PT-2037 - added test for the situation when both --system-only and --mysql-only are specified

Re-added fix for PT-1340 that was reverted by fix for PT-1398

.travis.yml

@@ -1,8 +1,7 @@
 language: go
 
 go:
-  - 1.15.x
-  - 1.14.x
+  - 1.17.x
   - tip
 
 services:

.whitesource

@@ -0,0 +1,24 @@
+{
+  "scanSettings": {
+    "configMode": "AUTO",
+    "configExternalURL": "",
+    "projectToken": "",
+    "baseBranches": [],
+    "enableLicenseViolations": true
+  },
+  "checkRunSettings": {
+    "vulnerableCheckRunConclusionLevel": "failure",
+    "displayMode": "diff"
+  },
+  "issueSettings": {
+    "minSeverityLevel": "NONE"
+  },
+  "remediateSettings": {
+    "enableRenovate": false,
+    "dependencyDashboard": true,
+    "extends": [
+      "github>whitesource/merge-confidence:beta",
+      "github>samq-ghdemo/renovate:demo"
+      ]
+  }
+}

bin/pt-diskstats

@@ -2243,8 +2243,10 @@ sub parse_diskstats_line {
    # linux kernel source => Documentation/iostats.txt
    # 2.6+   => 14 fields
    # 4.18+  => 18 fields
+   # 5.x+   => 20 fields (PT-1887)
+   my @num_fields = (14, 18, 20);
    my @dev_stats = split ' ', $line;
-   return unless @dev_stats == 14 or @dev_stats == 18;
+   return unless grep {$_ == scalar(@dev_stats)} @num_fields;
 
    my $read_bytes    = $dev_stats[READ_SECTORS]    * $block_size;
    my $written_bytes = $dev_stats[WRITTEN_SECTORS] * $block_size;

bin/pt-stalk

@@ -9,10 +9,10 @@ set -u
 # ###########################################################################
 # log_warn_die package
 # This package is a copy without comments from the original.  The original
-# with comments and its test file can be found in the Bazaar repository at,
+# with comments and its test file can be found in the GitHub repository at,
 #   lib/bash/log_warn_die.sh
 #   t/lib/bash/log_warn_die.sh
-# See https://launchpad.net/percona-toolkit for more information.
+# See https://github.com/percona/percona-toolkit for more information.
 # ###########################################################################
 
 
@@ -57,10 +57,10 @@ _d () {
 # ###########################################################################
 # subshell package
 # This package is a copy without comments from the original.  The original
-# with comments and its test file can be found in the Bazaar repository at,
+# with comments and its test file can be found in the GitHub repository at,
 #   lib/bash/subshell.sh
 #   t/lib/bash/subshell.sh
-# See https://launchpad.net/percona-toolkit for more information.
+# See https://github.com/percona/percona-toolkit for more information.
 # ###########################################################################
 
 
@@ -109,10 +109,10 @@ kill_all_subshells() {
 # ###########################################################################
 # parse_options package
 # This package is a copy without comments from the original.  The original
-# with comments and its test file can be found in the Bazaar repository at,
+# with comments and its test file can be found in the GitHub repository at,
 #   lib/bash/parse_options.sh
 #   t/lib/bash/parse_options.sh
-# See https://launchpad.net/percona-toolkit for more information.
+# See https://github.com/percona/percona-toolkit for more information.
 # ###########################################################################
 
 
@@ -128,7 +128,6 @@ OPT_ERRS=0        # How many command line option errors
 OPT_VERSION=""    # If --version was specified
 OPT_HELP=""       # If --help was specified
 OPT_ASK_PASS=""   # If --ask-pass was specified
-OPT_MYSQL_ONLY="" # If --mysql-only was specified
 PO_DIR=""         # Directory with program option spec files
 
 usage() {
@@ -335,7 +334,7 @@ _eval_po() {
             *)
                echo "Invalid attribute in $opt_spec: $line" >&2
                exit 1
-         esac
+         esac 
       done < "$opt_spec"
 
       if [ -z "$opt" ]; then
@@ -459,7 +458,6 @@ _parse_command_line() {
          else
             spec=$(grep "^short form:-$opt\$" "$PT_TMPDIR"/po/* | cut -d ':' -f 1)
             if [ -z "$spec"  ]; then
-               option_error "Unknown option: $real_opt"
                continue
             fi
          fi
@@ -475,7 +473,7 @@ _parse_command_line() {
             if [ "$val" ]; then
                option_error "Option $real_opt does not take a value"
                continue
-            fi
+            fi 
             if [ "$opt_is_negated" ]; then
                val=""
             else
@@ -518,10 +516,10 @@ size_to_bytes() {
 # ###########################################################################
 # mysql_options package
 # This package is a copy without comments from the original.  The original
-# with comments and its test file can be found in the Bazaar repository at,
+# with comments and its test file can be found in the GitHub repository at,
 #   lib/bash/mysql_options.sh
 #   t/lib/bash/mysql_options.sh
-# See https://launchpad.net/percona-toolkit for more information.
+# See https://github.com/percona/percona-toolkit for more information.
 # ###########################################################################
 
 
@@ -544,16 +542,23 @@ mysql_options() {
    if [ -n "$OPT_USER" ]; then
       MYSQL_ARGS="$MYSQL_ARGS --user=$OPT_USER"
    fi
-   if [ -n "$OPT_PASSWORD" ]; then
+   if [ -n "$OPT_ASK_PASS" ]; then
+      stty -echo
+      >&2 printf "Enter MySQL password: "
+      read GIVEN_PASS 
+      stty echo
+      printf "\n"
+      MYSQL_ARGS="$MYSQL_ARGS --password=$GIVEN_PASS"
+   elif [ -n "$OPT_PASSWORD" ]; then
       MYSQL_ARGS="$MYSQL_ARGS --password=$OPT_PASSWORD"
    fi
-
+   
    echo $MYSQL_ARGS
 }
 
 arrange_mysql_options() {
    local opts="$1"
-
+   
    local rearranged=""
    for opt in $opts; do
       if [ "$(echo $opt | awk -F= '{print $1}')" = "--defaults-file" ]; then
@@ -562,7 +567,7 @@ arrange_mysql_options() {
          rearranged="$rearranged $opt"
       fi
    done
-
+   
    echo "$rearranged"
 }
 
@@ -573,10 +578,10 @@ arrange_mysql_options() {
 # ###########################################################################
 # tmpdir package
 # This package is a copy without comments from the original.  The original
-# with comments and its test file can be found in the Bazaar repository at,
+# with comments and its test file can be found in the GitHub repository at,
 #   lib/bash/tmpdir.sh
 #   t/lib/bash/tmpdir.sh
-# See https://launchpad.net/percona-toolkit for more information.
+# See https://github.com/percona/percona-toolkit for more information.
 # ###########################################################################
 
 
@@ -614,10 +619,10 @@ rm_tmpdir() {
 # ###########################################################################
 # alt_cmds package
 # This package is a copy without comments from the original.  The original
-# with comments and its test file can be found in the Bazaar repository at,
+# with comments and its test file can be found in the GitHub repository at,
 #   lib/bash/alt_cmds.sh
 #   t/lib/bash/alt_cmds.sh
-# See https://launchpad.net/percona-toolkit for more information.
+# See https://github.com/percona/percona-toolkit for more information.
 # ###########################################################################
 
 
@@ -661,10 +666,10 @@ _which() {
 # ###########################################################################
 # safeguards package
 # This package is a copy without comments from the original.  The original
-# with comments and its test file can be found in the Bazaar repository at,
+# with comments and its test file can be found in the GitHub repository at,
 #   lib/bash/safeguards.sh
 #   t/lib/bash/safeguards.sh
-# See https://launchpad.net/percona-toolkit for more information.
+# See https://github.com/percona/percona-toolkit for more information.
 # ###########################################################################
 
 
@@ -717,10 +722,10 @@ check_disk_space() {
 # ###########################################################################
 # daemon package
 # This package is a copy without comments from the original.  The original
-# with comments and its test file can be found in the Bazaar repository at,
+# with comments and its test file can be found in the GitHub repository at,
 #   lib/bash/daemon.sh
 #   t/lib/bash/daemon.sh
-# See https://launchpad.net/percona-toolkit for more information.
+# See https://github.com/percona/percona-toolkit for more information.
 # ###########################################################################
 
 
@@ -766,10 +771,10 @@ remove_pid_file() {
 # ###########################################################################
 # collect package
 # This package is a copy without comments from the original.  The original
-# with comments and its test file can be found in the Bazaar repository at,
+# with comments and its test file can be found in the GitHub repository at,
 #   lib/bash/collect.sh
 #   t/lib/bash/collect.sh
-# See https://launchpad.net/percona-toolkit for more information.
+# See https://github.com/percona/percona-toolkit for more information.
 # ###########################################################################
 
 
@@ -796,9 +801,65 @@ collect() {
    local d="$1"  # directory to save results in
    local p="$2"  # prefix for each result file
 
-   local mysqld_pid=""
+   local cnt=$(($OPT_RUN_TIME / $OPT_SLEEP_COLLECT))
+   
+   if [ ! "$OPT_SYSTEM_ONLY" ]; then
+      local mysqld_pid=""
+      local mysql_version=""
+      local mysql_error_log=""
+      local tail_error_log_pid=""
+      local have_lock_waits_table=""
+      local have_oprofile=""
+      local mysqladmin_pid=""
+      local mutex=""
+      local tcpdump_pid=""
+      local ps_instrumentation_enabled=""
+
+      collect_mysql_data_one
+   fi
+
+   if [ ! "$OPT_MYSQL_ONLY" ]; then 
+      collect_system_data
+   fi 
+
+   log "Loop start: $(date +'TS %s.%N %F %T')"
+   local start_time=$(date +'%s')
+   local curr_time=$start_time
+   local ts="$(date +"TS %s.%N %F %T")"
+
+   while [ $((curr_time - start_time)) -lt $OPT_RUN_TIME ]; do
+      if [ ! "$OPT_MYSQL_ONLY" ]; then
+         collect_system_data_loop
+      fi
+
+      if [ ! "$OPT_SYSTEM_ONLY" ]; then
+         collect_mysql_data_loop
+      fi
+
+      curr_time=$(date +'%s')
+   done
+   log "Loop end: $(date +'TS %s.%N %F %T')"
+
+   if [ ! "$OPT_SYSTEM_ONLY" ]; then
+      collect_mysql_data_two
+   fi
+
+   hostname > "$d/$p-hostname"
+
+   wait_for_subshells $OPT_RUN_TIME
+   kill_all_subshells
+   for file in "$d/$p-"*; do
+      if [ -z "$(grep -v '^TS ' --max-count 10 "$file")" ]; then
+         log "Removing empty file $file";
+         rm "$file"
+      fi
+   done
+}
+
+collect_mysql_data_one() {
    if [ ! "$OPT_MYSQL_ONLY" ]; then
-      mysqld_pid=$(_pidof mysqld | awk '{print $1; exit;}')
+      port=$($CMD_MYSQL $EXT_ARGV -ss -e 'SELECT @@port')
+      mysqld_pid=$(lsof -i ":${port}" | grep -i listen | cut -f 3 -d" ")
    fi
 
    if [ "$CMD_PMAP" -a "$mysqld_pid" ]; then
@@ -820,27 +881,27 @@ collect() {
    collect_mysql_variables "$d/$p-variables" &
    sleep .5
 
-   local mysql_version="$(awk '/^version[^_]/{print substr($2,1,3)}' "$d/$p-variables")"
+   mysql_version="$(awk '/^version[^_]/{print substr($2,1,3)}' "$d/$p-variables")"
 
-   local mysql_error_log="$(awk '/^log_error/{print $2}' "$d/$p-variables")"
+   mysql_error_log="$(awk '/^log_error\s/{print $2}' "$d/$p-variables")"
    if [ -z "$mysql_error_log" -a "$mysqld_pid" ]; then
+      log $mysqld_pid
       mysql_error_log="$(ls -l /proc/$mysqld_pid/fd | awk '/ 2 ->/{print $NF}')"
    fi
 
-   local tail_error_log_pid=""
    if [ "$mysql_error_log" -a ! "$OPT_MYSQL_ONLY" ]; then
       log "The MySQL error log seems to be $mysql_error_log"
       tail -f "$mysql_error_log" >"$d/$p-log_error" &
       tail_error_log_pid=$!
 
-      $CMD_MYSQLADMIN $EXT_ARGV debug
+      $CMD_MYSQLADMIN $EXT_ARGV
    else
       log "Could not find the MySQL error log"
    fi 
    if [ "${mysql_version}" '>' "5.1" ]; then
-      local mutex="SHOW ENGINE INNODB MUTEX"
+      mutex="SHOW ENGINE INNODB MUTEX"
    else
-      local mutex="SHOW MUTEX STATUS"
+      mutex="SHOW MUTEX STATUS"
    fi
    innodb_status 1
    tokudb_status 1
@@ -849,7 +910,6 @@ collect() {
    $CMD_MYSQL $EXT_ARGV -e "$mutex" >> "$d/$p-mutex-status1" &
    open_tables                      >> "$d/$p-opentables1"   &
 
-   local tcpdump_pid=""
    if [ "$CMD_TCPDUMP" -a  "$OPT_COLLECT_TCPDUMP" ]; then
       local port=$(awk '/^port/{print $2}' "$d/$p-variables")
       if [ "$port" ]; then
@@ -858,7 +918,6 @@ collect() {
       fi
    fi
 
-   local have_oprofile=""
    if [ "$CMD_OPCONTROL" -a "$OPT_COLLECT_OPROFILE" ]; then
       if $CMD_OPCONTROL --init; then
          $CMD_OPCONTROL --start --no-vmlinux
@@ -869,114 +928,109 @@ collect() {
       local strace_pid=$!
    fi
 
-   if [ ! "$OPT_MYSQL_ONLY" ]; then 
-      ps -eaF  >> "$d/$p-ps"  &
-      top -bn${OPT_RUN_TIME} >> "$d/$p-top" &
-
-      [ "$mysqld_pid" ] && _lsof $mysqld_pid >> "$d/$p-lsof" &
-
-      if [ "$CMD_SYSCTL" ]; then
-         $CMD_SYSCTL -a >> "$d/$p-sysctl" &
-      fi
-
-      if [ "$CMD_DMESG" ]; then
-         local UPTIME=`cat /proc/uptime | awk '{ print $1 }'`
-         local START_TIME=$(echo "$UPTIME 60" | awk '{print ($1 - $2)}')
-         $CMD_DMESG  | perl -ne 'm/\[\s*(\d+)\./; if ($1 > '${START_TIME}') { print }' >> "$d/$p-dmesg" & 
-      fi
-
-      local cnt=$(($OPT_RUN_TIME / $OPT_SLEEP_COLLECT))
-      if [ "$CMD_VMSTAT" ]; then
-         $CMD_VMSTAT $OPT_SLEEP_COLLECT $cnt >> "$d/$p-vmstat" &
-         $CMD_VMSTAT $OPT_RUN_TIME 2 >> "$d/$p-vmstat-overall" &
-      fi
-      if [ "$CMD_IOSTAT" ]; then
-         $CMD_IOSTAT -dx $OPT_SLEEP_COLLECT $cnt >> "$d/$p-iostat" &
-         $CMD_IOSTAT -dx $OPT_RUN_TIME 2 >> "$d/$p-iostat-overall" &
-      fi
-      if [ "$CMD_MPSTAT" ]; then
-         $CMD_MPSTAT -P ALL $OPT_SLEEP_COLLECT $cnt >> "$d/$p-mpstat" &
-         $CMD_MPSTAT -P ALL $OPT_RUN_TIME 1 >> "$d/$p-mpstat-overall" &
-      fi
-
-      $CMD_MYSQLADMIN $EXT_ARGV ext -i$OPT_SLEEP_COLLECT -c$cnt >>"$d/$p-mysqladmin" &
-      local mysqladmin_pid=$!
-   fi 
-
-   local have_lock_waits_table=""
    $CMD_MYSQL $EXT_ARGV -e "SHOW TABLES FROM INFORMATION_SCHEMA" \
       | grep -i "INNODB_LOCK_WAITS" >/dev/null 2>&1
    if [ $? -eq 0 ]; then
       have_lock_waits_table="yes"
    fi
 
-   log "Loop start: $(date +'TS %s.%N %F %T')"
-   local start_time=$(date +'%s')
-   local curr_time=$start_time
-   local ps_instrumentation_enabled=$($CMD_MYSQL $EXT_ARGV -e 'SELECT ENABLED FROM performance_schema.setup_instruments WHERE NAME = "transaction";' \
+   $CMD_MYSQLADMIN $EXT_ARGV ext -i$OPT_SLEEP_COLLECT -c$cnt >>"$d/$p-mysqladmin" &
+   mysqladmin_pid=$!
+
+   ps_instrumentation_enabled=$($CMD_MYSQL $EXT_ARGV -e 'SELECT ENABLED FROM performance_schema.setup_instruments WHERE NAME = "transaction";' \
                                       | sed "2q;d" | sed 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/')
 
    if [ $ps_instrumentation_enabled != "yes" ]; then
       log "Performance Schema instrumentation is disabled"
    fi
+}
 
-   while [ $((curr_time - start_time)) -lt $OPT_RUN_TIME ]; do
-      if [ ! "$OPT_MYSQL_ONLY" ]; then
-         disk_space $d > $d/$p-disk-space
-         check_disk_space          \
-            $d/$p-disk-space       \
-            "$OPT_DISK_BYTES_FREE" \
-            "$OPT_DISK_PCT_FREE"   \
-            || break
+collect_system_data() {
+   ps -eaF  >> "$d/$p-ps"  &
+   top -bn${OPT_RUN_TIME} >> "$d/$p-top" &
 
-         sleep $(date +'%s.%N' | awk "{print $OPT_SLEEP_COLLECT - (\$1 % $OPT_SLEEP_COLLECT)}")
-         local ts="$(date +"TS %s.%N %F %T")"
+   [ "$mysqld_pid" ] && _lsof $mysqld_pid >> "$d/$p-lsof" &
 
-         if [ -d "/proc" ]; then
-            if [ -f "/proc/diskstats" ]; then
-               (echo $ts; cat /proc/diskstats) >> "$d/$p-diskstats" &
-            fi
-            if [ -f "/proc/stat" ]; then
-               (echo $ts; cat /proc/stat) >> "$d/$p-procstat" &
-            fi
-            if [ -f "/proc/vmstat" ]; then
-               (echo $ts; cat /proc/vmstat) >> "$d/$p-procvmstat" &
-            fi
-            if [ -f "/proc/meminfo" ]; then
-               (echo $ts; cat /proc/meminfo) >> "$d/$p-meminfo" &
-            fi
-            if [ -f "/proc/slabinfo" ]; then
-               (echo $ts; cat /proc/slabinfo) >> "$d/$p-slabinfo" &
-            fi
-            if [ -f "/proc/interrupts" ]; then
-               (echo $ts; cat /proc/interrupts) >> "$d/$p-interrupts" &
-            fi
-         fi
-         (echo $ts; df -k) >> "$d/$p-df" &
-         (echo $ts; netstat -antp) >> "$d/$p-netstat"   &
-         (echo $ts; netstat -s)    >> "$d/$p-netstat_s" &
+   if [ "$CMD_SYSCTL" ]; then
+      $CMD_SYSCTL -a >> "$d/$p-sysctl" &
+   fi
+
+   if [ "$CMD_DMESG" ]; then
+      local UPTIME=`cat /proc/uptime | awk '{ print $1 }'`
+      local START_TIME=$(echo "$UPTIME 60" | awk '{print ($1 - $2)}')
+      $CMD_DMESG  | perl -ne 'm/\[\s*(\d+)\./; if ($1 > '${START_TIME}') { print }' >> "$d/$p-dmesg" & 
+   fi
+
+   if [ "$CMD_VMSTAT" ]; then
+      $CMD_VMSTAT $OPT_SLEEP_COLLECT $cnt >> "$d/$p-vmstat" &
+      $CMD_VMSTAT $OPT_RUN_TIME 2 >> "$d/$p-vmstat-overall" &
+   fi
+   if [ "$CMD_IOSTAT" ]; then
+      $CMD_IOSTAT -dx $OPT_SLEEP_COLLECT $cnt >> "$d/$p-iostat" &
+      $CMD_IOSTAT -dx $OPT_RUN_TIME 2 >> "$d/$p-iostat-overall" &
+   fi
+   if [ "$CMD_MPSTAT" ]; then
+      $CMD_MPSTAT -P ALL $OPT_SLEEP_COLLECT $cnt >> "$d/$p-mpstat" &
+      $CMD_MPSTAT -P ALL $OPT_RUN_TIME 1 >> "$d/$p-mpstat-overall" &
+   fi
+}
+
+collect_mysql_data_loop() {
+   (echo $ts; $CMD_MYSQL $EXT_ARGV -e "SHOW FULL PROCESSLIST\G") \
+      >> "$d/$p-processlist" &
+   if [ "$have_lock_waits_table" ]; then
+      (echo $ts; lock_waits)   >>"$d/$p-lock-waits" &
+      (echo $ts; transactions) >>"$d/$p-transactions" &
+   fi
+
+   if [ "${mysql_version}" '>' "5.6" ] && [ $ps_instrumentation_enabled == "yes" ]; then
+      ps_locks_transactions "$d/$p-ps-locks-transactions"
+   fi
+
+   if [ "${mysql_version}" '>' "5.6" ]; then
+      (echo $ts; ps_prepared_statements) >> "$d/$p-prepared-statements" &
+   fi
+
+   slave_status "$d/$p-slave-status" "${mysql_version}" 
+}
+
+collect_system_data_loop() {
+   disk_space $d > $d/$p-disk-space
+   check_disk_space          \
+      $d/$p-disk-space       \
+      "$OPT_DISK_BYTES_FREE" \
+      "$OPT_DISK_PCT_FREE"   \
+      || break
+
+   sleep $(date +'%s.%N' | awk "{print $OPT_SLEEP_COLLECT - (\$1 % $OPT_SLEEP_COLLECT)}")
+   ts="$(date +"TS %s.%N %F %T")"
+
+   if [ -d "/proc" ]; then
+      if [ -f "/proc/diskstats" ]; then
+         (echo $ts; cat /proc/diskstats) >> "$d/$p-diskstats" &
       fi
-      (echo $ts; $CMD_MYSQL $EXT_ARGV -e "SHOW FULL PROCESSLIST\G") \
-         >> "$d/$p-processlist" &
-      if [ "$have_lock_waits_table" ]; then
-         (echo $ts; lock_waits)   >>"$d/$p-lock-waits" &
-         (echo $ts; transactions) >>"$d/$p-transactions" &
+      if [ -f "/proc/stat" ]; then
+         (echo $ts; cat /proc/stat) >> "$d/$p-procstat" &
       fi
-
-      if [ "${mysql_version}" '>' "5.6" ] && [ $ps_instrumentation_enabled == "yes" ]; then
-         ps_locks_transactions "$d/$p-ps-locks-transactions"
+      if [ -f "/proc/vmstat" ]; then
+         (echo $ts; cat /proc/vmstat) >> "$d/$p-procvmstat" &
       fi
-
-      if [ "${mysql_version}" '>' "5.6" ]; then
-         (echo $ts; ps_prepared_statements) >> "$d/$p-prepared-statements" &
+      if [ -f "/proc/meminfo" ]; then
+         (echo $ts; cat /proc/meminfo) >> "$d/$p-meminfo" &
       fi
+      if [ -f "/proc/slabinfo" ]; then
+         (echo $ts; cat /proc/slabinfo) >> "$d/$p-slabinfo" &
+      fi
+      if [ -f "/proc/interrupts" ]; then
+         (echo $ts; cat /proc/interrupts) >> "$d/$p-interrupts" &
+      fi
+   fi
+   (echo $ts; df -k) >> "$d/$p-df" &
+   (echo $ts; netstat -antp) >> "$d/$p-netstat"   &
+   (echo $ts; netstat -s)    >> "$d/$p-netstat_s" &
+}
 
-      slave_status "$d/$p-slave-status" "${mysql_version}" 
-
-      curr_time=$(date +'%s')
-   done
-   log "Loop end: $(date +'TS %s.%N %F %T')"
-
+collect_mysql_data_two() {
    if [ "$have_oprofile" ]; then
       $CMD_OPCONTROL --stop
       $CMD_OPCONTROL --dump
@@ -1020,20 +1074,9 @@ collect() {
    $CMD_MYSQL $EXT_ARGV -e "$mutex" >> "$d/$p-mutex-status2" &
    open_tables                      >> "$d/$p-opentables2"   &
 
-   kill $mysqladmin_pid
+   [ "$mysqladmin_pid" ] &&  kill $mysqladmin_pid
    [ "$tail_error_log_pid" ] && kill $tail_error_log_pid
    [ "$tcpdump_pid" ]        && kill $tcpdump_pid
-
-   hostname > "$d/$p-hostname"
-
-   wait_for_subshells $OPT_RUN_TIME
-   kill_all_subshells
-   for file in "$d/$p-"*; do
-      if [ -z "$(grep -v '^TS ' --max-count 10 "$file")" ]; then
-         log "Removing empty file $file";
-         rm "$file"
-      fi
-   done
 }
 
 open_tables() {
@@ -1087,8 +1130,13 @@ transactions() {
 tokudb_status() {
     local n=$1
 
-    $CMD_MYSQL $EXT_ARGV -e "SHOW ENGINE TOKUDB STATUS\G" \
-      >> "$d/$p-tokudbstatus$n" || rm -f "$d/$p-tokudbstatus$n"
+    has_tokudb=`$CMD_MYSQL $EXT_ARGV -e "SHOW ENGINES" | grep -i 'tokudb'`
+    exit_code=$?
+
+    if [ $exit_code -eq 0 ]; then
+       $CMD_MYSQL $EXT_ARGV -e "SHOW ENGINE TOKUDB STATUS\G" \
+         >> "$d/$p-tokudbstatus$n" || rm -f "$d/$p-tokudbstatus$n"
+    fi
 }
 
 innodb_status() {
@@ -1171,11 +1219,11 @@ slave_status() {
       echo -e "\n$sql\n" >> $outfile
       $CMD_MYSQL $EXT_ARGV -e "$sql" >> $outfile
 
-      sql="SELECT * FROM replication_connection_status\G"
+      sql="SELECT * FROM performance_schema.replication_connection_status\G"
       echo -e "\n$sql\n" >> $outfile
       $CMD_MYSQL $EXT_ARGV -e "$sql" >> $outfile
 
-      sql="SELECT * FROM replication_applier_status JOIN replication_applier_status_by_coordinator USING(channel_name)\G"
+      sql="SELECT * FROM performance_schema.replication_applier_status JOIN performance_schema.replication_applier_status_by_coordinator USING(channel_name)\G"
       echo -e "\n$sql\n" >> $outfile
       $CMD_MYSQL $EXT_ARGV -e "$sql" >> $outfile
    fi
@@ -1452,6 +1500,7 @@ stalk() {
          # ##################################################################
          log "Collect $ITER triggered"
          log "MYSQL_ONLY: $OPT_MYSQL_ONLY"
+         log "SYSTEM_ONLY: $OPT_SYSTEM_ONLY"
 
          # Send email to whomever that collect has been triggered.
          if [ "$OPT_NOTIFY_BY_EMAIL" ]; then
@@ -1468,6 +1517,8 @@ stalk() {
             if [ -n "$last_prefix" ]; then
                margin=$(du -mc "$OPT_DEST"/"$last_prefix"-* | tail -n 1 | awk '{print $1'})
             fi
+            # Disk space checked even if system data collection is OFF
+            # See https://jira.percona.com/browse/PT-1486
             disk_space "$OPT_DEST" > "$OPT_DEST/$prefix-disk-space"
             check_disk_space                  \
                "$OPT_DEST/$prefix-disk-space" \
@@ -1633,18 +1684,20 @@ if    [ "${0##*/}" = "$TOOL" ] \
    EXT_ARGV="$(arrange_mysql_options "$EXT_ARGV $MYSQL_ARGS")"
 
 
-   # Check that mysql and mysqladmin are in PATH.  If not, we're
-   # already dead in the water, so don't bother with cmd line opts,
-   # just error and exit.
-   [ -n "$(mysql --help)" ] \
-      || die "Cannot execute mysql.  Check that it is in PATH."
-   [ -n "$(mysqladmin --help)" ] \
-      || die "Cannot execute mysqladmin.  Check that it is in PATH."
+   if [ ! "$OPT_SYSTEM_ONLY" ]; then
+      # Check that mysql and mysqladmin are in PATH.  If not, we're
+      # already dead in the water, so don't bother with cmd line opts,
+      # just error and exit.
+      [ -n "$(mysql --help)" ] \
+         || die "Cannot execute mysql.  Check that it is in PATH."
+      [ -n "$(mysqladmin --help)" ] \
+         || die "Cannot execute mysqladmin.  Check that it is in PATH."
 
-   # Now that we have the cmd line opts, check that we can actually
-   # connect to MySQL.
-   [ -n "$(mysql $EXT_ARGV -e 'SELECT 1')" ] \
-      || die "Cannot connect to MySQL.  Check that MySQL is running and that the options after -- are correct."
+      # Now that we have the cmd line opts, check that we can actually
+      # connect to MySQL.
+      [ -n "$(mysql $EXT_ARGV -e 'SELECT 1')" ] \
+         || die "Cannot connect to MySQL.  Check that MySQL is running and that the options after -- are correct."
+   fi
 
    # Check existence and access to the --dest dir if we're collecting.
    if [ "$OPT_COLLECT" ]; then
@@ -2236,6 +2289,10 @@ L<"--disk-pct-free">, are still respected.
 
 See also L<"--collect">.
 
+=item --system-only
+
+Trigger only operating system related captures, ignoring all others.
+
 =item --threshold
 
 type: int; default: 25

bin/pt-upgrade

@@ -9386,6 +9386,7 @@ use Percona::Toolkit;
 use constant PTDEBUG => $ENV{PTDEBUG} || 0;
 
 use sigtrap 'handler', \&sig_int, 'normal-signals';
+binmode(STDOUT, "encoding(UTF-8)");
 
 # Global variables.  Only really essential variables should be here.
 my $oktorun     = 1;

lib/bash/collect.sh

@@ -49,10 +49,77 @@ collect() {
    local d="$1"  # directory to save results in
    local p="$2"  # prefix for each result file
 
-   local mysqld_pid=""
+   local cnt=$(($OPT_RUN_TIME / $OPT_SLEEP_COLLECT))
+   
+   if [ ! "$OPT_SYSTEM_ONLY" ]; then
+      local mysqld_pid=""
+      local mysql_version=""
+      local mysql_error_log=""
+      local tail_error_log_pid=""
+      local have_lock_waits_table=""
+      local have_oprofile=""
+      local mysqladmin_pid=""
+      local mutex=""
+      local tcpdump_pid=""
+      local ps_instrumentation_enabled=""
+
+      collect_mysql_data_one
+   fi
+
+   # Grab a few general things first.  Background all of these so we can start
+   # them all up as quickly as possible.  
+   if [ ! "$OPT_MYSQL_ONLY" ]; then 
+      collect_system_data
+   fi 
+
+   # This loop gathers data for the rest of the duration, and defines the time
+   # of the whole job.
+   log "Loop start: $(date +'TS %s.%N %F %T')"
+   local start_time=$(date +'%s')
+   local curr_time=$start_time
+   local ts="$(date +"TS %s.%N %F %T")"
+
+   while [ $((curr_time - start_time)) -lt $OPT_RUN_TIME ]; do
+      if [ ! "$OPT_MYSQL_ONLY" ]; then
+         collect_system_data_loop
+      fi
+
+      if [ ! "$OPT_SYSTEM_ONLY" ]; then
+         collect_mysql_data_loop
+      fi
+
+      curr_time=$(date +'%s')
+   done
+   log "Loop end: $(date +'TS %s.%N %F %T')"
+
+   if [ ! "$OPT_SYSTEM_ONLY" ]; then
+      collect_mysql_data_two
+   fi
+
+   # Finally, record what system we collected this data from.
+   hostname > "$d/$p-hostname"
+
+   # Remove "empty" files, i.e. ones that are truly empty or
+   # just contain timestamp lines.  When a command above fails,
+   # it may leave an empty file.  But first wait another --run-time
+   # seconds for any slow process to finish:
+   # https://bugs.launchpad.net/percona-toolkit/+bug/1047701
+   wait_for_subshells $OPT_RUN_TIME
+   kill_all_subshells
+   for file in "$d/$p-"*; do
+      # If there's not at least 1 line that's not a TS,
+      # then the file is empty.
+      if [ -z "$(grep -v '^TS ' --max-count 10 "$file")" ]; then
+         log "Removing empty file $file";
+         rm "$file"
+      fi
+   done
+}
+
+collect_mysql_data_one() {
    # Get pidof mysqld.
    if [ ! "$OPT_MYSQL_ONLY" ]; then
-      port=$(mysql -ss -e 'SELECT @@port')
+      port=$($CMD_MYSQL $EXT_ARGV -ss -e 'SELECT @@port')
       mysqld_pid=$(lsof -i ":${port}" | grep -i listen | cut -f 3 -d" ")
    fi
 
@@ -84,16 +151,16 @@ collect() {
 
    # Get the major.minor version number.  Version 3.23 doesn't matter for our
    # purposes, and other releases have x.x.x* version conventions so far.
-   local mysql_version="$(awk '/^version[^_]/{print substr($2,1,3)}' "$d/$p-variables")"
+   mysql_version="$(awk '/^version[^_]/{print substr($2,1,3)}' "$d/$p-variables")"
 
    # Is MySQL logging its errors to a file?  If so, tail that file.
-   local mysql_error_log="$(awk '/^log_error/{print $2}' "$d/$p-variables")"
+   mysql_error_log="$(awk '/^log_error\s/{print $2}' "$d/$p-variables")"
    if [ -z "$mysql_error_log" -a "$mysqld_pid" ]; then
+      log $mysqld_pid
       # Try getting it from the open filehandle...
       mysql_error_log="$(ls -l /proc/$mysqld_pid/fd | awk '/ 2 ->/{print $NF}')"
    fi
 
-   local tail_error_log_pid=""
    if [ "$mysql_error_log" -a ! "$OPT_MYSQL_ONLY" ]; then
       log "The MySQL error log seems to be $mysql_error_log"
       tail -f "$mysql_error_log" >"$d/$p-log_error" &
@@ -101,16 +168,16 @@ collect() {
 
       # Send a mysqladmin debug to the server so we can potentially learn about
       # locking etc.
-      $CMD_MYSQLADMIN $EXT_ARGV debug
+      $CMD_MYSQLADMIN $EXT_ARGV
    else
       log "Could not find the MySQL error log"
    fi 
    # Get a sample of these right away, so we can get these without interaction
    # with the other commands we're about to run.
    if [ "${mysql_version}" '>' "5.1" ]; then
-      local mutex="SHOW ENGINE INNODB MUTEX"
+      mutex="SHOW ENGINE INNODB MUTEX"
    else
-      local mutex="SHOW MUTEX STATUS"
+      mutex="SHOW MUTEX STATUS"
    fi
    innodb_status 1
    tokudb_status 1
@@ -120,7 +187,6 @@ collect() {
    open_tables                      >> "$d/$p-opentables1"   &
 
    # If TCP dumping is specified, start that on the server's port.
-   local tcpdump_pid=""
    if [ "$CMD_TCPDUMP" -a  "$OPT_COLLECT_TCPDUMP" ]; then
       local port=$(awk '/^port/{print $2}' "$d/$p-variables")
       if [ "$port" ]; then
@@ -131,7 +197,6 @@ collect() {
 
    # Next, start oprofile gathering data during the whole rest of this process.
    # The --init should be a no-op if it has already been init-ed.
-   local have_oprofile=""
    if [ "$CMD_OPCONTROL" -a "$OPT_COLLECT_OPROFILE" ]; then
       if $CMD_OPCONTROL --init; then
          $CMD_OPCONTROL --start --no-vmlinux
@@ -143,132 +208,123 @@ collect() {
       local strace_pid=$!
    fi
 
-   # Grab a few general things first.  Background all of these so we can start
-   # them all up as quickly as possible.  
-   if [ ! "$OPT_MYSQL_ONLY" ]; then 
-      ps -eaF  >> "$d/$p-ps"  &
-      top -bn${OPT_RUN_TIME} >> "$d/$p-top" &
-
-      [ "$mysqld_pid" ] && _lsof $mysqld_pid >> "$d/$p-lsof" &
-
-      if [ "$CMD_SYSCTL" ]; then
-         $CMD_SYSCTL -a >> "$d/$p-sysctl" &
-      fi
-
-      # collect dmesg events from 60 seconds ago until present
-      if [ "$CMD_DMESG" ]; then
-         local UPTIME=`cat /proc/uptime | awk '{ print $1 }'`
-         local START_TIME=$(echo "$UPTIME 60" | awk '{print ($1 - $2)}')
-         $CMD_DMESG  | perl -ne 'm/\[\s*(\d+)\./; if ($1 > '${START_TIME}') { print }' >> "$d/$p-dmesg" & 
-      fi
-
-      local cnt=$(($OPT_RUN_TIME / $OPT_SLEEP_COLLECT))
-      if [ "$CMD_VMSTAT" ]; then
-         $CMD_VMSTAT $OPT_SLEEP_COLLECT $cnt >> "$d/$p-vmstat" &
-         $CMD_VMSTAT $OPT_RUN_TIME 2 >> "$d/$p-vmstat-overall" &
-      fi
-      if [ "$CMD_IOSTAT" ]; then
-         $CMD_IOSTAT -dx $OPT_SLEEP_COLLECT $cnt >> "$d/$p-iostat" &
-         $CMD_IOSTAT -dx $OPT_RUN_TIME 2 >> "$d/$p-iostat-overall" &
-      fi
-      if [ "$CMD_MPSTAT" ]; then
-         $CMD_MPSTAT -P ALL $OPT_SLEEP_COLLECT $cnt >> "$d/$p-mpstat" &
-         $CMD_MPSTAT -P ALL $OPT_RUN_TIME 1 >> "$d/$p-mpstat-overall" &
-      fi
-
-      # Collect multiple snapshots of the status variables.  We use
-      # mysqladmin -c even though it is buggy and won't stop on its
-      # own in 5.1 and newer, because there is a chance that we will
-      # get and keep a connection to the database; in troubled times
-      # the database tends to exceed max_connections, so reconnecting
-      # in the loop tends not to work very well.
-      $CMD_MYSQLADMIN $EXT_ARGV ext -i$OPT_SLEEP_COLLECT -c$cnt >>"$d/$p-mysqladmin" &
-      local mysqladmin_pid=$!
-   fi 
-
-   local have_lock_waits_table=""
    $CMD_MYSQL $EXT_ARGV -e "SHOW TABLES FROM INFORMATION_SCHEMA" \
       | grep -i "INNODB_LOCK_WAITS" >/dev/null 2>&1
    if [ $? -eq 0 ]; then
       have_lock_waits_table="yes"
    fi
 
-   # This loop gathers data for the rest of the duration, and defines the time
-   # of the whole job.
-   log "Loop start: $(date +'TS %s.%N %F %T')"
-   local start_time=$(date +'%s')
-   local curr_time=$start_time
-   local ps_instrumentation_enabled=$($CMD_MYSQL $EXT_ARGV -e 'SELECT ENABLED FROM performance_schema.setup_instruments WHERE NAME = "transaction";' \
+   # Collect multiple snapshots of the status variables.  We use
+   # mysqladmin -c even though it is buggy and won't stop on its
+   # own in 5.1 and newer, because there is a chance that we will
+   # get and keep a connection to the database; in troubled times
+   # the database tends to exceed max_connections, so reconnecting
+   # in the loop tends not to work very well.
+   $CMD_MYSQLADMIN $EXT_ARGV ext -i$OPT_SLEEP_COLLECT -c$cnt >>"$d/$p-mysqladmin" &
+   mysqladmin_pid=$!
+
+   ps_instrumentation_enabled=$($CMD_MYSQL $EXT_ARGV -e 'SELECT ENABLED FROM performance_schema.setup_instruments WHERE NAME = "transaction";' \
                                       | sed "2q;d" | sed 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/')
 
    if [ $ps_instrumentation_enabled != "yes" ]; then
       log "Performance Schema instrumentation is disabled"
    fi
+}
 
-   while [ $((curr_time - start_time)) -lt $OPT_RUN_TIME ]; do
-      if [ ! "$OPT_MYSQL_ONLY" ]; then
-         # We check the disk, but don't exit, because we need to stop jobs if we
-         # need to exit.
-         disk_space $d > $d/$p-disk-space
-         check_disk_space          \
-            $d/$p-disk-space       \
-            "$OPT_DISK_BYTES_FREE" \
-            "$OPT_DISK_PCT_FREE"   \
-            || break
+collect_system_data() {
+   ps -eaF  >> "$d/$p-ps"  &
+   top -bn${OPT_RUN_TIME} >> "$d/$p-top" &
 
-         # Sleep between collect cycles.
-         # Synchronize ourselves onto the clock tick, so the sleeps are 1-second
-         sleep $(date +'%s.%N' | awk "{print $OPT_SLEEP_COLLECT - (\$1 % $OPT_SLEEP_COLLECT)}")
-         local ts="$(date +"TS %s.%N %F %T")"
+   [ "$mysqld_pid" ] && _lsof $mysqld_pid >> "$d/$p-lsof" &
 
-         # #####################################################################
-         # Collect data for this cycle.
-         # #####################################################################
-         if [ -d "/proc" ]; then
-            if [ -f "/proc/diskstats" ]; then
-               (echo $ts; cat /proc/diskstats) >> "$d/$p-diskstats" &
-            fi
-            if [ -f "/proc/stat" ]; then
-               (echo $ts; cat /proc/stat) >> "$d/$p-procstat" &
-            fi
-            if [ -f "/proc/vmstat" ]; then
-               (echo $ts; cat /proc/vmstat) >> "$d/$p-procvmstat" &
-            fi
-            if [ -f "/proc/meminfo" ]; then
-               (echo $ts; cat /proc/meminfo) >> "$d/$p-meminfo" &
-            fi
-            if [ -f "/proc/slabinfo" ]; then
-               (echo $ts; cat /proc/slabinfo) >> "$d/$p-slabinfo" &
-            fi
-            if [ -f "/proc/interrupts" ]; then
-               (echo $ts; cat /proc/interrupts) >> "$d/$p-interrupts" &
-            fi
-         fi
-         (echo $ts; df -k) >> "$d/$p-df" &
-         (echo $ts; netstat -antp) >> "$d/$p-netstat"   &
-         (echo $ts; netstat -s)    >> "$d/$p-netstat_s" &
+   if [ "$CMD_SYSCTL" ]; then
+      $CMD_SYSCTL -a >> "$d/$p-sysctl" &
+   fi
+
+   # collect dmesg events from 60 seconds ago until present
+   if [ "$CMD_DMESG" ]; then
+      local UPTIME=`cat /proc/uptime | awk '{ print $1 }'`
+      local START_TIME=$(echo "$UPTIME 60" | awk '{print ($1 - $2)}')
+      $CMD_DMESG  | perl -ne 'm/\[\s*(\d+)\./; if ($1 > '${START_TIME}') { print }' >> "$d/$p-dmesg" & 
+   fi
+
+   if [ "$CMD_VMSTAT" ]; then
+      $CMD_VMSTAT $OPT_SLEEP_COLLECT $cnt >> "$d/$p-vmstat" &
+      $CMD_VMSTAT $OPT_RUN_TIME 2 >> "$d/$p-vmstat-overall" &
+   fi
+   if [ "$CMD_IOSTAT" ]; then
+      $CMD_IOSTAT -dx $OPT_SLEEP_COLLECT $cnt >> "$d/$p-iostat" &
+      $CMD_IOSTAT -dx $OPT_RUN_TIME 2 >> "$d/$p-iostat-overall" &
+   fi
+   if [ "$CMD_MPSTAT" ]; then
+      $CMD_MPSTAT -P ALL $OPT_SLEEP_COLLECT $cnt >> "$d/$p-mpstat" &
+      $CMD_MPSTAT -P ALL $OPT_RUN_TIME 1 >> "$d/$p-mpstat-overall" &
+   fi
+}
+
+collect_mysql_data_loop() {
+   (echo $ts; $CMD_MYSQL $EXT_ARGV -e "SHOW FULL PROCESSLIST\G") \
+      >> "$d/$p-processlist" &
+   if [ "$have_lock_waits_table" ]; then
+      (echo $ts; lock_waits)   >>"$d/$p-lock-waits" &
+      (echo $ts; transactions) >>"$d/$p-transactions" &
+   fi
+
+   if [ "${mysql_version}" '>' "5.6" ] && [ $ps_instrumentation_enabled == "yes" ]; then
+      ps_locks_transactions "$d/$p-ps-locks-transactions"
+   fi
+
+   if [ "${mysql_version}" '>' "5.6" ]; then
+      (echo $ts; ps_prepared_statements) >> "$d/$p-prepared-statements" &
+   fi
+
+   slave_status "$d/$p-slave-status" "${mysql_version}" 
+}
+
+collect_system_data_loop() {
+   # We check the disk, but don't exit, because we need to stop jobs if we
+   # need to exit.
+   disk_space $d > $d/$p-disk-space
+   check_disk_space          \
+      $d/$p-disk-space       \
+      "$OPT_DISK_BYTES_FREE" \
+      "$OPT_DISK_PCT_FREE"   \
+      || break
+
+   # Sleep between collect cycles.
+   # Synchronize ourselves onto the clock tick, so the sleeps are 1-second
+   sleep $(date +'%s.%N' | awk "{print $OPT_SLEEP_COLLECT - (\$1 % $OPT_SLEEP_COLLECT)}")
+   ts="$(date +"TS %s.%N %F %T")"
+
+   # #####################################################################
+   # Collect data for this cycle.
+   # #####################################################################
+   if [ -d "/proc" ]; then
+      if [ -f "/proc/diskstats" ]; then
+         (echo $ts; cat /proc/diskstats) >> "$d/$p-diskstats" &
       fi
-      (echo $ts; $CMD_MYSQL $EXT_ARGV -e "SHOW FULL PROCESSLIST\G") \
-         >> "$d/$p-processlist" &
-      if [ "$have_lock_waits_table" ]; then
-         (echo $ts; lock_waits)   >>"$d/$p-lock-waits" &
-         (echo $ts; transactions) >>"$d/$p-transactions" &
+      if [ -f "/proc/stat" ]; then
+         (echo $ts; cat /proc/stat) >> "$d/$p-procstat" &
       fi
-
-      if [ "${mysql_version}" '>' "5.6" ] && [ $ps_instrumentation_enabled == "yes" ]; then
-         ps_locks_transactions "$d/$p-ps-locks-transactions"
+      if [ -f "/proc/vmstat" ]; then
+         (echo $ts; cat /proc/vmstat) >> "$d/$p-procvmstat" &
       fi
-
-      if [ "${mysql_version}" '>' "5.6" ]; then
-         (echo $ts; ps_prepared_statements) >> "$d/$p-prepared-statements" &
+      if [ -f "/proc/meminfo" ]; then
+         (echo $ts; cat /proc/meminfo) >> "$d/$p-meminfo" &
       fi
+      if [ -f "/proc/slabinfo" ]; then
+         (echo $ts; cat /proc/slabinfo) >> "$d/$p-slabinfo" &
+      fi
+      if [ -f "/proc/interrupts" ]; then
+         (echo $ts; cat /proc/interrupts) >> "$d/$p-interrupts" &
+      fi
+   fi
+   (echo $ts; df -k) >> "$d/$p-df" &
+   (echo $ts; netstat -antp) >> "$d/$p-netstat"   &
+   (echo $ts; netstat -s)    >> "$d/$p-netstat_s" &
+}
 
-      slave_status "$d/$p-slave-status" "${mysql_version}" 
-
-      curr_time=$(date +'%s')
-   done
-   log "Loop end: $(date +'TS %s.%N %F %T')"
-
+collect_mysql_data_two() {
    if [ "$have_oprofile" ]; then
       $CMD_OPCONTROL --stop
       $CMD_OPCONTROL --dump
@@ -316,28 +372,9 @@ collect() {
    open_tables                      >> "$d/$p-opentables2"   &
 
    # Kill backgrounded tasks.
-   kill $mysqladmin_pid
+   [ "$mysqladmin_pid" ] &&  kill $mysqladmin_pid
    [ "$tail_error_log_pid" ] && kill $tail_error_log_pid
    [ "$tcpdump_pid" ]        && kill $tcpdump_pid
-
-   # Finally, record what system we collected this data from.
-   hostname > "$d/$p-hostname"
-
-   # Remove "empty" files, i.e. ones that are truly empty or
-   # just contain timestamp lines.  When a command above fails,
-   # it may leave an empty file.  But first wait another --run-time
-   # seconds for any slow process to finish:
-   # https://bugs.launchpad.net/percona-toolkit/+bug/1047701
-   wait_for_subshells $OPT_RUN_TIME
-   kill_all_subshells
-   for file in "$d/$p-"*; do
-      # If there's not at least 1 line that's not a TS,
-      # then the file is empty.
-      if [ -z "$(grep -v '^TS ' --max-count 10 "$file")" ]; then
-         log "Removing empty file $file";
-         rm "$file"
-      fi
-   done
 }
 
 open_tables() {
@@ -391,8 +428,13 @@ transactions() {
 tokudb_status() {
     local n=$1
 
-    $CMD_MYSQL $EXT_ARGV -e "SHOW ENGINE TOKUDB STATUS\G" \
-      >> "$d/$p-tokudbstatus$n" || rm -f "$d/$p-tokudbstatus$n"
+    has_tokudb=`$CMD_MYSQL $EXT_ARGV -e "SHOW ENGINES" | grep -i 'tokudb'`
+    exit_code=$?
+
+    if [ $exit_code -eq 0 ]; then
+       $CMD_MYSQL $EXT_ARGV -e "SHOW ENGINE TOKUDB STATUS\G" \
+         >> "$d/$p-tokudbstatus$n" || rm -f "$d/$p-tokudbstatus$n"
+    fi
 }
 
 innodb_status() {
@@ -475,11 +517,11 @@ slave_status() {
       echo -e "\n$sql\n" >> $outfile
       $CMD_MYSQL $EXT_ARGV -e "$sql" >> $outfile
 
-      sql="SELECT * FROM replication_connection_status\G"
+      sql="SELECT * FROM performance_schema.replication_connection_status\G"
       echo -e "\n$sql\n" >> $outfile
       $CMD_MYSQL $EXT_ARGV -e "$sql" >> $outfile
 
-      sql="SELECT * FROM replication_applier_status JOIN replication_applier_status_by_coordinator USING(channel_name)\G"
+      sql="SELECT * FROM performance_schema.replication_applier_status JOIN performance_schema.replication_applier_status_by_coordinator USING(channel_name)\G"
       echo -e "\n$sql\n" >> $outfile
       $CMD_MYSQL $EXT_ARGV -e "$sql" >> $outfile
    fi

t/pt-stalk/pt-stalk.t

@@ -542,13 +542,13 @@ $retval = system("$trunk/bin/pt-stalk --no-stalk --run-time 2 --sleep 2 --dest $
 
 PerconaTest::wait_until(sub { !-f $pid_file });
 
-$output = `du -s $dest | wc -l`;
+$output = `ls -l $dest | wc -l`;
 
 $retval = system("$trunk/bin/pt-stalk --no-stalk --run-time 2 --dest $dest --retention-count 1 --pid $pid_file --iterations 1 -- --defaults-file=$cnf >$log_file 2>&1");
 
 PerconaTest::wait_until(sub { !-f $pid_file });
 
-$output = $output - `du -s $dest | wc -l`;
+$output = $output - `ls -l $dest | wc -l`;
 
 is(
    $output,
@@ -556,6 +556,73 @@ is(
    "Retention test 5: retention by count works as expected"
 );
 
+# ###########################################################################
+# Test if option --system-only works correctly
+# ###########################################################################
+
+cleanup();
+
+$retval = system("$trunk/bin/pt-stalk --no-stalk --system-only --run-time 10 --sleep 2 --dest $dest --pid $pid_file --iterations 1 -- --defaults-file=$cnf >$log_file 2>&1");
+
+PerconaTest::wait_until(sub { !-f $pid_file });
+
+$output = `ls $dest`;
+
+like(
+   $output,
+   qr/(df)|(meminfo)/,
+   "Option --system-only collects system data"
+);
+
+unlike(
+   $output,
+   qr/(innodbstatus)|(mysqladmin)/,
+   "Option --system-only does not collect MySQL data"
+);
+
+# ###########################################################################
+# Test if option --mysql-only works correctly
+# ###########################################################################
+
+cleanup();
+
+$retval = system("$trunk/bin/pt-stalk --no-stalk --mysql-only --run-time 10 --sleep 2 --dest $dest --pid $pid_file --iterations 1 -- --defaults-file=$cnf >$log_file 2>&1");
+
+PerconaTest::wait_until(sub { !-f $pid_file });
+
+$output = `ls $dest`;
+
+unlike(
+   $output,
+   qr/(df)|(meminfo)/,
+   "Option --mysql-only does not collect system data"
+);
+
+like(
+   $output,
+   qr/(innodbstatus)|(mysqladmin)/,
+   "Option --mysql-only collects MySQL data"
+);
+
+# ###########################################################################
+# Test if options --mysql-only and --system-only specified together,
+# pt-stalk collects only disk-space, hostname, output, and trigger
+# ###########################################################################
+
+cleanup();
+
+$retval = system("$trunk/bin/pt-stalk --no-stalk --mysql-only --system-only --run-time 10 --sleep 2 --dest $dest --pid $pid_file --iterations 1 --prefix test -- --defaults-file=$cnf >$log_file 2>&1");
+
+PerconaTest::wait_until(sub { !-f $pid_file });
+
+$output = `ls $dest`;
+
+is(
+   $output,
+   "test-disk-space\ntest-hostname\ntest-output\ntest-trigger\n",
+   "If both options --mysql-only and --system-only are specified only essential collections are triggered"
+);
+
 # ###########################################################################
 # Test report about performance schema transactions in MySQL 5.7+
 # ###########################################################################

util/update-modules

@@ -72,19 +72,19 @@ replace_pkg_in_tool() {
    if [ "$tool_lang" = "perl" ]; then
       echo "# $pkg package
 # This package is a copy without comments from the original.  The original
-# with comments and its test file can be found in the Bazaar repository at,
+# with comments and its test file can be found in the GitHub repository at,
 #   lib/$pkg_file_base.pm
 #   t/lib/$pkg_file_base.t
-# See https://launchpad.net/percona-toolkit for more information.
+# See https://github.com/percona/percona-toolkit for more information.
 # ###########################################################################
 {" >> $tmp_file
    else
       echo "# $pkg package
 # This package is a copy without comments from the original.  The original
-# with comments and its test file can be found in the Bazaar repository at,
+# with comments and its test file can be found in the GitHub repository at,
 #   lib/bash/$pkg.sh
 #   t/lib/bash/$pkg.sh
-# See https://launchpad.net/percona-toolkit for more information.
+# See https://github.com/percona/percona-toolkit for more information.
 # ###########################################################################
 " >> $tmp_file
    fi