Double free or corruption error when running run_test.py

[XunuoZhu]

Hi, yupeng. I encountered some problems when running run_test.py, it seems like a memory management issue in the program
Below is the output of the terminal.

Test DMRfind: *** Error in `/share/anaconda3/envs/methylpy/lib/python3.10/site-packages/methylpy-1.4.7-py3.10.egg/methylpy/run_rms_tests.out': double free or corruption (fasttop): 0x00000000011985f0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x7f98ad592329]
/share/anaconda3/envs/methylpy/lib/python3.10/site-packages/methylpy-1.4.7-py3.10.egg/methylpy/run_rms_tests.out[0x401f6c]
/share/anaconda3/envs/methylpy/lib/python3.10/site-packages/methylpy-1.4.7-py3.10.egg/methylpy/run_rms_tests.out[0x406077]
/share/anaconda3/envs/methylpy/lib/python3.10/site-packages/methylpy-1.4.7-py3.10.egg/methylpy/run_rms_tests.out[0x402927]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f98ad533555]
/share/anaconda3/envs/methylpy/lib/python3.10/site-packages/methylpy-1.4.7-py3.10.egg/methylpy/run_rms_tests.out[0x402b6f]
======= Memory map: ========
00400000-00408000 r-xp 00000000 00:2b 21847909692 /share/anaconda3/envs/methylpy/lib/python3.10/site-packages/methylpy-1.4.7-py3.10.egg/methylpy/run_rms_tests.out
00608000-00609000 r--p 00008000 00:2b 21847909692 /share/anaconda3/envs/methylpy/lib/python3.10/site-packages/methylpy-1.4.7-py3.10.egg/methylpy/run_rms_tests.out
00609000-0060a000 rw-p 00009000 00:2b 21847909692 /share/anaconda3/envs/methylpy/lib/python3.10/site-packages/methylpy-1.4.7-py3.10.egg/methylpy/run_rms_tests.out
01174000-011b7000 rw-p 00000000 00:00 0 [heap]
7f98a8000000-7f98a8021000 rw-p 00000000 00:00 0
7f98a8021000-7f98ac000000 ---p 00000000 00:00 0
7f98ac13f000-7f98ac184000 r-xp 00000000 fd:00 42164775 /usr/lib64/libquadmath.so.0.0.0
7f98ac184000-7f98ac384000 ---p 00045000 fd:00 42164775 /usr/lib64/libquadmath.so.0.0.0
7f98ac384000-7f98ac385000 r--p 00045000 fd:00 42164775 /usr/lib64/libquadmath.so.0.0.0
7f98ac385000-7f98ac386000 rw-p 00046000 fd:00 42164775 /usr/lib64/libquadmath.so.0.0.0
7f98ac386000-7f98ac39d000 r-xp 00000000 fd:00 42164760 /usr/lib64/libpthread-2.17.so
7f98ac39d000-7f98ac59c000 ---p 00017000 fd:00 42164760 /usr/lib64/libpthread-2.17.so
7f98ac59c000-7f98ac59d000 r--p 00016000 fd:00 42164760 /usr/lib64/libpthread-2.17.so
7f98ac59d000-7f98ac59e000 rw-p 00017000 fd:00 42164760 /usr/lib64/libpthread-2.17.so
7f98ac59e000-7f98ac5a2000 rw-p 00000000 00:00 0
7f98ac5a2000-7f98ac6c1000 r-xp 00000000 fd:00 42164580 /usr/lib64/libgfortran.so.3.0.0
7f98ac6c1000-7f98ac8c1000 ---p 0011f000 fd:00 42164580 /usr/lib64/libgfortran.so.3.0.0
7f98ac8c1000-7f98ac8c2000 r--p 0011f000 fd:00 42164580 /usr/lib64/libgfortran.so.3.0.0
7f98ac8c2000-7f98ac8c4000 rw-p 00120000 fd:00 42164580 /usr/lib64/libgfortran.so.3.0.0

7f98ac8c4000-7f98ad303000 r-xp 00000000 fd:00 92447082 /usr/lib64/atlas/libsatlas.so.3.10
7f98ad303000-7f98ad503000 ---p 00a3f000 fd:00 92447082 /usr/lib64/atlas/libsatlas.so.3.10
7f98ad503000-7f98ad508000 r--p 00a3f000 fd:00 92447082 /usr/lib64/atlas/libsatlas.so.3.10
7f98ad508000-7f98ad511000 rw-p 00a44000 fd:00 92447082 /usr/lib64/atlas/libsatlas.so.3.10
7f98ad511000-7f98ad6d5000 r-xp 00000000 fd:00 41944183 /usr/lib64/libc-2.17.so
7f98ad6d5000-7f98ad8d4000 ---p 001c4000 fd:00 41944183 /usr/lib64/libc-2.17.so
7f98ad8d4000-7f98ad8d8000 r--p 001c3000 fd:00 41944183 /usr/lib64/libc-2.17.so
7f98ad8d8000-7f98ad8da000 rw-p 001c7000 fd:00 41944183 /usr/lib64/libc-2.17.so
7f98ad8da000-7f98ad8df000 rw-p 00000000 00:00 0
7f98ad8df000-7f98ad8f5000 r-xp 00000000 fd:00 42164564 /usr/lib64/libgcc_s.so.1
7f98ad8f5000-7f98adaf5000 ---p 00016000 fd:00 42164564 /usr/lib64/libgcc_s.so.1
7f98adaf5000-7f98adaf6000 r--p 00016000 fd:00 42164564 /usr/lib64/libgcc_s.so.1
7f98adaf6000-7f98adaf7000 rw-p 00017000 fd:00 42164564 /usr/lib64/libgcc_s.so.1
7f98adaf7000-7f98adbf8000 r-xp 00000000 fd:00 42164687 /usr/lib64/libm-2.17.so
7f98adbf8000-7f98addf7000 ---p 00101000 fd:00 42164687 /usr/lib64/libm-2.17.so
7f98addf7000-7f98addf8000 r--p 00100000 fd:00 42164687 /usr/lib64/libm-2.17.so
7f98addf8000-7f98addf9000 rw-p 00101000 fd:00 42164687 /usr/lib64/libm-2.17.so
7f98addf9000-7f98ade35000 r-xp 00000000 fd:00 42164607 /usr/lib64/libgslcblas.so.0.0.0
7f98ade35000-7f98ae034000 ---p 0003c000 fd:00 42164607 /usr/lib64/libgslcblas.so.0.0.0
7f98ae034000-7f98ae035000 r--p 0003b000 fd:00 42164607 /usr/lib64/libgslcblas.so.0.0.0
7f98ae035000-7f98ae036000 rw-p 0003c000 fd:00 42164607 /usr/lib64/libgslcblas.so.0.0.0
7f98ae036000-7f98ae24b000 r-xp 00000000 fd:00 42164606 /usr/lib64/libgsl.so.0.16.0
7f98ae24b000-7f98ae44b000 ---p 00215000 fd:00 42164606 /usr/lib64/libgsl.so.0.16.0
7f98ae44b000-7f98ae44e000 r--p 00215000 fd:00 42164606 /usr/lib64/libgsl.so.0.16.0
7f98ae44e000-7f98ae45e000 rw-p 00218000 fd:00 42164606 /usr/lib64/libgsl.so.0.16.0
7f98ae45e000-7f98ae45f000 rw-p 00000000 00:00 0
7f98ae45f000-7f98ae481000 r-xp 00000000 fd:00 42189941 /usr/lib64/ld-2.17.so
7f98ae4af000-7f98ae4b6000 rw-p 00000000 00:00 0
7f98ae4b6000-7f98ae55c000 r--p 00000000 fd:00 44737546 /usr/lib64/libstdc++.so.6.0.30
7f98ae55c000-7f98ae5f0000 r-xp 000a6000 fd:00 44737546 /usr/lib64/libstdc++.so.6.0.30
7f98ae5f0000-7f98ae658000 r--p 0013a000 fd:00 44737546 /usr/lib64/libstdc++.so.6.0.30
7f98ae658000-7f98ae663000 r--p 001a1000 fd:00 44737546 /usr/lib64/libstdc++.so.6.0.30
7f98ae663000-7f98ae667000 rw-p 001ac000 fd:00 44737546 /usr/lib64/libstdc++.so.6.0.30
7f98ae667000-7f98ae66b000 rw-p 00000000 00:00 0
7f98ae67e000-7f98ae680000 rw-p 00000000 00:00 0
7f98ae680000-7f98ae681000 r--p 00021000 fd:00 42189941 /usr/lib64/ld-2.17.so
7f98ae681000-7f98ae682000 rw-p 00022000 fd:00 42189941 /usr/lib64/ld-2.17.so
7f98ae682000-7f98ae683000 rw-p 00000000 00:00 0
7ffc72c3e000-7ffc72c5f000 rw-p 00000000 00:00 0 [stack]
7ffc72db3000-7ffc72db5000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
failed
Test reidentify-DMR: failed

test_error_msg.txt
test_output_msg.txt

Any advice or suggestions would be appreciated. Looking forward to your reply.

[yupenghe]

Could you try recompiling run_rms_tests.out to see if the issue is fixed?
https://github.com/yupenghe/methylpy#optional-step---compile-rmscpp