Memory error

[Jiawei-Xing]

Hi, I got this error when I run mkdssp:

*** Error in `./mkdssp': munmap_chunk(): invalid pointer: 0x000000000216f030 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7f474)[0x2b5a3bc1a474]
./mkdssp[0x43f676]
./mkdssp[0x4a9574]
./mkdssp[0x4aa80d]
./mkdssp[0x41c536]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b5a3bbbd555]
./mkdssp[0x421b08]
======= Memory map: ========
00400000-00571000 r-xp 00000000 00:31 28096106542                        /home/xing.232/Pfam-structure/2nd-structure/mkdssp
00771000-00783000 r--p 00171000 00:31 28096106542                        /home/xing.232/Pfam-structure/2nd-structure/mkdssp
00783000-0078c000 rw-p 00183000 00:31 28096106542                        /home/xing.232/Pfam-structure/2nd-structure/mkdssp
0078c000-00790000 rw-p 00000000 00:00 0 
0215d000-0218f000 rw-p 00000000 00:00 0                                  [heap]
2b5a3b459000-2b5a3b47b000 r-xp 00000000 fd:00 50332529                   /usr/lib64/ld-2.17.so
2b5a3b47b000-2b5a3b47d000 rw-p 00000000 00:00 0 
2b5a3b496000-2b5a3b497000 rw-p 00000000 00:00 0 
2b5a3b497000-2b5a3b49a000 r--p 00000000 00:30 7254892574                 /home/modules/anaconda3-2020.02/lib/libz.so.1.2.11
2b5a3b49a000-2b5a3b4ae000 r-xp 00003000 00:30 7254892574                 /home/modules/anaconda3-2020.02/lib/libz.so.1.2.11
2b5a3b4ae000-2b5a3b4b5000 r--p 00017000 00:30 7254892574                 /home/modules/anaconda3-2020.02/lib/libz.so.1.2.11
2b5a3b4b5000-2b5a3b4b6000 r--p 0001d000 00:30 7254892574                 /home/modules/anaconda3-2020.02/lib/libz.so.1.2.11
2b5a3b4b6000-2b5a3b4b7000 rw-p 0001e000 00:30 7254892574                 /home/modules/anaconda3-2020.02/lib/libz.so.1.2.11
2b5a3b4b7000-2b5a3b559000 r--p 00000000 00:30 7253655610                 /home/modules/anaconda3-2020.02/lib/libstdc++.so.6.0.26
2b5a3b559000-2b5a3b5d8000 r-xp 000a2000 00:30 7253655610                 /home/modules/anaconda3-2020.02/lib/libstdc++.so.6.0.26
2b5a3b5d8000-2b5a3b619000 r--p 00121000 00:30 7253655610                 /home/modules/anaconda3-2020.02/lib/libstdc++.so.6.0.26
2b5a3b619000-2b5a3b624000 r--p 00161000 00:30 7253655610                 /home/modules/anaconda3-2020.02/lib/libstdc++.so.6.0.26
2b5a3b624000-2b5a3b628000 rw-p 0016c000 00:30 7253655610                 /home/modules/anaconda3-2020.02/lib/libstdc++.so.6.0.26
2b5a3b628000-2b5a3b62c000 rw-p 00000000 00:00 0 
2b5a3b62c000-2b5a3b62f000 r--p 00000000 00:30 7253349033                 /home/modules/anaconda3-2020.02/lib/libgcc_s.so.1
2b5a3b62f000-2b5a3b63b000 r-xp 00003000 00:30 7253349033                 /home/modules/anaconda3-2020.02/lib/libgcc_s.so.1
2b5a3b63b000-2b5a3b63e000 r--p 0000f000 00:30 7253349033                 /home/modules/anaconda3-2020.02/lib/libgcc_s.so.1
2b5a3b63e000-2b5a3b63f000 r--p 00011000 00:30 7253349033                 /home/modules/anaconda3-2020.02/lib/libgcc_s.so.1
2b5a3b63f000-2b5a3b640000 rw-p 00012000 00:30 7253349033                 /home/modules/anaconda3-2020.02/lib/libgcc_s.so.1
2b5a3b640000-2b5a3b645000 rw-p 00000000 00:00 0 
2b5a3b67a000-2b5a3b67b000 r--p 00021000 fd:00 50332529                   /usr/lib64/ld-2.17.so
2b5a3b67b000-2b5a3b67c000 rw-p 00022000 fd:00 50332529                   /usr/lib64/ld-2.17.so
2b5a3b67c000-2b5a3b67d000 rw-p 00000000 00:00 0 
2b5a3b67d000-2b5a3b694000 r-xp 00000000 fd:00 51280953                   /usr/lib64/libpthread-2.17.so
2b5a3b694000-2b5a3b893000 ---p 00017000 fd:00 51280953                   /usr/lib64/libpthread-2.17.so
2b5a3b893000-2b5a3b894000 r--p 00016000 fd:00 51280953                   /usr/lib64/libpthread-2.17.so
2b5a3b894000-2b5a3b895000 rw-p 00017000 fd:00 51280953                   /usr/lib64/libpthread-2.17.so
2b5a3b895000-2b5a3b899000 rw-p 00000000 00:00 0 
2b5a3b899000-2b5a3b99a000 r-xp 00000000 fd:00 51280745                   /usr/lib64/libm-2.17.so
2b5a3b99a000-2b5a3bb99000 ---p 00101000 fd:00 51280745                   /usr/lib64/libm-2.17.so
2b5a3bb99000-2b5a3bb9a000 r--p 00100000 fd:00 51280745                   /usr/lib64/libm-2.17.so
2b5a3bb9a000-2b5a3bb9b000 rw-p 00101000 fd:00 51280745                   /usr/lib64/libm-2.17.so
2b5a3bb9b000-2b5a3bd5f000 r-xp 00000000 fd:00 50874781                   /usr/lib64/libc-2.17.so
2b5a3bd5f000-2b5a3bf5e000 ---p 001c4000 fd:00 50874781                   /usr/lib64/libc-2.17.so
2b5a3bf5e000-2b5a3bf62000 r--p 001c3000 fd:00 50874781                   /usr/lib64/libc-2.17.so
2b5a3bf62000-2b5a3bf64000 rw-p 001c7000 fd:00 50874781                   /usr/lib64/libc-2.17.so
2b5a3bf64000-2b5a3bf69000 rw-p 00000000 00:00 0 
7ffe5ebbb000-7ffe5ebdd000 rw-p 00000000 00:00 0                          [stack]
7ffe5ebe3000-7ffe5ebe5000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)

[mhekkel]

Thanks for reporting. However, would it be possible to give a bit more details? Like, what version of dssp are you using? Did you build it yourself or did you download it from elsewhere? What what the input file? What OS are you using? Anything else that might help us to investigate this problem?

[drlemmus]

Stale