➜ kstar git:(main) ✗ python3 kstar.boundedMem.py
WARNING: Using incubator modules: jdk.incubator.foreign
OSPREY 3.2-dev, Python 3.9.6, Java 16, Linux-4.15.0-153-generic-x86_64-with-glibc2.27
Using up to 1280 MiB heap memory: 128 MiB for garbage, 1152 MiB for storage
COFFEE-0: node started on cluster COFFEE-job-858290664, addr=[152.3.140.121]:5701, hostname=saiyan
COFFEE-0: waiting for cluster to assemble ...
COFFEE-0: computing Z matrix for state: complex
COFFEE-0: computing static-static ...
COFFEE-0: static-static finished
COFFEE-0: computing 30 singles ...
Progress: 100.0% ETA: 0 ns
Finished in 5.9 ms
COFFEE-0: singles finished
COFFEE-0: computing 269 pairs ...
Progress: 24.9% ETA: 14.9 s
Progress: 49.8% ETA: 10.8 s
Progress: 86.6% ETA: 3.3 s
Progress: 100.0% ETA: 690.0 ms
Finished in 17.2 s
COFFEE-0: pairs finished
COFFEE-0: computing Z matrix for state: design
COFFEE-0: computing static-static ...
COFFEE-0: static-static finished
COFFEE-0: computing 30 singles ...
Progress: 100.0% ETA: 0 ns
Finished in 2.3 ms
COFFEE-0: singles finished
COFFEE-0: computing 269 pairs ...
Progress: 100.0% ETA: 21.0 ms
Finished in 1.0 s
COFFEE-0: pairs finished
COFFEE-0: computing Z matrix for state: target
COFFEE-0: computing static-static ...
COFFEE-0: static-static finished
COFFEE-0: computing 0 singles ...
COFFEE-0: singles finished
COFFEE-0: computing 0 pairs ...
COFFEE-0: pairs finished
COFFEE-0: Computing free energies for 10 sequences...
COFFEE-0: wild-type sequence ...
COFFEE-0: Processing state target
COFFEE-0: G [-2.323,-2.323] width 0.000000 of 0.000000 nodedb 0.0% time 508.92 ms
COFFEE-0: target: [-2.323282,-2.323282] (w 0.000000) kcal/mol
COFFEE-0: Processing state design, sequence [13 LEU=leu 16 ILE=ile 1 ALA=ala]
COFFEE-0: G [-1653.358,-1653.284] width 0.073544 of 0.000000 nodedb 0.0% time 504.31 ms
COFFEE-0: design: [-1653.358036,-1653.284492] (w 0.073544) kcal/mol
COFFEE-0: Processing state complex, sequence [13 LEU=leu 16 ILE=ile 1 ALA=ala]
COFFEE-0: G [-1705.618,Infinity] width Infinity of 0.000000 nodedb 0.0% time 501.96 ms
COFFEE-0: G [-1705.139,-1703.090] width 2.048888 of 0.000000 nodedb 0.0% time 1.00 s
COFFEE-0: G [-1704.136,-1703.389] width 0.747564 of 0.000000 nodedb 0.0% time 1.51 s
COFFEE-0: G [-1703.593,-1703.405] width 0.188597 of 0.000000 nodedb 0.0% time 2.01 s
COFFEE-0: G [-1703.477,-1703.405] width 0.072075 of 0.000000 nodedb 0.0% time 2.51 s
java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 157
at edu.duke.cs.osprey.confspace.compiled.AssignedCoords.lambda$toMol$0(AssignedCoords.java:162)
at edu.duke.cs.osprey.confspace.compiled.AssignedCoords.toMol(AssignedCoords.java:171)
at edu.duke.cs.osprey.structure.PDBIO.lambda$writeEcoords$8(PDBIO.java:717)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1625)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:913)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682)
at edu.duke.cs.osprey.structure.PDBIO.writeEcoords(PDBIO.java:717)
at edu.duke.cs.osprey.structure.PDBIO.writeFileEcoords(PDBIO.java:728)
at edu.duke.cs.osprey.coffee.directors.PfuncDirector.saveEnsemble(PfuncDirector.java:327)
at edu.duke.cs.osprey.coffee.directors.PfuncDirector.calc(PfuncDirector.java:296)
at edu.duke.cs.osprey.coffee.directors.KStarDirector.calcG(KStarDirector.java:336)
at edu.duke.cs.osprey.coffee.directors.KStarDirector.direct(KStarDirector.java:268)
at edu.duke.cs.osprey.coffee.Coffee.run(Coffee.java:362)
COFFEE-0: Error encountered, stopping cluster ...
COFFEE-0: COFFEE Finished in 39.99 s
COFFEE-0: node finished
➜ kstar git:(main) ✗
Invoked as
python3 kstar.boundedMem.py