Troubleshooting

General error while installing/compiling Xmipp (non-development installations)

If you are getting an error during the Xmipp compilation, consider to read compilationLog.txt file located in the xmipp folder (by default in scipion3/software/em)/xmippSrc). You can also review the requirements of Xmipp.

Alternatively, you can go with the plugin manager or by running

scipion3 installb xmippSrc

If ERROR: Could not find target xmippSrc is gotten, try to run

scipion3 installp -p scipion-em-xmipp

If the problem persist, don’t hesitate to contact us.

HDF5

We sometimes see issues regarding the HDF5 dependency. We recommend removing all hdf5 versions and install just hdf5-devel. To do that:

sudo apt remove hdf5
sudo apt remove hdf5-devel
pip uninstall h5py

Remove all files related to hdf5 in /usr/lib64/libhdf5*, /usr/include/hdf5* and …/anaconda3/include/hdf5*.

We strongy recommend you to install it via your default package manager:

sudo apt-get install libhdf5-dev

If you install it using other package management system (such as Conda), it might lead to compile/link time issues caused by incompatible version being fetched.

libstdc++.so. version GLIBCXX_3.4.30 not found

When an error like this appear:

libstdc++.so.6: version GLIBCXX_3.4.30 not found (required by /usr/bin/cmake)

It is because the version of libstdc++.so.6 found (in scipion3 enviroment) is older than the one of the system. This usually happens when the library is recently installed in the Scipion environment but with an older version.

The message could be masked by this message

>>> WARNING: XmippImage library not found!
> Please install Xmipp to get full functionality for cryo electron microscopy workflows. Otherwise ignore this.

If this message arise, please run this command to confirm the cause:

./scipion3 python
import xmippLib

The best way to resolve this issue is to update the library in the scipion enviroment.

scipion3 run conda install -c conda-forge libstdcxx-ng

Another less stable option is

mv libstdc++.so.VERSION. libstdc++.so.VERSION.old

Cannot compile with Java

Checking Java configuration...
/usr/lib/jvm/java-11-openjdk-amd64/bin/javac Xmipp.java
/bin/sh: 1: /usr/lib/jvm/java-11-openjdk-amd64/bin/javac: not found
Check the JAVAC
Cannot compile with Java

Java compiler is missing. Needs to install the jdk-devel version. In ubuntu would be like:

sudo apt-get install default-jdk

or activate a jdk with javac using alternatives.

If this is not the case, and you have <SCIPION_HOME>/config/scipion.conf (optional), review the JAVA_XXX variables there. They might be pointing to a non existing JAVA home.