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.

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.