Hello,
I am running the cryosparc tutorial and cannot get past the motion correction step. All of the import jobs seem to work, however, motion correction does not. I have tried resetting the path to direct to both cryosparc and cuda, however, it does not seem to change the error message.
[CPU: 221.8 MB] Error occurred while processing J1/imported/14sep05c_00024sq_00003hl_00002es.frames.tif
Traceback (most recent call last):
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/tools.py", line 429, in context_dependent_memoize
return ctx_dict[cur_ctx][args]
KeyError: <pycuda._driver.Context object at 0x2aaad73bb1b0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pytools/prefork.py", line 50, in call_capture_output
stderr=PIPE)
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/subprocess.py", line 800, in __init__
restore_signals, start_new_session)
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/subprocess.py", line 1551, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'nvcc': 'nvcc'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data1/cryosparc_user/v3/cryosparc_worker/cryosparc_compute/jobs/pipeline.py", line 59, in exec
return self.process(item)
File "cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_patch.py", line 190, in cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
File "cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_patch.py", line 193, in cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
File "cryosparc_worker/cryosparc_compute/jobs/motioncorrection/run_patch.py", line 195, in cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
File "cryosparc_worker/cryosparc_compute/jobs/motioncorrection/patchmotion.py", line 251, in cryosparc_compute.jobs.motioncorrection.patchmotion.unbend_motion_correction
File "cryosparc_worker/cryosparc_compute/jobs/motioncorrection/patchmotion.py", line 260, in cryosparc_compute.jobs.motioncorrection.patchmotion.unbend_motion_correction
File "cryosparc_worker/cryosparc_compute/jobs/motioncorrection/patchmotion.py", line 117, in cryosparc_compute.jobs.motioncorrection.patchmotion.prepare_movie_for_processing
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/gpuarray.py", line 549, in fill
func = elementwise.get_fill_kernel(self.dtype)
File "<decorator-gen-120>", line 2, in get_fill_kernel
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/tools.py", line 433, in context_dependent_memoize
result = func(*args)
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/elementwise.py", line 498, in get_fill_kernel
"fill")
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/elementwise.py", line 163, in get_elwise_kernel
arguments, operation, name, keep, options, **kwargs)
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/elementwise.py", line 149, in get_elwise_kernel_and_types
keep, options, **kwargs)
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/elementwise.py", line 76, in get_elwise_module
options=options, keep=keep, no_extern_c=True)
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/compiler.py", line 291, in __init__
arch, code, cache_dir, include_dirs)
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/compiler.py", line 254, in compile
return compile_plain(source, options, keep, nvcc, cache_dir, target)
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/compiler.py", line 78, in compile_plain
checksum.update(preprocess_source(source, options, nvcc).encode("utf-8"))
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/compiler.py", line 50, in preprocess_source
result, stdout, stderr = call_capture_output(cmdline, error_on_nonzero=False)
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pytools/prefork.py", line 227, in call_capture_output
return forker.call_capture_output(cmdline, cwd, error_on_nonzero)
File "/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pytools/prefork.py", line 61, in call_capture_output
% (" ".join(cmdline), e))
pytools.prefork.ExecError: error invoking 'nvcc --preprocess -arch sm_75 -I/data1/cryosparc_user/v3/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/cuda /tmp/tmp0i5ikmg6.cu --compiler-options -P': [Errno 2] No such file or directory: 'nvcc': 'nvcc'
Marking J1/imported/14sep05c_00024sq_00003hl_00002es.frames.tif as incomplete and continuing...
Any insight into what the problem is or the solution would help! Thank you so much!