Open cymon opened 1 year ago
I've made some notes about this issue in a GoogleDoc (request access): InterProScan version needs updating
Here the issue is that the version of IPS in MGF v.1.0.0 uses version 5.57-90.0 which contains an Prosite binary package that is incompatible with AMD EPYC cpus (specifically 7643 cpus (launched 2021), but presumably others with the same architecture). According to this post, the ProSite pftools library needs to be updated to v3.2.11. The latest version of IPS is 5.64-96.0.
This exact error is noted in the IPS documentation:
Additionally on some systems, specially on cluster environments, the following error has been reported Error setting affinity! Error running prosite binary bin/prosite/pfsearchV3 This means the provided binary is not compatible with your system. We have included alternative binaries that you can try, by updating you interproscan.properties file to point to the alternative binaries: binary.prosite.pfscanv3.path=${bin.directory}/prosite/altbin/pfscanV3.noaf binary.prosite.pfsearchv3.path=${bin.directory}/prosite/altbin/pfsearchV3.noaf If the problem persist, you may need to compile those binaries from source, making sure to build without affinity by compiling with the flag cmake -DUSE_AFFINITY=OFF ..
ACTION: We need to make the above changes to IPS version 5.64-96.0 and rebuild the docker image. However, changes to Docker mean that the current Dockerfile will no longer compile - the issue is this command: RUN echo "localhost" > /etc/hostname && echo "127.0.0.1\tlocalhost" > /etc/hosts Using this command is no longer persistent in the resulting image. I think (this is beyond my understanding of Docker) it needs to be set via a parameter in the docker run command, or in the docker-compose config.
Re-opening...
MetaGOflow v1.0 aborts with an error on cluster using AMD EPYC 7643 cpus due to the following Prosite binary incompatibility in InterProScan:
This seems to be due to a Prosite binary incompatibility as reported elsewhere with this version of IPS..
The version of IPS in v1.0 is 5.57-90.0 from Aug 2022. Unfortunately, even if this problem has been resolved in newer versions of IPS (latest: June 2023), changes to Docker mean that the current Dockerfile for IPS in MetaGOflow will not compile the newer versions of IPS.
The only way to resolve this for MetaGOflow v.1.0 would be to recompile the Prosite binaries with the newer compatible libraries and rebuild the IPS 5.57-90.0 container. This may not be worth the effort at this stage with more than half of the first EMO BON batch of data already analysed.
However, this should be resolved for MetaGOflow v1.1 (or whatever version we use to analyses the second EMO BON data tranch).