NWChem + Chimbuko Docker image now allows the user to pass a write dir for the provDB. Coupled with mounting an external directory allows persistence of the provenance data

Author: giltirn

docker/ubuntu18.04/openmpi4.0.4/Dockerfile.chimbuko.nwchem

@@ -23,12 +23,12 @@ RUN apt-get update && apt-get install -y gdb emacs-nox vim
 
 WORKDIR /
 
-RUN echo "INVALIDATE_7" > /dev/null
+RUN echo "INVALIDATE_10" > /dev/null
 COPY run_nwchem_chimbuko.sh /
 COPY sos_filter.txt /
 COPY chimbuko_config.templ /
 
 EXPOSE 5000
 
 ENTRYPOINT [ "./run_nwchem_chimbuko.sh" ]
-CMD [ "5", "50000", "SST", "false", "12", "10", "1000", "/test" ]
+CMD [ "5", "50000", "SST", "false", "12", "10", "1000", "/test", "chimbuko/provdb" ]

docker/ubuntu18.04/openmpi4.0.4/chimbuko_config.templ

@@ -29,7 +29,7 @@ provdb_nshards=4  #number of database shards
 provdb_ninstances=1 #number of database server instances. Shards are distributed over instances
 provdb_engine="ofi+tcp;ofi_rxm"  #the OFI libfabric provider used for the Mochi stack
 provdb_port=5001 #the port of the provenance database
-provdb_writedir=chimbuko/provdb #the directory in which the provenance database is written. Chimbuko creates chimbuko/provdb which can be used as a default
+provdb_writedir=<PROVDB_WRITEDIR> #the directory in which the provenance database is written. Chimbuko creates chimbuko/provdb which can be used as a default
 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
 
 #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)

docker/ubuntu18.04/openmpi4.0.4/run_nwchem_chimbuko.sh

@@ -29,6 +29,7 @@ AD_SIGMA=${5:-6}
 AD_WINSZ=${6:-10}
 AD_INTERVAL=${7:-1000}
 BATCH_DIR=${8:-/test}
+PROVDB_WRITEDIR=${9:-chimbuko/provdb}
 
 echo "============================"
 echo "NMPIS: ${NMPIS}"
@@ -39,6 +40,7 @@ echo "AD SIGMA: ${AD_SIGMA}"
 echo "AD WINSZ: ${AD_WINSZ}"
 echo "AD INTERVAL: ${AD_INTERVAL} msec"
 echo "BATCH DIR: ${BATCH_DIR}"
+echo "PROVDB WRITEDIR : ${PROVDB_WRITEDIR}"
 echo "============================"
 sleep 1
 
@@ -63,7 +65,7 @@ cd $BATCH_DIR
 rm -rf *
 
 # #Override config script with user options
-cat /chimbuko_config.templ | sed "s/<TAU_ADIOS2_ENGINE>/${ADIOS_MODE}/" | sed "s/<AD_WIN_SIZE>/${AD_WINSZ}/" | sed "s/<AD_SIGMA>/${AD_SIGMA}/" | sed "s/<AD_INTERVAL>/${AD_INTERVAL}/" | sed "s|<VIZ_ROOT>|${VIZ_ROOT}|" > chimbuko_config.sh
+cat /chimbuko_config.templ | sed "s/<TAU_ADIOS2_ENGINE>/${ADIOS_MODE}/" | sed "s/<AD_WIN_SIZE>/${AD_WINSZ}/" | sed "s/<AD_SIGMA>/${AD_SIGMA}/" | sed "s/<AD_INTERVAL>/${AD_INTERVAL}/" | sed "s|<VIZ_ROOT>|${VIZ_ROOT}|" | sed "s|<PROVDB_WRITEDIR>|${PROVDB_WRITEDIR}|" > chimbuko_config.sh
 export CHIMBUKO_CONFIG=chimbuko_config.sh
 source ${CHIMBUKO_CONFIG}
 
@@ -113,4 +115,7 @@ else
 fi
 
 wait
+echo "Setting ownership of provdb data"
+chown `stat -c "%u:%g" ${PROVDB_WRITEDIR}` ${PROVDB_WRITEDIR}/provdb*
+
 echo "Bye~~!!"