*** Error in `../FastK': free(): corrupted unsorted chunks: 0x0000000001687480 *** when profiling sequences #8
Comments
|
Well shoot. I downloaded the data and ran it on my Mac laptop.
Unfortunately it ran just fine, with all output exactly corresponding
to yours save the seg-fault :-).
The problem is a very small one, so I doubt it is a disk space issue.
Can you please tell me what compiler, what OS, and what hardware?
If you know how to use your local debugger, compiling for debug (with -g),
and giving me a stack trace would potentially be useful.
Otherwise we could zoom and I could try to debug interactively with you
as my copilot. What time zone are you in? (I'm in Germany).
…-- Gene
On 4/9/21, 7:44 PM, chrisquince wrote:
Thanks for creating yet another incredibly useful looking bit of a
software :) I have been searching for a program with all this
functionality for a while but I have run into this issue. I have
created this as a new issue as I believe it is separate to the file
write to /tmp problem raised previously. I am getting corrupted memory
faults when try to profile the following sequences downloadable as:
wget https://ebitutorial.s3.climb.ac.uk/graph5.fasta
Running the command:
FastK -k51 graph5.fasta -v -T1 -p
I get:
------------------------------------------------------------------------
Partitioning 1 .fasta file into 1 parts
Determining minimizer scheme & partition for graph5
Estimate 1.703M 51-mers
Handling data in a single block
Using 5-minimizers with 1024 core prefixes
Phase 1: Partitioning K-mers into 1 Super-mer Files
There are 38 reads totalling 1,705,389 bps
| Part: 51-mer super-mers ave. length
0: 1,703,489 81,679 20.9
Sum: 1,703,489 81,679 20.9
Range 1,703,489 - 1,703,489 (0.00%)
|
Resources for phase: 0.076u 0.016s 0.108w 84.7%
Phase 2: Sorting & Counting K-mers in 1 blocks
| Part: wgt'd k-mers savings
0: 988,833 1.7
All: 988,833 1.7
|
Resources for phase: 0.312u 0.028s 0.368w 92.1%
Phase 4 (-p option): Merging Profile Fragments
The profiles occupy 160.35 KB
Segmentation fault (core dumped)
That may be the /tmp dir problem. If I point it at a drive with a
large amount (1 Tbp of free space) as temp dir with -P I get:
FastK -k51 graph5.fasta -v -P/mnt/chris-native/chris/tmp/ -T1 -p
Partitioning 1 .fasta file into 1 parts
Determining minimizer scheme & partition for graph5
Estimate 1.703M 51-mers
Handling data in a single block
Using 5-minimizers with 1024 core prefixes
Phase 1: Partitioning K-mers into 1 Super-mer Files
There are 38 reads totalling 1,705,389 bps
| Part: 51-mer super-mers ave. length
0: 1,703,489 81,679 20.9
Sum: 1,703,489 81,679 20.9
Range 1,703,489 - 1,703,489 (0.00%)
|
Resources for phase: 0.088u 0.008s 0.356w 26.9%
Phase 2: Sorting & Counting K-mers in 1 blocks
| Part: wgt'd k-mers savings
0: 988,833 1.7
All: 988,833 1.7
|
Resources for phase: 0.400u 0.076s 0.551w 86.4%
Phase 4 (-p option): Merging Profile Fragments
The profiles occupy 160.35 KB
*** Error in `../FastK': free(): corrupted unsorted chunks:
0x0000000001687480 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777f5)[0x7fb467d637f5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8038a)[0x7fb467d6c38a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7fb467d7058c]
../FastK[0x418bbb]
../FastK[0x40438a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fb467d0c840]
../FastK[0x404819]
======= Memory map: ========
00400000-004b2000 r-xp 00000000 00:2b 474411334
/mnt/gpfs/chris/repos/FASTK/FastK
006b1000-006b2000 r--p 000b1000 00:2b 474411334
/mnt/gpfs/chris/repos/FASTK/FastK
006b2000-006b3000 rw-p 000b2000 00:2b 474411334
/mnt/gpfs/chris/repos/FASTK/FastK
006b3000-006b6000 rw-p 00000000 00:00 0
01664000-02eac000 rw-p 00000000 00:00 0 [heap]
7fb35c000000-7fb35c021000 rw-p 00000000 00:00 0
7fb35c021000-7fb360000000 ---p 00000000 00:00 0
7fb361e85000-7fb461e86000 rw-p 00000000 00:00 0
7fb461e86000-7fb461e87000 ---p 00000000 00:00 0
7fb461e87000-7fb462687000 rw-p 00000000 00:00 0
7fb462df9000-7fb462e10000 r-xp 00000000 08:02 656120
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fb462e10000-7fb46300f000 ---p 00017000 08:02 656120
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fb46300f000-7fb463010000 r--p 00016000 08:02 656120
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fb463010000-7fb463011000 rw-p 00017000 08:02 656120
/lib/x86_64-linux-gnu/libgcc_s.so.1
7fb463011000-7fb46301a000 r-xp 00000000 08:02 654573
/lib/x86_64-linux-gnu/libcrypt-2.23.so
7fb46301a000-7fb463219000 ---p 00009000 08:02 654573
/lib/x86_64-linux-gnu/libcrypt-2.23.so
7fb463219000-7fb46321a000 r--p 00008000 08:02 654573
/lib/x86_64-linux-gnu/libcrypt-2.23.so
7fb46321a000-7fb46321b000 rw-p 00009000 08:02 654573
/lib/x86_64-linux-gnu/libcrypt-2.23.so
7fb46321b000-7fb463249000 rw-p 00000000 00:00 0
7fb463249000-7fb463319000 r-xp 00000000 08:02 134403
/usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
7fb463319000-7fb463518000 ---p 000d0000 08:02 134403
/usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
7fb463518000-7fb46351b000 r--p 000cf000 08:02 134403
/usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
7fb46351b000-7fb46351d000 rw-p 000d2000 08:02 134403
/usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
7fb46351d000-7fb46351e000 rw-p 00000000 00:00 0
7fb46351e000-7fb463565000 r-xp 00000000 08:02 137969
/usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
7fb463565000-7fb463764000 ---p 00047000 08:02 137969
/usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
7fb463764000-7fb463766000 r--p 00046000 08:02 137969
/usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
7fb463766000-7fb463768000 rw-p 00048000 08:02 137969
/usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
7fb463768000-7fb463769000 rw-p 00000000 00:00 0
7fb463769000-7fb463777000 r-xp 00000000 08:02 137959
/usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
7fb463777000-7fb463976000 ---p 0000e000 08:02 137959
/usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
7fb463976000-7fb463977000 r--p 0000d000 08:02 137959
/usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
7fb463977000-7fb463978000 rw-p 0000e000 08:02 137959
/usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
7fb463978000-7fb46399f000 r-xp 00000000 08:02 137965
/usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
7fb46399f000-7fb463b9f000 ---p 00027000 08:02 137965
/usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
7fb463b9f000-7fb463ba0000 r--p 00027000 08:02 137965
/usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
7fb463ba0000-7fb463ba1000 rw-p 00028000 08:02 137965
/usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
7fb463ba1000-7fb463ba8000 r-xp 00000000 08:02 133165
/usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7fb463ba8000-7fb463da7000 ---p 00007000 08:02 133165
/usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7fb463da7000-7fb463da8000 r--p 00006000 08:02 133165
/usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7fb463da8000-7fb463da9000 rw-p 00007000 08:02 133165
/usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7fb463da9000-7fb463dbe000 r-xp 00000000 08:02 145811
/usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
7fb463dbe000-7fb463fbd000 ---p 00015000 08:02 145811
/usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
7fb463fbd000-7fb463fbe000 r--p 00014000 08:02 145811
/usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
7fb463fbe000-7fb463fbf000 rw-p 00015000 08:02 145811
/usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
7fb463fbf000-7fb463fef000 r-xp 00000000 08:02 137955
/usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
7fb463fef000-7fb4641ef000 ---p 00030000 08:02 137955
/usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
7fb4641ef000-7fb4641f0000 r--p 00030000 08:02 137955
/usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
7fb4641f0000-7fb4641f1000 rw-p 00031000 08:02 137955
/usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
7fb4641f1000-7fb4641f2000 rw-p 00000000 00:00 0
7fb4641f2000-7fb464291000 r-xp 00000000 08:02 137952
/usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
7fb464291000-7fb464490000 ---p 0009f000 08:02 137952
/usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
7fb464490000-7fb464491000 r--p 0009e000 08:02 137952
/usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
7fb464491000-7fb464494000 rw-p 0009f000 08:02 137952
/usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
7fb464494000-7fb464518000 r-xp 00000000 08:02 137974
/usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
7fb464518000-7fb464717000 ---p 00084000 08:02 137974
/usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
7fb464717000-7fb46471a000 r--p 00083000 08:02 137974
/usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
7fb46471a000-7fb46471d000 rw-p 00086000 08:02 137974
/usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
7fb46471d000-7fb46471e000 rw-p 00000000 00:00 0
7fb46471e000-7fb464726000 r-xp 00000000 08:02 137979
/usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
7fb464726000-7fb464925000 ---p 00008000 08:02 137979
/usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
7fb464925000-7fb464926000 r--p 00007000 08:02 137979
/usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
7fb464926000-7fb464927000 rw-p 00008000 08:02 137979
/usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
7fb464927000-7fb46492a000 r-xp 00000000 08:02 660056
/lib/x86_64-linux-gnu/libkeyutils.so.1.5
7fb46492a000-7fb464b29000 ---p 00003000 08:02 660056
/lib/x86_64-linux-gnu/libkeyutils.so.1.5
7fb464b29000-7fb464b2a000 r--p 00002000 08:02 660056
/lib/x86_64-linux-gnu/libkeyutils.so.1.5
7fb464b2a000-7fb464b2b000 rw-p 00003000 08:02 660056
/lib/x86_64-linux-gnu/libkeyutils.so.1.5
7fb464b2b000-7fb464b3c000 r-xp 00000000 08:02 131781
/usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
7fb464b3c000-7fb464d3c000 ---p 00011000 08:02 131781
/usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
7fb464d3c000-7fb464d3d000 r--p 00011000 08:02 131781
/usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
7fb464d3d000-7fb464d3e000 rw-p 00012000 08:02 131781
/usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
7fb464d3e000-7fb464d97000 r-xp 00000000 08:02 137411
/usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
7fb464d97000-7fb464f96000 ---p 00059000 08:02 137411
/usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
7fb464f96000-7fb464fa0000 r--p 00058000 08:02 137411
/usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
7fb464fa0000-7fb464fa2000 rw-p 00062000 08:02 137411
/usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
7fb464fa2000-7fb464fdf000 r-xp 00000000 08:02 137984
/usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
7fb464fdf000-7fb4651df000 ---p 0003d000 08:02 137984
/usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
7fb4651df000-7fb4651e0000 r--p 0003d000 08:02 137984
/usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
7fb4651e0000-7fb4651e2000 rw-p 0003e000 08:02 137984
/usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
7fb4651e2000-7fb4651e3000 rw-p 00000000 00:00 0
7fb4651e3000-7fb4651fc000 r-xp 00000000 08:02 132347
/usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
7fb4651fc000-7fb4653fc000 ---p 00019000 08:02 132347
/usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
7fb4653fc000-7fb4653fd000 r--p 00019000 08:02 132347
/usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
7fb4653fd000-7fb4653fe000 rw-p 0001a000 08:02 132347
/usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
7fb4653fe000-7fb465415000 r-xp 00000000 08:02 655434
/lib/x86_64-linux-gnu/libresolv-2.23.so
7fb465415000-7fb465615000 ---p 00017000 08:02 655434
/lib/x86_64-linux-gnu/libresolv-2.23.so
7fb465615000-7fb465616000 r--p 00017000 08:02 655434
/lib/x86_64-linux-gnu/libresolv-2.23.so
7fb465616000-7fb465617000 rw-p 00018000 08:02 655434
/lib/x86_64-linux-gnu/libresolv-2.23.so
7fb465617000-7fb465619000 rw-p 00000000 00:00 0
7fb465619000-7fb465623000 r-xp 00000000 08:02 134938
/usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7fb465623000-7fb465822000 ---p 0000a000 08:02 134938
/usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7fb465822000-7fb465823000 r--p 00009000 08:02 134938
/usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7fb465823000-7fb465824000 rw-p 0000a000 08:02 134938
/usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7fb465824000-7fb465827000 r-xp 00000000 08:02 654290
/lib/x86_64-linux-gnu/libcom_err.so.2.1
7fb465827000-7fb465a26000 ---p 00003000 08:02 654290
/lib/x86_64-linux-gnu/libcom_err.so.2.1
7fb465a26000-7fb465a27000 r--p 00002000 08:02 654290
/lib/x86_64-linux-gnu/libcom_err.so.2.1
7fb465a27000-7fb465a28000 rw-p 00003000 08:02 654290
/lib/x86_64-linux-gnu/libcom_err.so.2.1
7fb465a28000-7fb465a54000 r-xp 00000000 08:02 132856
/usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7fb465a54000-7fb465c53000 ---p 0002c000 08:02 132856
/usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7fb465c53000-7fb465c55000 r--p 0002b000 08:02 132856
/usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7fb465c55000-7fb465c56000 rw-p 0002d000 08:02 132856
/usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7fb465c56000-7fb465c57000 rw-p 00000000 00:00 0
7fb465c57000-7fb465d1a000 r-xp 00000000 08:02 137943
/usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7fb465d1a000-7fb465f1a000 ---p 000c3000 08:02 137943
/usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7fb465f1a000-7fb465f27000 r--p 000c3000 08:02 137943
/usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7fb465f27000-7fb465f29000 rw-p 000d0000 08:02 137943
/usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7fb465f29000-7fb465fa8000 r-xp 00000000 08:02 133173
/usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
7fb465fa8000-7fb4661a7000 ---p 0007f000 08:02 133173
/usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
7fb4661a7000-7fb4661a8000 r--p 0007e000 08:02 133173
/usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
7fb4661a8000-7fb4661a9000 rw-p 0007f000 08:02 133173
/usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
7fb4661a9000-7fb4661dd000 r-xp 00000000 08:02 133193
/usr/lib/x86_64-linux-gnu/libnettle.so.6.2
7fb4661dd000-7fb4663dc000 ---p 00034000 08:02 133193
/usr/lib/x86_64-linux-gnu/libnettle.so.6.2
7fb4663dc000-7fb4663de000 r--p 00033000 08:02 133193
/usr/lib/x86_64-linux-gnu/libnettle.so.6.2
7fb4663de000-7fb4663df000 rw-p 00035000 08:02 133193
/usr/lib/x86_64-linux-gnu/libnettle.so.6.2
7fb4663df000-7fb466411000 r-xp 00000000 08:02 133179
/usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
7fb466411000-7fb466610000 ---p 00032000 08:02 133179
/usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
7fb466610000-7fb466611000 r--p 00031000 08:02 133179
/usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
7fb466611000-7fb466612000 rw-p 00032000 08:02 133179
/usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
7fb466612000-7fb466735000 r-xp 00000000 08:02 134875
/usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7fb466735000-7fb466934000 ---p 00123000 08:02 134875
/usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7fb466934000-7fb46693f000 r--p 00122000 08:02 134875
/usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7fb46693f000-7fb466941000 rw-p 0012d000 08:02 134875
/usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7fb466941000-7fb466942000 rw-p 00000000 00:00 0
7fb466942000-7fb46698f000 r-xp 00000000 08:02 131120
/usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
7fb46698f000-7fb466b8e000 ---p 0004d000 08:02 131120
/usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
7fb466b8e000-7fb466b90000 r--p 0004c000 08:02 131120
/usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
7fb466b90000-7fb466b91000 rw-p 0004e000 08:02 131120
/usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
7fb466b91000-7fb466b93000 rw-p 00000000 00:00 0
7fb466b93000-7fb466ba0000 r-xp 00000000 08:02 131171
/usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
7fb466ba0000-7fb466da0000 ---p 0000d000 08:02 131171
/usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
7fb466da0000-7fb466da1000 r--p 0000d000 08:02 131171
/usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
7fb466da1000-7fb466da2000 rw-p 0000e000 08:02 131171
/usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
7fb466da2000-7fb466de9000 r-xp 00000000 08:02 137935
/usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7fb466de9000-7fb466fe8000 ---p 00047000 08:02 137935
/usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7fb466fe8000-7fb466fea000 r--p 00046000 08:02 137935
/usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7fb466fea000-7fb466fec000 rw-p 00048000 08:02 137935
/usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7fb466fec000-7fb467207000 r-xp 00000000 08:02 654731
/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7fb467207000-7fb467406000 ---p 0021b000 08:02 654731
/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7fb467406000-7fb467422000 r--p 0021a000 08:02 654731
/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7fb467422000-7fb46742e000 rw-p 00236000 08:02 654731
/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7fb46742e000-7fb467431000 rw-p 00000000 00:00 0
7fb467431000-7fb46748f000 r-xp 00000000 08:02 654734
/lib/x86_64-linux-gnu/libssl.so.1.0.0
7fb46748f000-7fb46768f000 ---p 0005e000 08:02 654734
/lib/x86_64-linux-gnu/libssl.so.1.0.0
7fb46768f000-7fb467693000 r--p 0005e000 08:02 654734
/lib/x86_64-linux-gnu/libssl.so.1.0.0
7fb467693000-7fb467699000 rw-p 00062000 08:02 654734
/lib/x86_64-linux-gnu/libssl.so.1.0.0
7fb467699000-7fb4676b4000 r-xp 00000000 08:02 135071
/usr/lib/x86_64-linux-gnu/librtmp.so.1
7fb4676b4000-7fb4678b3000 ---p 0001b000 08:02 135071
/usr/lib/x86_64-linux-gnu/librtmp.so.1
7fb4678b3000-7fb4678b4000 r--p 0001a000 08:02 135071
/usr/lib/x86_64-linux-gnu/librtmp.so.1
7fb4678b4000-7fb4678b5000 rw-p 0001b000 08:02 135071
/usr/lib/x86_64-linux-gnu/librtmp.so.1
7fb4678b5000-7fb4678e6000 r-xp 00000000 08:02 161247
/usr/lib/x86_64-linux-gnu/libidn.so.11.6.15
7fb4678e6000-7fb467ae6000 ---p 00031000 08:02 161247
/usr/lib/x86_64-linux-gnu/libidn.so.11.6.15
7fb467ae6000-7fb467ae7000 r--p 00031000 08:02 161247
/usr/lib/x86_64-linux-gnu/libidn.so.11.6.15
7fb467ae7000-7fb467ae8000 rw-p 00032000 08:02 161247
/usr/lib/x86_64-linux-gnu/libidn.so.11.6.15
7fb467ae8000-7fb467aeb000 r-xp 00000000 08:02 654528
/lib/x86_64-linux-gnu/libdl-2.23.so
7fb467aeb000-7fb467cea000 ---p 00003000 08:02 654528
/lib/x86_64-linux-gnu/libdl-2.23.so
7fb467cea000-7fb467ceb000 r--p 00002000 08:02 654528
/lib/x86_64-linux-gnu/libdl-2.23.so
7fb467ceb000-7fb467cec000 rw-p 00003000 08:02 654528
/lib/x86_64-linux-gnu/libdl-2.23.so
7fb467cec000-7fb467eac000 r-xp 00000000 08:02 654530
/lib/x86_64-linux-gnu/libc-2.23.so
7fb467eac000-7fb4680ac000 ---p 001c0000 08:02 654530
/lib/x86_64-linux-gnu/libc-2.23.so
7fb4680ac000-7fb4680b0000 r--p 001c0000 08:02 654530
/lib/x86_64-linux-gnu/libc-2.23.so
7fb4680b0000-7fb4680b2000 rw-p 001c4000 08:02 654530
/lib/x86_64-linux-gnu/libc-2.23.so
7fb4680b2000-7fb4680b6000 rw-p 00000000 00:00 0
7fb4680b6000-7fb468124000 r-xp 00000000 08:02 137680
/usr/lib/x86_64-linux-gnu/libcurl.so.4.4.0
7fb468124000-7fb468324000 ---p 0006e000 08:02 137680
/usr/lib/x86_64-linux-gnu/libcurl.so.4.4.0
7fb468324000-7fb468327000 r--p 0006e000 08:02 137680
/usr/lib/x86_64-linux-gnu/libcurl.so.4.4.0
7fb468327000-7fb468328000 rw-p 00071000 08:02 137680
/usr/lib/x86_64-linux-gnu/libcurl.so.4.4.0
7fb468328000-7fb468349000 r-xp 00000000 08:02 654615
/lib/x86_64-linux-gnu/liblzma.so.5.0.0
7fb468349000-7fb468548000 ---p 00021000 08:02 654615
/lib/x86_64-linux-gnu/liblzma.so.5.0.0
7fb468548000-7fb468549000 r--p 00020000 08:02 654615
/lib/x86_64-linux-gnu/liblzma.so.5.0.0
7fb468549000-7fb46854a000 rw-p 00021000 08:02 654615
/lib/x86_64-linux-gnu/liblzma.so.5.0.0
7fb46854a000-7fb468559000 r-xp 00000000 08:02 654186
/lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fb468559000-7fb468758000 ---p 0000f000 08:02 654186
/lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fb468758000-7fb468759000 r--p 0000e000 08:02 654186
/lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fb468759000-7fb46875a000 rw-p 0000f000 08:02 654186
/lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fb46875a000-7fb468773000 r-xp 00000000 08:02 654834
/lib/x86_64-linux-gnu/libz.so.1.2.8
7fb468773000-7fb468972000 ---p 00019000 08:02 654834
/lib/x86_64-linux-gnu/libz.so.1.2.8
7fb468972000-7fb468973000 r--p 00018000 08:02 654834
/lib/x86_64-linux-gnu/libz.so.1.2.8
7fb468973000-7fb468974000 rw-p 00019000 08:02 654834
/lib/x86_64-linux-gnu/libz.so.1.2.8
7fb468974000-7fb46898c000 r-xp 00000000 08:02 654534
/lib/x86_64-linux-gnu/libpthread-2.23.so
7fb46898c000-7fb468b8b000 ---p 00018000 08:02 654534
/lib/x86_64-linux-gnu/libpthread-2.23.so
7fb468b8b000-7fb468b8c000 r--p 00017000 08:02 654534
/lib/x86_64-linux-gnu/libpthread-2.23.so
7fb468b8c000-7fb468b8d000 rw-p 00018000 08:02 654534
/lib/x86_64-linux-gnu/libpthread-2.23.so
7fb468b8d000-7fb468b91000 rw-p 00000000 00:00 0
7fb468b91000-7fb468bb7000 r-xp 00000000 08:02 655423
/lib/x86_64-linux-gnu/ld-2.23.so
7fb468d88000-7fb468d9b000 rw-p 00000000 00:00 0
7fb468db5000-7fb468db6000 rw-p 00000000 00:00 0
7fb468db6000-7fb468db7000 r--p 00025000 08:02 655423
/lib/x86_64-linux-gnu/ld-2.23.so
7fb468db7000-7fb468db8000 rw-p 00026000 08:02 655423
/lib/x86_64-linux-gnu/ld-2.23.so
7fb468db8000-7fb468db9000 rw-p 00000000 00:00 0
7ffd617cb000-7ffd6181f000 rw-p 00000000 00:00 0 [stack]
7ffd61932000-7ffd61934000 r--p 00000000 00:00 0 [vvar]
7ffd61934000-7ffd61936000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-fffffffff
Sorry for the long post but I have though the above may be helpful.
This is compiled with gcc:
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.12) 5.4.0 20160609
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Thanks for the quick response. I was able to reproduce this on a clean VM. So I can give you an exact set-up. The VM is running Ubuntu 16.04 and I installed all required libraries through apt except HTSLIB that I compiled from source. gcc is: gcc (Ubuntu 5.4.0-6ubuntu1~16.04.12) 5.4.0 20160609 I will have a go at generating a stack trace this afternoon. I may be able to do that or it may be beyond my limited C debugging capability. If you could e-mail me c.quince at warwick.ac.uk your public ssh key I could give you access to the VM? I am in the UK so zoom is definitely possible. I will also try an Ubuntu 18.04 VM in case it is version specific. Chris |
|
Here is the stack trace when running the command: FastK -k51 graph5.fasta -v -P/home/ubuntu/tmp/ -T1 -p On the Ubuntu 16.04 VM#0 0x00007ffff6f67438 in __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:54 |
|
Hi Chris,
So it is crashing right at the end of the merge step when it is
cleaning up by freeing the
memory it was using. This suggests that there was either an overwrite
of a memory block
header or ... I did a bit of poking around to see if any writes were
outside the bounds of
a given data structure and didn't see anything (albeit not exhaustive).
What I did notice
is that the object being freed at the crash is about 4.2GB. This is
just a bit bigger than what
can be held in a 32-bit integer. Could you check that for your version
of Ubuntu that
64-bit ints are supported (i.e. sizeof(long long int) should = 8) and
that malloc takes
a 64-bit int as its size argument? Another thing to try would be to set
say -M4 which
would reduce the size of the big object and hence also test if this is a
64-bit vs 32-bit issue.
…-- Gene
On 4/12/21, 7:39 PM, chrisquince wrote:
Here is the stack trace when running the command:
FastK -k51 graph5.fasta -v -P/home/ubuntu/tmp/ -T1 -p
On the Ubuntu 16.04 VM
#0 0x00007ffff6f67438 in __GI_raise ***@***.***=6) at
../sysdeps/unix/sysv/linux/raise.c:54
#1 <#1> 0x00007ffff6f6903a
in __GI_abort () at abort.c:89
#2 <#2> 0x00007ffff6fa97fa
in __libc_message (do_abort=2, ***@***.***=0x7ffff70c2f98 "*** Error
in `%s': %s: 0x%s ***\n") at ../sysdeps/posix/libc_fatal.c:175
#3 <#3> 0x00007ffff6fb2c81
in malloc_printerr (ar_ptr=0x7ffff72f6b20 <main_arena>, ptr=,
str=0x7ffff70bfd52 "corrupted double-linked list", action=3) at
malloc.c:5020
#4 <#4> _int_free
(av=0x7ffff72f6b20 <main_arena>, p=, have_lock=0) at malloc.c:4021
#5 <#5> 0x00007ffff6fb658c
in __GI___libc_free (mem=) at malloc.c:2975
#6 <#6> 0x000000000041c450
in Merge_Profiles (dpwd=0x6b95d0 ".", dbrt=0x6b9500 "graph5") at
merge.c:832
#7 <#7> 0x0000000000405af3
in main (argc=2, argv=0x7fffffffe558) at FastK.c:490
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Hi Gene, I am sure this is a 64 bit VM and sizeof(long long int) returns 8. I ran FastK through valgrind which is a program I used to use to find memory errors and it returned the following with the args above: ==2752== Warning: set address range perms: large range [0x395d8040, 0x1395d8030) (undefined) 124%==2752== Invalid write of size 1 Does that help at all? I can also run valgrind with more intensive options than the default? Thanks, |
|
Well alright, that certainly identified a bug-- I was freeing a small
block and then immediately
using it right at the end. On a Mac this doesn't cause a problem as the
block is still there, but
obviously Ubuntu is different. I fixed that and committed to the
master. Could you pull the
revision and see if that fixed it? And thanks, I know valgrind, it's
really handy.
-- Gene
…On 4/13/21, 2:01 PM, chrisquince wrote:
Hi Gene,
I am sure this is a 64 bit VM and sizeof(long long int) returns 8.
I ran FastK through valgrind which is a program I used to use to find
memory errors and it returned the following with the args above:
==2752== Warning: set address range perms: large range [0x395d8040,
0x1395d8030) (undefined)
124%==2752== Invalid write of size 1
==2752== at 0x4C35035: __GI_mempcpy (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==2752== by 0x59906DD: _IO_default_xsputn (genops.c:438)
==2752== by 0x596351A: vfprintf (vfprintf.c:1632)
==2752== by 0x59851DA: vsprintf (iovsprintf.c:42)
==2752== by 0x596A9D6: sprintf (sprintf.c:32)
==2752== by 0x41B638: merge_profile_thread (merge.c:608)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752== Address 0xd7e2e07 is 23 bytes inside a block of size 124 free'd
==2752== at 0x4C2EDEB: free (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==2752== by 0x41B614: merge_profile_thread (merge.c:605)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752== Block was alloc'd at
==2752== at 0x4C2DB8F: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==2752== by 0x41E8E6: Malloc (gene_core.c:22)
==2752== by 0x41A42B: merge_profile_thread (merge.c:128)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752==
==2752== Invalid write of size 1
==2752== at 0x599068B: _IO_default_xsputn (genops.c:450)
==2752== by 0x596293C: vfprintf (vfprintf.c:1663)
==2752== by 0x59851DA: vsprintf (iovsprintf.c:42)
==2752== by 0x596A9D6: sprintf (sprintf.c:32)
==2752== by 0x41B638: merge_profile_thread (merge.c:608)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752== Address 0xd7e2e08 is 24 bytes inside a block of size 124 free'd
==2752== at 0x4C2EDEB: free (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==2752== by 0x41B614: merge_profile_thread (merge.c:605)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752== Block was alloc'd at
==2752== at 0x4C2DB8F: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==2752== by 0x41E8E6: Malloc (gene_core.c:22)
==2752== by 0x41A42B: merge_profile_thread (merge.c:128)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752==
==2752== Invalid write of size 1
==2752== at 0x599068B: _IO_default_xsputn (genops.c:450)
==2752== by 0x5962E0F: vfprintf (vfprintf.c:1631)
==2752== by 0x59851DA: vsprintf (iovsprintf.c:42)
==2752== by 0x596A9D6: sprintf (sprintf.c:32)
==2752== by 0x41B638: merge_profile_thread (merge.c:608)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752== Address 0xd7e2e0d is 29 bytes inside a block of size 124 free'd
==2752== at 0x4C2EDEB: free (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==2752== by 0x41B614: merge_profile_thread (merge.c:605)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752== Block was alloc'd at
==2752== at 0x4C2DB8F: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==2752== by 0x41E8E6: Malloc (gene_core.c:22)
==2752== by 0x41A42B: merge_profile_thread (merge.c:128)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752==
==2752== Invalid write of size 1
==2752== at 0x59851E9: vsprintf (iovsprintf.c:43)
==2752== by 0x596A9D6: sprintf (sprintf.c:32)
==2752== by 0x41B638: merge_profile_thread (merge.c:608)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752== Address 0xd7e2e0e is 30 bytes inside a block of size 124 free'd
==2752== at 0x4C2EDEB: free (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==2752== by 0x41B614: merge_profile_thread (merge.c:605)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752== Block was alloc'd at
==2752== at 0x4C2DB8F: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==2752== by 0x41E8E6: Malloc (gene_core.c:22)
==2752== by 0x41A42B: merge_profile_thread (merge.c:128)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752==
==2752== Syscall param unlink(pathname) points to unaddressable byte(s)
==2752== at 0x5A0DB57: unlink (syscall-template.S:84)
==2752== by 0x41B644: merge_profile_thread (merge.c:609)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752== Address 0xd7e2df0 is 0 bytes inside a block of size 124 free'd
==2752== at 0x4C2EDEB: free (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==2752== by 0x41B614: merge_profile_thread (merge.c:605)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752== Block was alloc'd at
==2752== at 0x4C2DB8F: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==2752== by 0x41E8E6: Malloc (gene_core.c:22)
==2752== by 0x41A42B: merge_profile_thread (merge.c:128)
==2752== by 0x41C122: Merge_Profiles (merge.c:789)
==2752== by 0x405AF2: main (FastK.c:490)
==2752==
Does that help at all? I can also run valgrind with more intensive
options than the default?
Thanks,
Chris
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Hi Gene, That is great! I pulled the latest version recompiled and it ran through without errors. Thanks very much for your help. Looking forward to playing around with the profiles now. Best, |
Thanks for creating yet another incredibly useful looking bit of a software :) I have been searching for a program with all this functionality for a while but I have run into this issue. I have created this as a new issue as I believe it is separate to the file write to /tmp problem raised previously. I am getting corrupted memory faults when try to profile the following sequences downloadable as:
wget https://ebitutorial.s3.climb.ac.uk/graph5.fasta
Running the command:
FastK -k51 graph5.fasta -v -T1 -p
I get:
Partitioning 1 .fasta file into 1 parts
Determining minimizer scheme & partition for graph5
Estimate 1.703M 51-mers
Handling data in a single block
Using 5-minimizers with 1024 core prefixes
Phase 1: Partitioning K-mers into 1 Super-mer Files
There are 38 reads totalling 1,705,389 bps
Resources for phase: 0.076u 0.016s 0.108w 84.7%
Phase 2: Sorting & Counting K-mers in 1 blocks
Resources for phase: 0.312u 0.028s 0.368w 92.1%
Phase 4 (-p option): Merging Profile Fragments
The profiles occupy 160.35 KB
Segmentation fault (core dumped)
That may be the /tmp dir problem. If I point it at a drive with a large amount (1 Tbp of free space) as temp dir with -P I get:
FastK -k51 graph5.fasta -v -P/mnt/chris-native/chris/tmp/ -T1 -p
Partitioning 1 .fasta file into 1 parts
Determining minimizer scheme & partition for graph5
Estimate 1.703M 51-mers
Handling data in a single block
Using 5-minimizers with 1024 core prefixes
Phase 1: Partitioning K-mers into 1 Super-mer Files
There are 38 reads totalling 1,705,389 bps
Resources for phase: 0.088u 0.008s 0.356w 26.9%
Phase 2: Sorting & Counting K-mers in 1 blocks
Resources for phase: 0.400u 0.076s 0.551w 86.4%
Phase 4 (-p option): Merging Profile Fragments
The profiles occupy 160.35 KB
*** Error in `../FastK': free(): corrupted unsorted chunks: 0x0000000001687480 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777f5)[0x7fb467d637f5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8038a)[0x7fb467d6c38a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7fb467d7058c]
../FastK[0x418bbb]
../FastK[0x40438a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fb467d0c840]
../FastK[0x404819]
======= Memory map: ========
00400000-004b2000 r-xp 00000000 00:2b 474411334 /mnt/gpfs/chris/repos/FASTK/FastK
006b1000-006b2000 r--p 000b1000 00:2b 474411334 /mnt/gpfs/chris/repos/FASTK/FastK
006b2000-006b3000 rw-p 000b2000 00:2b 474411334 /mnt/gpfs/chris/repos/FASTK/FastK
006b3000-006b6000 rw-p 00000000 00:00 0
01664000-02eac000 rw-p 00000000 00:00 0 [heap]
7fb35c000000-7fb35c021000 rw-p 00000000 00:00 0
7fb35c021000-7fb360000000 ---p 00000000 00:00 0
7fb361e85000-7fb461e86000 rw-p 00000000 00:00 0
7fb461e86000-7fb461e87000 ---p 00000000 00:00 0
7fb461e87000-7fb462687000 rw-p 00000000 00:00 0
7fb462df9000-7fb462e10000 r-xp 00000000 08:02 656120 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fb462e10000-7fb46300f000 ---p 00017000 08:02 656120 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fb46300f000-7fb463010000 r--p 00016000 08:02 656120 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fb463010000-7fb463011000 rw-p 00017000 08:02 656120 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fb463011000-7fb46301a000 r-xp 00000000 08:02 654573 /lib/x86_64-linux-gnu/libcrypt-2.23.so
7fb46301a000-7fb463219000 ---p 00009000 08:02 654573 /lib/x86_64-linux-gnu/libcrypt-2.23.so
7fb463219000-7fb46321a000 r--p 00008000 08:02 654573 /lib/x86_64-linux-gnu/libcrypt-2.23.so
7fb46321a000-7fb46321b000 rw-p 00009000 08:02 654573 /lib/x86_64-linux-gnu/libcrypt-2.23.so
7fb46321b000-7fb463249000 rw-p 00000000 00:00 0
7fb463249000-7fb463319000 r-xp 00000000 08:02 134403 /usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
7fb463319000-7fb463518000 ---p 000d0000 08:02 134403 /usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
7fb463518000-7fb46351b000 r--p 000cf000 08:02 134403 /usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
7fb46351b000-7fb46351d000 rw-p 000d2000 08:02 134403 /usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
7fb46351d000-7fb46351e000 rw-p 00000000 00:00 0
7fb46351e000-7fb463565000 r-xp 00000000 08:02 137969 /usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
7fb463565000-7fb463764000 ---p 00047000 08:02 137969 /usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
7fb463764000-7fb463766000 r--p 00046000 08:02 137969 /usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
7fb463766000-7fb463768000 rw-p 00048000 08:02 137969 /usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
7fb463768000-7fb463769000 rw-p 00000000 00:00 0
7fb463769000-7fb463777000 r-xp 00000000 08:02 137959 /usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
7fb463777000-7fb463976000 ---p 0000e000 08:02 137959 /usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
7fb463976000-7fb463977000 r--p 0000d000 08:02 137959 /usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
7fb463977000-7fb463978000 rw-p 0000e000 08:02 137959 /usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
7fb463978000-7fb46399f000 r-xp 00000000 08:02 137965 /usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
7fb46399f000-7fb463b9f000 ---p 00027000 08:02 137965 /usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
7fb463b9f000-7fb463ba0000 r--p 00027000 08:02 137965 /usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
7fb463ba0000-7fb463ba1000 rw-p 00028000 08:02 137965 /usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
7fb463ba1000-7fb463ba8000 r-xp 00000000 08:02 133165 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7fb463ba8000-7fb463da7000 ---p 00007000 08:02 133165 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7fb463da7000-7fb463da8000 r--p 00006000 08:02 133165 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7fb463da8000-7fb463da9000 rw-p 00007000 08:02 133165 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7fb463da9000-7fb463dbe000 r-xp 00000000 08:02 145811 /usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
7fb463dbe000-7fb463fbd000 ---p 00015000 08:02 145811 /usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
7fb463fbd000-7fb463fbe000 r--p 00014000 08:02 145811 /usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
7fb463fbe000-7fb463fbf000 rw-p 00015000 08:02 145811 /usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
7fb463fbf000-7fb463fef000 r-xp 00000000 08:02 137955 /usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
7fb463fef000-7fb4641ef000 ---p 00030000 08:02 137955 /usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
7fb4641ef000-7fb4641f0000 r--p 00030000 08:02 137955 /usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
7fb4641f0000-7fb4641f1000 rw-p 00031000 08:02 137955 /usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
7fb4641f1000-7fb4641f2000 rw-p 00000000 00:00 0
7fb4641f2000-7fb464291000 r-xp 00000000 08:02 137952 /usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
7fb464291000-7fb464490000 ---p 0009f000 08:02 137952 /usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
7fb464490000-7fb464491000 r--p 0009e000 08:02 137952 /usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
7fb464491000-7fb464494000 rw-p 0009f000 08:02 137952 /usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
7fb464494000-7fb464518000 r-xp 00000000 08:02 137974 /usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
7fb464518000-7fb464717000 ---p 00084000 08:02 137974 /usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
7fb464717000-7fb46471a000 r--p 00083000 08:02 137974 /usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
7fb46471a000-7fb46471d000 rw-p 00086000 08:02 137974 /usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
7fb46471d000-7fb46471e000 rw-p 00000000 00:00 0
7fb46471e000-7fb464726000 r-xp 00000000 08:02 137979 /usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
7fb464726000-7fb464925000 ---p 00008000 08:02 137979 /usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
7fb464925000-7fb464926000 r--p 00007000 08:02 137979 /usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
7fb464926000-7fb464927000 rw-p 00008000 08:02 137979 /usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
7fb464927000-7fb46492a000 r-xp 00000000 08:02 660056 /lib/x86_64-linux-gnu/libkeyutils.so.1.5
7fb46492a000-7fb464b29000 ---p 00003000 08:02 660056 /lib/x86_64-linux-gnu/libkeyutils.so.1.5
7fb464b29000-7fb464b2a000 r--p 00002000 08:02 660056 /lib/x86_64-linux-gnu/libkeyutils.so.1.5
7fb464b2a000-7fb464b2b000 rw-p 00003000 08:02 660056 /lib/x86_64-linux-gnu/libkeyutils.so.1.5
7fb464b2b000-7fb464b3c000 r-xp 00000000 08:02 131781 /usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
7fb464b3c000-7fb464d3c000 ---p 00011000 08:02 131781 /usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
7fb464d3c000-7fb464d3d000 r--p 00011000 08:02 131781 /usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
7fb464d3d000-7fb464d3e000 rw-p 00012000 08:02 131781 /usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
7fb464d3e000-7fb464d97000 r-xp 00000000 08:02 137411 /usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
7fb464d97000-7fb464f96000 ---p 00059000 08:02 137411 /usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
7fb464f96000-7fb464fa0000 r--p 00058000 08:02 137411 /usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
7fb464fa0000-7fb464fa2000 rw-p 00062000 08:02 137411 /usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
7fb464fa2000-7fb464fdf000 r-xp 00000000 08:02 137984 /usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
7fb464fdf000-7fb4651df000 ---p 0003d000 08:02 137984 /usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
7fb4651df000-7fb4651e0000 r--p 0003d000 08:02 137984 /usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
7fb4651e0000-7fb4651e2000 rw-p 0003e000 08:02 137984 /usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
7fb4651e2000-7fb4651e3000 rw-p 00000000 00:00 0
7fb4651e3000-7fb4651fc000 r-xp 00000000 08:02 132347 /usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
7fb4651fc000-7fb4653fc000 ---p 00019000 08:02 132347 /usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
7fb4653fc000-7fb4653fd000 r--p 00019000 08:02 132347 /usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
7fb4653fd000-7fb4653fe000 rw-p 0001a000 08:02 132347 /usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
7fb4653fe000-7fb465415000 r-xp 00000000 08:02 655434 /lib/x86_64-linux-gnu/libresolv-2.23.so
7fb465415000-7fb465615000 ---p 00017000 08:02 655434 /lib/x86_64-linux-gnu/libresolv-2.23.so
7fb465615000-7fb465616000 r--p 00017000 08:02 655434 /lib/x86_64-linux-gnu/libresolv-2.23.so
7fb465616000-7fb465617000 rw-p 00018000 08:02 655434 /lib/x86_64-linux-gnu/libresolv-2.23.so
7fb465617000-7fb465619000 rw-p 00000000 00:00 0
7fb465619000-7fb465623000 r-xp 00000000 08:02 134938 /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7fb465623000-7fb465822000 ---p 0000a000 08:02 134938 /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7fb465822000-7fb465823000 r--p 00009000 08:02 134938 /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7fb465823000-7fb465824000 rw-p 0000a000 08:02 134938 /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7fb465824000-7fb465827000 r-xp 00000000 08:02 654290 /lib/x86_64-linux-gnu/libcom_err.so.2.1
7fb465827000-7fb465a26000 ---p 00003000 08:02 654290 /lib/x86_64-linux-gnu/libcom_err.so.2.1
7fb465a26000-7fb465a27000 r--p 00002000 08:02 654290 /lib/x86_64-linux-gnu/libcom_err.so.2.1
7fb465a27000-7fb465a28000 rw-p 00003000 08:02 654290 /lib/x86_64-linux-gnu/libcom_err.so.2.1
7fb465a28000-7fb465a54000 r-xp 00000000 08:02 132856 /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7fb465a54000-7fb465c53000 ---p 0002c000 08:02 132856 /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7fb465c53000-7fb465c55000 r--p 0002b000 08:02 132856 /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7fb465c55000-7fb465c56000 rw-p 0002d000 08:02 132856 /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7fb465c56000-7fb465c57000 rw-p 00000000 00:00 0
7fb465c57000-7fb465d1a000 r-xp 00000000 08:02 137943 /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7fb465d1a000-7fb465f1a000 ---p 000c3000 08:02 137943 /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7fb465f1a000-7fb465f27000 r--p 000c3000 08:02 137943 /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7fb465f27000-7fb465f29000 rw-p 000d0000 08:02 137943 /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7fb465f29000-7fb465fa8000 r-xp 00000000 08:02 133173 /usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
7fb465fa8000-7fb4661a7000 ---p 0007f000 08:02 133173 /usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
7fb4661a7000-7fb4661a8000 r--p 0007e000 08:02 133173 /usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
7fb4661a8000-7fb4661a9000 rw-p 0007f000 08:02 133173 /usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
7fb4661a9000-7fb4661dd000 r-xp 00000000 08:02 133193 /usr/lib/x86_64-linux-gnu/libnettle.so.6.2
7fb4661dd000-7fb4663dc000 ---p 00034000 08:02 133193 /usr/lib/x86_64-linux-gnu/libnettle.so.6.2
7fb4663dc000-7fb4663de000 r--p 00033000 08:02 133193 /usr/lib/x86_64-linux-gnu/libnettle.so.6.2
7fb4663de000-7fb4663df000 rw-p 00035000 08:02 133193 /usr/lib/x86_64-linux-gnu/libnettle.so.6.2
7fb4663df000-7fb466411000 r-xp 00000000 08:02 133179 /usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
7fb466411000-7fb466610000 ---p 00032000 08:02 133179 /usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
7fb466610000-7fb466611000 r--p 00031000 08:02 133179 /usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
7fb466611000-7fb466612000 rw-p 00032000 08:02 133179 /usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
7fb466612000-7fb466735000 r-xp 00000000 08:02 134875 /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7fb466735000-7fb466934000 ---p 00123000 08:02 134875 /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7fb466934000-7fb46693f000 r--p 00122000 08:02 134875 /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7fb46693f000-7fb466941000 rw-p 0012d000 08:02 134875 /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7fb466941000-7fb466942000 rw-p 00000000 00:00 0
7fb466942000-7fb46698f000 r-xp 00000000 08:02 131120 /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
7fb46698f000-7fb466b8e000 ---p 0004d000 08:02 131120 /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
7fb466b8e000-7fb466b90000 r--p 0004c000 08:02 131120 /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
7fb466b90000-7fb466b91000 rw-p 0004e000 08:02 131120 /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
7fb466b91000-7fb466b93000 rw-p 00000000 00:00 0
7fb466b93000-7fb466ba0000 r-xp 00000000 08:02 131171 /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
7fb466ba0000-7fb466da0000 ---p 0000d000 08:02 131171 /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
7fb466da0000-7fb466da1000 r--p 0000d000 08:02 131171 /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
7fb466da1000-7fb466da2000 rw-p 0000e000 08:02 131171 /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
7fb466da2000-7fb466de9000 r-xp 00000000 08:02 137935 /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7fb466de9000-7fb466fe8000 ---p 00047000 08:02 137935 /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7fb466fe8000-7fb466fea000 r--p 00046000 08:02 137935 /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7fb466fea000-7fb466fec000 rw-p 00048000 08:02 137935 /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7fb466fec000-7fb467207000 r-xp 00000000 08:02 654731 /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7fb467207000-7fb467406000 ---p 0021b000 08:02 654731 /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7fb467406000-7fb467422000 r--p 0021a000 08:02 654731 /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7fb467422000-7fb46742e000 rw-p 00236000 08:02 654731 /lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7fb46742e000-7fb467431000 rw-p 00000000 00:00 0
7fb467431000-7fb46748f000 r-xp 00000000 08:02 654734 /lib/x86_64-linux-gnu/libssl.so.1.0.0
7fb46748f000-7fb46768f000 ---p 0005e000 08:02 654734 /lib/x86_64-linux-gnu/libssl.so.1.0.0
7fb46768f000-7fb467693000 r--p 0005e000 08:02 654734 /lib/x86_64-linux-gnu/libssl.so.1.0.0
7fb467693000-7fb467699000 rw-p 00062000 08:02 654734 /lib/x86_64-linux-gnu/libssl.so.1.0.0
7fb467699000-7fb4676b4000 r-xp 00000000 08:02 135071 /usr/lib/x86_64-linux-gnu/librtmp.so.1
7fb4676b4000-7fb4678b3000 ---p 0001b000 08:02 135071 /usr/lib/x86_64-linux-gnu/librtmp.so.1
7fb4678b3000-7fb4678b4000 r--p 0001a000 08:02 135071 /usr/lib/x86_64-linux-gnu/librtmp.so.1
7fb4678b4000-7fb4678b5000 rw-p 0001b000 08:02 135071 /usr/lib/x86_64-linux-gnu/librtmp.so.1
7fb4678b5000-7fb4678e6000 r-xp 00000000 08:02 161247 /usr/lib/x86_64-linux-gnu/libidn.so.11.6.15
7fb4678e6000-7fb467ae6000 ---p 00031000 08:02 161247 /usr/lib/x86_64-linux-gnu/libidn.so.11.6.15
7fb467ae6000-7fb467ae7000 r--p 00031000 08:02 161247 /usr/lib/x86_64-linux-gnu/libidn.so.11.6.15
7fb467ae7000-7fb467ae8000 rw-p 00032000 08:02 161247 /usr/lib/x86_64-linux-gnu/libidn.so.11.6.15
7fb467ae8000-7fb467aeb000 r-xp 00000000 08:02 654528 /lib/x86_64-linux-gnu/libdl-2.23.so
7fb467aeb000-7fb467cea000 ---p 00003000 08:02 654528 /lib/x86_64-linux-gnu/libdl-2.23.so
7fb467cea000-7fb467ceb000 r--p 00002000 08:02 654528 /lib/x86_64-linux-gnu/libdl-2.23.so
7fb467ceb000-7fb467cec000 rw-p 00003000 08:02 654528 /lib/x86_64-linux-gnu/libdl-2.23.so
7fb467cec000-7fb467eac000 r-xp 00000000 08:02 654530 /lib/x86_64-linux-gnu/libc-2.23.so
7fb467eac000-7fb4680ac000 ---p 001c0000 08:02 654530 /lib/x86_64-linux-gnu/libc-2.23.so
7fb4680ac000-7fb4680b0000 r--p 001c0000 08:02 654530 /lib/x86_64-linux-gnu/libc-2.23.so
7fb4680b0000-7fb4680b2000 rw-p 001c4000 08:02 654530 /lib/x86_64-linux-gnu/libc-2.23.so
7fb4680b2000-7fb4680b6000 rw-p 00000000 00:00 0
7fb4680b6000-7fb468124000 r-xp 00000000 08:02 137680 /usr/lib/x86_64-linux-gnu/libcurl.so.4.4.0
7fb468124000-7fb468324000 ---p 0006e000 08:02 137680 /usr/lib/x86_64-linux-gnu/libcurl.so.4.4.0
7fb468324000-7fb468327000 r--p 0006e000 08:02 137680 /usr/lib/x86_64-linux-gnu/libcurl.so.4.4.0
7fb468327000-7fb468328000 rw-p 00071000 08:02 137680 /usr/lib/x86_64-linux-gnu/libcurl.so.4.4.0
7fb468328000-7fb468349000 r-xp 00000000 08:02 654615 /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7fb468349000-7fb468548000 ---p 00021000 08:02 654615 /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7fb468548000-7fb468549000 r--p 00020000 08:02 654615 /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7fb468549000-7fb46854a000 rw-p 00021000 08:02 654615 /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7fb46854a000-7fb468559000 r-xp 00000000 08:02 654186 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fb468559000-7fb468758000 ---p 0000f000 08:02 654186 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fb468758000-7fb468759000 r--p 0000e000 08:02 654186 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fb468759000-7fb46875a000 rw-p 0000f000 08:02 654186 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7fb46875a000-7fb468773000 r-xp 00000000 08:02 654834 /lib/x86_64-linux-gnu/libz.so.1.2.8
7fb468773000-7fb468972000 ---p 00019000 08:02 654834 /lib/x86_64-linux-gnu/libz.so.1.2.8
7fb468972000-7fb468973000 r--p 00018000 08:02 654834 /lib/x86_64-linux-gnu/libz.so.1.2.8
7fb468973000-7fb468974000 rw-p 00019000 08:02 654834 /lib/x86_64-linux-gnu/libz.so.1.2.8
7fb468974000-7fb46898c000 r-xp 00000000 08:02 654534 /lib/x86_64-linux-gnu/libpthread-2.23.so
7fb46898c000-7fb468b8b000 ---p 00018000 08:02 654534 /lib/x86_64-linux-gnu/libpthread-2.23.so
7fb468b8b000-7fb468b8c000 r--p 00017000 08:02 654534 /lib/x86_64-linux-gnu/libpthread-2.23.so
7fb468b8c000-7fb468b8d000 rw-p 00018000 08:02 654534 /lib/x86_64-linux-gnu/libpthread-2.23.so
7fb468b8d000-7fb468b91000 rw-p 00000000 00:00 0
7fb468b91000-7fb468bb7000 r-xp 00000000 08:02 655423 /lib/x86_64-linux-gnu/ld-2.23.so
7fb468d88000-7fb468d9b000 rw-p 00000000 00:00 0
7fb468db5000-7fb468db6000 rw-p 00000000 00:00 0
7fb468db6000-7fb468db7000 r--p 00025000 08:02 655423 /lib/x86_64-linux-gnu/ld-2.23.so
7fb468db7000-7fb468db8000 rw-p 00026000 08:02 655423 /lib/x86_64-linux-gnu/ld-2.23.so
7fb468db8000-7fb468db9000 rw-p 00000000 00:00 0
7ffd617cb000-7ffd6181f000 rw-p 00000000 00:00 0 [stack]
7ffd61932000-7ffd61934000 r--p 00000000 00:00 0 [vvar]
7ffd61934000-7ffd61936000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-fffffffff
Sorry for the long post but I have though the above may be helpful. This is compiled with gcc:
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.12) 5.4.0 20160609
The text was updated successfully, but these errors were encountered: