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wtsi-npg / baton

iRODS client programs and API
http://wtsi-npg.github.io/baton
GNU General Public License v2.0
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munmap_chunk(): invalid pointer error when running baton-do #204

Closed kript closed 5 years ago

kript commented 6 years ago

Not sure if I'm holding this wrong, and apologies if so, but I get a rather unexpected error when running baton-do;

cat /tmp/jc18_JSDC_test//CPLVQ5.json | jq .
{
  "target": [
    {
      "data_object": "0.txt",
      "file": "0.txt",
      "collection:": "/seq-dev/home/jc18#Sanger1",
      "directory": "/tmp/jc18_JSDC_test/CPLVQ5"
    },
    {
      "data_object": "1.txt",
      "file": "1.txt",
      "collection:": "/seq-dev/home/jc18#Sanger1",
      "directory": "/tmp/jc18_JSDC_test/CPLVQ5"
    },
    {
      "data_object": "2.txt",
      "file": "2.txt",
      "collection:": "/seq-dev/home/jc18#Sanger1",
      "directory": "/tmp/jc18_JSDC_test/CPLVQ5"
    },
    {
      "data_object": "3.txt",
      "file": "3.txt",
      "collection:": "/seq-dev/home/jc18#Sanger1",
      "directory": "/tmp/jc18_JSDC_test/CPLVQ5"
    },
    {
      "data_object": "4.txt",
      "file": "4.txt",
      "collection:": "/seq-dev/home/jc18#Sanger1",
      "directory": "/tmp/jc18_JSDC_test/CPLVQ5"
    },
    {
      "data_object": "5.txt",
      "file": "5.txt",
      "collection:": "/seq-dev/home/jc18#Sanger1",
      "directory": "/tmp/jc18_JSDC_test/CPLVQ5"
    },
    {
      "data_object": "6.txt",
      "file": "6.txt",
      "collection:": "/seq-dev/home/jc18#Sanger1",
      "directory": "/tmp/jc18_JSDC_test/CPLVQ5"
    },
    {
      "data_object": "7.txt",
      "file": "7.txt",
      "collection:": "/seq-dev/home/jc18#Sanger1",
      "directory": "/tmp/jc18_JSDC_test/CPLVQ5"
    },
    {
      "data_object": "8.txt",
      "file": "8.txt",
      "collection:": "/seq-dev/home/jc18#Sanger1",
      "directory": "/tmp/jc18_JSDC_test/CPLVQ5"
    },
    {
      "data_object": "9.txt",
      "file": "9.txt",
      "collection:": "/seq-dev/home/jc18#Sanger1",
      "directory": "/tmp/jc18_JSDC_test/CPLVQ5"
    }
  ],
  "operation": "put"
}
cat /tmp/jc18_JSDC_test//CPLVQ5.json | /software/npg/20180625/bin/baton-do --verbose
*** glibc detected *** /software/npg/20180625/bin/baton-do: munmap_chunk(): invalid pointer: 0x00007ffd154d3ef0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7da66)[0x7fac3d015a66]
/software/sciops/pkg/baton/1.1.0/bin/../lib/libbaton.so.0(baton_json_dispatch_op+0x40)[0x7fac3ed453b0]
/software/sciops/pkg/baton/1.1.0/bin/../lib/libbaton.so.0(do_operation+0xd4)[0x7fac3ed44754]
/software/npg/20180625/bin/baton-do[0x40141b]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fac3cfb97ed]
/software/npg/20180625/bin/baton-do[0x4014b5]
======= Memory map: ========
00400000-00403000 r-xp 00000000 00:17 35030860                           /software/sciops/pkg/baton/1.1.0/bin/baton-do
00602000-00603000 rw-p 00002000 00:17 35030860                           /software/sciops/pkg/baton/1.1.0/bin/baton-do
0167c000-0171c000 rw-p 00000000 00:00 0                                  [heap]
7fac3b6b0000-7fac3b7f6000 r-xp 00000000 08:06 151036985                  /opt/renci/icommands/plugins/auth/libkrb.so
7fac3b7f6000-7fac3b9f6000 ---p 00146000 08:06 151036985                  /opt/renci/icommands/plugins/auth/libkrb.so
7fac3b9f6000-7fac3b9fb000 r--p 00146000 08:06 151036985                  /opt/renci/icommands/plugins/auth/libkrb.so
7fac3b9fb000-7fac3ba03000 rw-p 0014b000 08:06 151036985                  /opt/renci/icommands/plugins/auth/libkrb.so
7fac3ba03000-7fac3ba0c000 rw-p 00000000 00:00 0 
7fac3ba10000-7fac3ba32000 r-xp 00000000 08:06 201883666                  /opt/renci/icommands/plugins/network/libtcp.so
7fac3ba32000-7fac3bc31000 ---p 00022000 08:06 201883666                  /opt/renci/icommands/plugins/network/libtcp.so
7fac3bc31000-7fac3bc33000 r--p 00021000 08:06 201883666                  /opt/renci/icommands/plugins/network/libtcp.so
7fac3bc33000-7fac3bc34000 rw-p 00023000 08:06 201883666                  /opt/renci/icommands/plugins/network/libtcp.so
7fac3bc38000-7fac3bc3f000 r-xp 00000000 08:06 251723810                  /lib/x86_64-linux-gnu/libnss_dns-2.15.so
7fac3bc3f000-7fac3be3e000 ---p 00007000 08:06 251723810                  /lib/x86_64-linux-gnu/libnss_dns-2.15.so
7fac3be3e000-7fac3be3f000 r--p 00006000 08:06 251723810                  /lib/x86_64-linux-gnu/libnss_dns-2.15.so
7fac3be3f000-7fac3be40000 rw-p 00007000 08:06 251723810                  /lib/x86_64-linux-gnu/libnss_dns-2.15.so
7fac3be40000-7fac3be4b000 r-xp 00000000 08:06 251730967                  /lib/x86_64-linux-gnu/libnss_files-2.15.so
7fac3be4b000-7fac3c04a000 ---p 0000b000 08:06 251730967                  /lib/x86_64-linux-gnu/libnss_files-2.15.so
7fac3c04a000-7fac3c04b000 r--p 0000a000 08:06 251730967                  /lib/x86_64-linux-gnu/libnss_files-2.15.so
7fac3c04b000-7fac3c04c000 rw-p 0000b000 08:06 251730967                  /lib/x86_64-linux-gnu/libnss_files-2.15.so
7fac3c050000-7fac3c068000 r-xp 00000000 08:06 251723814                  /lib/x86_64-linux-gnu/libresolv-2.15.so
7fac3c068000-7fac3c268000 ---p 00018000 08:06 251723814                  /lib/x86_64-linux-gnu/libresolv-2.15.so
7fac3c268000-7fac3c269000 r--p 00018000 08:06 251723814                  /lib/x86_64-linux-gnu/libresolv-2.15.so
7fac3c269000-7fac3c26a000 rw-p 00019000 08:06 251723814                  /lib/x86_64-linux-gnu/libresolv-2.15.so
7fac3c26a000-7fac3c270000 rw-p 00000000 00:00 0 
7fac3c270000-7fac3c273000 r-xp 00000000 08:06 251659316                  /lib/x86_64-linux-gnu/libkeyutils.so.1.4
7fac3c273000-7fac3c472000 ---p 00003000 08:06 251659316                  /lib/x86_64-linux-gnu/libkeyutils.so.1.4
7fac3c472000-7fac3c473000 r--p 00002000 08:06 251659316                  /lib/x86_64-linux-gnu/libkeyutils.so.1.4
7fac3c473000-7fac3c474000 rw-p 00003000 08:06 251659316                  /lib/x86_64-linux-gnu/libkeyutils.so.1.4
7fac3c477000-7fac3c478000 rw-p 00000000 00:00 0 
7fac3c478000-7fac3c47f000 r-xp 00000000 08:06 150996055                  /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7fac3c47f000-7fac3c67e000 ---p 00007000 08:06 150996055                  /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7fac3c67e000-7fac3c67f000 r--p 00006000 08:06 150996055                  /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7fac3c67f000-7fac3c680000 rw-p 00007000 08:06 150996055                  /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7fac3c680000-7fac3c683000 r-xp 00000000 08:06 251659286                  /lib/x86_64-linux-gnu/libcom_err.so.2.1
7fac3c683000-7fac3c882000 ---p 00003000 08:06 251659286                  /lib/x86_64-linux-gnu/libcom_err.so.2.1
7fac3c882000-7fac3c883000 r--p 00002000 08:06 251659286                  /lib/x86_64-linux-gnu/libcom_err.so.2.1
7fac3c883000-7fac3c884000 rw-p 00003000 08:06 251659286                  /lib/x86_64-linux-gnu/libcom_err.so.2.1
7fac3c888000-7fac3c8ad000 r-xp 00000000 08:06 150995992                  /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7fac3c8ad000-7fac3caad000 ---p 00025000 08:06 150995992                  /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7fac3caad000-7fac3caae000 r--p 00025000 08:06 150995992                  /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7fac3caae000-7fac3caaf000 rw-p 00026000 08:06 150995992                  /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7fac3caaf000-7fac3cab0000 rw-p 00000000 00:00 0 
7fac3cab0000-7fac3cb74000 r-xp 00000000 08:06 150996052                  /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7fac3cb74000-7fac3cd73000 ---p 000c4000 08:06 150996052                  /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7fac3cd73000-7fac3cd7d000 r--p 000c3000 08:06 150996052                  /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7fac3cd7d000-7fac3cd7e000 rw-p 000cd000 08:06 150996052                  /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7fac3cd80000-7fac3cd96000 r-xp 00000000 08:06 251659337                  /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fac3cd96000-7fac3cf95000 ---p 00016000 08:06 251659337                  /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fac3cf95000-7fac3cf96000 r--p 00015000 08:06 251659337                  /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fac3cf96000-7fac3cf97000 rw-p 00016000 08:06 251659337                  /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fac3cf98000-7fac3d14f000 r-xp 00000000 08:06 251730949                  /lib/x86_64-linux-gnu/libc-2.15.so
7fac3d14f000-7fac3d34e000 ---p 001b7000 08:06 251730949                  /lib/x86_64-linux-gnu/libc-2.15.so
7fac3d34e000-7fac3d352000 r--p 001b6000 08:06 251730949                  /lib/x86_64-linux-gnu/libc-2.15.so
7fac3d352000-7fac3d354000 rw-p 001ba000 08:06 251730949                  /lib/x86_64-linux-gnu/libc-2.15.so
7fac3d354000-7fac3d359000 rw-p 00000000 00:00 0 
7fac3d360000-7fac3d375000 r-xp 00000000 08:06 251659284                  /lib/x86_64-linux-gnu/libgcc_s.so.1
7fac3d375000-7fac3d574000 ---p 00015000 08:06 251659284                  /lib/x86_64-linux-gnu/libgcc_s.so.1
7fac3d574000-7fac3d575000 r--p 00014000 08:06 251659284                  /lib/x86_64-linux-gnu/libgcc_s.so.1
7fac3d575000-7fac3d576000 rw-p 00015000 08:06 251659284                  /lib/x86_64-linux-gnu/libgcc_s.so.1
7fac3d578000-7fac3d65a000 r-xp 00000000 08:06 150995987                  /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7fac3d65a000-7fac3d859000 ---p 000e2000 08:06 150995987                  /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7fac3d859000-7fac3d861000 r--p 000e1000 08:06 150995987                  /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7fac3d861000-7fac3d863000 rw-p 000e9000 08:06 150995987                  /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16
7fac3d863000-7fac3d878000 rw-p 00000000 00:00 0 
7fac3d878000-7fac3d87f000 r-xp 00000000 08:06 251661329                  /lib/x86_64-linux-gnu/librt-2.15.so
7fac3d87f000-7fac3da7e000 ---p 00007000 08:06 251661329                  /lib/x86_64-linux-gnu/librt-2.15.so
7fac3da7e000-7fac3da7f000 r--p 00006000 08:06 251661329                  /lib/x86_64-linux-gnu/librt-2.15.so
7fac3da7f000-7fac3da80000 rw-p 00007000 08:06 251661329                  /lib/x86_64-linux-gnu/librt-2.15.so
7fac3da80000-7fac3db7b000 r-xp 00000000 08:06 251730953                  /lib/x86_64-linux-gnu/libm-2.15.so
7fac3db7b000-7fac3dd7a000 ---p 000fb000 08:06 251730953                  /lib/x86_64-linux-gnu/libm-2.15.so
7fac3dd7a000-7fac3dd7b000 r--p 000fa000 08:06 251730953                  /lib/x86_64-linux-gnu/libm-2.15.so
7fac3dd7b000-7fac3dd7c000 rw-p 000fb000 08:06 251730953                  /lib/x86_64-linux-gnu/libm-2.15.so
7fac3dd80000-7fac3dd82000 r-xp 00000000 08:06 251723806                  /lib/x86_64-linux-gnu/libdl-2.15.so
7fac3dd82000-7fac3df82000 ---p 00002000 08:06 251723806                  /lib/x86_64-linux-gnu/libdl-2.15.so
7fac3df82000-7fac3df83000 r--p 00002000 08:06 251723806                  /lib/x86_64-linux-gnu/libdl-2.15.so
7fac3df83000-7fac3df84000 rw-p 00003000 08:06 251723806                  /lib/x86_64-linux-gnu/libdl-2.15.so
7fac3df88000-7fac3dfa0000 r-xp 00000000 08:06 251730961                  /lib/x86_64-linux-gnu/libpthread-2.15.so
7fac3dfa0000-7fac3e19f000 ---p 00018000 08:06 251730961                  /lib/x86_64-linux-gnu/libpthread-2.15.so
7fac3e19f000-7fac3e1a0000 r--p 00017000 08:06 251730961                  /lib/x86_64-linux-gnu/libpthread-2.15.so
7fac3e1a0000-7fac3e1a1000 rw-p 00018000 08:06 251730961                  /lib/x86_64-linux-gnu/libpthread-2.15.so
7fac3e1a1000-7fac3e1a5000 rw-p 00000000 00:00 0 
7fac3e1a8000-7fac3e1e3000 r-xp 00000000 08:06 150996045                  /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7fac3e1e3000-7fac3e3e3000 ---p 0003b000 08:06 150996045                  /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7fac3e3e3000-7fac3e3e4000 r--p 0003b000 08:06 150996045                  /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7fac3e3e4000-7fac3e3e6000 rw-p 0003c000 08:06 150996045                  /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7fac3e3e8000-7fac3e3f4000 r-xp 00000000 00:17 18629151                   /software/sciops/pkg/baton/1.1.0/lib/libjansson.so.4.10.0
7fac3e3f4000-7fac3e5f4000 ---p 0000c000 00:17 18629151                   /software/sciops/pkg/baton/1.1.0/lib/libjansson.so.4.10.0
7fac3e5f4000-7fac3e5f5000 rw-p 0000c000 00:17 18629151                   /software/sciops/pkg/baton/1.1.0/lib/libjansson.so.4.10.0
7fac3e5f8000-7fac3e7ab000 r-xp 00000000 08:06 251660631                  /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7fac3e7ab000-7fac3e9ab000 ---p 001b3000 08:06 251660631                  /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7fac3e9ab000-7fac3e9c6000 r--p 001b3000 08:06 251660631                  /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7fac3e9c6000-7fac3e9d1000 rw-p 001ce000 08:06 251660631                  /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7fac3e9d1000-7fac3e9d5000 rw-p 00000000 00:00 0 
7fac3e9d8000-7fac3ea2d000 r-xp 00000000 08:06 251660633                  /lib/x86_64-linux-gnu/libssl.so.1.0.0
7fac3ea2d000-7fac3ec2d000 ---p 00055000 08:06 251660633                  /lib/x86_64-linux-gnu/libssl.so.1.0.0
7fac3ec2d000-7fac3ec30000 r--p 00055000 08:06 251660633                  /lib/x86_64-linux-gnu/libssl.so.1.0.0
7fac3ec30000-7fac3ec37000 rw-p 00058000 08:06 251660633                  /lib/x86_64-linux-gnu/libssl.so.1.0.0
7fac3ec38000-7fac3eefa000 r-xp 00000000 00:17 18629157                   /software/sciops/pkg/baton/1.1.0/lib/libbaton.so.0.0.0
7fac3eefa000-7fac3f0fa000 ---p 002c2000 00:17 18629157                   /software/sciops/pkg/baton/1.1.0/lib/libbaton.so.0.0.0
7fac3f0fa000-7fac3f111000 rw-p 002c2000 00:17 18629157                   /software/sciops/pkg/baton/1.1.0/lib/libbaton.so.0.0.0
7fac3f111000-7fac3f118000 rw-p 00000000 00:00 0 
7fac3f118000-7fac3f13a000 r-xp 00000000 08:06 251730965                  /lib/x86_64-linux-gnu/ld-2.15.so
7fac3f332000-7fac3f33a000 rw-p 00000000 00:00 0 
7fac3f33a000-7fac3f33b000 r--p 00022000 08:06 251730965                  /lib/x86_64-linux-gnu/ld-2.15.so
7fac3f33b000-7fac3f33d000 rw-p 00023000 08:06 251730965                  /lib/x86_64-linux-gnu/ld-2.15.so
7fac3f33d000-7fac3f342000 rw-p 00000000 00:00 0 
7ffd154b4000-7ffd154d5000 rw-p 00000000 00:00 0                          [stack]
7ffd155f8000-7ffd155f9000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted
keithj commented 6 years ago

Fixed by #205