I did
cd $CRYOSPARC_HOME
cd cryosparc_worker
./bin/cryosparcw install-3dflex
but, it didin’t work.
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 82, in cryosparc_compute.run.main
File “/home/cryosparc/cryosparc_worker/cryosparc_compute/jobs/jobregister.py”, line 448, in get_run_function
runmod = importlib.import_module(“…”+modname, name)
File “/home/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/importlib/init.py”, line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File “”, line 1014, in _gcd_import
File “”, line 991, in _find_and_load
File “”, line 975, in _find_and_load_unlocked
File “”, line 671, in _load_unlocked
File “”, line 1174, in exec_module
File “”, line 219, in _call_with_frames_removed
File “cryosparc_master/cryosparc_compute/jobs/flex_refine/run_train.py”, line 12, in init cryosparc_compute.jobs.flex_refine.run_train
File “cryosparc_master/cryosparc_compute/jobs/flex_refine/flexmod.py”, line 19, in init cryosparc_compute.jobs.flex_refine.flexmod
ModuleNotFoundError: No module named ‘torch’
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 82, in cryosparc_compute.run.main
File “/home/cryosparc/cryosparc_worker/cryosparc_compute/jobs/jobregister.py”, line 448, in get_run_function
runmod = importlib.import_module(“…”+modname, name)
File “/home/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/importlib/init.py”, line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File “”, line 1014, in _gcd_import
File “”, line 991, in _find_and_load
File “”, line 975, in _find_and_load_unlocked
File “”, line 671, in _load_unlocked
File “”, line 1174, in exec_module
File “”, line 219, in _call_with_frames_removed
File “cryosparc_master/cryosparc_compute/jobs/flex_refine/run_train.py”, line 12, in init cryosparc_compute.jobs.flex_refine.run_train
File “cryosparc_master/cryosparc_compute/jobs/flex_refine/flexmod.py”, line 19, in init cryosparc_compute.jobs.flex_refine.flexmod
ModuleNotFoundError: No module named ‘torch’
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 82, in cryosparc_compute.run.main
File “/home/cryosparc/cryosparc_worker/cryosparc_compute/jobs/jobregister.py”, line 448, in get_run_function
runmod = importlib.import_module(“…”+modname, name)
File “/home/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/importlib/init.py”, line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File “”, line 1014, in _gcd_import
File “”, line 991, in _find_and_load
File “”, line 975, in _find_and_load_unlocked
File “”, line 671, in _load_unlocked
File “”, line 1174, in exec_module
File “”, line 219, in _call_with_frames_removed
File “cryosparc_master/cryosparc_compute/jobs/flex_refine/run_train.py”, line 12, in init cryosparc_compute.jobs.flex_refine.run_train
File “cryosparc_master/cryosparc_compute/jobs/flex_refine/flexmod.py”, line 19, in init cryosparc_compute.jobs.flex_refine.flexmod
ModuleNotFoundError: No module named ‘torch’
Installing 3D Flex Refine dependencies…
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.5.0
Please update conda by running
$ conda update -n base -c defaults conda
Package Plan
environment location: /home/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env
added / updated specs:
- cuda-nvcc=11.8
- cuda-toolkit=11.8
The following NEW packages will be INSTALLED:
cuda-cccl nvidia/label/cuda-11.8.0/linux-64::cuda-cccl-11.8.89-0
cuda-command-line~ nvidia/label/cuda-11.8.0/linux-64::cuda-command-line-tools-11.8.0-0
cuda-compiler nvidia/label/cuda-11.8.0/linux-64::cuda-compiler-11.8.0-0
cuda-cudart nvidia/label/cuda-11.8.0/linux-64::cuda-cudart-11.8.89-0
cuda-cudart-dev nvidia/label/cuda-11.8.0/linux-64::cuda-cudart-dev-11.8.89-0
cuda-cuobjdump nvidia/label/cuda-11.8.0/linux-64::cuda-cuobjdump-11.8.86-0
cuda-cupti nvidia/label/cuda-11.8.0/linux-64::cuda-cupti-11.8.87-0
cuda-cuxxfilt nvidia/label/cuda-11.8.0/linux-64::cuda-cuxxfilt-11.8.86-0
cuda-documentation nvidia/label/cuda-11.8.0/linux-64::cuda-documentation-11.8.86-0
cuda-driver-dev nvidia/label/cuda-11.8.0/linux-64::cuda-driver-dev-11.8.89-0
cuda-gdb nvidia/label/cuda-11.8.0/linux-64::cuda-gdb-11.8.86-0
cuda-libraries nvidia/label/cuda-11.8.0/linux-64::cuda-libraries-11.8.0-0
cuda-libraries-dev nvidia/label/cuda-11.8.0/linux-64::cuda-libraries-dev-11.8.0-0
cuda-memcheck nvidia/label/cuda-11.8.0/linux-64::cuda-memcheck-11.8.86-0
cuda-nsight nvidia/label/cuda-11.8.0/linux-64::cuda-nsight-11.8.86-0
cuda-nsight-compu~ nvidia/label/cuda-11.8.0/linux-64::cuda-nsight-compute-11.8.0-0
cuda-nvcc nvidia/label/cuda-11.8.0/linux-64::cuda-nvcc-11.8.89-0
cuda-nvdisasm nvidia/label/cuda-11.8.0/linux-64::cuda-nvdisasm-11.8.86-0
cuda-nvml-dev nvidia/label/cuda-11.8.0/linux-64::cuda-nvml-dev-11.8.86-0
cuda-nvprof nvidia/label/cuda-11.8.0/linux-64::cuda-nvprof-11.8.87-0
cuda-nvprune nvidia/label/cuda-11.8.0/linux-64::cuda-nvprune-11.8.86-0
cuda-nvrtc nvidia/label/cuda-11.8.0/linux-64::cuda-nvrtc-11.8.89-0
cuda-nvrtc-dev nvidia/label/cuda-11.8.0/linux-64::cuda-nvrtc-dev-11.8.89-0
cuda-nvtx nvidia/label/cuda-11.8.0/linux-64::cuda-nvtx-11.8.86-0
cuda-nvvp nvidia/label/cuda-11.8.0/linux-64::cuda-nvvp-11.8.87-0
cuda-profiler-api nvidia/label/cuda-11.8.0/linux-64::cuda-profiler-api-11.8.86-0
cuda-sanitizer-api nvidia/label/cuda-11.8.0/linux-64::cuda-sanitizer-api-11.8.86-0
cuda-toolkit nvidia/label/cuda-11.8.0/linux-64::cuda-toolkit-11.8.0-0
cuda-tools nvidia/label/cuda-11.8.0/linux-64::cuda-tools-11.8.0-0
cuda-visual-tools nvidia/label/cuda-11.8.0/linux-64::cuda-visual-tools-11.8.0-0
gds-tools nvidia/label/cuda-11.8.0/linux-64::gds-tools-1.4.0.31-0
libcublas nvidia/label/cuda-11.8.0/linux-64::libcublas-11.11.3.6-0
libcublas-dev nvidia/label/cuda-11.8.0/linux-64::libcublas-dev-11.11.3.6-0
libcufft nvidia/label/cuda-11.8.0/linux-64::libcufft-10.9.0.58-0
libcufft-dev nvidia/label/cuda-11.8.0/linux-64::libcufft-dev-10.9.0.58-0
libcufile nvidia/label/cuda-11.8.0/linux-64::libcufile-1.4.0.31-0
libcufile-dev nvidia/label/cuda-11.8.0/linux-64::libcufile-dev-1.4.0.31-0
libcurand nvidia/label/cuda-11.8.0/linux-64::libcurand-10.3.0.86-0
libcurand-dev nvidia/label/cuda-11.8.0/linux-64::libcurand-dev-10.3.0.86-0
libcusolver nvidia/label/cuda-11.8.0/linux-64::libcusolver-11.4.1.48-0
libcusolver-dev nvidia/label/cuda-11.8.0/linux-64::libcusolver-dev-11.4.1.48-0
libcusparse nvidia/label/cuda-11.8.0/linux-64::libcusparse-11.7.5.86-0
libcusparse-dev nvidia/label/cuda-11.8.0/linux-64::libcusparse-dev-11.7.5.86-0
libnpp nvidia/label/cuda-11.8.0/linux-64::libnpp-11.8.0.86-0
libnpp-dev nvidia/label/cuda-11.8.0/linux-64::libnpp-dev-11.8.0.86-0
libnvjpeg nvidia/label/cuda-11.8.0/linux-64::libnvjpeg-11.9.0.86-0
libnvjpeg-dev nvidia/label/cuda-11.8.0/linux-64::libnvjpeg-dev-11.9.0.86-0
nsight-compute nvidia/label/cuda-11.8.0/linux-64::nsight-compute-2022.3.0.22-0
The following packages will be UPDATED:
ca-certificates conda-forge::ca-certificates-2022.12.~ → pkgs/main::ca-certificates-2024.3.11-h06a4308_0
certifi conda-forge/noarch::certifi-2022.12.7~ → pkgs/main/linux-64::certifi-2024.6.2-py38h06a4308_0
openssl conda-forge::openssl-1.1.1s-h0b41bf4_1 → pkgs/main::openssl-1.1.1w-h7f8727e_0
Preparing transaction: done
Verifying transaction: failed
>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/site-packages/conda/exceptions.py", line 1082, in __call__
return func(*args, **kwargs)
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/site-packages/conda/cli/main.py", line 87, in _main
exit_code = do_call(args, p)
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 84, in do_call
return getattr(module, func_name)(args, parser)
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/site-packages/conda/cli/main_install.py", line 20, in execute
install(args, parser, 'install')
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/site-packages/conda/cli/install.py", line 316, in install
handle_txn(unlink_link_transaction, prefix, args, newenv)
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/site-packages/conda/cli/install.py", line 345, in handle_txn
unlink_link_transaction.execute()
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/site-packages/conda/core/link.py", line 277, in execute
self.verify()
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/site-packages/conda/core/link.py", line 238, in verify
exceptions = self._verify(self.prefix_setups, self.prefix_action_groups)
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/site-packages/conda/core/link.py", line 622, in _verify
for exc in self.verify_executor.map(UnlinkLinkTransaction._verify_individual_level,
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/site-packages/conda/common/io.py", line 525, in map
yield func(thing)
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/site-packages/conda/core/link.py", line 443, in _verify_individual_level
error_result = axn.verify()
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/site-packages/conda/core/path_actions.py", line 409, in verify
mkdir_p(self.transaction_context['temp_dir'])
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/site-packages/conda/gateways/disk/__init__.py", line 68, in mkdir_p
os.makedirs(path)
File "/home/cryosparc/cryosparc_worker/deps/anaconda/lib/python3.8/os.py", line 223, in makedirs
mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/home/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/.condatmp'
$ /home/cryosparc/cryosparc_worker/deps/anaconda/bin/conda install -y cuda-nvcc=11.8 cuda-toolkit=11.8 -c nvidia/label/cuda-11.8.0
environment variables:
CIO_TEST=
CONDA_DEFAULT_ENV=cryosparc_worker_env
CONDA_EXE=/home/cryosparc/cryosparc_worker/deps/anaconda/bin/conda
CONDA_PREFIX=/home/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_e
nv
CONDA_PROMPT_MODIFIER=(cryosparc_worker_env)
CONDA_PYTHON_EXE=/home/cryosparc/cryosparc_worker/deps/anaconda/bin/python
CONDA_ROOT=/home/cryosparc/cryosparc_worker/deps/anaconda
CONDA_SHLVL=1
CRYOSPARC_CUDA_PATH=/usr/local/cuda-11.5
CRYOSPARC_PATH=/home/cryosparc/cryosparc_worker/bin
CURL_CA_BUNDLE=
LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:/apps/IMOD/lib:/apps/bsoft/lib:/usr/local/cuda/
lib64
MANPATH=/usr/share/man/openmpi-x86_64:/apps/IMOD/man:/usr/local/cuda/share/man
:
MODULEPATH=/etc/scl/modulefiles:/usr/share/Modules/modulefiles:/etc/modulefiles:/
usr/share/modulefiles:/apps/modulefiles:/apps/oneAPI
PATH=/home/cryosparc/cryosparc_worker/deps/anaconda/bin:/home/cryosparc/cry
osparc_worker/bin:/home/cryosparc/cryosparc_worker/deps/anaconda/envs/
cryosparc_worker_env/bin:/home/cryosparc/cryosparc_worker/deps/anacond
a/condabin:/home/cryosparc/cryosparc_master/bin:/apps/relion-3.1.3/bin
:/usr/lib64/openmpi/bin:/apps/IMOD/bin:/apps/bsoft/bin:/home/cryosparc
/.local/bin:/home/cryosparc/bin:/usr/share/Modules/bin:/usr/local/cuda
/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig
PYTHONNOUSERSITE=true
PYTHONPATH=/home/cryosparc/cryosparc_worker
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
__MODULES_SHARE_MANPATH=:2
active environment : cryosparc_worker_env
active env location : /home/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env
shell level : 1
user config file : /home/cryosparc/.condarc
populated config files : /home/cryosparc/cryosparc_worker/deps/anaconda/.condarc
conda version : 4.12.0
conda-build version : not installed
python version : 3.8.13.final.0
virtual packages : __cuda=11.5=0
__linux=4.18.0=0
__glibc=2.28=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/cryosparc/cryosparc_worker/deps/anaconda (read only)
conda av data dir : /home/cryosparc/cryosparc_worker/deps/anaconda/etc/conda
conda av metadata url : None
/home/cryosparc/cryosparc_worker/deps/anaconda/pkgs
/home/cryosparc/.conda/pkgs
envs directories : /home/cryosparc/.conda/envs
/home/cryosparc/cryosparc_worker/deps/anaconda/envs
platform : linux-64
user-agent : conda/4.12.0 requests/2.27.1 CPython/3.8.13 Linux/4.18.0-348.2.1.el8_5.x86_64 rocky/8.5 glibc/2.28
UID:GID : 1001:1001
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
Upload successful.
Specifying gpu test
Enabling PyTorch test
Running worker tests…
2024-07-01 00:05:35,973 log CRITICAL | Worker test results
2024-07-01 00:05:35,973 log CRITICAL | yoshinobu
2024-07-01 00:05:35,973 log CRITICAL | ✕ GPU
2024-07-01 00:05:35,973 log CRITICAL | Error: No module named ‘torch’
2024-07-01 00:05:35,973 log CRITICAL | See P13 J86 for more information