V4.6.2 installation error

peizhou · January 11, 2025, 4:44am

Hi,

I am encountering issues with cryosparc v4.6.2 installation. I used the command “cryosparcm update --override”. The installation went smoothly after the message of mongodb 3.6.23 installation successful. Here is the remaining message.

Any suggestions?

Thanks,

Pei

>>>>

(success messages above)
  Extracting all conda packages...
  ------------------------------------------------------------------------
.................................................................................................
  ------------------------------------------------------------------------
    Done.
    conda packages installation successful.
  ------------------------------------------------------------------------
  Main dependency installation completed. Continuing...
  ------------------------------------------------------------------------
  Completed.
  Currently checking hash for mongodb
  Forcing reinstall for dependency mongodb...
  ------------------------------------------------------------------------
  mongodb 3.6.23 installation successful.
  ------------------------------------------------------------------------
  Completed.
  Completed dependency check.
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/opt/CryoSparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/libtiff/__init__.py", line 21, in <module>
    from .tiff import TIFFfile, TIFFimage, TiffArray
  File "/opt/CryoSparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/libtiff/tiff.py", line 25, in <module>
    from .tiff_file import TIFFfile
  File "/opt/CryoSparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/libtiff/tiff_file.py", line 15, in <module>
    from numpy.testing.utils import memusage
ModuleNotFoundError: No module named 'numpy.testing.utils'

wtempel · January 13, 2025, 2:47pm

@peizhou Please can you provide additional background information

output of the command, under the Linux account designated for the CryoSPARC installation:
```
env | grep PATH
```
the CryoSPARC version under which this instance last operated
the motivation for using the update --override option in this specific case
the date when cryosparcm update was last run without the --override flag

peizhou · January 13, 2025, 10:46pm

[em@gemini CryoSparc]$ env | grep PATH
LD_LIBRARY_PATH=/opt/pymol/lib64:/usr/local/lib:/usr/local/cuda-8.0/lib64:/usr/local/cuda-11.1/lib64:/opt/relion/3.1/lib:/opt/openmpi/4.0.5/lib64:/opt/pymol/lib64:/usr/local/lib:/usr/local/cuda-8.0/lib64:/usr/local/cuda-11.1/lib64:/opt/IMOD/lib:
PATH=/home/xtal/phenix-1.19.2-4158/build/bin:/opt/CryoSparc/cryosparc_master/bin:/opt/pyem/:/data/Programs/ColabFold/localcolabfold/colabfold-conda/bin:/opt/bin:/opt/pymol/bin:/opt/cistem/1.0.0:/opt/frealign/9.11/bin:/opt/relion/3.1/bin:/usr/local/cuda-11.1/bin:/usr/local/cuda-8.0/bin:/opt/openmpi/4.0.5/bin:/usr/lib64/qt-3.3/bin:/home/em/perl5/bin:/opt/IMOD/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/em/.local/bin:/home/em/bin
MODULEPATH=/opt/sp/modulefiles:/usr/share/Modules/modulefiles:/etc/modulefiles
LIBTBX_OPATH=
QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins

Previous version: v4.5.3

I restored the previous version and tried “cryosparcm update” and got the same error below. (Hence, today is the last run without the --override flag.)

Here is the last part of the installation log (with Conda package installation successful.)

....
Transaction finished

To activate this environment, use:

    micromamba activate /opt/CryoSparc/cryosparc_master/deps/anaconda

Or to execute a single command in this environment, use:

    micromamba run -p /opt/CryoSparc/cryosparc_master/deps/anaconda mycommand

installation finished.
  ------------------------------------------------------------------------
    Done.
    anaconda python installation successful.
  ------------------------------------------------------------------------
  Extracting all conda packages...
  ------------------------------------------------------------------------
.................................................................................................
  ------------------------------------------------------------------------
    Done.
    conda packages installation successful.
  ------------------------------------------------------------------------
  Main dependency installation completed. Continuing...
  ------------------------------------------------------------------------
  Completed.
  Currently checking hash for mongodb
  Dependencies for mongodb have not changed.
  Completed dependency check.
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/opt/CryoSparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/libtiff/__init__.py", line 21, in <module>
    from .tiff import TIFFfile, TIFFimage, TiffArray
  File "/opt/CryoSparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/libtiff/tiff.py", line 25, in <module>
    from .tiff_file import TIFFfile
  File "/opt/CryoSparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/libtiff/tiff_file.py", line 15, in <module>
    from numpy.testing.utils import memusage
ModuleNotFoundError: No module named 'numpy.testing.utils'

wtempel · January 14, 2025, 6:37pm

Thanks @peizhou Please can you run these commands and post their outputs

whoami
which python3
python3 -m pip list
/opt/CryoSparc/cryosparc_master/bin/cryosparcm call python -c "import sys, numpy; print(sys.path, numpy.__file__)"

peizhou · January 14, 2025, 7:35pm

I think my python path/version and packages are probably the source of issues. Here are the output.

[em@gemini CryoSparc]$ whoami
em

[em@gemini CryoSparc]$ which python3
/data/Programs/ColabFold/localcolabfold/colabfold-conda/bin/python3

[em@gemini CryoSparc]$ which python3
/data/Programs/ColabFold/localcolabfold/colabfold-conda/bin/python3

[em@gemini CryoSparc]$ python3 -m pip list
Package                      Version
---------------------------- ---------------------
absl-py                      1.4.0
aiohappyeyeballs             2.4.4
aiohttp                      3.11.11
aiosignal                    1.3.2
alphafold-colabfold          2.3.5
antlr4-python3-runtime       4.9.3
appdirs                      1.4.4
astunparse                   1.6.3
async-timeout                5.0.1
attrs                        24.3.0
biopython                    1.84
boltz                        0.4.0
cachetools                   5.3.1
certifi                      2023.5.7
charset-normalizer           3.1.0
chex                         0.1.6
click                        8.1.7
colabfold                    1.5.2
contextlib2                  21.6.0
contourpy                    1.1.0
cycler                       0.11.0
dm-haiku                     0.0.9
dm-tree                      0.1.8
docker                       6.1.3
docker-pycreds               0.4.0
einops                       0.8.0
einx                         0.3.0
fairscale                    0.4.13
filelock                     3.16.1
flatbuffers                  23.5.26
fonttools                    4.40.0
frozendict                   2.4.6
frozenlist                   1.5.0
fsspec                       2024.12.0
gast                         0.4.0
gitdb                        4.0.11
GitPython                    3.1.43
google-auth                  2.21.0
google-auth-oauthlib         1.0.0
google-pasta                 0.2.0
grpcio                       1.56.0
h5py                         3.9.0
hydra-core                   1.3.2
idna                         3.4
ihm                          1.8
immutabledict                2.2.4
importlib-metadata           4.13.0
jax                          0.3.25
jaxlib                       0.3.25+cuda11.cudnn82
Jinja2                       3.1.5
jmp                          0.0.4
keras                        2.12.0
kiwisolver                   1.4.4
libclang                     16.0.0
lightning-utilities          0.11.9
Markdown                     3.4.3
MarkupSafe                   2.1.3
mashumaro                    3.14
matplotlib                   3.7.1
ml-collections               0.1.1
ml-dtypes                    0.2.0
modelcif                     1.2
mpmath                       1.3.0
msgpack                      1.1.0
multidict                    6.1.0
networkx                     3.4.2
numpy                        1.26.3
nvidia-cublas-cu12           12.4.5.8
nvidia-cuda-cupti-cu12       12.4.127
nvidia-cuda-nvrtc-cu12       12.4.127
nvidia-cuda-runtime-cu12     12.4.127
nvidia-cudnn-cu12            9.1.0.70
nvidia-cufft-cu12            11.2.1.3
nvidia-curand-cu12           10.3.5.147
nvidia-cusolver-cu12         11.6.1.9
nvidia-cusparse-cu12         12.3.1.170
nvidia-nccl-cu12             2.21.5
nvidia-nvjitlink-cu12        12.4.127
nvidia-nvtx-cu12             12.4.127
oauthlib                     3.2.2
omegaconf                    2.3.0
OpenMM                       7.7.0
opt-einsum                   3.3.0
packaging                    23.1
pandas                       2.2.3
pdbfixer                     1.8.1
Pillow                       10.0.0
pip                          23.1.2
platformdirs                 4.3.6
propcache                    0.2.1
protobuf                     4.23.3
psutil                       6.1.1
py3Dmol                      2.0.3
pyasn1                       0.5.0
pyasn1-modules               0.3.0
pyparsing                    3.1.0
python-dateutil              2.8.2
pytorch-lightning            2.4.0
pytz                         2023.3
PyYAML                       6.0.2
rdkit                        2024.3.2
requests                     2.32.3
requests-oauthlib            1.3.1
rsa                          4.9
scipy                        1.13.1
sentry-sdk                   2.19.2
setproctitle                 1.3.4
setuptools                   67.8.0
six                          1.16.0
smmap                        5.0.1
sympy                        1.13.1
tabulate                     0.9.0
tensorboard                  2.12.3
tensorboard-data-server      0.7.1
tensorflow                   2.12.0
tensorflow-cpu               2.12.0
tensorflow-estimator         2.12.0
tensorflow-io-gcs-filesystem 0.32.0
termcolor                    2.3.0
toolz                        0.12.0
torch                        2.5.1
torchmetrics                 1.6.1
tqdm                         4.65.0
triton                       3.1.0
types-requests               2.32.0.20241016
typing_extensions            4.12.2
tzdata                       2024.2
urllib3                      2.3.0
wandb                        0.18.7
websocket-client             1.6.1
Werkzeug                     2.3.6
wheel                        0.38.4
wrapt                        1.14.1
yarl                         1.18.3
zipp                         3.15.0

wtempel · January 14, 2025, 7:59pm

Thanks. Please can you also post the output of

/opt/CryoSparc/cryosparc_master/bin/cryosparcm call python -c "import sys, numpy; print(sys.path, numpy.__file__)"

peizhou · January 14, 2025, 9:39pm

Here is the outcome:

/opt/CryoSparc/cryosparc_master/bin/cryosparcm call python -c "import sys, numpy; print(sys.path, numpy.__file__)"
['', '/opt/CryoSparc/cryosparc_master', '/opt/CryoSparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python310.zip', '/opt/CryoSparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10', '/opt/CryoSparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/lib-dynload', '/opt/CryoSparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages'] /opt/CryoSparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/numpy/__init__.py

peizhou · January 14, 2025, 9:41pm

I noticed the html edit changed the text. Here is the corrected one. The bold font actually indicates the name with two underlines before and after.

wtempel · January 14, 2025, 9:47pm

Thanks for posting the output.

You are seeing the effect of markdown formatting.

wtempel · January 15, 2025, 10:20pm

A possible workaround might be to set the PYTHONNOUSERSITE variable and finish the installation with the command

PYTHONNOUSERSITE=true cryosparcm install

Does this help?

peizhou · January 16, 2025, 1:57am

I tried this from my restored v4.5.3. It worked fine, but it did not update to v.4.6.2.

My question is: should I use “PYTHONNOUSERSITE=true cryosparcm update” or should I download the v.4.6.2 tar.gz files and then run “PYTHONNOUSERSITE=true cryosparcm install”.

Please advise. Thanks!

peizhou · January 16, 2025, 2:59am

Thanks a lot for your help!!!

“PYTHONNOUSERSITE=true cryosparcm update” worked for me. I was able to update to v4.6.2. Cheers!