crash at dump

[jodyphelan]

kmtricks dump seems to crash with the following error:

terminate called after throwing an instance of 'km::IOError'
  what():  std::exception
[2023-03-31 07:43:20.178] [error] Killed after receive Aborted:SIGABRT(6) signal. Demangled backtrace dumped at ./kmtricks_backtrace.log. If the problem persists, please open an issue with the return of 'kmtricks infos' and the content of ./kmtricks_backtrace.log

kmtricks infos:

kmtricks v1.3.0

- HOST -
build host: Linux-6.1.3
run host: Linux 4.15.0-197-generic

- BUILD -
c compiler: GNU 11.2.0
cxx compiler: GNU 11.2.0
conda: ON
static: OFF
native: OFF
modules: ON
socks: ON
howde: ON
dev: OFF
kmer: 32,64,96,128,160,192,224,256
max_c: 4294967295

- GIT SHA1 / VERSION -
kmtricks: 92d7894
sdsl: c32874c
bcli: 3e4f493
fmt: 0544a227
kff: 97d135e
lz4: 4de56b3
spdlog: v1.2.1-1811-g5b4c4f3f
xxhash: 6853ddc
gtest: release-1.8.0-2774-g96f4ce02
croaring: v0.3.3-17-g2d5c927
robin-hood-hasing: 24b3f50
turbop: 4ab9f5b
cfrcat: 2f9da97
indicators: v1.9-36-gcdcff01

Contact: teo.lemane@inria.fr

Backtrace:

Backtrace:
1 0x00007f549d83cf10 (null) + 140001396641552
2 0x00007f549d83ce87 gsignal + 199
3 0x00007f549d83e7f1 abort + 321
4 0x00007f549e4ae036 __gnu_cxx::__verbose_terminate_handler() + 192
5 0x00007f549e4ac524 (null) + 140001409680676
6 0x00007f549e4ac576 (null) + 140001409680758
7 0x00007f549e4ac768 __cxa_rethrow + 0
8 0x00000000005411b6 void km::check_fstream_good<std::basic_ifstream<char, std::char_traits<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_ifstream<char, std::char_traits<char> > const&) + 198
9 0x00000000005a8d99 (null) + 5934489
10 0x00000000005aa5cf (null) + 5940687
11 0x00000000005ace4b (null) + 5951051
12 0x00000000004c9132 main + 914
13 0x00007f549d81fc87 __libc_start_main + 231
14 0x00000000004cbdc4 (null) + 5029316

[tlemane]

Hello,

Can you tell me the commands you used? For matrix construction and dump.

Teo

[jodyphelan]

This is for matrix construction:

kmtricks pipeline --file list_files.txt --run-dir run

This is for the dump:

kmtricks dump  --run-dir out --input run/matrices/matrix_0.count

[tlemane]

Hello,

The --run-dir option of kmtricks dump must indicate the kmtrticks run, in your example it should be --run-dir run. The output is stdout by default, you can specify it using --output.

I realize that kmtricks dump checks that --run-dir exists but does not check that it is a kmtricks run. When I use your commands, I get the same error if the out directory exists but it is not a kmtricks run. I will add more checks in the next release.

I hope this help.

Teo

[jodyphelan]

Sorry thought I'd gotten back to you already. Yes this works nicely!