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Various fixes in the stats wf #430

Merged
claudio.atzori merged 12 commits from antonis.lempesis/dnet-hadoop:beta into beta 2024-05-08 13:41:03 +02:00
Conversation 0 Commits 12 Files Changed 13 +132 -152
4 changed files with 132 additions and 152 deletions
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71
dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh
View File

@ -67,24 +67,21 @@ function copydb() {
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
rm -f error.log
return 1
exit 2
fi
# Make Impala aware of the deletion of the old DB immediately.
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
# Using max-bandwidth of: 50 * 100 Mb/s = 5 Gb/s
# Using max memory of: 50 * 6144 = 300 Gb
# Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
# Using max memory of: 70 * 6144 = 430 Gb
# Using 1MB as a buffer-size.
# The " -Ddistcp.dynamic.recordsPerChunk=50" arg is not available in our version of hadoop
# The " -Ddistcp.dynamic.recordsPerChunk=N" arg is not available in our version of hadoop
# The "ug" args cannot be used as we get a "User does not belong to hive" error.
# The "p" argument cannot be used, as it blocks the files from being used, giving a "sticky bit"-error, even after applying chmod and chown onm the files.
hadoop distcp -Dmapreduce.map.memory.mb=6144 -m 70 -bandwidth 150 \
-numListstatusThreads 40 \
-copybuffersize 1048576 \
-strategy dynamic \
-blocksperchunk 8 \
-pb \
${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
@ -92,9 +89,9 @@ function copydb() {
if [ $? -eq 0 ]; then
echo -e "\nSuccessfully copied the files of '${db}'.\n"
else
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT WITH EXIT STATUS: $?\n\n"
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
return 2
exit 3
fi
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
@ -105,14 +102,11 @@ function copydb() {
# create the new database (with the same name)
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
# Make Impala aware of the creation of the new DB immediately.
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
sleep 1
# Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
# So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
all_create_view_statements=()
num_tables=0
entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'` # Get the tables and views without any potential the "WARN" logs.
for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
@ -129,9 +123,11 @@ function copydb() {
all_create_view_statements+=("$create_view_statement")
else
echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
((num_tables++))
CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' | head -1`
if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@ -142,74 +138,73 @@ function copydb() {
fi
done
echo -e "\nAll tables have been created, going to create the views..\n"
previous_num_of_views_to_retry=${#all_create_view_statements[@]}
if [[ $num_tables -gt 0 ]]; then
echo -e "\nAll ${num_tables} tables have been created, for db '${db}', going to create the ${previous_num_of_views_to_retry} views..\n"
else
echo -e "\nDB '${db}' does not have any tables, moving on to create the ${previous_num_of_views_to_retry} views..\n"
fi
# Time to loop through the views and create them.
# At this point all table-schemas should have been created.
previous_num_of_views_to_retry=${#all_create_view_statements}
if [[ $previous_num_of_views_to_retry -gt 0 ]]; then
echo -e "\nAll_create_view_statements:\n\n${all_create_view_statements[@]}\n" # DEBUG
# Make Impala aware of the new tables, so it knows them when creating the views.
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
sleep 1
echo -e "\nAll_create_view_statements (${previous_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n" # DEBUG
else
echo -e "\nDB '${db}' does not contain any views.\n"
fi
level_counter=0
while [[ ${#all_create_view_statements[@]} -gt 0 ]]; do
while [[ $previous_num_of_views_to_retry -gt 0 ]]; do
((level_counter++))
# The only accepted reason for a view to not be created, is if it depends on another view, which has not been created yet.
# In this case, we should retry creating this particular view again.
should_retry_create_view_statements=()
new_num_of_views_to_retry=0
for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
if [ -n "$specific_errors" ]; then
echo -e "\nspecific_errors: ${specific_errors}\n"
echo -e "\nView '$(cat error.log | grep "CREATE VIEW " | sed 's/CREATE VIEW //g' | sed 's/ as select .*//g')' failed to be created, possibly because it depends on another view.\n"
should_retry_create_view_statements+=("$create_view_statement")
echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
else
all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}") # Remove the current successful statement from the list.
sleep 1 # Wait a bit for Impala to register that the view was created, before possibly referencing it by another view.
fi
done
new_num_of_views_to_retry=${#should_retry_create_view_statements}
all_create_view_statements=("$(echo "${all_create_view_statements[@]}" | grep -v '^[\s]*$')") # Re-index the array, filtering-out any empty elements.
# Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
return 3
exit 5
elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
echo -e "\nTo be retried \"create_view_statements\":\n\n${should_retry_create_view_statements[@]}\n"
previous_num_of_views_to_retry=$new_num_of_views_to_retry
echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
else
echo -e "\nFinished creating views, for db: '${db}', in level-${level_counter}.\n"
fi
all_create_view_statements=("${should_retry_create_view_statement[@]}") # This is needed in any case to either move forward with the rest of the views or stop at 0 remaining views.
previous_num_of_views_to_retry=$new_num_of_views_to_retry
done
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
sleep 1
echo -e "\nComputing stats for tables..\n"
entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
# Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"` # This grep works here, as we do not want to match multiple-lines.
if [ -z "$create_view_statement" ]; then # If it's a table, then go load the data to it.
# Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
fi
done
# Check if the entities in both clusters are the same, down to the exact names, not just the counts. (they are sorted in the same way both in hive and impala)
if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
echo -e "\nAll entities have been copied to Impala cluster.\n"
else
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
return 4
exit 6
fi
rm -f error.log

71
dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh
View File

@ -66,24 +66,21 @@ function copydb() {
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
rm -f error.log
return 1
exit 2
fi
# Make Impala aware of the deletion of the old DB immediately.
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
# Using max-bandwidth of: 50 * 100 Mb/s = 5 Gb/s
# Using max memory of: 50 * 6144 = 300 Gb
# Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
# Using max memory of: 70 * 6144 = 430 Gb
# Using 1MB as a buffer-size.
# The " -Ddistcp.dynamic.recordsPerChunk=50" arg is not available in our version of hadoop
# The " -Ddistcp.dynamic.recordsPerChunk=N" arg is not available in our version of hadoop
# The "ug" args cannot be used as we get a "User does not belong to hive" error.
# The "p" argument cannot be used, as it blocks the files from being used, giving a "sticky bit"-error, even after applying chmod and chown onm the files.
hadoop distcp -Dmapreduce.map.memory.mb=6144 -m 70 -bandwidth 150 \
-numListstatusThreads 40 \
-copybuffersize 1048576 \
-strategy dynamic \
-blocksperchunk 8 \
-pb \
${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
@ -91,9 +88,9 @@ function copydb() {
if [ $? -eq 0 ]; then
echo -e "\nSuccessfully copied the files of '${db}'.\n"
else
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT WITH EXIT STATUS: $?\n\n"
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
return 2
exit 3
fi
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
@ -104,14 +101,11 @@ function copydb() {
# create the new database (with the same name)
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
# Make Impala aware of the creation of the new DB immediately.
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
sleep 1
# Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
# So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
all_create_view_statements=()
num_tables=0
entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'` # Get the tables and views without any potential the "WARN" logs.
for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
@ -128,9 +122,11 @@ function copydb() {
all_create_view_statements+=("$create_view_statement")
else
echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
((num_tables++))
CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' | head -1`
if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@ -141,74 +137,73 @@ function copydb() {
fi
done
echo -e "\nAll tables have been created, going to create the views..\n"
previous_num_of_views_to_retry=${#all_create_view_statements[@]}
if [[ $num_tables -gt 0 ]]; then
echo -e "\nAll ${num_tables} tables have been created, for db '${db}', going to create the ${previous_num_of_views_to_retry} views..\n"
else
echo -e "\nDB '${db}' does not have any tables, moving on to create the ${previous_num_of_views_to_retry} views..\n"
fi
# Time to loop through the views and create them.
# At this point all table-schemas should have been created.
previous_num_of_views_to_retry=${#all_create_view_statements}
if [[ $previous_num_of_views_to_retry -gt 0 ]]; then
echo -e "\nAll_create_view_statements:\n\n${all_create_view_statements[@]}\n" # DEBUG
# Make Impala aware of the new tables, so it knows them when creating the views.
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
sleep 1
echo -e "\nAll_create_view_statements (${previous_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n" # DEBUG
else
echo -e "\nDB '${db}' does not contain any views.\n"
fi
level_counter=0
while [[ ${#all_create_view_statements[@]} -gt 0 ]]; do
while [[ $previous_num_of_views_to_retry -gt 0 ]]; do
((level_counter++))
# The only accepted reason for a view to not be created, is if it depends on another view, which has not been created yet.
# In this case, we should retry creating this particular view again.
should_retry_create_view_statements=()
new_num_of_views_to_retry=0
for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
if [ -n "$specific_errors" ]; then
echo -e "\nspecific_errors: ${specific_errors}\n"
echo -e "\nView '$(cat error.log | grep "CREATE VIEW " | sed 's/CREATE VIEW //g' | sed 's/ as select .*//g')' failed to be created, possibly because it depends on another view.\n"
should_retry_create_view_statements+=("$create_view_statement")
echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
else
all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}") # Remove the current successful statement from the list.
sleep 1 # Wait a bit for Impala to register that the view was created, before possibly referencing it by another view.
fi
done
new_num_of_views_to_retry=${#should_retry_create_view_statements}
all_create_view_statements=("$(echo "${all_create_view_statements[@]}" | grep -v '^[\s]*$')") # Re-index the array, filtering-out any empty elements.
# Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
return 3
exit 5
elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
echo -e "\nTo be retried \"create_view_statements\":\n\n${should_retry_create_view_statements[@]}\n"
previous_num_of_views_to_retry=$new_num_of_views_to_retry
echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
else
echo -e "\nFinished creating views, for db: '${db}', in level-${level_counter}.\n"
fi
all_create_view_statements=("${should_retry_create_view_statement[@]}") # This is needed in any case to either move forward with the rest of the views or stop at 0 remaining views.
previous_num_of_views_to_retry=$new_num_of_views_to_retry
done
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
sleep 1
echo -e "\nComputing stats for tables..\n"
entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
# Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"` # This grep works here, as we do not want to match multiple-lines.
if [ -z "$create_view_statement" ]; then # If it's a table, then go load the data to it.
# Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
fi
done
# Check if the entities in both clusters are the same, down to the exact names, not just the counts. (they are sorted in the same way both in hive and impala)
if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
echo -e "\nAll entities have been copied to Impala cluster.\n"
else
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
return 4
exit 6
fi
rm -f error.log

71
dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh
View File

@ -66,24 +66,21 @@ function copydb() {
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
rm -f error.log
return 1
exit 2
fi
# Make Impala aware of the deletion of the old DB immediately.
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
# Using max-bandwidth of: 50 * 100 Mb/s = 5 Gb/s
# Using max memory of: 50 * 6144 = 300 Gb
# Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
# Using max memory of: 70 * 6144 = 430 Gb
# Using 1MB as a buffer-size.
# The " -Ddistcp.dynamic.recordsPerChunk=50" arg is not available in our version of hadoop
# The " -Ddistcp.dynamic.recordsPerChunk=N" arg is not available in our version of hadoop
# The "ug" args cannot be used as we get a "User does not belong to hive" error.
# The "p" argument cannot be used, as it blocks the files from being used, giving a "sticky bit"-error, even after applying chmod and chown onm the files.
hadoop distcp -Dmapreduce.map.memory.mb=6144 -m 70 -bandwidth 150 \
-numListstatusThreads 40 \
-copybuffersize 1048576 \
-strategy dynamic \
-blocksperchunk 8 \
-pb \
${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
@ -91,9 +88,9 @@ function copydb() {
if [ $? -eq 0 ]; then
echo -e "\nSuccessfully copied the files of '${db}'.\n"
else
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT WITH EXIT STATUS: $?\n\n"
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
return 2
exit 3
fi
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
@ -104,14 +101,11 @@ function copydb() {
# create the new database (with the same name)
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
# Make Impala aware of the creation of the new DB immediately.
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
sleep 1
# Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
# So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
all_create_view_statements=()
num_tables=0
entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'` # Get the tables and views without any potential the "WARN" logs.
for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
@ -128,9 +122,11 @@ function copydb() {
all_create_view_statements+=("$create_view_statement")
else
echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
((num_tables++))
CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' | head -1`
if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@ -141,74 +137,73 @@ function copydb() {
fi
done
echo -e "\nAll tables have been created, going to create the views..\n"
previous_num_of_views_to_retry=${#all_create_view_statements[@]}
if [[ $num_tables -gt 0 ]]; then
echo -e "\nAll ${num_tables} tables have been created, for db '${db}', going to create the ${previous_num_of_views_to_retry} views..\n"
else
echo -e "\nDB '${db}' does not have any tables, moving on to create the ${previous_num_of_views_to_retry} views..\n"
fi
# Time to loop through the views and create them.
# At this point all table-schemas should have been created.
previous_num_of_views_to_retry=${#all_create_view_statements}
if [[ $previous_num_of_views_to_retry -gt 0 ]]; then
echo -e "\nAll_create_view_statements:\n\n${all_create_view_statements[@]}\n" # DEBUG
# Make Impala aware of the new tables, so it knows them when creating the views.
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
sleep 1
echo -e "\nAll_create_view_statements (${previous_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n" # DEBUG
else
echo -e "\nDB '${db}' does not contain any views.\n"
fi
level_counter=0
while [[ ${#all_create_view_statements[@]} -gt 0 ]]; do
while [[ $previous_num_of_views_to_retry -gt 0 ]]; do
((level_counter++))
# The only accepted reason for a view to not be created, is if it depends on another view, which has not been created yet.
# In this case, we should retry creating this particular view again.
should_retry_create_view_statements=()
new_num_of_views_to_retry=0
for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
if [ -n "$specific_errors" ]; then
echo -e "\nspecific_errors: ${specific_errors}\n"
echo -e "\nView '$(cat error.log | grep "CREATE VIEW " | sed 's/CREATE VIEW //g' | sed 's/ as select .*//g')' failed to be created, possibly because it depends on another view.\n"
should_retry_create_view_statements+=("$create_view_statement")
echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
else
all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}") # Remove the current successful statement from the list.
sleep 1 # Wait a bit for Impala to register that the view was created, before possibly referencing it by another view.
fi
done
new_num_of_views_to_retry=${#should_retry_create_view_statements}
all_create_view_statements=("$(echo "${all_create_view_statements[@]}" | grep -v '^[\s]*$')") # Re-index the array, filtering-out any empty elements.
# Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
return 3
exit 5
elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
echo -e "\nTo be retried \"create_view_statements\":\n\n${should_retry_create_view_statements[@]}\n"
previous_num_of_views_to_retry=$new_num_of_views_to_retry
echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
else
echo -e "\nFinished creating views, for db: '${db}', in level-${level_counter}.\n"
fi
all_create_view_statements=("${should_retry_create_view_statement[@]}") # This is needed in any case to either move forward with the rest of the views or stop at 0 remaining views.
previous_num_of_views_to_retry=$new_num_of_views_to_retry
done
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
sleep 1
echo -e "\nComputing stats for tables..\n"
entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
# Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"` # This grep works here, as we do not want to match multiple-lines.
if [ -z "$create_view_statement" ]; then # If it's a table, then go load the data to it.
# Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
fi
done
# Check if the entities in both clusters are the same, down to the exact names, not just the counts. (they are sorted in the same way both in hive and impala)
if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
echo -e "\nAll entities have been copied to Impala cluster.\n"
else
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
return 4
exit 6
fi
rm -f error.log

71
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
View File

@ -68,24 +68,21 @@ function copydb() {
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
rm -f error.log
return 1
exit 2
fi
# Make Impala aware of the deletion of the old DB immediately.
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
# Using max-bandwidth of: 50 * 100 Mb/s = 5 Gb/s
# Using max memory of: 50 * 6144 = 300 Gb
# Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
# Using max memory of: 70 * 6144 = 430 Gb
# Using 1MB as a buffer-size.
# The " -Ddistcp.dynamic.recordsPerChunk=50" arg is not available in our version of hadoop
# The " -Ddistcp.dynamic.recordsPerChunk=N" arg is not available in our version of hadoop
# The "ug" args cannot be used as we get a "User does not belong to hive" error.
# The "p" argument cannot be used, as it blocks the files from being used, giving a "sticky bit"-error, even after applying chmod and chown onm the files.
hadoop distcp -Dmapreduce.map.memory.mb=6144 -m 70 -bandwidth 150 \
-numListstatusThreads 40 \
-copybuffersize 1048576 \
-strategy dynamic \
-blocksperchunk 8 \
-pb \
${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
@ -93,9 +90,9 @@ function copydb() {
if [ $? -eq 0 ]; then
echo -e "\nSuccessfully copied the files of '${db}'.\n"
else
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT WITH EXIT STATUS: $?\n\n"
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
return 2
exit 3
fi
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
@ -106,14 +103,11 @@ function copydb() {
# create the new database (with the same name)
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
# Make Impala aware of the creation of the new DB immediately.
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
sleep 1
# Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
# So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
all_create_view_statements=()
num_tables=0
entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'` # Get the tables and views without any potential the "WARN" logs.
for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
@ -130,9 +124,11 @@ function copydb() {
all_create_view_statements+=("$create_view_statement")
else
echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
((num_tables++))
CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' | head -1`
if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@ -143,74 +139,73 @@ function copydb() {
fi
done
echo -e "\nAll tables have been created, going to create the views..\n"
previous_num_of_views_to_retry=${#all_create_view_statements[@]}
if [[ $num_tables -gt 0 ]]; then
echo -e "\nAll ${num_tables} tables have been created, for db '${db}', going to create the ${previous_num_of_views_to_retry} views..\n"
else
echo -e "\nDB '${db}' does not have any tables, moving on to create the ${previous_num_of_views_to_retry} views..\n"
fi
# Time to loop through the views and create them.
# At this point all table-schemas should have been created.
previous_num_of_views_to_retry=${#all_create_view_statements}
if [[ $previous_num_of_views_to_retry -gt 0 ]]; then
echo -e "\nAll_create_view_statements:\n\n${all_create_view_statements[@]}\n" # DEBUG
# Make Impala aware of the new tables, so it knows them when creating the views.
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
sleep 1
echo -e "\nAll_create_view_statements (${previous_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n" # DEBUG
else
echo -e "\nDB '${db}' does not contain any views.\n"
fi
level_counter=0
while [[ ${#all_create_view_statements[@]} -gt 0 ]]; do
while [[ $previous_num_of_views_to_retry -gt 0 ]]; do
((level_counter++))
# The only accepted reason for a view to not be created, is if it depends on another view, which has not been created yet.
# In this case, we should retry creating this particular view again.
should_retry_create_view_statements=()
new_num_of_views_to_retry=0
for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
if [ -n "$specific_errors" ]; then
echo -e "\nspecific_errors: ${specific_errors}\n"
echo -e "\nView '$(cat error.log | grep "CREATE VIEW " | sed 's/CREATE VIEW //g' | sed 's/ as select .*//g')' failed to be created, possibly because it depends on another view.\n"
should_retry_create_view_statements+=("$create_view_statement")
echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
else
all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}") # Remove the current successful statement from the list.
sleep 1 # Wait a bit for Impala to register that the view was created, before possibly referencing it by another view.
fi
done
new_num_of_views_to_retry=${#should_retry_create_view_statements}
all_create_view_statements=("$(echo "${all_create_view_statements[@]}" | grep -v '^[\s]*$')") # Re-index the array, filtering-out any empty elements.
# Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
return 3
exit 5
elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
echo -e "\nTo be retried \"create_view_statements\":\n\n${should_retry_create_view_statements[@]}\n"
previous_num_of_views_to_retry=$new_num_of_views_to_retry
echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
else
echo -e "\nFinished creating views, for db: '${db}', in level-${level_counter}.\n"
fi
all_create_view_statements=("${should_retry_create_view_statement[@]}") # This is needed in any case to either move forward with the rest of the views or stop at 0 remaining views.
previous_num_of_views_to_retry=$new_num_of_views_to_retry
done
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
sleep 1
echo -e "\nComputing stats for tables..\n"
entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
# Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"` # This grep works here, as we do not want to match multiple-lines.
if [ -z "$create_view_statement" ]; then # If it's a table, then go load the data to it.
# Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
sleep 1
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
fi
done
# Check if the entities in both clusters are the same, down to the exact names, not just the counts. (they are sorted in the same way both in hive and impala)
if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
echo -e "\nAll entities have been copied to Impala cluster.\n"
else
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
return 4
exit 6
fi
rm -f error.log