Renamed some variables in chimbuko_config for consistency and added commenting

Updated ubuntu18.04 Mochi Dockerfile to reflect new source for sds repo
Services script now checks the variables passed from config to the AD are defined

Author: giltirn

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

@@ -9,15 +9,15 @@ RUN echo FORCE_REDOWNLOAD_10_30_20_12_53 >> /dev/null && \
 
 RUN source /spack/spack/share/spack/setup-env.sh && \
     mkdir /sds && cd /sds && \
-    git clone https://xgitlab.cels.anl.gov/sds/sds-repo.git && \
-    spack repo add sds-repo
+    git clone https://github.com/mochi-hpc/mochi-spack-packages.git && \
+    spack repo add mochi-spack-packages
 
 COPY packages.yaml /root/.spack/
 
 RUN source /spack/spack/share/spack/setup-env.sh && \
         spack install mercury ^libfabric@1.9.0 && \
-	spack install mochi-sonata@master ^libfabric@1.9.0 && \
-	spack install py-mochi-sonata ^mochi-sonata@master ^python@3.6.0 ^libfabric@1.9.0 && \
+	spack install mochi-sonata ^libfabric@1.9.0 && \
+	spack install py-mochi-sonata ^python@3.6.0 ^libfabric@1.9.0 && \
 	spack gc -y && spack clean -a
 
 WORKDIR /

scripts/launch/chimbuko_config.sh

@@ -39,15 +39,14 @@ provdb_domain=mlx5_0 #only needed for verbs provider   <------------ ***SET ME (
 pserver_extra_args="" #any extra command line arguments to pass
 pserver_port=5559  #port for parameter server
 pserver_nt=2 #number of worker threads
-pserver_ad="hbos"
 ####################################
 #Options for the AD module
 ####################################
-ad_extra_args="-perf_outputpath chimbuko/logs -perf_step 1" #any extra command line arguments to pass. chimbuko/logs is automatically created by services script
-ad_outlier_sigma=12 #number of standard deviations that defines an outlier
-ad_win_size=5  #number of events around an anomaly to store; provDB entry size is proportional to this
-ad_alg=${pserver_ad}
-hbos_thres=0.99
+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
+ad_win_size=5  #number of events around an anomaly to store; provDB entry size is proportional to this so keep it small!
+ad_alg="hbos" #the anomaly detection algorithm. Valid values are "hbos" and "sstd"
+ad_outlier_hbos_threshold=0.99  #the percentile of events outside of which are considered anomalies by the HBOS algorithm
+ad_outlier_sstd_sigma=12 #number of standard deviations that defines an outlier in the SSTD algorithm
 ####################################
 #Options for TAU
 #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

scripts/launch/run_services.sh

@@ -194,8 +194,9 @@ if (( 1 )); then
     echo "==========================================="
     echo "Chimbuko Services: Pserver $pserver_addr"
 
+    pserver_alg=${ad_alg} #Pserver AD algorithm choice must match that used for the driver
     pserver_addr="tcp://${ip}:${pserver_port}"  #address for parameter server in format "tcp://IP:PORT"
-    pserver -ad ${pserver_ad} -nt ${pserver_nt} -logdir ${log_dir} -port ${pserver_port} ${ps_extra_args} 2>&1 | tee ${log_dir}/pserver.log  &
+    pserver -ad ${pserver_alg} -nt ${pserver_nt} -logdir ${log_dir} -port ${pserver_port} ${ps_extra_args} 2>&1 | tee ${log_dir}/pserver.log  &
 
     ps_pid=$!
     extra_args+=" -pserver_addr ${pserver_addr}"
@@ -204,10 +205,15 @@ fi
 
 #echo "Chimbuko Services: Processes are: " $(ps)
 
+#Check that the variables passed to the AD from the config file are defined
+testit=${ad_outlier_sstd_sigma}
+testit=${ad_win_size}
+testit=${ad_alg}
+testit=${ad_outlier_hbos_threshold}
 
 ############################################
 #Generate the command to launch the AD module
-ad_opts="${extra_args} -err_outputpath ${log_dir} -outlier_sigma ${ad_outlier_sigma} -anom_win_size ${ad_win_size} -ad_algorithm ${ad_alg} -hbos_threshold ${hbos_thres}"
+ad_opts="${extra_args} -err_outputpath ${log_dir} -outlier_sigma ${ad_outlier_sstd_sigma} -anom_win_size ${ad_win_size} -ad_algorithm ${ad_alg} -hbos_threshold ${ad_outlier_hbos_threshold}"
 ad_cmd="driver ${TAU_ADIOS2_ENGINE} ${TAU_ADIOS2_PATH} ${TAU_ADIOS2_FILE_PREFIX}-${EXE_NAME} ${ad_opts} 2>&1 | tee ${log_dir}/ad.log"
 echo ${ad_cmd} > ${var_dir}/chimbuko_ad_cmdline.var