sitarapersad
sitarapersad
Hi Tatyana! Are you using the GPU version? The non-GPU does use sparse matrices so I will check on this asap for you!
Hi Tatyana - thanks for catching this! I think that somehow the non-sparse matrix version ended up being the one pushed most recently. I will fix this ASAP and push...
Hi - just providing an update on this. I misunderstood which matrix the sparsity error was coming from. The kernel matrix itself is sparse, but the A_ and B_ matrices...
Just updated the CPU version to use sparse matrices - the current issue is that it's a bit slower than the CPU version without sparse matrices on small inputs since...
Hi! Sorry for the delay in this, will take a look into it and see what's going on with the 'plot' module!
Hi! Can you confirm that it prints out "("Welcome to SEACells GPU!"), just to make sure the correct version is being called? Also, what is the size of your dataset?...
This is a bit curious, as we were able to run 120k cells on a cluster with 200GB of memory, so memory-wise, you should be fine. It may be slow...
Gotcha - yes sorry it only prints every 10 iterations or so, which might be confusing! Let me know if it still does not work. A GPU sped up version...
Hi Sayyam! I think this is likely because there are too many SEACells. We recommend about 1 SEACell for every 100 cells, so for your dataset, something on the order...
Ahh yes, sorry about that! I will remove the extra dependencies and test it out this week. Will update this soon!