Upside-MD
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John-Jumper
error when running simulation
I got this error for several pdb files. Any suggestions as what the problem may be?
upside/obj/upside --duration 1e7 --frame-interval 1e2 --temperature 0.5 --seed $RANDOM simulation.up invocation: upside/obj/upside --duration 1e7 --frame-interval 1e2 --temperature 0.5 --seed 28633 simulation.up random seed: 28633
ERROR: while adding 'hbond_coverage', dimensions of 'interaction_param', expected (2, 20, 30) but got (2, 20, 54) HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0: #000: ../../src/H5D.c line 391 in H5Dclose(): not a dataset major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0: #000: ../../src/H5D.c line 391 in H5Dclose(): not a dataset major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0: #000: ../../src/H5D.c line 391 in H5Dclose(): not a dataset major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0: #000: ../../src/H5D.c line 391 in H5Dclose(): not a dataset major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0: #000: ../../src/H5G.c line 809 in H5Gclose(): not a group major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0: #000: ../../src/H5F.c line 2047 in H5Fclose(): invalid file identifier major: Invalid arguments to routine minor: Inappropriate type
I did get it to work, but I don't recall what the problem was. I will have to look back through email from the developers. Obviously, the correspondence was not on this issues page. I will see what I can find and post it here.
Replacing the compile command with
rm -rf ../obj/* && CXXFLAGS=-DPARAM_OLD cmake ../src && make -j
seemed to do the trick. It appears the config scripts are still writing 'old-style' parameters (whatever that means).
