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Added benchmark_suite miniapp demonstrating anomalies in an openMP threaded region
Added openmp build of Tau to ubuntu-18.04 Dockerfile
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‎benchmark_suite/openmp_cpu/Makefile‎

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main: main.C
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tau_cxx.sh main.C -o main -g -fopenmp
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main_notau: main.C
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mpic++ main.C -o main -g -fopenmp
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clean:
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rm main

‎benchmark_suite/openmp_cpu/chimbuko_config.sh‎

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#Note: This configuration file is sourced into the bash environment for Chimbuko startup scripts, thus the user must follow correct shell conventions
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#Please do not remove any of the variables!
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#IMPORTANT NOTE: Variables that cannot be left as default are marked as <------------ ***SET ME***
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service_node_iface=eth0 #network interface upon which communication to the service node is performed <------------ ***SET ME***
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####################################
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#Options for visualization module
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####################################
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use_viz=0 #enable or disable the visualization
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viz_root=/opt/chimbuko/viz #the root directory of the visualization module <------------ ***SET ME (if using viz)***
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viz_worker_port=6379 #the port on which to run the redis server for the visualization backend
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viz_port=5002 #the port on which to run the webserver
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export C_FORCE_ROOT=1 #required only for docker runs, allows celery to execute properly as root user <----------------- *** SET ME (if using Docker)
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############################################################
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#General options for Chimbuko backend (pserver, ad, provdb)
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############################################################
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backend_root="infer" #The root install directory of the PerformanceAnalysis libraries. If set to "infer" it will be inferred from the path of the executables
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chimbuko_services="infer" #The location of the Chimbuko service script. If set to "infer" it will be inferred from backend_root
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####################################
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#Options for the provenance database
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####################################
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use_provdb=1 #enable or disable the provDB. If disabled the provenance data will be written as JSON ASCII into the ${provdb_writedir} set below
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provdb_extra_args="" #any extra command line arguments to pass
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provdb_nshards=4 #number of database shards
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provdb_engine="ofi+tcp;ofi_rxm" #the OFI libfabric provider used for the Mochi stack
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provdb_port=5000 #the port of the provenance database
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provdb_nthreads=4 #number of worker threads; should be >= the number of shards
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provdb_writedir=chimbuko/provdb #the directory in which the provenance database is written. Chimbuko creates chimbuko/provdb which can be used as a default
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provdb_commit_freq=10000 #frequency ms at which the provenance database is committed to disk. If set to 0 it will commit only at the end
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#With "verbs" provider (used for infiniband, iWarp, etc) we need to also specify the domain, which can be found by running fi_info (on a compute node)
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provdb_domain=mlx5_0 #only needed for verbs provider <------------ ***SET ME (if using verbs)***
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####################################
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#Options for the parameter server
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####################################
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use_pserver=1 #enable or disable the pserver
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pserver_extra_args="" #any extra command line arguments to pass
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pserver_port=5559 #port for parameter server
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pserver_nt=2 #number of worker threads
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####################################
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#Options for the AD module
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####################################
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ad_extra_args="-perf_outputpath chimbuko/logs -perf_step 1" #any extra command line arguments to pass. Note: chimbuko/logs is automatically created by services script
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ad_win_size=5 #number of events around an anomaly to store; provDB entry size is proportional to this so keep it small!
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ad_alg="hbos" #the anomaly detection algorithm. Valid values are "hbos" and "sstd"
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ad_outlier_hbos_threshold=0.99 #the percentile of events outside of which are considered anomalies by the HBOS algorithm
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ad_outlier_sstd_sigma=12 #number of standard deviations that defines an outlier in the SSTD algorithm
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####################################
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#Options for TAU
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#Note: Only the TAU_ADIOS2_PATH, TAU_ADIOS2_FILE_PREFIX, EXE_NAME and TAU_ADIOS2_ENGINE variables are used by the Chimbuko services script and there only to generate the suggested
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# command to launch the AD (output to chimbuko/vars/chimbuko_ad_cmdline.var); they can be overridden by the run script if desired providing the appropriate modifications
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# are made to the AD launch command. The remainder of the variables are used only by TAU and can be freely overridden.
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####################################
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export TAU_ADIOS2_ENGINE=SST #online communication engine (alternative BP4 although this goes through the disk system and may be slower unless the BPfiles are stored on a burst disk)
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export TAU_ADIOS2_ONE_FILE=FALSE #a different connection file for each rank
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export TAU_ADIOS2_PERIODIC=1 #enable/disable ADIOS2 periodic output
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export TAU_ADIOS2_PERIOD=1000000 #period in us between ADIOS2 io steps
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export TAU_THREAD_PER_GPU_STREAM=1 #force GPU streams to appear as different TAU virtual threads
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export TAU_THROTTLE=0 #enable/disable throttling of short-running functions
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export TAU_MAKEFILE=/opt/tau2/x86_64/lib/Makefile.tau-papi-mpi-pthread-pdt-openmp-adios2 #The TAU makefile to use <------------ ***SET ME***
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#Note: the following 2 variables are not used by the service script but are included here for use from the user's run script allowing the application to be launched with either "${TAU_EXEC} <app>" or "${TAU_PYTHON} <app>"
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#Note: the "binding" -T ... is used by Tau to find the appropriate configuration. It can typically be inferred from the name of the Makefile. If using a non-MPI job the 'mpi' should be changed to 'serial' and a non-MPI build of
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# ADIOS2/TAU must exist
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#Suggestion: It is useful to test the command without Chimbuko first to ensure TAU picks up the correct binding; this can be done by 'export TAU_ADIOS2_ENGINE=BPFile' and then running the application with Tau but without Chimbuko.
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TAU_EXEC="tau_exec -T papi,mpi,pthread,pdt,openmp,adios2 -adios2_trace" #how to execute tau_exec; the -T arguments should mirror the makefile name <------------ ***SET ME***
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TAU_PYTHON="tau_python -T papi,mpi,pthread,pdt,adios2 -tau-python-interpreter=python3 -adios2_trace -tau-python-args=-u" #how to execute tau_python. Note that passing -u to python forces it to not buffer stdout so we can pipe it
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#to tee in realtime <--- SET ME (if !python3)
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export EXE_NAME=main #the name of the executable (without path) <------------ ***SET ME***
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TAU_ADIOS2_PATH=chimbuko/adios2 #path where the adios2 files are to be stored. Chimbuko services creates the directory chimbuko/adios2 in the working directory and this should be used by default
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TAU_ADIOS2_FILE_PREFIX=tau-metrics #the prefix of tau adios2 files; full filename is ${TAU_ADIOS2_PREFIX}-${EXE_NAME}-${RANK}.bp
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###########################################################################
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# NON-USER VARIABLES BELOW = DON'T MODIFY THESE!!
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###########################################################################
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#Extra processing
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export TAU_ADIOS2_FILENAME="${TAU_ADIOS2_PATH}/${TAU_ADIOS2_FILE_PREFIX}"
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if [[ ${backend_root} == "infer" ]]; then
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backend_root=$( readlink -f $(which provdb_admin | sed 's/provdb_admin//')/../ )
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fi
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if [[ ${chimbuko_services} == "infer" ]]; then
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chimbuko_services="${backend_root}/scripts/launch/run_services.sh"
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if [ ! -f "${chimbuko_services}" ]; then
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echo "Could not infer service script location: service script does not exist at ${chimbuko_services}!"
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exit 1
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fi
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fi
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‎benchmark_suite/openmp_cpu/main.C‎

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//In this example a function is executed with a chosen number of distinct modes in a random pattern, and anomalies are inserted as points far away from these modes
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#include<chrono>
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#include<thread>
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#include<iostream>
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#include<sstream>
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#include<random>
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#include<mpi.h>
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#include<omp.h>
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#include <sys/select.h>
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template<typename T>
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T strToAny(const std::string &s){
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T out;
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std::stringstream ss; ss << s; ss >> out;
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if(ss.fail()) throw std::runtime_error("Failed to parse \"" + s + "\"");
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return out;
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}
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void sleep_100ms(){
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std::this_thread::sleep_for(std::chrono::milliseconds(100));
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}
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void the_function(const int sleep_ms){
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int nsleep = sleep_ms / 100;
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for(int i=0;i<nsleep;i++)
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sleep_100ms();
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}
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int main(int argc, char **argv){
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if(argc < 6){
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std::cout << "Usage: <binary> <ncycles> <mode times (comma separated)> <anom time> <anom freq> <threads>" << std::endl;
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std::cout << "Times are in *milliseconds* and will be rounded to the nearest 100ms" << std::endl;
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exit(0);
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}
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MPI_Init(&argc, &argv);
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int cycles = strToAny<int>(argv[1]);
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std::stringstream ss;
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ss << argv[2];
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std::cout << "Mode times: ";
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std::vector<int> mode_times;
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while(ss.good()) {
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std::string substr;
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getline(ss, substr, ','); //get first string delimited by comma
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mode_times.push_back(strToAny<int>(substr));
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std::cout << mode_times.back() << " ";
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}
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std::cout << std::endl;
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int anom_time = strToAny<int>(argv[3]);
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int anom_freq = strToAny<int>(argv[4]);
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int threads = strToAny<int>(argv[5]);
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//Round the times
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anom_time = ( (anom_time + 50) / 100 ) * 100;
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std::cout << "Anom time rounded to " << anom_time << " ms" << std::endl;
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for(int i=0;i<mode_times.size();i++){
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mode_times[i] = ( (mode_times[i] + 50) / 100 ) * 100;
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std::cout << "Mode " << i << " time rounded to " << mode_times[i] << " ms" << std::endl;
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}
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omp_set_num_threads(threads);
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#pragma omp parallel
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{
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int me = omp_get_thread_num();
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std::mt19937 gen(me*1234);
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std::uniform_int_distribution<> dist(0, mode_times.size()-1);
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for(int i=0;i<cycles;i++){
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int time;
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if(i > 0 && i % anom_freq == 0) time = anom_time;
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else{
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int mode = dist(gen);
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time = mode_times[mode];
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}
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std::cout << "Thread " << me << " cycle " << i << " " << time << std::endl;
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the_function(time);
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}
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}
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MPI_Finalize();
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}

‎benchmark_suite/openmp_cpu/run.sh‎

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#!/bin/bash
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set -e
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############## USER VARIABLES ####################
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ranks=1 #number of MPI ranks
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cycles=100 #number of loops in main program
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anom_freq=30 #how many loop cycles beween anomalies
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modetimes="200,500" #function execution times in ms for "normal executions" (each cycle randomly chosen over modes)
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anom_time=10000 #function execution time in ms for anomalous execution
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threads=3
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############## END OF USER VARIABLES #################
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rm -rf chimbuko
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export CHIMBUKO_CONFIG=chimbuko_config.sh
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source ${CHIMBUKO_CONFIG}
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if (( 1 )); then
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echo "Running services"
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${chimbuko_services} 2>&1 | tee services.log &
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echo "Waiting"
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while [ ! -f chimbuko/vars/chimbuko_ad_cmdline.var ]; do sleep 1; done
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ad_cmd=$(cat chimbuko/vars/chimbuko_ad_cmdline.var)
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fi
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if (( 1 )); then
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echo "Instantiating AD"
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eval "mpirun --allow-run-as-root -n ${ranks} ${ad_cmd} &"
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sleep 2
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fi
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#Run the main program
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if (( 1 )); then
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mkdir -p chimbuko/adios2 chimbuko/logs
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echo "Running main"
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mpirun --allow-run-as-root -n ${ranks} ${TAU_EXEC} ./main ${cycles} ${modetimes} ${anom_time} ${anom_freq} ${threads} 2>&1 | tee main.log
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fi
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wait

‎docker/ubuntu18.04/openmpi4.0.4/Dockerfile.tau2‎

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RUN echo "FORCE REDOWNLOAD 10_30_20_16_39" > /dev/null && git clone https://github.com/UO-OACISS/tau2.git
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WORKDIR /Downloads/tau2
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#Use known working version of tau2
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RUN git checkout 6756ea1e2790dc83580f0e437a443a29039798fc
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#pthread+mpi
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RUN ./configure -cc=mpicc -c++=mpic++ -fortran=gfortran -mpi \
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-pthread -bfd=download -unwind=download -pdt=/opt/pdt \
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-papi=/opt/papi \
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&& make -j$JOBS install
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#openmp+mpi
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RUN ./configure -cc=mpicc -c++=mpic++ -fortran=gfortran -mpi \
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-openmp -bfd=download -unwind=download -pdt=/opt/pdt \
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-pdt_c++=g++ -prefix=/opt/tau2 -adios=/opt/adios2 \
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-papi=/opt/papi \
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&& make -j$JOBS install
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RUN git log | head -1 > /opt/tau2/git_version
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FROM chimbuko/adios2:ubuntu18.04

‎include/chimbuko/util/PerfStats.hpp‎

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#include <map>
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#include "chimbuko/util/RunMetric.hpp"
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#endif
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#include<string>
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namespace chimbuko{
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