Hello,
I’ll preface this by noting that this may be an NVIDIA issue and not a cryosparc issue. That said, I’m looking for any possible solution.
I’m trying to run a Patch Motion on a newly installed cryosparc instance on a freshly installed Linux Mint 20 (Ulyana). CUDA version is 10.2 and I run into the following error
> [CPU: 883.3 MB] Traceback (most recent call last):
> File "cryosparc2_compute/jobs/runcommon.py", line 1685, in run_with_except_hook
> run_old(*args, **kw)
> File "/home/vamsee/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/threading.py", line 754, in run
> self.__target(*self.__args, **self.__kwargs)
> File "cryosparc2_compute/jobs/pipeline.py", line 165, in thread_work
> work = processor.process(item)
> File "cryosparc2_worker/cryosparc2_compute/jobs/motioncorrection/run_patch.py", line 157, in cryosparc2_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
> File "cryosparc2_worker/cryosparc2_compute/jobs/motioncorrection/run_patch.py", line 160, in cryosparc2_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
> File "cryosparc2_worker/cryosparc2_compute/jobs/motioncorrection/run_patch.py", line 161, in cryosparc2_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
> File "cryosparc2_worker/cryosparc2_compute/jobs/motioncorrection/patchmotion.py", line 77, in cryosparc2_compute.jobs.motioncorrection.patchmotion.unbend_motion_correction
> File "cryosparc2_worker/cryosparc2_compute/jobs/motioncorrection/patchmotion.py", line 103, in cryosparc2_compute.jobs.motioncorrection.patchmotion.unbend_motion_correction
> File "/home/vamsee/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/gpuarray.py", line 549, in fill
> func = elementwise.get_fill_kernel(self.dtype)
> File "<decorator-gen-124>", line 2, in get_fill_kernel
> File "/home/vamsee/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/tools.py", line 432, in context_dependent_memoize
> result = func(*args)
> File "/home/vamsee/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/elementwise.py", line 496, in get_fill_kernel
> "fill")
> File "/home/vamsee/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/elementwise.py", line 161, in get_elwise_kernel
> arguments, operation, name, keep, options, **kwargs)
> File "/home/vamsee/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/elementwise.py", line 147, in get_elwise_kernel_and_types
> keep, options, **kwargs)
> File "/home/vamsee/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/elementwise.py", line 75, in get_elwise_module
> options=options, keep=keep)
> File "/home/vamsee/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/compiler.py", line 291, in __init__
> arch, code, cache_dir, include_dirs)
> File "/home/vamsee/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/compiler.py", line 254, in compile
> return compile_plain(source, options, keep, nvcc, cache_dir, target)
> File "/home/vamsee/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/compiler.py", line 78, in compile_plain
> checksum.update(preprocess_source(source, options, nvcc).encode("utf-8"))
> File "/home/vamsee/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/compiler.py", line 55, in preprocess_source
> cmdline, stderr=stderr)
> CompileError: nvcc preprocessing of /tmp/tmpZ5hkbR.cu failed
> [command: nvcc --preprocess -arch sm_75 -I/home/vamsee/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/cuda /tmp/tmpZ5hkbR.cu --compiler-options -P]
> [stderr:
> In file included from /usr/local/cuda-10.2/bin/../targets/x86_64-linux/include/cuda_runtime.h:83,
> from <command-line>:
> /usr/local/cuda-10.2/bin/../targets/x86_64-linux/include/crt/host_config.h:138:2: error: #error -- unsupported GNU version! gcc versions later than 8 are not supported!
> 138 | #error -- unsupported GNU version! gcc versions later than 8 are not supported!
> | ^~~~~
> ]
This error clearly states that the CUDA version doesn’t support GCC versions > 8. The default GCC version in LM20 is 9.3. Anyway, I could force cryosparc/CUDA to look for an older version and run the Patch Motion? or do I need to go all the way back to reinstalling an older LM version?
Thanks,
Vamsee