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LinearDesignSoftware / LinearDesign

The LinearDesign mRNA design software.
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Length limit #5

Open Davood-Norouzi opened 1 year ago

Davood-Norouzi commented 1 year ago

Thanks for this great tool!

When I try to run lineardesign on a protein of length 1384 aa (mRNA length 4152 nt), the program doesn't do anything. I have a powerful computer, with 64GB RAM and an intel i7 processor.

Is there anyway I can run it on the whole sequence?

Thank you in advance, -Davood

PhatBrett commented 1 year ago

Any resolution? Encountering same issue

tangweijr commented 1 year ago

same issue, even can't run testseq(spike2P)

cwyc commented 1 year ago

On my machine, it looks like the length limit is just oom-killer stopping the program, because it's consumed all of my memory. I wonder if you have something like what I have on your dmesg logs:

[   52.773416] Out of memory: Killed process 480 (LinearDesign_2D) total-vm:9203056kB, anon-rss:7276232kB, file-rss:0kB, shmem-rss:0kB, UID:1000 pgtables:18044kB oom_score_adj:0

I think this is happening in the parse function in beam_cky_parser.cc. Maybe the developers could optimize memory allocation here. Or maybe we all have to buy more RAM.

Tanyazwantig commented 9 months ago

Hi, were you able to solve this? I am having the same issue.

Davood-Norouzi commented 9 months ago

I used an AWS EC2 instance with 192GB RAM and it worked. Great tool, but it is not memory optimized.