Nailgun
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installed Nailgun on the cluster. I did the following in /nfs/home/stefan/NAILGUN/nailgun-master 1) Install with maven $ /nfs/home/stefan/NAILGUN/apache-maven-3.6.3/bin/mvn clean install Since we have Java 1.8 on the cluster, the Build worked out. 2) This is what we've been missing so far: We need to generate a class path containing the server and the classes we want to run with nailgun: $ export CLASSPATH="/nfs/home/stefan/NAILGUN/nailgun-master/nailgun-server/target/classes:/nfs/home/stefan/NAILGUN/nailgun-master/nailgun-examples/target/classes:/nfs/soft/jchem/jchem-19.15/lib/*" 3) Start the server: $ java com.facebook.nailgun.NGServer & 4) Now you can run the classes with the nailgun client ./nailgun-client/target/ng com.facebook.nailgun.examples.HelloWorld Just as an example that this actually is faster as compared to "classic" java: Classic Java $ time java com.facebook.nailgun.examples.HelloWorld Hello, world! real 0m1.794s user 0m0.336s sys 0m1.414s Nailgun $ time ./nailgun-client/target/ng com.facebook.nailgun.examples.HelloWorld Hello, world! real 0m0.025s user 0m0.001s sys 0m0.005s So it seems to speed up things. As for Jchem, I don't know why it works, but it does :) Normal execution of cxcalc $ time cxcalc Calculator, (C) 1998-2019 ChemAxon Ltd. version 19.15.0 ... real 0m22.604s user 0m28.868s sys 0m19.380s Normal execution with Java $ time java chemaxon.marvin.Calculator Calculator, (C) 1998-2019 ChemAxon Ltd. version 19.15.0 ... real 0m19.084s user 0m28.498s sys 0m19.360s First execution with nailgun $ time ./nailgun-client/target/ng chemaxon.marvin.Calculator Calculator, (C) 1998-2019 ChemAxon Ltd. version 19.15.0 ... real 0m12.016s user 0m0.000s sys 0m0.008s Subsequent execution with nailgun $ time ./nailgun-client/target/ng chemaxon.marvin.Calculator Calculator, (C) 1998-2019 ChemAxon Ltd. version 19.15.0 ... real 0m0.014s user 0m0.001s sys 0m0.004s So the speedup of opening cxcalc multiple times within the server is 1000-fold???