Installation problem

lmilewski · October 31, 2019, 6:27pm

Hi,
I searched all internet and I don’t have a solution. I have an error when using install.sh script. Everything is ok, until:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
  ------------------------------------------------------------------------
    Done.
    conda packages installation successful.
  ------------------------------------------------------------------------
  Preparing to install all pip packages...
  ------------------------------------------------------------------------
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
**Processing ./deps_bundle/python/python_packages/pip_packages/Flask-JSONRPC-0.3.1.tar.gz**
**Processing ./deps_bundle/python/python_packages/pip_packages/Flask-PyMongo-0.5.1.tar.gz**
**Processing ./deps_bundle/python/python_packages/pip_packages/libtiff-0.4.2.tar.gz**
**    Complete output from command python setup.py egg_info:**
**    Traceback (most recent call last):**
**      File "<string>", line 1, in <module>**
**      File "/tmp/pip-req-build-UEjLdg/setup.py", line 77, in <module>**
**        from numpy.distutils.core import setup, Extension**
**    ImportError: No module named numpy.distutils.core**
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-req-build-UEjLdg/
  ------------------------------------------------------------------------
    Done.
    pip packages installation successful.
  ------------------------------------------------------------------------
  Main dependency installation completed. Continuing...
  ------------------------------------------------------------------------
  Completed.
  Currently checking hash for mongodb
  Dependencies for mongodb have changed - reinstalling...
  ------------------------------------------------------------------------
  mongodb 3.4.10 installation successful.
  ------------------------------------------------------------------------
  Completed.
  Completed dependency check.

After this it said that cryoSPARC is installed, but when I try cryosparcm start I have this:

Starting cryoSPARC...

Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named pymongo

What I can do now?

This is my install script:

./install.sh --standalone --license $LICENSE_ID --worker_path /home/cryosparc_user/software/cryosparc2_worker --cudapath /usr/local/cuda-10.1 --ssdpath /scratch/cryosparc_cache/ --initial_email my@mail --initial_password mypassw--initial_name "myname"

Thank you in advance,
Lukasz

stephan · November 1, 2019, 4:49pm

Hi @lmilewski,

Can you please answer:
What OS is this?
Is there cryoSPARC already installed on this system?
Are your GPUs set up correctly? (i.e. does nvidia-smi work?)

lmilewski · November 2, 2019, 3:58am

Hi, @stephan,
Ubuntu 18,
cryosparc was not previously installed, its fresh OS.
GPUs are set up correctly

ronnie · April 6, 2020, 12:52pm

I’d love to bump this one, as I’m having the same issue.

System is Ubuntu 18.04, GPUs set up fine (eg Relion and Scipion works fine).
I basically get the same error message as lmilewski, see below. Any thoughts on how to fix this?

Best,
Ronnie

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Done.
conda packages installation successful.

Preparing to install all pip packages…

DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won’t be maintained after that date. A future version of pip will drop support for Python 2.7.
Processing ./deps_bundle/python/python_packages/pip_packages/Flask-JSONRPC-0.3.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/Flask-PyMongo-0.5.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/libtiff-0.4.2.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File “”, line 1, in
File “/tmp/pip-req-build-oONzJO/setup.py”, line 77, in
from numpy.distutils.core import setup, Extension
ImportError: No module named numpy.distutils.core

----------------------------------------

Command “python setup.py egg_info” failed with error code 1 in /tmp/pip-req-build-oONzJO/

Done.
pip packages installation successful.

Main dependency installation completed. Continuing…

Completed.
Currently checking hash for mongodb
Dependencies for mongodb have changed - reinstalling…

mongodb 3.4.10 installation successful.

Completed.
Completed dependency check.

************ CRYOSPARC MASTER INSTALLATION COMPLETE **************

CryoSPARC System master has now been installed.
Add bin directory to your ~/.bashrc ?

Yes
No
#? 1

The following lines were appended to your ~/.bashrc:
export PATH=/home/ronnie/software/cryosparc/cryosparc2_master/bin:$PATH

************ CRYOSPARC SYSTEM: STANDALONE INSTALLER **************

The installer will now download, install and connect the worker
package on this machine. The worker package will allow cryoSPARC
to run compute jobs.

Starting cryoSPARC…

Starting cryoSPARC System master process…
CryoSPARC is not already running.
database: started
Traceback (most recent call last):
File “”, line 1, in
ImportError: No module named pymongo

stephan · April 6, 2020, 2:30pm

Hi @ronnie,

Is it possible your situation is related to this:

If so, please make sure your anaconda environments have been deactivated before reinstalling cryoSPARC. Sorry for the inconvenience!

ronnie · April 7, 2020, 8:30am

Hi @stephan,

Thank you for the tip. I’ve now tried to deactivate my existing anaconda environment by running conda deactivate before reinstalling cryosparc using “cryosparcm update --override”. Did not really help though, as I now get similar error message as user in the thread you mentioned:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
  ------------------------------------------------------------------------
    Done.
    conda packages installation successful.
  ------------------------------------------------------------------------
  Preparing to install all pip packages...
  ------------------------------------------------------------------------
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Processing ./deps_bundle/python/python_packages/pip_packages/Flask-JSONRPC-0.3.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/Flask-PyMongo-0.5.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/libtiff-0.4.2.tar.gz
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-req-build-7ufWdZ/setup.py", line 77, in <module>
        from numpy.distutils.core import setup, Extension
    ImportError: No module named numpy.distutils.core
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-req-build-7ufWdZ/
  ------------------------------------------------------------------------
    Done.
    pip packages installation successful.
  ------------------------------------------------------------------------
  Main dependency installation completed. Continuing...
  ------------------------------------------------------------------------
  Completed.
  Currently checking hash for mongodb
  Forcing reinstall for dependency mongodb...
  ------------------------------------------------------------------------
  mongodb 3.4.10 installation successful.
  ------------------------------------------------------------------------
  Completed.
  Completed dependency check. 
 
===================================================
Successfully updated master from version v2.14.2 to version v2.14.2.
===================================================
 
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named pymongo

I’m again unfortunately a bit at a loss on how to fix it… Any help would be appreciated

stephan · April 15, 2020, 3:34pm

Hey @ronnie,

I’m not sure if you’ve already figure this out, but it may be worth checking your .bashrc, which will be found in your home folder. It may be overriding a python path, which may be causing the anaconda installation to fail. If thats not the case, I would suggest deleting the cryosparc2_master and cryosparc2_worker folders, re-extracting the archives, and starting from scratch. But before you start, check what happens when you type which conda or which python.