terminate called after throwing an instance of 'std::bad_alloc'

[ThWacker]

Hi,
I tried to run Raven on Nanopore data (quite a big file, 85GB roughly) on a HPCC with a Torque Scheduler. The run was aborted with the following StdErr:

[raven::] loaded 9087491 sequences 640.684164s
[raven::Graph::Construct] minimized 0 - 244845 / 9087491 359.047807s
[raven::Graph::Construct] mapped sequences 1918.468984s
[raven::Graph::Construct] minimized 244845 - 485704 / 9087491 369.553781s
[raven::Graph::Construct] mapped sequences 4952.626360s
[raven::Graph::Construct] minimized 485704 - 730713 / 9087491 422.459109s
[raven::Graph::Construct] mapped sequences 8062.137459s
[raven::Graph::Construct] minimized 730713 - 970097 / 9087491 365.644221s
[raven::Graph::Construct] mapped sequences 11157.831874s
[raven::Graph::Construct] minimized 970097 - 1205546 / 9087491 408.545256s
[raven::Graph::Construct] mapped sequences 14233.668864s
[raven::Graph::Construct] minimized 1205546 - 1444410 / 9087491 425.380612s
[raven::Graph::Construct] mapped sequences 17397.713790s
[raven::Graph::Construct] minimized 1444410 - 1678744 / 9087491 356.319257s
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
/var/spool/torque/mom_priv/jobs/1752457.mgmt01.cluster.local.SC: line 4: 2272 Aborted "$@"

I am a bit at a loss why. Could it be that I run out of memory? Any help is appreciated!!
Thank you!

Best wishes

[rvaser]

Hello,
how much RAM does your machine have?

Best regards,
Robert

[ThWacker]

Hello, Thanks for your response! It is either 128 or 256 GB. I will have to ask the people maintaining the server which computing node the parallel queue is actually using. But based on the Canu output I got, which lists what hosts, cores and memory capacity it found, I would assume 128. Best regards Theresa

…

On 6 May 2020, at 17:28, Robert Vaser ***@***.***> wrote: Hello, how much RAM does your machine have? Best regards, Robert — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#19 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIRG3IC3AKIZ5NTSNXYG22DRQF62HANCNFSM4M2RCEKA>.

[rvaser]

Hi Theresa,
128GB might not be enough. Is the file you have compressed or is the 85GB uncompressed size? Raven's memory requirements are around 1.3 * .FASTQ + 16GB.

Best regards,
Robert

[ThWacker]

Hi Robert, I tried submitting it to the high memory queue; if it works there, we know it was the memory. It is uncompressed 85GB, actually. Thank you for your help!! Best regards Theresa

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On 6 May 2020, at 18:58, Robert Vaser ***@***.***> wrote: Hi Theresa, 128GB might not be enough. Is the file you have compressed or is the 85GB uncompressed size? Raven's memory requirements are around 1.3 * .FASTQ + 16GB. Best regards, Robert — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#19 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIRG3IAPFSO5QSUYYKNRH7DRQGJLRANCNFSM4M2RCEKA>.