Problem:
When using the Find Neurite building block, it's possible to calculate all the various neurite associated features. When processing using the Image Analysis view the relevant features are correctly calculated and displayed. However, when running the batch analysis using the external HCP cluster, although the job status page states that the analysis has "completed" the Find Neurite BB feature output is not present in the results file. The Find Neurite BB features are marked as either 0 or n/a.
Example error as shown in the Acapella analysis log files:
2024-02-14 13:08:16.416 4 {31/0} [neurite/run] WARN: Retry 1/10: an error occurred while executing CSIRO external wrapper for DetectNeurites2 (/SImA/app1/Acapella/AcapellaResources/AcapellaNeuriteAnalysis/Bin/NeuriteAnalysisShim): exit code 0x00007F00: /SImA/app1/Acapella/AcapellaResources/AcapellaNeuriteAnalysis/Bin/NeuriteAnalysisShim: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory |PID=30638|TID=30953|SESS=0|
Solution:
Check to see if the same batch analysis can be processed using a local batch analysis job queue e.g. SImA default. If that works, and the relevant Neurite detection features are calculated and defined then this confirms that the issue is related to running the analysis on the HCP cluster.
The libjpeg library which is required by the CSIRO Neurite detection algorithm is not installed on the external cluster nodes.
Check the external cluster nodes to make sure that the required library is installed, if it is not, install it
Example for RHEL:
$ dnf install libjpeg-turbo
Example for Ubuntu:
$ apt install libjpeg62
Note, the libjpeg library will need to be installed on all of the nodes used in the HCP cluster.
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