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cosmo-team / cosmo

Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.
GNU General Public License v3.0
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No space left on device error #12

Open winni2k opened 7 years ago

winni2k commented 7 years ago

When I run cosmo-build:

./cosmo-build input.ctx -m 10000 -o output.cosmo -k 47

I get this output culminating in an error message:

cosmo-build compiled with supported colors=128 [STXXL-MSG] STXXL v1.4.99 (prerelease/Release) (git 0a80a8c55993948f7f2f6c2c5a51ff45b403045b) + gnu parallel(20170814) [STXXL-ERRMSG] Warning: no config file found. [STXXL-ERRMSG] Using default disk configuration. [STXXL-MSG] Disk '/var/tmp/stxxl' is allocated, space: 1000 MiB, I/O implementation: syscall delete_on_exit queue=0 devid=0 input.ctx looks like a raw file.Reading input and creating runs...[STXXL-ERRMSG] External memory block allocation error: 2621440000 bytes requested, 1048576000 bytes free. Trying to extend the external memory space... [STXXL-ERRMSG] External memory block allocation error: 2621440000 bytes requested, 1048576000 bytes free. Trying to extend the external memory space... [STXXL-ERRMSG] External memory block allocation error: 2621440000 bytes requested, 1048576000 bytes free. Trying to extend the external memory space... [STXXL-ERRMSG] External memory block allocation error: 2621440000 bytes requested, 1048576000 bytes free. Trying to extend the external memory space... [STXXL-ERRMSG] External memory block allocation error: 2621440000 bytes requested, 1048576000 bytes free. Trying to extend the external memory space... [STXXL-ERRMSG] External memory block allocation error: 2621440000 bytes requested, 1048576000 bytes free. Trying to extend the external memory space... Building from 620016348 edges...Merging runs...[STXXL-ERRMSG] External memory block allocation error: 2057306112 bytes requested, 1048576000 bytes free. Trying to extend the external memory space... [STXXL-ERRMSG] External memory block allocation error: 2057306112 bytes requested, 1048576000 bytes free. Trying to extend the external memory space... [STXXL-ERRMSG] External memory block allocation error: 9921626112 bytes requested, 1048576000 bytes free. Trying to extend the external memory space... Materializing table B...terminate called after throwing an instance of 'stxxl::io_error' what(): Error in virtual void stxxl::syscall_file::serve(void*, stxxl::file::offset_type, stxxl::file::size_type, stxxl::request_interface::request_type) : this=0x1820a80 call=::write(fd,buffer,bytes) path=/var/tmp/stxxl fd=5 offset=23873978368 buffer=0x2b01e03cd000 bytes=2097152 type=WRITE rc=-1 : No space left on device: iostream error: iostream error

I have a TB left on my device, so I'm pretty sure that's not the problem. Maybe /var/tmp is getting full. How can I change the temporary directory?

GuillaumeHolley commented 6 years ago

Hello everyone,

I am getting the same issue as @winni2k here: my /var/tmp/ directory gets full and the program stops because of that. How can I change the temporary directory?

GuillaumeHolley commented 6 years ago

Here is the solution: https://stxxl.org/tags/1.4.1/install_config.html