Error in `python': double free or corruption (out): 0x00002aaab2137e20

[msantorsola]

Hello @RMBarnard,

I am trying to run rareSim on:

NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"

with the following setup

name: RAREsim_env
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - conda-forge::r-base=4.2.2
  - conda-forge::r-devtools=2.4.5
  - conda-forge::python=3.11.0
  - conda-forge::cython=0.29.32

After the installion

python setup.py install

I tried to run raresim on the test data:

python convert.py -i lib/raresim/test/data/Simulated_80k_9.controls.haps.gz -o Simulated_80k_9.controls.haps.gz.sm

getting the error

*** Error in `python': double free or corruption (out): 0x00002aaab2137e20 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x2aaaab87d489]
/home/santorsola/.conda/envs/RAREsim_env/lib/libz.so.1(+0xf02e)[0x2aaaaac7402e]
/home/santorsola/.conda/envs/RAREsim_env/lib/libz.so.1(gzclose_r+0x3d)[0x2aaaaac74e6d]
/home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/site-packages/rareSim-0.0.0-py3.11-linux-x86_64.egg/rareSim.cpython-311-x86_64-linux-gnu.so(read_compressed_matrix+0xf8)[0x2aaaaac46708]
/home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/site-packages/rareSim-0.0.0-py3.11-linux-x86_64.egg/rareSim.cpython-311-x86_64-linux-gnu.so(+0x162bf)[0x2aaaaac542bf]
python(_PyObject_MakeTpCall+0x22b)[0x55555573187b]
python(_PyEval_EvalFrameDefault+0x319e)[0x55555574169e]
python(+0x1e61fb)[0x55555573a1fb]
python(PyEval_EvalCode+0x9f)[0x5555558049af]
python(+0x2d3479)[0x555555827479]
python(+0x2cf724)[0x555555823724]
python(+0x2e47d2)[0x5555558387d2]
python(_PyRun_SimpleFileObject+0x1af)[0x55555583812f]
python(_PyRun_AnyFileObject+0x43)[0x555555837f03]
python(Py_RunMain+0x2ec)[0x55555583206c]
python(Py_BytesMain+0x39)[0x5555557f33f9]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2aaaab81e3d5]
python(+0x29f2a1)[0x5555557f32a1]
======= Memory map: ========
2aaaaaaab000-2aaaaaacd000 r-xp 00000000 08:06 134218507                  /usr/lib64/ld-2.17.so
2aaaaaacd000-2aaaaaacf000 r-xp 00000000 00:00 0                          [vdso]
2aaaaaacf000-2aaaaaaf2000 rw-p 00000000 00:00 0 
2aaaaaaf4000-2aaaaac3e000 rw-p 00000000 00:00 0 
2aaaaac3e000-2aaaaac44000 r--p 00000000 00:2a 17283055499167043404       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/site-packages/rareSim-0.0.0-py3.11-linux-x86_64.egg/rareSim.cpython-311-x86_64-linux-gnu.so
2aaaaac44000-2aaaaac5a000 r-xp 00006000 00:2a 17283055499167043404       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/site-packages/rareSim-0.0.0-py3.11-linux-x86_64.egg/rareSim.cpython-311-x86_64-linux-gnu.so
2aaaaac5a000-2aaaaac62000 r--p 0001c000 00:2a 17283055499167043404       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/site-packages/rareSim-0.0.0-py3.11-linux-x86_64.egg/rareSim.cpython-311-x86_64-linux-gnu.so
2aaaaac62000-2aaaaac63000 r--p 00024000 00:2a 17283055499167043404       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/site-packages/rareSim-0.0.0-py3.11-linux-x86_64.egg/rareSim.cpython-311-x86_64-linux-gnu.so
2aaaaac63000-2aaaaac65000 rw-p 00025000 00:2a 17283055499167043404       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/site-packages/rareSim-0.0.0-py3.11-linux-x86_64.egg/rareSim.cpython-311-x86_64-linux-gnu.so
2aaaaac65000-2aaaaac68000 r--p 00000000 00:2a 3087942793824374416        /home/santorsola/.conda/envs/RAREsim_env/lib/libz.so.1.2.13
2aaaaac68000-2aaaaac76000 r-xp 00003000 00:2a 3087942793824374416        /home/santorsola/.conda/envs/RAREsim_env/lib/libz.so.1.2.13
2aaaaac76000-2aaaaac7d000 r--p 00011000 00:2a 3087942793824374416        /home/santorsola/.conda/envs/RAREsim_env/lib/libz.so.1.2.13
2aaaaac7d000-2aaaaac7e000 r--p 00017000 00:2a 3087942793824374416        /home/santorsola/.conda/envs/RAREsim_env/lib/libz.so.1.2.13
2aaaaac7e000-2aaaaac7f000 rw-p 00018000 00:2a 3087942793824374416        /home/santorsola/.conda/envs/RAREsim_env/lib/libz.so.1.2.13
2aaaaac7f000-2aaaaac81000 r--p 00000000 00:2a 12791344906923180067       /home/santorsola/.conda/envs/RAREsim_env/lib/libbz2.so.1.0.8
2aaaaac81000-2aaaaac8f000 r-xp 00002000 00:2a 12791344906923180067       /home/santorsola/.conda/envs/RAREsim_env/lib/libbz2.so.1.0.8
2aaaaac8f000-2aaaaac91000 r--p 00010000 00:2a 12791344906923180067       /home/santorsola/.conda/envs/RAREsim_env/lib/libbz2.so.1.0.8
2aaaaac91000-2aaaaac92000 r--p 00011000 00:2a 12791344906923180067       /home/santorsola/.conda/envs/RAREsim_env/lib/libbz2.so.1.0.8
2aaaaac92000-2aaaaac93000 rw-p 00012000 00:2a 12791344906923180067       /home/santorsola/.conda/envs/RAREsim_env/lib/libbz2.so.1.0.8
2aaaaac93000-2aaaaac97000 r--p 00000000 00:2a 2712163331505818732        /home/santorsola/.conda/envs/RAREsim_env/lib/liblzma.so.5.2.6
2aaaaac97000-2aaaaacae000 r-xp 00004000 00:2a 2712163331505818732        /home/santorsola/.conda/envs/RAREsim_env/lib/liblzma.so.5.2.6
2aaaaacae000-2aaaaacb9000 r--p 0001b000 00:2a 2712163331505818732        /home/santorsola/.conda/envs/RAREsim_env/lib/liblzma.so.5.2.6
2aaaaacb9000-2aaaaacba000 ---p 00026000 00:2a 2712163331505818732        /home/santorsola/.conda/envs/RAREsim_env/lib/liblzma.so.5.2.6
2aaaaacba000-2aaaaacbb000 r--p 00026000 00:2a 2712163331505818732        /home/santorsola/.conda/envs/RAREsim_env/lib/liblzma.so.5.2.6
2aaaaacbb000-2aaaaacbc000 rw-p 00027000 00:2a 2712163331505818732        /home/santorsola/.conda/envs/RAREsim_env/lib/liblzma.so.5.2.6
2aaaaacbc000-2aaaaacbe000 r--p 00000000 00:2a 7526024194282183601        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_bisect.cpython-311-x86_64-linux-gnu.so
2aaaaacbe000-2aaaaacbf000 r-xp 00002000 00:2a 7526024194282183601        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_bisect.cpython-311-x86_64-linux-gnu.so
2aaaaacbf000-2aaaaacc0000 r--p 00003000 00:2a 7526024194282183601        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_bisect.cpython-311-x86_64-linux-gnu.so
2aaaaacc0000-2aaaaacc1000 r--p 00003000 00:2a 7526024194282183601        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_bisect.cpython-311-x86_64-linux-gnu.so
2aaaaacc1000-2aaaaacc2000 rw-p 00004000 00:2a 7526024194282183601        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_bisect.cpython-311-x86_64-linux-gnu.so
2aaaaacc2000-2aaaaacc4000 r--p 00000000 00:2a 14480133864851379061       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_random.cpython-311-x86_64-linux-gnu.so
2aaaaacc4000-2aaaaacc6000 r-xp 00002000 00:2a 14480133864851379061       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_random.cpython-311-x86_64-linux-gnu.so
2aaaaacc6000-2aaaaacc7000 r--p 00004000 00:2a 14480133864851379061       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_random.cpython-311-x86_64-linux-gnu.so
2aaaaacc7000-2aaaaacc8000 r--p 00004000 00:2a 14480133864851379061       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_random.cpython-311-x86_64-linux-gnu.so
2aaaaacc8000-2aaaaacc9000 rw-p 00005000 00:2a 14480133864851379061       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_random.cpython-311-x86_64-linux-gnu.so
2aaaaaccc000-2aaaaaccd000 r--p 00021000 08:06 134218507                  /usr/lib64/ld-2.17.so
2aaaaaccd000-2aaaaacce000 rw-p 00022000 08:06 134218507                  /usr/lib64/ld-2.17.so
2aaaaacce000-2aaaaaccf000 rw-p 00000000 00:00 0 
2aaaaaccf000-2aaaaace6000 r-xp 00000000 08:06 134218581                  /usr/lib64/libpthread-2.17.so
2aaaaace6000-2aaaaaee5000 ---p 00017000 08:06 134218581                  /usr/lib64/libpthread-2.17.so
2aaaaaee5000-2aaaaaee6000 r--p 00016000 08:06 134218581                  /usr/lib64/libpthread-2.17.so
2aaaaaee6000-2aaaaaee7000 rw-p 00017000 08:06 134218581                  /usr/lib64/libpthread-2.17.so
2aaaaaee7000-2aaaaaeeb000 rw-p 00000000 00:00 0 
2aaaaaeeb000-2aaaaaeed000 r-xp 00000000 08:06 134218534                  /usr/lib64/libdl-2.17.so
2aaaaaeed000-2aaaab0ed000 ---p 00002000 08:06 134218534                  /usr/lib64/libdl-2.17.so
2aaaab0ed000-2aaaab0ee000 r--p 00002000 08:06 134218534                  /usr/lib64/libdl-2.17.so
2aaaab0ee000-2aaaab0ef000 rw-p 00003000 08:06 134218534                  /usr/lib64/libdl-2.17.so
2aaaab0ef000-2aaaab0f1000 r-xp 00000000 08:06 134218603                  /usr/lib64/libutil-2.17.so
2aaaab0f1000-2aaaab2f0000 ---p 00002000 08:06 134218603                  /usr/lib64/libutil-2.17.so
2aaaab2f0000-2aaaab2f1000 r--p 00001000 08:06 134218603                  /usr/lib64/libutil-2.17.so
2aaaab2f1000-2aaaab2f2000 rw-p 00002000 08:06 134218603                  /usr/lib64/libutil-2.17.so
2aaaab2f2000-2aaaab2f9000 r-xp 00000000 08:06 134218589                  /usr/lib64/librt-2.17.so
2aaaab2f9000-2aaaab4f8000 ---p 00007000 08:06 134218589                  /usr/lib64/librt-2.17.so
2aaaab4f8000-2aaaab4f9000 r--p 00006000 08:06 134218589                  /usr/lib64/librt-2.17.so
2aaaab4f9000-2aaaab4fa000 rw-p 00007000 08:06 134218589                  /usr/lib64/librt-2.17.so
2aaaab4fa000-2aaaab5fb000 r-xp 00000000 08:06 134218538                  /usr/lib64/libm-2.17.so
2aaaab5fb000-2aaaab7fa000 ---p 00101000 08:06 134218538                  /usr/lib64/libm-2.17.so
2aaaab7fa000-2aaaab7fb000 r--p 00100000 08:06 134218538                  /usr/lib64/libm-2.17.so
2aaaab7fb000-2aaaab7fc000 rw-p 00101000 08:06 134218538                  /usr/lib64/libm-2.17.so
2aaaab7fc000-2aaaab9be000 r-xp 00000000 08:06 134218522                  /usr/lib64/libc-2.17.so
2aaaab9be000-2aaaabbbe000 ---p 001c2000 08:06 134218522                  /usr/lib64/libc-2.17.so
2aaaabbbe000-2aaaabbc2000 r--p 001c2000 08:06 134218522                  /usr/lib64/libc-2.17.so
2aaaabbc2000-2aaaabbc4000 rw-p 001c6000 08:06 134218522                  /usr/lib64/libc-2.17.so
2aaaabbc4000-2aaaabbc9000 rw-p 00000000 00:00 0 
2aaaabbc9000-2aaab20f3000 r--p 00000000 08:06 1073742623                 /usr/lib/locale/locale-archive
2aaab20f3000-2aaab21f3000 rw-p 00000000 00:00 0 
2aaab21f3000-2aaab21f7000 r--p 00000000 00:2a 9662580320724510658        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/math.cpython-311-x86_64-linux-gnu.so
2aaab21f7000-2aaab21ff000 r-xp 00004000 00:2a 9662580320724510658        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/math.cpython-311-x86_64-linux-gnu.so
2aaab21ff000-2aaab2204000 r--p 0000c000 00:2a 9662580320724510658        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/math.cpython-311-x86_64-linux-gnu.so
2aaab2204000-2aaab2205000 r--p 00010000 00:2a 9662580320724510658        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/math.cpython-311-x86_64-linux-gnu.so
2aaab2205000-2aaab2206000 rw-p 00011000 00:2a 9662580320724510658        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/math.cpython-311-x86_64-linux-gnu.so
2aaab2206000-2aaab2208000 r--p 00000000 00:2a 14467581900901550953       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_sha512.cpython-311-x86_64-linux-gnu.so
2aaab2208000-2aaab220c000 r-xp 00002000 00:2a 14467581900901550953       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_sha512.cpython-311-x86_64-linux-gnu.so
2aaab220c000-2aaab220d000 r--p 00006000 00:2a 14467581900901550953       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_sha512.cpython-311-x86_64-linux-gnu.so
2aaab220d000-2aaab220e000 r--p 00006000 00:2a 14467581900901550953       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_sha512.cpython-311-x86_64-linux-gnu.so
2aaab220e000-2aaab220f000 rw-p 00007000 00:2a 14467581900901550953       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_sha512.cpython-311-x86_64-linux-gnu.so
2aaab220f000-2aaab230f000 rw-p 00000000 00:00 0 
2aaab230f000-2aaab2312000 r--p 00000000 00:2a 15069737546547859123       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/zlib.cpython-311-x86_64-linux-gnu.so
2aaab2312000-2aaab2316000 r-xp 00003000 00:2a 15069737546547859123       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/zlib.cpython-311-x86_64-linux-gnu.so
2aaab2316000-2aaab2319000 r--p 00007000 00:2a 15069737546547859123       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/zlib.cpython-311-x86_64-linux-gnu.so
2aaab2319000-2aaab231a000 r--p 00009000 00:2a 15069737546547859123       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/zlib.cpython-311-x86_64-linux-gnu.so
2aaab231a000-2aaab231b000 rw-p 0000a000 00:2a 15069737546547859123       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/zlib.cpython-311-x86_64-linux-gnu.so
2aaab231b000-2aaab231d000 r--p 00000000 00:2a 8937699498426330701        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_bz2.cpython-311-x86_64-linux-gnu.so
2aaab231d000-2aaab231f000 r-xp 00002000 00:2a 8937699498426330701        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_bz2.cpython-311-x86_64-linux-gnu.so
2aaab231f000-2aaab2321000 r--p 00004000 00:2a 8937699498426330701        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_bz2.cpython-311-x86_64-linux-gnu.so
2aaab2321000-2aaab2322000 r--p 00005000 00:2a 8937699498426330701        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_bz2.cpython-311-x86_64-linux-gnu.so
2aaab2322000-2aaab2323000 rw-p 00006000 00:2a 8937699498426330701        /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_bz2.cpython-311-x86_64-linux-gnu.so
2aaab2323000-2aaab2326000 r--p 00000000 00:2a 13037353082354309650       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_lzma.cpython-311-x86_64-linux-gnu.so
2aaab2326000-2aaab232b000 r-xp 00003000 00:2a 13037353082354309650       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_lzma.cpython-311-x86_64-linux-gnu.so
2aaab232b000-2aaab232e000 r--p 00008000 00:2a 13037353082354309650       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_lzma.cpython-311-x86_64-linux-gnu.so
2aaab232e000-2aaab232f000 r--p 0000a000 00:2a 13037353082354309650       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_lzma.cpython-311-x86_64-linux-gnu.so
2aaab232f000-2aaab2330000 rw-p 0000b000 00:2a 13037353082354309650       /home/santorsola/.conda/envs/RAREsim_env/lib/python3.11/lib-dynload/_lzma.cpython-311-x86_64-linux-gnu.so
2aaab2330000-2aaab2334000 r--p 00000000 00:2a 471252549003562817         /home/santorsola/.conda/envs/RAREsim_env/lib/libgcc_s.so.1
2aaab2334000-2aaab2344000 r-xp 00004000 00:2a 471252549003562817         /home/santorsola/.conda/envs/RAREsim_env/lib/libgcc_s.so.1
2aaab2344000-2aaab2347000 r--p 00014000 00:2a 471252549003562817         /home/santorsola/.conda/envs/RAREsim_env/lib/libgcc_s.so.1
2aaab2347000-2aaab2348000 r--p 00016000 00:2a 471252549003562817         /home/santorsola/.conda/envs/RAREsim_env/lib/libgcc_s.so.1
2aaab2348000-2aaab2349000 rw-p 00017000 00:2a 471252549003562817         /home/santorsola/.conda/envs/RAREsim_env/lib/libgcc_s.so.1
2aaab4000000-2aaab4021000 rw-p 00000000 00:00 0 
2aaab4021000-2aaab8000000 ---p 00000000 00:00 0 
555555554000-555555644000 r--p 00000000 00:2a 1583022007723825179        /home/santorsola/.conda/envs/RAREsim_env/bin/python3.11
555555644000-555555895000 r-xp 000f0000 00:2a 1583022007723825179        /home/santorsola/.conda/envs/RAREsim_env/bin/python3.11
555555895000-555555982000 r--p 00341000 00:2a 1583022007723825179        /home/santorsola/.conda/envs/RAREsim_env/bin/python3.11
555555982000-5555559b1000 r--p 0042e000 00:2a 1583022007723825179        /home/santorsola/.conda/envs/RAREsim_env/bin/python3.11
5555559b1000-555555ae1000 rw-p 0045d000 00:2a 1583022007723825179        /home/santorsola/.conda/envs/RAREsim_env/bin/python3.11
555555ae1000-555555ce8000 rw-p 00000000 00:00 0                          [heap]
7ffffffdd000-7ffffffff000 rw-p 00000000 00:00 0                          [stack]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)

How can I fix it? Thank you

[RMBarnard]

Try to run using "python3" instead of "python" and let me know if that changes anything.

[msantorsola]

*** Error in `python3': double free or corruption (out): 0x00002aaab2137e20 ***

[msantorsola]

A similar error when using test data in https://github.com/meganmichelle/RAREsim

python /home/santorsola/data_simulation/tools/raresim/convert.py -i Simulated_example.controls.haps.gz     -o Simulated_example.controls.haps.gz.sm

*** Error in `python': munmap_chunk(): invalid pointer: 0x00002aaab22591f0***

[RMBarnard]

I see that you are using Python 3.11 which raresim has not yet been tested on. I have done all of my building and testing using Python 3.10. Perhaps changing to this version might help resolve this issue?