gpu memory issue - 8M cell 24G GPU out of memory during umap

[yubin-ai]

Code I used: sc.tl.umap(ad,min_dist=0.1,method='rapids',neighbors_key='neighbors')

AWS G5 4xlarge 1 GPU 24G GPU memory.

During the process the GPU usage is 4G/24G but at the end, it crashed saying out of memory.

---------------------------------------------------------------------------

MemoryError                               Traceback (most recent call last)
Cell In[11], line 1
----> 1 sc.tl.umap(ad,min_dist=0.1,method='rapids',neighbors_key='neighbors')

File ~/mambaforge/envs/rapids-23.08/lib/python3.10/site-packages/scanpy/tools/_umap.py:237, in umap(adata, min_dist, spread, n_components, maxiter, alpha, gamma, negative_sample_rate, init_pos, random_state, a, b, copy, method, neighbors_key)
    222     X_contiguous = np.ascontiguousarray(X, dtype=np.float32)
    223     umap = UMAP(
    224         n_neighbors=n_neighbors,
    225         n_components=n_components,
   (...)
    235         random_state=random_state,
    236     )
--> 237     X_umap = umap.fit_transform(X_contiguous)
    238 adata.obsm['X_umap'] = X_umap  # annotate samples with UMAP coordinates
    239 logg.info(
    240     '    finished',
    241     time=start,
    242     deep=('added\n' "    'X_umap', UMAP coordinates (adata.obsm)"),
    243 )

File ~/mambaforge/envs/rapids-23.08/lib/python3.10/site-packages/cuml/internals/api_decorators.py:188, in _make_decorator_function.<locals>.decorator_function.<locals>.decorator_closure.<locals>.wrapper(*args, **kwargs)
    185     set_api_output_dtype(output_dtype)
    187 if process_return:
--> 188     ret = func(*args, **kwargs)
    189 else:
    190     return func(*args, **kwargs)

File ~/mambaforge/envs/rapids-23.08/lib/python3.10/site-packages/cuml/internals/api_decorators.py:393, in enable_device_interop.<locals>.dispatch(self, *args, **kwargs)
    391 if hasattr(self, "dispatch_func"):
    392     func_name = gpu_func.__name__
--> 393     return self.dispatch_func(func_name, gpu_func, *args, **kwargs)
    394 else:
    395     return gpu_func(self, *args, **kwargs)

File ~/mambaforge/envs/rapids-23.08/lib/python3.10/site-packages/cuml/internals/api_decorators.py:190, in _make_decorator_function.<locals>.decorator_function.<locals>.decorator_closure.<locals>.wrapper(*args, **kwargs)
    188         ret = func(*args, **kwargs)
    189     else:
--> 190         return func(*args, **kwargs)
    192 return cm.process_return(ret)

File base.pyx:665, in cuml.internals.base.UniversalBase.dispatch_func()

File umap.pyx:658, in cuml.manifold.umap.UMAP.fit_transform()

File ~/mambaforge/envs/rapids-23.08/lib/python3.10/site-packages/cuml/internals/api_decorators.py:188, in _make_decorator_function.<locals>.decorator_function.<locals>.decorator_closure.<locals>.wrapper(*args, **kwargs)
    185     set_api_output_dtype(output_dtype)
    187 if process_return:
--> 188     ret = func(*args, **kwargs)
    189 else:
    190     return func(*args, **kwargs)

File ~/mambaforge/envs/rapids-23.08/lib/python3.10/site-packages/cuml/internals/api_decorators.py:393, in enable_device_interop.<locals>.dispatch(self, *args, **kwargs)
    391 if hasattr(self, "dispatch_func"):
    392     func_name = gpu_func.__name__
--> 393     return self.dispatch_func(func_name, gpu_func, *args, **kwargs)
    394 else:
    395     return gpu_func(self, *args, **kwargs)

File ~/mambaforge/envs/rapids-23.08/lib/python3.10/site-packages/cuml/internals/api_decorators.py:190, in _make_decorator_function.<locals>.decorator_function.<locals>.decorator_closure.<locals>.wrapper(*args, **kwargs)
    188         ret = func(*args, **kwargs)
    189     else:
--> 190         return func(*args, **kwargs)
    192 return cm.process_return(ret)

File base.pyx:665, in cuml.internals.base.UniversalBase.dispatch_func()

File umap.pyx:595, in cuml.manifold.umap.UMAP.fit()

MemoryError: std::bad_alloc: out_of_memory: CUDA error at: /home/ec2-user/mambaforge/envs/rapids-23.08/include/rmm/mr/device/cuda_memory_resource.hpp

[yubin-ai]

had to use this to avoid out of memory.

import cupy as cp
import rmm
rmm.reinitialize(managed_memory=True)
cp.cuda.set_allocator(rmm.rmm_cupy_allocator)