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Gmx distance error：double free or corruption (!prev): 0x0000000001386d60 ***
- 若水无风
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2 years 9 months ago - 2 years 9 months ago #9066
by 若水无风
Gmx distance error：double free or corruption (!prev): 0x0000000001386d60 *** was created by 若水无风
I am working on the Martini force field parameterization of polymers. When I used the 'gmx distance' command to calculate the distribution of bond lengths, I encountered such an error. I will be very grateful if you can give some suggestions. This is my input file and error message.
trajpbc.xtc
C_bonds.ndx
PS：when select another group，everything is ok.
GROMACS: gmx distance, version 2018.8
Executable: /sob/gmx2018.8/bin/gmx
Data prefix: /sob/gmx2018.8
Working dir: /sob
Command line:
gmx distance -f trajpbc.xtc -len 0.35 -tol 0.8 -n C_bonds.ndx -oh bonds_BR2.xvg
Available static index groups:
Group 0 "bonds_BR1" (2000 atoms)
Group 1 "bonds_BR2" (1800 atoms)
Specify any number of selections for option 'select'
(Position pairs to calculate distances for):
(one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end)
> 1
Selection '1' parsed
Reading frame 1 time 20.000 *** Error in `gmx': double free or corruption (!prev): 0x0000000001386d60 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x7f0a2832f489]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN13gmx_ana_pos_tD1Ev+0x1f)[0x7f0a2995849f]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN3gmx8internal13SelectionDataD2Ev+0x34)[0x7f0a2995d0f4]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN3gmx19SelectionCollection4ImplD1Ev+0x89)[0x7f0a2995f059]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN3gmx19SelectionCollectionD1Ev+0x19)[0x7f0a2995faf9]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(+0x6aab78)[0x7f0a29986b78]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(+0x15189d)[0x7f0a2942d89d]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZNSt8_Rb_treeISsSt4pairIKSsSt10unique_ptrIN3gmx18ICommandLineModuleESt14default_deleteIS4_EEESt10_Select1stIS8_ESt4lessISsESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E+0x4a)[0x7f0a2942bfba]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN3gmx24CommandLineModuleManagerD1Ev+0x246)[0x7f0a29429236]
gmx[0x40ddcd]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f0a282d03d5]
gmx[0x40de16]
======= Memory map: ========
00400000-00438000 r-xp 00000000 fd:00 37284055 /sob/gmx2018.8/bin/gmx
00637000-00638000 r--p 00037000 fd:00 37284055 /sob/gmx2018.8/bin/gmx
00638000-00639000 rw-p 00038000 fd:00 37284055 /sob/gmx2018.8/bin/gmx
00639000-0063a000 rw-p 00000000 00:00 0
01341000-013c3000 rw-p 00000000 00:00 0 [heap]
7f0a20000000-7f0a20021000 rw-p 00000000 00:00 0
7f0a20021000-7f0a24000000 ---p 00000000 00:00 0
7f0a27a92000-7f0a27c91000 r-xp 00000000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f0a27c91000-7f0a27e90000 ---p 001ff000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f0a27e90000-7f0a27ea1000 r--p 001fe000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f0a27ea1000-7f0a27ea2000 rw-p 0020f000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f0a27ea2000-7f0a27ea9000 r-xp 00000000 fd:00 33674031 /usr/lib64/librt-2.17.so
7f0a27ea9000-7f0a280a8000 ---p 00007000 fd:00 33674031 /usr/lib64/librt-2.17.so
7f0a280a8000-7f0a280a9000 r--p 00006000 fd:00 33674031 /usr/lib64/librt-2.17.so
7f0a280a9000-7f0a280aa000 rw-p 00007000 fd:00 33674031 /usr/lib64/librt-2.17.so
7f0a280aa000-7f0a280ac000 r-xp 00000000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7f0a280ac000-7f0a282ac000 ---p 00002000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7f0a282ac000-7f0a282ad000 r--p 00002000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7f0a282ad000-7f0a282ae000 rw-p 00003000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7f0a282ae000-7f0a28470000 r-xp 00000000 fd:00 33665201 /usr/lib64/libc-2.17.so
7f0a28470000-7f0a28670000 ---p 001c2000 fd:00 33665201 /usr/lib64/libc-2.17.so
7f0a28670000-7f0a28674000 r--p 001c2000 fd:00 33665201 /usr/lib64/libc-2.17.so
7f0a28674000-7f0a28676000 rw-p 001c6000 fd:00 33665201 /usr/lib64/libc-2.17.so
7f0a28676000-7f0a2867b000 rw-p 00000000 00:00 0
7f0a2867b000-7f0a28692000 r-xp 00000000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7f0a28692000-7f0a28891000 ---p 00017000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7f0a28891000-7f0a28892000 r--p 00016000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7f0a28892000-7f0a28893000 rw-p 00017000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7f0a28893000-7f0a28897000 rw-p 00000000 00:00 0
7f0a28897000-7f0a288ac000 r-xp 00000000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f0a288ac000-7f0a28aab000 ---p 00015000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f0a28aab000-7f0a28aac000 r--p 00014000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f0a28aac000-7f0a28aad000 rw-p 00015000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f0a28aad000-7f0a28ad2000 r-xp 00000000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7f0a28ad2000-7f0a28cd1000 ---p 00025000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7f0a28cd1000-7f0a28cd2000 r--p 00024000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7f0a28cd2000-7f0a28cd3000 rw-p 00025000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7f0a28cd3000-7f0a28dd4000 r-xp 00000000 fd:00 33665209 /usr/lib64/libm-2.17.so
7f0a28dd4000-7f0a28fd3000 ---p 00101000 fd:00 33665209 /usr/lib64/libm-2.17.so
7f0a28fd3000-7f0a28fd4000 r--p 00100000 fd:00 33665209 /usr/lib64/libm-2.17.so
7f0a28fd4000-7f0a28fd5000 rw-p 00101000 fd:00 33665209 /usr/lib64/libm-2.17.so
7f0a28fd5000-7f0a290be000 r-xp 00000000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7f0a290be000-7f0a292bd000 ---p 000e9000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7f0a292bd000-7f0a292c5000 r--p 000e8000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7f0a292c5000-7f0a292c7000 rw-p 000f0000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7f0a292c7000-7f0a292dc000 rw-p 00000000 00:00 0
7f0a292dc000-7f0a29f25000 r-xp 00000000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f0a29f25000-7f0a2a125000 ---p 00c49000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f0a2a125000-7f0a2a136000 r--p 00c49000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f0a2a136000-7f0a2a156000 rw-p 00c5a000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f0a2a156000-7f0a2a158000 rw-p 00000000 00:00 0
7f0a2a158000-7f0a2a17a000 r-xp 00000000 fd:00 33665194 /usr/lib64/ld-2.17.so
7f0a2a35a000-7f0a2a362000 rw-p 00000000 00:00 0
7f0a2a375000-7f0a2a379000 rw-p 00000000 00:00 0
7f0a2a379000-7f0a2a37a000 r--p 00021000 fd:00 33665194 /usr/lib64/ld-2.17.so
7f0a2a37a000-7f0a2a37b000 rw-p 00022000 fd:00 33665194 /usr/lib64/ld-2.17.so
7f0a2a37b000-7f0a2a37c000 rw-p 00000000 00:00 0
7ffc74cbb000-7ffc74cdc000 rw-p 00000000 00:00 0 [stack]Aborted (core dumped)
trajpbc.xtc
C_bonds.ndx
PS：when select another group，everything is ok.
GROMACS: gmx distance, version 2018.8
Executable: /sob/gmx2018.8/bin/gmx
Data prefix: /sob/gmx2018.8
Working dir: /sob
Command line:
gmx distance -f trajpbc.xtc -len 0.35 -tol 0.8 -n C_bonds.ndx -oh bonds_BR2.xvg
Available static index groups:
Group 0 "bonds_BR1" (2000 atoms)
Group 1 "bonds_BR2" (1800 atoms)
Specify any number of selections for option 'select'
(Position pairs to calculate distances for):
(one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end)
> 1
Selection '1' parsed
Reading frame 1 time 20.000 *** Error in `gmx': double free or corruption (!prev): 0x0000000001386d60 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x7f0a2832f489]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN13gmx_ana_pos_tD1Ev+0x1f)[0x7f0a2995849f]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN3gmx8internal13SelectionDataD2Ev+0x34)[0x7f0a2995d0f4]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN3gmx19SelectionCollection4ImplD1Ev+0x89)[0x7f0a2995f059]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN3gmx19SelectionCollectionD1Ev+0x19)[0x7f0a2995faf9]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(+0x6aab78)[0x7f0a29986b78]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(+0x15189d)[0x7f0a2942d89d]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZNSt8_Rb_treeISsSt4pairIKSsSt10unique_ptrIN3gmx18ICommandLineModuleESt14default_deleteIS4_EEESt10_Select1stIS8_ESt4lessISsESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E+0x4a)[0x7f0a2942bfba]
/sob/gmx2018.8/bin/../lib64/libgromacs.so.3(_ZN3gmx24CommandLineModuleManagerD1Ev+0x246)[0x7f0a29429236]
gmx[0x40ddcd]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f0a282d03d5]
gmx[0x40de16]
======= Memory map: ========
00400000-00438000 r-xp 00000000 fd:00 37284055 /sob/gmx2018.8/bin/gmx
00637000-00638000 r--p 00037000 fd:00 37284055 /sob/gmx2018.8/bin/gmx
00638000-00639000 rw-p 00038000 fd:00 37284055 /sob/gmx2018.8/bin/gmx
00639000-0063a000 rw-p 00000000 00:00 0
01341000-013c3000 rw-p 00000000 00:00 0 [heap]
7f0a20000000-7f0a20021000 rw-p 00000000 00:00 0
7f0a20021000-7f0a24000000 ---p 00000000 00:00 0
7f0a27a92000-7f0a27c91000 r-xp 00000000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f0a27c91000-7f0a27e90000 ---p 001ff000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f0a27e90000-7f0a27ea1000 r--p 001fe000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f0a27ea1000-7f0a27ea2000 rw-p 0020f000 fd:00 100838348 /sob/fftw338/lib/libfftw3f.so.3.5.8
7f0a27ea2000-7f0a27ea9000 r-xp 00000000 fd:00 33674031 /usr/lib64/librt-2.17.so
7f0a27ea9000-7f0a280a8000 ---p 00007000 fd:00 33674031 /usr/lib64/librt-2.17.so
7f0a280a8000-7f0a280a9000 r--p 00006000 fd:00 33674031 /usr/lib64/librt-2.17.so
7f0a280a9000-7f0a280aa000 rw-p 00007000 fd:00 33674031 /usr/lib64/librt-2.17.so
7f0a280aa000-7f0a280ac000 r-xp 00000000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7f0a280ac000-7f0a282ac000 ---p 00002000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7f0a282ac000-7f0a282ad000 r--p 00002000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7f0a282ad000-7f0a282ae000 rw-p 00003000 fd:00 33665207 /usr/lib64/libdl-2.17.so
7f0a282ae000-7f0a28470000 r-xp 00000000 fd:00 33665201 /usr/lib64/libc-2.17.so
7f0a28470000-7f0a28670000 ---p 001c2000 fd:00 33665201 /usr/lib64/libc-2.17.so
7f0a28670000-7f0a28674000 r--p 001c2000 fd:00 33665201 /usr/lib64/libc-2.17.so
7f0a28674000-7f0a28676000 rw-p 001c6000 fd:00 33665201 /usr/lib64/libc-2.17.so
7f0a28676000-7f0a2867b000 rw-p 00000000 00:00 0
7f0a2867b000-7f0a28692000 r-xp 00000000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7f0a28692000-7f0a28891000 ---p 00017000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7f0a28891000-7f0a28892000 r--p 00016000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7f0a28892000-7f0a28893000 rw-p 00017000 fd:00 33674027 /usr/lib64/libpthread-2.17.so
7f0a28893000-7f0a28897000 rw-p 00000000 00:00 0
7f0a28897000-7f0a288ac000 r-xp 00000000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f0a288ac000-7f0a28aab000 ---p 00015000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f0a28aab000-7f0a28aac000 r--p 00014000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f0a28aac000-7f0a28aad000 rw-p 00015000 fd:00 33554509 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f0a28aad000-7f0a28ad2000 r-xp 00000000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7f0a28ad2000-7f0a28cd1000 ---p 00025000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7f0a28cd1000-7f0a28cd2000 r--p 00024000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7f0a28cd2000-7f0a28cd3000 rw-p 00025000 fd:00 33701332 /usr/lib64/libgomp.so.1.0.0
7f0a28cd3000-7f0a28dd4000 r-xp 00000000 fd:00 33665209 /usr/lib64/libm-2.17.so
7f0a28dd4000-7f0a28fd3000 ---p 00101000 fd:00 33665209 /usr/lib64/libm-2.17.so
7f0a28fd3000-7f0a28fd4000 r--p 00100000 fd:00 33665209 /usr/lib64/libm-2.17.so
7f0a28fd4000-7f0a28fd5000 rw-p 00101000 fd:00 33665209 /usr/lib64/libm-2.17.so
7f0a28fd5000-7f0a290be000 r-xp 00000000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7f0a290be000-7f0a292bd000 ---p 000e9000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7f0a292bd000-7f0a292c5000 r--p 000e8000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7f0a292c5000-7f0a292c7000 rw-p 000f0000 fd:00 33687522 /usr/lib64/libstdc++.so.6.0.19
7f0a292c7000-7f0a292dc000 rw-p 00000000 00:00 0
7f0a292dc000-7f0a29f25000 r-xp 00000000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f0a29f25000-7f0a2a125000 ---p 00c49000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f0a2a125000-7f0a2a136000 r--p 00c49000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f0a2a136000-7f0a2a156000 rw-p 00c5a000 fd:00 2354367 /sob/gmx2018.8/lib64/libgromacs.so.3.5.0
7f0a2a156000-7f0a2a158000 rw-p 00000000 00:00 0
7f0a2a158000-7f0a2a17a000 r-xp 00000000 fd:00 33665194 /usr/lib64/ld-2.17.so
7f0a2a35a000-7f0a2a362000 rw-p 00000000 00:00 0
7f0a2a375000-7f0a2a379000 rw-p 00000000 00:00 0
7f0a2a379000-7f0a2a37a000 r--p 00021000 fd:00 33665194 /usr/lib64/ld-2.17.so
7f0a2a37a000-7f0a2a37b000 rw-p 00022000 fd:00 33665194 /usr/lib64/ld-2.17.so
7f0a2a37b000-7f0a2a37c000 rw-p 00000000 00:00 0
7ffc74cbb000-7ffc74cdc000 rw-p 00000000 00:00 0 [stack]Aborted (core dumped)
Last edit: 2 years 9 months ago by 若水无风.
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