thegenemyers
commented
3 years ago 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).
-- GeneOn 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 -pPartitioning 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-fffffffffSorry 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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chrisquince
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