e01d509000-14e01d709000 rw-p 00000000 00:00 0
14e01d709000-14e01d70a000 ---p 00000000 00:00 0
14e01d70a000-14e01d90a000 rw-p 00000000 00:00 0
14e01d90a000-14e01d90b000 ---p 00000000 00:00 0
14e01d90b000-14e01db0b000 rw-p 00000000 00:00 0
14e01db0b000-14e01db0c000 ---p 00000000 00:00 0
14e01db0c000-14e01dd0c000 rw-p 00000000 00:00 0
14e01dd0c000-14e01dd0d000 ---p 00000000 00:00 0
14e01dd0d000-14e01df0d000 rw-p 00000000 00:00 0
14e01df0d000-14e01df0e000 ---p 00000000 00:00 0
14e01df0e000-14e01e10e000 rw-p 00000000 00:00 0
14e01e10e000-14e01e10f000 ---p 00000000 00:00 0
14e01e10f000-14e01e30f000 rw-p 00000000 00:00 0
14e01e30f000-14e01e310000 ---p 00000000 00:00 0
14e01e310000-14e01e510000 rw-p 00000000 00:00 0
14e01e510000-14e01e511000 ---p 00000000 00:00 0
14e01e511000-14e01e711000 rw-p 00000000 00:00 0
14e01e711000-14e01e712000 ---p 00000000 00:00 0
14e01e712000-14e01e912000 rw-p 00000000 00:00 0
14e01e912000-14e01e913000 ---p 00000000 00:00 0
14e01e913000-14e01eb13000 rw-p 00000000 00:00 0
14e01eb13000-14e01eb14000 ---p 00000000 00:00 0
14e01eb14000-14e01ed14000 rw-p 00000000 00:00 0
14e01ed14000-14e01ed15000 ---p 00000000 00:00 0
14e01ed15000-14e01ef15000 rw-p 00000000 00:00 0
14e01ef15000-14e01ef16000 ---p 00000000 00:00 0
14e01ef16000-14e01f116000 rw-p 00000000 00:00 0
14e01f116000-14e01f117000 ---p 00000000 00:00 0
14e01f117000-14e01f317000 rw-p 00000000 00:00 0
14e01f317000-14e01f318000 ---p 00000000 00:00 0
14e01f318000-14e01f518000 rw-p 00000000 00:00 0
14e020519000-14e0229ae000 rw-p 00000000 00:00 0
14e022a72000-14e022a73000 ---p 00000000 00:00 0
14e022a73000-14e022c73000 rw-p 00000000 00:00 0
14e022c73000-14e022c74000 ---p 00000000 00:00 0
14e022c74000-14e022e74000 rw-p 00000000 00:00 0
14e022e74000-14eb79754000 r--p 00000000 00:2f 1099807198645 /large/___SCRATCH___/area/fbarone/foldseek/orfeo_benchmark/cores_scalability/48_cores/tmpFolder/9749724961102201013/pref
14eb79754000-14eb79be8000 rw-p 00000000 00:00 0
14eb79be8000-14eb7dfce000 r--p 00000000 00:2f 1099805755019 /large/___SCRATCH___/area/fbarone/foldseek/databases/swiss_200k/swiss_200k_ss
14eb7dfce000-14eb7e462000 rw-p 00000000 00:00 0
14eb7e462000-14eb7e463000 ---p 00000000 00:00 0
14eb7e463000-14eb7e663000 rw-p 00000000 00:00 0
14eb7e663000-14eb7e664000 ---p 00000000 00:00 0
14eb7e664000-14eb7e864000 rw-p 00000000 00:00 0
14eb7e864000-14eb7e865000 ---p 00000000 00:00 0
14eb7e865000-14eb7ea65000 rw-p 00000000 00:00 0
14eb7ee10000-14eb831f6000 r--p 00000000 00:2f 1099805755028 /large/___SCRATCH___/area/fbarone/foldseek/databases/swiss_200k/swiss_200k
14eb831f6000-14eb831f8000 r-xp 00000000 08:03 33555708 /usr/lib64/libfreebl3.so
14eb831f8000-14eb833f7000 ---p 00002000 08:03 33555708 /usr/lib64/libfreebl3.so
14eb833f7000-14eb833f8000 r--p 00001000 08:03 33555708 /usr/lib64/libfreebl3.so
14eb833f8000-14eb833f9000 rw-p 00002000 08:03 33555708 /usr/lib64/libfreebl3.so
14eb833f9000-14eb833fb000 r-xp 00000000 08:03 33655353 /usr/lib64/libutil-2.17.so
14eb833fb000-14eb835fa000 ---p 00002000 08:03 33655353 /usr/lib64/libutil-2.17.so
14eb835fa000-14eb835fb000 r--p 00001000 08:03 33655353 /usr/lib64/libutil-2.17.so
14eb835fb000-14eb835fc000 rw-p 00002000 08:03 33655353 /usr/lib64/libutil-2.17.so
14eb835fc000-14eb83603000 r-xp 00000000 08:03 33655349 /usr/lib64/librt-2.17.so
14eb83603000-14eb83802000 ---p 00007000 08:03 33655349 /usr/lib64/librt-2.17.so
14eb83802000-14eb83803000 r--p 00006000 08:03 33655349 /usr/lib64/librt-2.17.so
14eb83803000-14eb83804000 rw-p 00007000 08:03 33655349 /usr/lib64/librt-2.17.so
14eb83804000-14eb83a3a000 r-xp 00000000 08:03 33556322 /usr/lib64/libcrypto.so.1.0.2k
14eb83a3a000-14eb83c3a000 ---p 00236000 08:03 33556322 /usr/lib64/libcrypto.so.1.0.2k
14eb83c3a000-14eb83c56000 r--p 00236000 08:03 33556322 /usr/lib64/libcrypto.so.1.0.2k
14eb83c56000-14eb83c63000 rw-p 00252000 08:03 33556322 /usr/lib64/libcrypto.so.1.0.2k
14eb83c63000-14eb83c67000 rw-p 00000000 00:00 0
14eb83c67000-14eb83c6f000 r-xp 00000000 08:03 33556005 /usr/lib64/libcrypt-2.17.so
14eb83c6f000-14eb83e6e000 ---p 00008000 08:03 33556005 /usr/lib64/libcrypt-2.17.so
14eb83e6e000-14eb83e6f000 r--p 00007000 08:03 33556005 /usr/lib64/libcrypt-2.17.so
14eb83e6f000-14eb83e70000 rw-p 00008000 08:03 33556005 /usr/lib64/libcrypt-2.17.so
14eb83e70000-14eb83e9e000 rw-p 00000000 00:00 0
14eb83e9e000-14eb83ea0000 r-xp 00000000 08:03 33556007 /usr/lib64/libdl-2.17.so
14eb83ea0000-14eb840a0000 ---p 00002000 08:03 33556007 /usr/lib64/libdl-2.17.so
14eb840a0000-14eb840a1000 r--p 00002000 08:03 33556007 /usr/lib64/libdl-2.17.so
14eb840a1000-14eb840a2000 rw-p 00003000 08:03 33556007 /usr/lib64/libdl-2.17.so
14eb840a2000-14eb840f6000 r-xp 00000000 08:03 68030406 /opt/pbs/lib/libpbs.so.0.0.0
14eb840f6000-14eb842f6000 ---p 00054000 08:03 68030406 /opt/pbs/lib/libpbs.so.0.0.0
14eb842f6000-14eb842f7000 r--p 00054000 08:03 68030406 /opt/pbs/lib/libpbs.so.0.0.0
14eb842f7000-14eb842fd000 rw-p 00055000 08:03 68030406 /opt/pbs/lib/libpbs.so.0.0.0
14eb842fd000-14eb84300000 rw-p 00000000 00:00 0
14eb84300000-14eb84588000 r-xp 00000000 00:35 71165492 /opt/area/shared/libraries/openmpi/4.1.2/lib/libopen-pal.so.40.30.2
14eb84588000-14eb84787000 ---p 00288000 00:35 71165492 /opt/area/shared/libraries/openmpi/4.1.2/lib/libopen-pal.so.40.30.2
14eb84787000-14eb8478d000 r--p 00287000 00:35 71165492 /opt/area/shared/libraries/openmpi/4.1.2/lib/libopen-pal.so.40.30.2
14eb8478d000-14eb8479f000 rw-p 0028d000 00:35 71165492 /opt/area/shared/libraries/openmpi/4.1.2/lib/libopen-pal.so.40.30.2
14eb8479f000-14eb847aa000 rw-p 00000000 00:00 0
14eb847aa000-14eb848c1000 r-xp 00000000 00:35 71165498 /opt/area/shared/libraries/openmpi/4.1.2/lib/libopen-rte.so.40.30.2
14eb848c1000-14eb84ac1000 ---p 00117000 00:35 71165498 /opt/area/shared/libraries/openmpi/4.1.2/lib/libopen-rte.so.40.30.2
14eb84ac1000-14eb84ac3000 r--p 00117000 00:35 71165498 /opt/area/shared/libraries/openmpi/4.1.2/lib/libopen-rte.so.40.30.2
14eb84ac3000-14eb84ace000 rw-p 00119000 00:35 71165498 /opt/area/shared/libraries/openmpi/4.1.2/lib/libopen-rte.so.40.30.2
14eb84ace000-14eb84ad1000 rw-p 00000000 00:00 0
14eb84ad1000-14eb84c94000 r-xp 00000000 08:03 33556000 /usr/lib64/libc-2.17.so
14eb84c94000-14eb84e94000 ---p 001c3000 08:03 33556000 /usr/lib64/libc-2.17.so
14eb84e94000-14eb84e98000 r--p 001c3000 08:03 33556000 /usr/lib64/libc-2.17.so
14eb84e98000-14eb84e9a000 rw-p 001c7000 08:03 33556000 /usr/lib64/libc-2.17.so
14eb84e9a000-14eb84e9f000 rw-p 00000000 00:00 0
14eb84e9f000-14eb84eb6000 r-xp 00000000 08:03 33655345 /usr/lib64/libpthread-2.17.so
14eb84eb6000-14eb850b5000 ---p 00017000 08:03 33655345 /usr/lib64/libpthread-2.17.so
14eb850b5000-14eb850b6000 r--p 00016000 08:03 33655345 /usr/lib64/libpthread-2.17.so
14eb850b6000-14eb850b7000 rw-p 00017000 08:03 33655345 /usr/lib64/libpthread-2.17.so
14eb850b7000-14eb850bb000 rw-p 00000000 00:00 0
14eb850bb000-14eb850d2000 r-xp 00000000 00:35 36596276 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libgcc_s.so.1
14eb850d2000-14eb852d1000 ---p 00017000 00:35 36596276 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libgcc_s.so.1
14eb852d1000-14eb852d2000 r--p 00016000 00:35 36596276 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libgcc_s.so.1
14eb852d2000-14eb852d3000 rw-p 00017000 00:35 36596276 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libgcc_s.so.1
14eb852d3000-14eb85307000 r-xp 00000000 00:35 36596283 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libgomp.so.1.0.0
14eb85307000-14eb85507000 ---p 00034000 00:35 36596283 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libgomp.so.1.0.0
14eb85507000-14eb85508000 r--p 00034000 00:35 36596283 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libgomp.so.1.0.0
14eb85508000-14eb85509000 rw-p 00035000 00:35 36596283 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libgomp.so.1.0.0
14eb85509000-14eb8560a000 r-xp 00000000 08:03 33556011 /usr/lib64/libm-2.17.so
14eb8560a000-14eb85809000 ---p 00101000 08:03 33556011 /usr/lib64/libm-2.17.so
14eb85809000-14eb8580a000 r--p 00100000 08:03 33556011 /usr/lib64/libm-2.17.so
14eb8580a000-14eb8580b000 rw-p 00101000 08:03 33556011 /usr/lib64/libm-2.17.so
14eb8580b000-14eb859d4000 r-xp 00000000 00:35 36789011 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libstdc++.so.6.0.28
14eb859d4000-14eb85bd4000 ---p 001c9000 00:35 36789011 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libstdc++.so.6.0.28
14eb85bd4000-14eb85bdf000 r--p 001c9000 00:35 36789011 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libstdc++.so.6.0.28
14eb85bdf000-14eb85be2000 rw-p 001d4000 00:35 36789011 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libstdc++.so.6.0.28
14eb85be2000-14eb85be5000 rw-p 00000000 00:00 0
14eb85be5000-14eb85eb1000 r-xp 00000000 00:35 70489492 /opt/area/shared/libraries/openmpi/4.1.2/lib/libmpi.so.40.30.2
14eb85eb1000-14eb860b1000 ---p 002cc000 00:35 70489492 /opt/area/shared/libraries/openmpi/4.1.2/lib/libmpi.so.40.30.2
14eb860b1000-14eb860b4000 r--p 002cc000 00:35 70489492 /opt/area/shared/libraries/openmpi/4.1.2/lib/libmpi.so.40.30.2
14eb860b4000-14eb860d6000 rw-p 002cf000 00:35 70489492 /opt/area/shared/libraries/openmpi/4.1.2/lib/libmpi.so.40.30.2
14eb860d6000-14eb860ed000 rw-p 00000000 00:00 0
14eb860ed000-14eb860fc000 r-xp 00000000 08:03 33556381 /usr/lib64/libbz2.so.1.0.6
14eb860fc000-14eb862fb000 ---p 0000f000 08:03 33556381 /usr/lib64/libbz2.so.1.0.6
14eb862fb000-14eb862fc000 r--p 0000e000 08:03 33556381 /usr/lib64/libbz2.so.1.0.6
14eb862fc000-14eb862fd000 rw-p 0000f000 08:03 33556381 /usr/lib64/libbz2.so.1.0.6
14eb862fd000-14eb86312000 r-xp 00000000 08:03 33556064 /usr/lib64/libz.so.1.2.7
14eb86312000-14eb86511000 ---p 00015000 08:03 33556064 /usr/lib64/libz.so.1.2.7
14eb86511000-14eb86512000 r--p 00014000 08:03 33556064 /usr/lib64/libz.so.1.2.7
14eb86512000-14eb86513000 rw-p 00015000 08:03 33556064 /usr/lib64/libz.so.1.2.7
14eb86513000-14eb86519000 r-xp 00000000 00:35 36596272 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libatomic.so.1.2.0
14eb86519000-14eb86718000 ---p 00006000 00:35 36596272 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libatomic.so.1.2.0
14eb86718000-14eb86719000 r--p 00005000 00:35 36596272 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libatomic.so.1.2.0
14eb86719000-14eb8671a000 rw-p 00006000 00:35 36596272 /opt/area/shared/programs/x86_64/gnu/gcc/9.3.0/lib64/libatomic.so.1.2.0
14eb8671a000-14eb8671b000 rw-p 00000000 00:00 0
14eb8671b000-14eb8673d000 r-xp 00000000 08:03 33555711 /usr/lib64/ld-2.17.so
14eb86795000-14eb86929000 rw-p 00000000 00:00 0
14eb86936000-14eb8693c000 rw-p 00000000 00:00 0
14eb8693c000-14eb8693d000 r--p 00021000 08:03 33555711 /usr/lib64/ld-2.17.so
14eb8693d000-14eb8693e000 rw-p 00022000 08:03 33555711 /usr/lib64/ld-2.17.so
14eb8693e000-14eb8693f000 rw-p 00000000 00:00 0
7ffd097ea000-7ffd0980e000 rw-p 00000000 00:00 0 [stack]
7ffd09861000-7ffd09865000 r--p 00000000 00:00 0 [vvar]
7ffd09865000-7ffd09867000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node ct1pt-tnode006 exited on signal 6 (Aborted).
--------------------------------------------------------------------------
Raw
stdout.log
Mon Sep 12 13:12:07 CEST 2022
Running swiss_200k versus swiss_200k - thin node 48c cores
Create directory tmpFolder
search /scratch/area/fbarone/foldseek/databases/swiss_200k/swiss_200k /scratch/area/fbarone/foldseek/databases/swiss_200k/swiss_200k /scratch/area/fbarone/foldseek/orfeo_benchmark/cores_scalability/48_cores/alignments tmpFolder -s 7.5 --max-seqs 20000 --mpi-runner mpirun -map-by ppr:1:node:pe=24 --split 2 --split-mode 1
MMseqs Version: a8eb6812b8f0a64f4ce767051af7a5540167500d-MPI
Seq. id. threshold 0
Coverage threshold 0
Coverage mode 0
Max reject 2147483647
Max accept 2147483647
Add backtrace false
TMscore threshold 0
TMalign fast 1
Preload mode 0
Threads 24
Verbosity 3
Substitution matrix aa:3di.out,nucl:3di.out
Alignment mode 3
Alignment mode 0
E-value threshold 0.001
Min alignment length 0
Seq. id. mode 0
Alternative alignments 0
Max sequence length 65535
Compositional bias 1
Compositional bias 1
Gap open cost aa:10,nucl:10
Gap extension cost aa:1,nucl:1
Compressed 0
Seed substitution matrix aa:3di.out,nucl:3di.out
Sensitivity 7.5
k-mer length 6
k-score seq:2147483647,prof:2147483647
Max results per query 20000
Split database 2
Split mode 1
Split memory limit 0
Diagonal scoring true
Exact k-mer matching 0
Mask residues 0
Mask residues probability 0.99995
Mask lower case residues 1
Minimum diagonal score 15
Selected taxa
Spaced k-mers 1
Spaced k-mer pattern
Local temporary path
Search iterations 1
Alignment type 2
Remove temporary files true
MPI runner mpirun -map-by ppr:1:node:pe=24
Force restart with latest tmp false
MPI Init
Rank: 0 Size: 2
prefilter /scratch/area/fbarone/foldseek/databases/swiss_200k/swiss_200k_ss /scratch/area/fbarone/foldseek/databases/swiss_200k/swiss_200k_ss tmpFolder/9749724961102201013/pref --sub-mat 'aa:3di.out,nucl:3di.out' --seed-sub-mat 'aa:3di.out,nucl:3di.out' -s 7.5 -k 6 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 20000 --split 2 --split-mode 1 --split-memory-limit 0 -c 0 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 0.15 --diag-score 1 --exact-kmer-matching 0 --mask 0 --mask-prob 0.99995 --mask-lower-case 1 --min-ungapped-score 15 --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: 200000 type: Aminoacid
Query split mode. Searching through 2 splits
Estimated memory consumption: 1G
Target database size: 200000 type: Aminoacid
Index table k-mer threshold: 96 at k-mer size 6
Index table: counting k-mers
[=================================================================] 200.00K 0s 343ms
Index table: Masked residues: 0
Index table: fill
[=================================================================] 200.00K 0s 738ms
Index statistics
Entries: 57067789
DB size: 814 MB
Avg k-mer size: 0.891684
Top 10 k-mers
LVLVVV 76135
SVSVVV 69276
DDDDPP 42891
VLVLLL 39000
VVVSVS 37573
NVSVVV 35386
VLVLLV 30782
VSVSVV 30146
VSVSSV 24158
LVSVVV 23727
Time for index table init: 0h 0m 1s 712ms
Process prefiltering step 1 of 2
k-mer similarity threshold: 96
Starting prefiltering scores calculation (step 1 of 2)
Query db start 1 to 106284
Target db start 1 to 200000
[=================================================================] 106.28K 10m 6s 828ms
879.051139 k-mers per position
2926067 DB matches per sequence
61107 overflows
0 queries produce too many hits (truncated result)
17804 sequences passed prefiltering per query sequence
20000 median result list length
0 sequences with 0 size result lists
Time for merging to pref_tmp_0: 0h 0m 18s 348ms
Time for merging to pref: 0h 1m 19s 135ms
Time for processing: 0h 11m 46s 840ms
structurealign /scratch/area/fbarone/foldseek/databases/swiss_200k/swiss_200k /scratch/area/fbarone/foldseek/databases/swiss_200k/swiss_200k tmpFolder/9749724961102201013/pref tmpFolder/9749724961102201013/aln --tmscore-threshold 0 --sub-mat 'aa:3di.out,nucl:3di.out' -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 0.5 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:10,nucl:10 --gap-extend aa:1,nucl:1 --zdrop 40 --threads 24 --compressed 0 -v 3
structurealign /scratch/area/fbarone/foldseek/databases/swiss_200k/swiss_200k /scratch/area/fbarone/foldseek/databases/swiss_200k/swiss_200k tmpFolder/9749724961102201013/pref tmpFolder/9749724961102201013/aln --tmscore-threshold 0 --sub-mat 'aa:3di.out,nucl:3di.out' -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 0.5 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:10,nucl:10 --gap-extend aa:1,nucl:1 --zdrop 40 --threads 24 --compressed 0 -v 3
[=[================================================================================================================================] 200.00K 4h 5m 20s 222ms
Error: Alignment step died
elapsed time: 15450 seconds
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