Hi, all
I got error when I run the 3D flex reconstruction.
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 96, in cryosparc_compute.run.main
File “/kumquat/boshu/cryosparc/cryosparc_worker/cryosparc_compute/jobs/flex_refine/run_highres.py”, line 150, in run
flexmod.do_hr_refinement_flex(numiter=params[‘flex_bfgs_num_iters’])
File “cryosparc_master/cryosparc_compute/jobs/flex_refine/flexmod.py”, line 1640, in cryosparc_compute.jobs.flex_refine.flexmod.do_hr_refinement_flex.lambda7
File “/kumquat/boshu/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/scipy/optimize/_lbfgsb_py.py”, line 199, in fmin_l_bfgs_b
res = _minimize_lbfgsb(fun, x0, args=args, jac=jac, bounds=bounds,
File “/kumquat/boshu/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/scipy/optimize/_lbfgsb_py.py”, line 308, in _minimize_lbfgsb
sf = _prepare_scalar_function(fun, x0, jac=jac, args=args, epsilon=eps,
File “/kumquat/boshu/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/scipy/optimize/_optimize.py”, line 263, in _prepare_scalar_function
sf = ScalarFunction(fun, x0, args, grad, hess,
File “/kumquat/boshu/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/scipy/optimize/_differentiable_functions.py”, line 158, in init
self._update_fun()
File “/kumquat/boshu/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/scipy/optimize/_differentiable_functions.py”, line 251, in _update_fun
self._update_fun_impl()
File “/kumquat/boshu/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/scipy/optimize/_differentiable_functions.py”, line 155, in update_fun
self.f = fun_wrapped(self.x)
File “/kumquat/boshu/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/scipy/optimize/_differentiable_functions.py”, line 137, in fun_wrapped
fx = fun(np.copy(x), *args)
File “/kumquat/boshu/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/scipy/optimize/_optimize.py”, line 76, in call
self._compute_if_needed(x, *args)
File “/kumquat/boshu/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/scipy/optimize/_optimize.py”, line 70, in _compute_if_needed
fg = self.fun(x, *args)
File “cryosparc_master/cryosparc_compute/jobs/flex_refine/flexmod.py”, line 1640, in cryosparc_compute.jobs.flex_refine.flexmod.do_hr_refinement_flex.lambda7
File “cryosparc_master/cryosparc_compute/jobs/flex_refine/flexmod.py”, line 1621, in cryosparc_compute.jobs.flex_refine.flexmod.errfunc_flex
File “/kumquat/boshu/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/torch/_tensor.py”, line 488, in backward
torch.autograd.backward(
File “/kumquat/boshu/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/torch/autograd/init.py”, line 197, in backward
Variable._execution_engine.run_backward( # Calls into the C++ engine to run the backward pass
torch.cuda.OutOfMemoryError: CUDA out of memory. Tried to allocate 1.72 GiB (GPU 0; 9.78 GiB total capacity; 7.24 GiB already allocated; 604.56 MiB free; 8.12 GiB reserved in total by PyTorch) If reserved memory is >> allocated memory try setting max_split_size_mb to avoid fragmentation. See documentation for Memory Management and PYTORCH_CUDA_ALLOC_CONF
Do you have any ideas to solve this problem?
Thanks in advance!
boshu
