Hi,
this is the output of those commands
keck@keck-cryo2:~$ /home/keck/cryosparc/cryosparc_worker/bin/cryosparcw call which nvcc
/home/keck/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin/nvcc
keck@keck-cryo2:~$ echo "" | /home/keck/cryosparc/cryosparc_worker/bin/cryosparcw call nvcc -v -E -
#$ _NVVM_BRANCH_=nvvm
#$ _SPACE_=
#$ _CUDART_=cudart
#$ _HERE_=/home/keck/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin
#$ _THERE_=/home/keck/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin
#$ _TARGET_SIZE_=
#$ _TARGET_DIR_=
#$ _TARGET_SIZE_=64
#$ TOP=/home/keck/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin/..
#$ NVVMIR_LIBRARY_DIR=/home/keck/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin/../nvvm/libdevice
#$ LD_LIBRARY_PATH=/home/keck/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin/../lib:/usr/local/cuda/lib64:/home/keck/cryosparc/cryosparc_worker/deps/external/cudnn/lib
#$ PATH=/home/keck/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin/../nvvm/bin:/home/keck/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin:/usr/local/cuda/bin:/home/keck/cryosparc/cryosparc_worker/bin:/home/keck/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin:/home/keck/cryosparc/cryosparc_worker/deps/anaconda/condabin:/home/keck/cryosparc/cryosparc_master/bin:/home/keck/cryosparc/cryosparc_master/bin:/home/keck/cryosparc/cryosparc_master/bin:/home/keck/cryosparc/cryosparc_master/bin:/home/keck/cryosparc/cryosparc_master/bin:/home/keck/cryosparc/cryosparc_master/bin:/home/keck/cryosparc/cryosparc_master/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin
#$ INCLUDES="-I/home/keck/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin/../include"
#$ LIBRARIES= "-L/home/keck/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin/../lib/stubs" "-L/home/keck/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/bin/../lib"
#$ CUDAFE_FLAGS=
#$ PTXAS_FLAGS=
nvcc fatal : Don't know what to do with '/tmp/tmpxft_0000df21_00000000-1_stdin'
So I was able to get the job patch motion correction running after I did this:
Update ubuntu from 20.04 to 22.04
Purge cuda
reinstall nvidia cuda toolkit
reinstall driver
install nvidia utils → which inturn removed nvidia cuda toolkit
(if I tried to reinstall nvidia cuda toolkit it said it will remove nvidia util - I dont know what to do at this point)
Right now if I run command
nvcc --version
it said:
Command 'nvcc' not found, but can be installed with:
sudo apt install nvidia-cuda-toolkit
what do you think? will I have problem running my jobs upstream in the future?