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)?
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)?