SConsEnvironmentError: No module named compilation_db:

[jpellman]

Hi,

I'm getting the following error when I attempt to compile xmippCore in an Ubuntu 20.04 environment with CUDA 11.4.3:

Compiling XmippCore--------
/usr/bin/scons:104: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  import pkg_resources
scons: Reading SConscript files ...
SConsEnvironmentError: No module named compilation_db:
  File "/opt/scipion/xmipp-bundle/src/xmippCore/SConstruct", line 388:
    env.SConscript('SConscript', exports='env')
  File "/usr/lib/scons/SCons/Script/SConscript.py", line 597:
    return _SConscript(self.fs, *files, **subst_kw)
  File "/usr/lib/scons/SCons/Script/SConscript.py", line 286:
    exec(compile(scriptdata, scriptname, 'exec'), call_stack[-1].globals)
  File "/opt/scipion/xmipp-bundle/src/xmippCore/SConscript", line 116:
    addLib('XmippCore',
  File "/opt/scipion/xmipp-bundle/src/xmippCore/SConscript", line 92:
    lib = env.AddCppLibrary(name, **kwargs)
  File "/usr/lib/scons/SCons/Environment.py", line 219:
    return self.method(*nargs, **kwargs)
  File "/opt/scipion/xmipp-bundle/src/xmippCore/SConstruct", line 216:
    env2.Tool('compilation_db')
  File "/usr/lib/scons/SCons/Environment.py", line 1809:
    tool = SCons.Tool.Tool(tool, toolpath, **kw)
  File "/usr/lib/scons/SCons/Tool/__init__.py", line 122:
    module = self._tool_module()
  File "/usr/lib/scons/SCons/Tool/__init__.py", line 221:
    raise SCons.Errors.SConsEnvironmentError(error_string)

This compilation happens as part of a broader procedure for installing Scipion. These are the instructions I was given to accomplish this:

1. Clone the repository with git clone https://github.com/I2PC/xmipp.git xmipp-bundle && cd xmipp-bundle
2. Run scipion3 run ./xmipp config
3. Edit xmipp.conf to remove the problematic compilation flags
4. Run scipion3 run ./xmipp
5. Link the installation to Scipion with scipion3 installp -p src/scipion-em-xmipp --devel"

This stack trace is thrown during step 4 of this process. I've attached a log that might have more info. I'm using a conda environment to run the installer and the following command was used to install dependencies:

apt-get install -y gcc-10 g++-10 libopenmpi-dev make scons libfftw3-dev libhdf5-dev python3-numpy python3-dev libtiff5-dev libsqlite3-dev default-jdk git cmake curl wget rsync 

Is there anything else I should be doing/installing to get this to compile?

compileLOG.txt

Many thanks, John Pellman

[albertmena]

Hi John and sorry for the long wait for the answer, We are completely changing the installer of Xmipp,if you going to install the devel branch of xmipp you just need to try to install xmipp again following these steps: steps xmipp dev

[albertmena]

We remove sconbs as installer tool