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: libhdf5.so: undefined reference to …

We sometimes see issues regarding the HDF5 dependency related some incompatibility with hdf5 and curl

hdf5/serial/libhdf5.so: undefined reference to `curl_easy_setopt@CURL_OPENSSL_4

If hdf5 is installed on the Scipion3 enviroment, remove and reinstall it (it might lead to compile/link time issues caused by incompatible version being fetched)
scipion3 conda remove hdf5 scipion3 conda install -c conda-forge hdf5
If you have install hdf5 just in your system, we recommend to install hdf5 in the Scipion enviroment. To do that:
scipion3 conda install -c conda-forge hdf5
If you have installed hdf5 in your system and you can not use conda, please remove hdf5 an all files it creates and reinstall it:
sudo apt remove hdf5-devel
Remove all files related to hdf5 in /usr/lib64/libhdf5*, /usr/include/hdf5* /lib/x86_64-linux-gnu/libhdf5_serial.so and …/anaconda3/include/hdf5*.

We strongy recommend you to install it via your default package manager:
sudo apt-get install libhdf5-dev

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.

ImportError: cannot import name ‘cmake’ from ‘cmake’ (unknown location)

This error occurs because a Python package named cmake (installed via pip) conflicts with the real system-wide CMake tool. The cmake package from pip is not the real CMake; it is a deprecated wrapper. More details on

Check the location of the CMake executable:
```
which cmake
```
If the output shows a path like /home/user/.local/bin/cmake, it means you are using the incorrect version installed via pip.
Uninstall the incorrect version:
```
pip uninstall cmake
```
Verify that you are now using the correct CMake version:
```
which cmake
```
The binary should be located at /usr/bin/cmake or another system directory.

If CMake is not installed, install it from the appropriate source:

sudo apt install cmake