Greetings Cryosparc Community,
I have recently run into an error while running Cryosparc Live. I am quite new to this process, so any direction would be immensely appreciated.
When I run CTF correction I get the following output error:
Traceback (most recent call last):
File "/home/cryosparcusr/cryosparc/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: (dtype('float32'),)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "cryosparc_worker/cryosparc_compute/jobs/rtp_workers/run.py", line 376, in cryosparc_compute.jobs.rtp_workers.run.rtp_worker
File "cryosparc_worker/cryosparc_compute/jobs/rtp_workers/run.py", line 439, in cryosparc_compute.jobs.rtp_workers.run.process_movie
File "cryosparc_worker/cryosparc_compute/jobs/rtp_workers/run.py", line 585, in cryosparc_compute.jobs.rtp_workers.run.do_patch_motion
File "cryosparc_worker/cryosparc_compute/jobs/rtp_workers/run.py", line 590, in cryosparc_compute.jobs.rtp_workers.run.do_patch_motion
File "cryosparc_worker/cryosparc_compute/jobs/motioncorrection/patchmotion.py", line 255, in cryosparc_compute.jobs.motioncorrection.patchmotion.unbend_motion_correction
File "cryosparc_worker/cryosparc_compute/jobs/motioncorrection/patchmotion.py", line 264, in cryosparc_compute.jobs.motioncorrection.patchmotion.unbend_motion_correction
File "cryosparc_worker/cryosparc_compute/jobs/motioncorrection/patchmotion.py", line 121, in cryosparc_compute.jobs.motioncorrection.patchmotion.prepare_movie_for_processing
File "/home/cryosparcusr/cryosparc/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-13>", line 2, in get_fill_kernel
File "/home/cryosparcusr/cryosparc/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 "/home/cryosparcusr/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/elementwise.py", line 498, in get_fill_kernel
"fill")
File "/home/cryosparcusr/cryosparc/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 "/home/cryosparcusr/cryosparc/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 "/home/cryosparcusr/cryosparc/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 "/home/cryosparcusr/cryosparc/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 "/home/cryosparcusr/cryosparc/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 "/home/cryosparcusr/cryosparc/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 "/home/cryosparcusr/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/compiler.py", line 55, in preprocess_source
cmdline, stderr=stderr)
pycuda.driver.CompileError: nvcc preprocessing of /tmp/tmpkx366p8_.cu failed
[command: nvcc --preprocess -arch sm_75 -I/home/cryosparcusr/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pycuda/cuda /tmp/tmpkx366p8_.cu --compiler-options -P]
[stderr:
b"In file included from /usr/local/cuda-11.2/bin/../targets/x86_64-linux/include/cuda_runtime.h:83,\n from <command-line>:\n/usr/local/cuda-11.2/bin/../targets/x86_64-linux/include/crt/host_config.h:139:2: error: #error -- unsupported GNU version! gcc versions later than 10 are not supported! The nvcc flag '-allow-unsupported-compiler' can be used to override this version check; however, using an unsupported host compiler may cause compilation failure or incorrect run time execution. Use at your own risk.\n 139 | #error -- unsupported GNU version! gcc versions later than 10 are not supported! The nvcc flag '-allow-unsupported-compiler' can be used to override this version check; however, using an unsupported host compiler may cause compilation failure or incorrect run time execution. Use at your own risk.\n | ^~~~~\n"]
The secondary exception I understand to be a version warning, it is the first error that is throwing me off. It appears that when sending context data to pycuda the software is throwing a datatype error.
If there is any additional information needed to help diagnose this information, I would be happy to provide it.
Thank you for your guidance,
Ali