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Create output report and visualizations for GLIPH2 module on Cirro #18

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RachelKarchin opened this issue Nov 22, 2024 · 1 comment
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@RachelKarchin
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@dltamayo dltamayo self-assigned this Nov 26, 2024
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from @dltamayo:

While I ran this without issue locally, Gliph2 failed on >Cirro with this error:

 .command.sh: line 32:  693 Segmentation fault   (core dumped) /opt/gliph2/irtools -c tcrtoolkit-bulk_2025-01-16_07:37:09.cfg

Despite increasing the cpu and memory in different configurations, 4 cpus/16 GB memory was the only configuration that I could get Gliph2 to complete on Cirro
When I ran Gliph2 locally, it took about an hour with the test data. However, on Cirro it took a little over 4 hours to successfully complete with 4 cpus/16 GB.
Given the lack of open source code for Gliph2 as well, it may be difficult to troubleshoot further, even if I can get it to work now. Also, I don't know how well Gliph2 would scale with larger datasets, given the length of time it takes right now. I'll test out turboGliph and see how it compares.

@dltamayo dltamayo transferred this issue from break-through-cancer/btc-TCRtoolkit-Bulk Mar 25, 2025
@dimalvovs dimalvovs transferred this issue from another repository Mar 25, 2025
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