Open funnell opened 1 month ago
The only modification I made to the program was that I needed to remove this line:
#include <malloc.h>
I had to do this to get any of the programs to compile, but this didn't seem to affect any other program as they all seemed to run fine after modification.
Hi Tyler, Sorry to hear it's not working for you. I'm glad any of it works on Mac though, since I hadn't tested that! Also, thanks for the tip about malloc.h, it looks like that's actually deprecated so I will be deleting that and re-checking all my programs as soon as I have time. Regarding the error, it could be Mac issues - if you can try it on a Linux that would be useful; it may be something as simple as incompatible text formats for newlines. I really don't know much about Mac. Another thing could be that it's struggling for memory; squish can use a lot (I think it would give a different error in that case but it's worth checking). Again, I don't know how to monitor that on Mac but I guess you do. Or very likely it's a bug in my code, mis-allocating memory. One quick test would be to try it with >1 thread - I always run it with multiple threads so it's possible I forgot to test with 1, and made some dumb mistake! Otherwise, the problem is it's been working for me so I'd need to try it with your data to find the problem. Would you be happy to share your files with me? We could make contact off github to transfer files privately if the data is confidential. Regards, Kate
Hi Kate, Thanks so much for the quick response! Running with multiple threads didn't work though unfortunately :'( and I don't see any issues with running out of memory with the input I'm using. I will give it a try on Linux and report back.
Happy to share the input files in the meantime off Github, what email address should I send them to?
No worries Tyler, I thought I'd hunted down your address at mskcc but it bounced. :( My Monash email is the one I want to give you but I don't want to write it in plain text on a web forum, but you should be able to see it by googling me (It's probably online already but we have to try, right?? Make the web scrapers work for their money...) I've also sent you a LinkedIn invite. So let me know if none of that works to help us connect. Thanks, Kate
Hello,
I'm getting this error:
When running squish like so:
This is the full output:
squish was compiled like this on my M3 MacBook Air:
where: