Regarding the Principal component analysis with CPPTRAJ

[satyajitkhatua09]

Hi Users/Developers,

I am having issues running PCA analysis with CPPTRAJ. It always stops showing the segmentation fault.

I am only considering the CA atoms of protein and P atoms of nucleic acid (a total of 28486 atoms). Therefore, my Covariance Matrix Size is 85,308 × 85,308 (3 × 28486 = 85,308), consuming a substantial memory of

Memory (bytes) = (85,308 × 85,308) ×size of a double-precision float (typically 8 bytes) ≈ 58GB.

This prompts me to do the analysis on ANDES HPC in Oak Ridge National Laboratory. However, the run still fails to produce results. The error message remains the same. So, are there any limitations on the number of atoms to be considered for the PCA analysis in CPPTRAJ? If so, how to change that (if possible)?

[drroe]

Hi, sorry for the delay here.

I haven't delved into the code yet but my suspicion is that there is an int somewhere being used in matrix indexing; max size of an int is 2147483647, which is much smaller than the size of your matrix. I'll try to get to this ASAP. Thanks for the report!