Here is the output, current version is v4.5.1
(base) [cryosparc_user@dhvi-r124848 ~]$ cd cryosparc/cryosparc_worker
(base) [cryosparc_user@dhvi-r124848 cryosparc_worker]$ cat version
v4.5.1
Thanks @ml705. Please can you post the answers to questions (2.) and (3.) in Child process with PID terminated unexpectedly on v4.5 - #14 by wtempel.
(There’s no need to re-run nvidia-smi.)
Question 2: I tried to restart the job after the following the commands given in question 3 and it worked.
Question 3 outputs are below
It is working now. Thank you so much for your help. Can I know in a simple terminology what has actually happened?
/path/to/cryosparc_worker/bin/cryosparcw callenv| grep PATH
LD_LIBRARY_PATH=/usr/lib/wsl/lib:/usr/local/relion-4.0/lib:/usr/local/cuda/lib:/usr/local/cuda/lib64:/usr/local/cuda-11.2/lib:/usr/local/cuda-11.2/lib64:/usr/local/cuda-11.1/lib:/usr/local/cuda-11.1/lib64:/usr/local/cuda-11.0/lib:/usr/local/cuda-11.0/lib64:/usr/local/cuda-10.1/lib:/usr/local/cuda-10.1/lib64:/usr/local/relion-4.0/lib:/usr/local/cuda/lib:/usr/local/cuda/lib64:/usr/local/cuda-11.2/lib:/usr/local/cuda-11.2/lib64:/usr/local/cuda-11.1/lib:/usr/local/cuda-11.1/lib64:/usr/local/cuda-11.0/lib:/usr/local/cuda-11.0/lib64:/usr/local/cuda-10.1/lib:/usr/local/cuda-10.1/lib64:/usr/local/relion-4.0/lib:/usr/local/cuda/lib:/usr/local/cuda/lib64:/usr/local/cuda-11.2/lib:/usr/local/cuda-11.2/lib64:/usr/local/cuda-11.1/lib:/usr/local/cuda-11.1/lib64:/usr/local/cuda-11.0/lib:/usr/local/cuda-11.0/lib64:/usr/local/cuda-10.1/lib:/usr/local/cuda-10.1/lib64:
MODULES_RUN_QUARANTINE=LD_LIBRARY_PATHLD_PRELOAD
CRYOSPARC_PATH=/home/cryosparc_user/cryosparc/cryosparc_worker/bin
WINDOWPATH=2
PYTHONPATH=/home/cryosparc_user/cryosparc/cryosparc_worker
MANPATH=/usr/local/IMOD/man::
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/usr/share/modulefiles
MODULEPATH_modshare=/usr/share/Modules/modulefiles:2:/etc/modulefiles:2:/usr/share/modulefiles:2
NUMBA_CUDA_INCLUDE_PATH=/home/cryosparc_user/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/include
PATH=/home/cryosparc_user/cryosparc/cryosparc_worker/bin:/home/cryosparc_user/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin:/home/cryosparc_user/cryosparc/cryosparc_worker/deps/anaconda/condabin:/home/cryosparc_user/cryosparc/cryosparc_master/bin:/usr/local/relion-4.0/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/EMAN_2.91/bin:/usr/local/EMAN_2.91/condabin:/home/cryosparc_user/cryosparc/cryosparc_master/bin:/home/cryosparc_user/.local/bin:/home/cryosparc_user/bin:/usr/local/relion-4.0/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/relion-4.0/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/share/Modules/bin:/usr/local/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.18/bin:/usr/local/ResMap:/usr/local/cistem-1.0.0-beta:/usr/local/EMAN_2.91/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.18/bin:/usr/local/ResMap:/usr/local/cistem-1.0.0-beta:/usr/local/EMAN_2.91/bin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.18/bin:/usr/local/ResMap:/usr/local/cistem-1.0.0-beta:/usr/local/EMAN_2.91/bin
/path/to/cryosparc_worker/bin/cryosparcw call numba –s
/home/cryosparc_user/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/numba/core/config.py:178: UserWarning: CUDA Python bindings requested (the environment variable NUMBA_CUDA_USE_NVIDIA_BINDING is set), but they are not importable: No module named ‘cuda’.
/path/to/cryosparc_worker/bin/cryosparcw call python -c“from numba import cuda; cuda.cudadrv.libs.test()”
(base) [cryosparc_user@dhvi-r124848 ~]$ /home/cryosparc_user/cryosparc/cryosparc_worker/bin/cryosparcw call python -c “from numba import cuda; cuda.cudadrv.libs.test()”
/home/cryosparc_user/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/numba/core/config.py:178: UserWarning: CUDA Python bindings requested (the environment variable NUMBA_CUDA_USE_NVIDIA_BINDING is set), but they are not importable: No module named ‘cuda’.
warnings.warn(msg)
Finding driver from candidates:
libcuda.so
libcuda.so.1
/usr/lib/libcuda.so
/usr/lib/libcuda.so.1
/usr/lib64/libcuda.so
/usr/lib64/libcuda.so.1
Using loader <class ‘ctypes.CDLL’>
Trying to load driver… ok
Loaded from libcuda.so
Mapped libcuda.so paths:
/usr/lib64/libcuda.so.580.126.18
Finding nvvm from Conda environment
Located at /home/cryosparc_user/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/libnvvm.so.4.0.0
Trying to open library… ok
Finding nvrtc from Conda environment
Located at /home/cryosparc_user/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/libnvrtc.so.11.8.89
Trying to open library… ok
Finding cudart from Conda environment
Located at /home/cryosparc_user/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/libcudart.so.11.8.89
Trying to open library… ok
Finding cudadevrt from Conda environment
Located at /home/cryosparc_user/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/libcudadevrt.a
Checking library… ok
Finding libdevice from Conda environment
Located at /home/cryosparc_user/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/libdevice.10.bc
Checking library… ok
/sbin/ldconfig -p | grep -u libcuda
(base) [cryosparc_user@dhvi-r124848 ~]$ /sbin/ldconfig -p | grep -u libcuda
libcudart.so.11.0 (libc6,x86-64) => /usr/local/cuda-11.0/targets/x86_64-linux/lib/libcudart.so.11.0
libcudart.so.11.0 (libc6,x86-64) => /usr/local/cuda-11.1/targets/x86_64-linux/lib/libcudart.so.11.0
libcudart.so.11.0 (libc6,x86-64) => /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudart.so.11.0
libcudart.so.11.0 (libc6,x86-64) => /usr/local/cuda-11.6/targets/x86_64-linux/lib/libcudart.so.11.0
libcudart.so.10.1 (libc6,x86-64) => /usr/local/cuda-10.1/targets/x86_64-linux/lib/libcudart.so.10.1
libcudart.so (libc6,x86-64) => /usr/local/cuda-10.1/targets/x86_64-linux/lib/libcudart.so
libcudart.so (libc6,x86-64) => /usr/local/cuda-11.0/targets/x86_64-linux/lib/libcudart.so
libcudart.so (libc6,x86-64) => /usr/local/cuda-11.1/targets/x86_64-linux/lib/libcudart.so
libcudart.so (libc6,x86-64) => /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudart.so
libcudart.so (libc6,x86-64) => /usr/local/cuda-11.6/targets/x86_64-linux/lib/libcudart.so
libcudadebugger.so.1 (libc6,x86-64) => /lib64/libcudadebugger.so.1
libcuda.so.1 (libc6,x86-64) => /lib64/libcuda.so.1
libcuda.so.1 (libc6) => /lib/libcuda.so.1
libcuda.so (libc6,x86-64) => /lib64/libcuda.so
libcuda.so (libc6) => /lib/libcuda.so
The commands were intended for the collection of diagnostic information. I did not expect that the commands would fix anything. Please can you confirm that patch motion correction works on the dhvi-r124848 computer?
Patch motion correction job shows complete, but I do see the some incomplete movies. Since the log is too long, I attached complete log of this job in word file in a link. Please check the link. thank you
Thanks @ml705 . Please can you share the job report for that job?
Uploaded into box folder. Please let me know if you can’t access it. Thank you.
Thanks @ml705 I fetched the report. You may disable the download links if you wish.
The logs indicate read errors for one of the files. Can you try (via Import Movies), importing the single file
FoilHole_13874182_Data_13873307_7_20260414_162154_EER.eer
specifically and then running Patch Motion Correction?
