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This paper reports on the design and implementation of the HPC performance monitoring system deployed to continuously monitor performance metrics of all jobs on the HPC systems at the Max Planck Computing and Data Facility (MPCDF). Thereby it reveals important information to various stakeholders, in particular to users, application support, system administrators, and management. On each compute node, hardware and software performance monitoring data is collected by our newly developed lightweight open-source hpcmd middleware which builds upon standard Linux tools. The data is transported via rsyslog, and aggregated and processed by a Splunk system, enabling detailed per-cluster and per-job interactive analysis in a web browser. Additionally, performance reports are provided to the users as PDF files. Finally, we report on practical experience and benefits from large-scale deployments on MPCDF HPC systems, demonstrating how our solution can be useful to any HPC center., Comment: 13 pages, 3 figures

Cryo-electron microscopy is a revolutionary technique that can provide 3D density maps at near-atomic resolution. However, map validation is still an open issue in the field. Despite several efforts from the community, it is possible to overfit the reconstructions to noisy data. Here, inspired by modern statistics, we develop a novel methodology that uses a small independent particle set to validate the 3D maps. The main idea is to monitor how the map probability evolves over the control set during the refinement. The method is complementary to the gold-standard procedure, which generates two reconstructions at each iteration. We low-pass filter the two reconstructions for different frequency cutoffs, and we calculate the probability of each filtered map given the control set. For high-quality maps, the probability should increase as a function of the frequency cutoff and of the refinement iteration. We also compute the similarity between the probability distributions of the two reconstructions. As higher frequencies are added to the maps, more dissimilar are the distributions. We optimized the BioEM software package to perform these calculations, and tested the method on several systems, some which were overfitted. Our results show that our method is able to discriminate the overfitted sets from the non-overfitted ones. We conclude that having a control particle set, not used for the refinement, is essential for cross-validating cryo-EM maps.

The supercomputing platforms available for high performance computing based research evolve at a great rate. However, this rapid development of novel technologies requires constant adaptations and optimizations of the existing codes for each new machine architecture. In such context, minimizing time of efficiently porting the code on a new platform is of crucial importance. A possible solution for this common challenge is to use simulations of the application that can assist in detecting performance bottlenecks. Due to prohibitive costs of classical cycle-accurate simulators, coarse-grain simulations are more suitable for large parallel and distributed systems. We present a procedure of implementing the profiling for openQCD code [1] through simulation, which will enable the global reduction of the cost of profiling and optimizing this code commonly used in the lattice QCD community. Our approach is based on well-known SimGrid simulator [2], which allows for fast and accurate performance predictions of HPC codes. Additionally, accurate estimations of the program behavior on some future machines, not yet accessible to us, are anticipated.