watch_server added to repo

utility/watch_server/watch_abinit.yaml

+log_name: out #whatever you call your 2>&1 out file
+dropoff: 20 #minutes since last status change to no longer find log
+host: 128.219.185.137 #current CNMS influxdb server
+port: 8086 #influx db port
+root_dir: /your/root/dir
+user_name: your_id
+job_prefix: 'abinit' #generally the code
+job_suffix: 'condo' #generally the server
+influx: True
+start: 'ABINIT is a project of the Universite Catholique de Louvain'
+header: 
+  'npfft, npband, npspinor and npkpt': [[6, 'npfft'],[7, 'npband'],[8, 'npspinor'],[9, 'npkpt']]
+  'npkt=': [[2, 'kpoints']]
+  'natom =': [[3, 'natoms']]
+  'mband =': [[4, 'nband']]
+parse:
+# regex: column, tick_name
+  'ETOT': [[3, 'toten'], [4, 'eacc']]
+finish:
+- 'JOB DONE'
+idle_count: 30
+find_sleep: 60

utility/watch_server/watch_espresso.yaml

+log_name: out
+dropoff: 20 #minutes since last status change to no longer find log
+host: 128.219.185.137
+port: 8086
+root_dir: /your/calculation/root/dir
+user_name: your id
+job_prefix: 'espresso' #generally the code
+job_suffix: 'condo' #generally the server
+influx: True
+start: 'PWSCF.*starts'
+init:
+  'tcpu': 0
+header: 
+  'Parallel version (MPI), running on   640 processors': [[6, 'nproc']]
+  'K-points.*npool': [[5, 'kpar']]
+  'number of k points': [[5, 'kpoints']]
+  'number of atoms/cell': [[5, 'natoms']]
+  'number of Kohn-Sham states': [[5, 'nstates']]
+parse:
+# regex: column, tick_name
+  'total cpu time spent': [[9, 'tcpu']]
+  'total energy': [[4, 'toten']]
+  'estimated': [[5, 'eacc']]
+  'Total force': [[4, 'tforce']]
+finish:
+- 'JOB DONE'
+idle_count: 30
+find_sleep: 60

utility/watch_server/watch_server.influx

+37859  curl -i -XPOST http://128.219.185.137:8086/query --data-urlencode "q=CREATE DATABASE \"jobs\""
+create datatbabse jobs
+select moving_average("value",10) INTO "toten_ma" FROM "toten" GROUP BY "job_name","user_name","code"
+select "value" INTO "toten_ma" FROM "toten" GROUP BY "job_name","user_name","code"
+

utility/watch_server/watch_server.py

+import sys
+import yaml
+import re
+import time
+import subprocess
+import os
+import multiprocessing as mp
+import socket
+import requests
+from ws_pygtail import Pygtail
+
+def read_output(log):
+    ld = config['launch_dir']
+    print "Watching: {}".format(log)
+    (directory, out_file) = os.path.split(log)
+    job_name = os.path.basename(directory)
+    job_tag = "{}.{}.{}.{}".format(config['user_name'],
+                                   config['job_prefix'],
+                                   job_name,
+                                   config['job_suffix'])
+    print "job tag: {}".format(job_tag)
+    sock = socket.create_connection((config['host'],config['port']))
+    print "Peer Name", sock.getpeername()
+    print "Sock Name", sock.getsockname()
+    watch_log = open(os.path.join(ld,"{}.log".format(job_tag)),'w')
+    watch_log.write("Watching {}\n".format(log))
+    while True:
+        offset_file = os.path.join(ld,"{}.off".format(job_tag))
+        for line in Pygtail(log,
+                            offset_file=offset_file):
+            for find_this, then_do in config['parse'].iteritems():
+                match = re.search(find_this, line)
+                if match:
+                    the_value = (line.split())[then_do[0]-1]
+                    the_value = re.sub(r':',r'',the_value)
+                    print "{} {}".format(then_do[1], the_value)
+                    watch_log.write("{}: {}\n".format(then_do[1], the_value))
+                    sock.sendall("{}.{} {} {}\n".format(job_tag,
+                                                   then_do[1],
+                                                   the_value,
+                                                   int(time.time())))
+        
+
+        watch_log.flush()
+        time.sleep(10)                                          
+
+def read_output_influx(log):
+    ld = config['launch_dir']
+    print "Watching: {}".format(log)
+    (directory, out_file) = os.path.split(log)
+    job_name = os.path.basename(directory)
+    job_tag = "{}.{}.{}.{}".format(config['user_name'],
+                                   config['job_prefix'],
+                                   job_name,
+                                   config['job_suffix'])
+    print "job tag: {}".format(job_tag)
+    watch_log = open(os.path.join(ld,"{}.log".format(job_tag)),'w')
+    watch_log.write("Watching {}\n".format(log))
+    watch_start = ('start' in config)
+    header_element_found = {x:False for x in config['header']}
+    while True:
+        offset_file = os.path.join(ld,"{}.off".format(job_tag))
+        influx_lines = []
+        for line in Pygtail(log,
+                            offset_file=offset_file):
+            if watch_start:
+                match = re.search(config['start'],line)
+                if match:
+                    if 'init' in config:
+                        for measurement, value in config['init'].iteritems():
+                            influx_point = ("{},user_name={},code={},"
+                                            "job_name={},host={} value={} {}\n"
+                                            .format(measurement,
+                                                    config['user_name'],
+                                                    config['job_prefix'],
+                                                    job_name,
+                                                    config['job_suffix'],
+                                                    value,
+                                                    int(time.time())))
+                            influx_lines.append(influx_point)
+                            influx_point = ("header,user_name={},code={},"
+                                            "host={} job_name=\"{}\" {}\n"
+                                            .format(config['user_name'],
+                                                    config['job_prefix'],
+                                                    config['job_suffix'],
+                                                    job_name,
+                                                    int(time.time())))
+                            influx_lines.append(influx_point)             
+                if 'header' in config:
+                    for find_this, then_do in config['header'].iteritems():
+                        match = re.search(find_this, line)
+                        if match:
+                            try:
+                                the_value = (line.split())[then_do[0]-1]
+                                print line.split()
+                                the_value = re.sub(r':',r'',the_value)
+                                print "Header -- {}: {}".format(then_do[1], the_value)
+                                influx_point = ("header,user_name={},code={},"
+                                                "host={} {}={} {}\n"
+                                                .format(config['user_name'],
+                                                        config['job_prefix'],
+                                                        config['job_suffix'],
+                                                        then_do[1],
+                                                        the_value,
+                                                        int(time.time())))
+                                influx_lines.append(influx_point)                   
+                                watch_log.write("Header -- {}: {}\n".format(then_do[1], the_value))
+                            except IndexError as ie:
+                                print "found", find_this, "index error, no column ", ie, " in: "
+                                print line
+                                        
+            for find_this, then_do in config['parse'].iteritems():
+                match = re.search(find_this, line)
+                if match:
+                    try:
+                        for aindex, label in then_do:
+                            the_value = (line.split())[aindex-1]
+                            the_value = re.sub(r':',r'',the_value)
+                            print "{} {}".format(label, the_value)
+                            influx_point = ("{},user_name={},code={},"
+                                            "job_name={},host={} value={} {}\n"
+                                            .format(label,
+                                                    config['user_name'],
+                                                    config['job_prefix'],
+                                                    job_name,
+                                                    config['job_suffix'],
+                                                    the_value,
+                                                    int(time.time())))
+                            influx_lines.append(influx_point)                   
+                            watch_log.write("{}: {}\n".format(label, the_value))
+                    except IndexError as ie:
+                        print "found", find_this, "index error, no column ", ie, " in: "
+                        print line
+        
+        if len(influx_lines) > 0:
+            r = requests.post("http://{}:{}/write?db=jobs&precision=s".format(config['host'],config['port']), data="".join(influx_lines))
+            print r.text
+            watch_log.flush()
+        time.sleep(10)                                          
+
+        
+if __name__ == '__main__':
+    conf_file = open(sys.argv[1],'r')
+    config = yaml.load(conf_file)
+    config['launch_dir'] = os.getcwd()
+    if 'root_dir' in config:
+        os.chdir(config['root_dir'])
+        match = re.search('lustre',  config['root_dir'])
+        if match:
+            config['lustre'] = True
+    if 'dropoff' in config:
+        dropoff = "-{}".format(int(config['dropoff']))
+    else:
+        dropoff = "-20"            
+
+    print "CONFIG -- WATCH SERVER"
+    print config
+
+    #Lists used in main loop
+    watch_list = [] #what is the difference
+    watch_idlers = {}
+    log_2_process = {}
+
+    
+    while True:
+        logs = []
+        
+        if 'lustre' in config:
+            lustre_logs = subprocess.check_output(['lfs','find', '-ctime', '-1', '-name', config['log_name'], './'])
+            lustre_logs = lustre_logs.splitlines()
+            print lustre_logs
+            for lustre_log in lustre_logs:
+                mod_seconds = time.time() - os.stat(lustre_log).st_mtime
+                print time.time(),'-',os.stat(lustre_log).st_ctime, mod_seconds, (-1 * int(dropoff) * 60)
+                if mod_seconds < -1 * int(dropoff) * 60:
+                    logs.append(lustre_log)
+        else:    
+            logs = subprocess.check_output(['find', './' ,'-name', config['log_name'], '-cmin', dropoff])
+            logs = logs.split('\n')
+
+        found_activity = []
+        real_logs = [log for log in logs if len(log) > 1]
+        for log in real_logs:
+            if log in log_2_process and log_2_process[log].is_alive():
+                found_activity.append(log)
+                if log in watch_idlers:
+                    del watch_idlers[log]                    
+            else:
+                if 'influx' in config:
+                    log_2_process[log] = mp.Process(target=read_output_influx, args=[log])
+                else:
+                    log_2_process[log] = mp.Process(target=read_output, args=[log])
+                log_2_process[log].daemon = True
+                log_2_process[log].start()
+                found_activity.append(log)
+
+        for proc_log in [idle_log for idle_log in log_2_process if idle_log not in found_activity]:
+            if idle_log in watch_idlers:
+                watch_idlers[idle_log] += 1
+            else:
+                watch_idlers[idle_log] = 1
+            if watch_idlers[idle_log] > config["idle_count"]:
+                del watch_idlers[idle_log]
+                log_2_process[log].terminate()
+                del log_2_process[log]
+                #delete offset file here
+                
+        print "sleeping..."
+        time.sleep(config['find_sleep'])
+
+            
+        
+	       

utility/watch_server/watch_vasp.yaml

+log_name: OUTCAR
+dropoff: 20 #minutes since last status change to no longer find log
+host: 128.219.185.137
+port: 8086
+root_dir: /lustre/or-hydra/cades-cnms/your_directory
+user_name: your_name
+influx: True
+job_prefix: 'vasp' #generally the code
+job_suffix: 'condo' #generally the server
+start: 'executed on'
+header: 
+  'running on': [[3, 'nproc']]
+  'distrk': [[7, 'kpar']]
+  'distr': [[6, 'ncores_per_band']]
+  'NKPTS': [[4, 'n_kpts']]
+  'NIONS': [[11, 'n_ions']]
+parse:
+# regex: column, tick_name
+  'LOOP:': [[4, 'loop']]
+  'LOOP\+:': [[4, 'loop_plus']]
+  'TOTEN': [[5, 'toten']]
+finish:
+- 'General timing and accounting'
+idle_count: 30 #number of minutes after dropoff to kill a log watcher process
+find_sleep: 60

utility/watch_server/ws_pygtail.py

+#!/usr/bin/python -tt
+# -*- coding: utf-8 -*-
+
+# pygtail - a python "port" of logtail2
+# Copyright (C) 2011 Brad Greenlee <brad@footle.org>
+#
+# Derived from logcheck <http://logcheck.org>
+# Copyright (C) 2003 Jonathan Middleton <jjm@ixtab.org.uk>
+# Copyright (C) 2001 Paul Slootman <paul@debian.org>
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+from __future__ import print_function
+from os import stat
+from os.path import exists, getsize
+import sys
+import glob
+import gzip
+from optparse import OptionParser
+
+__version__ = '0.7.0'
+
+
+PY3 = sys.version_info[0] == 3
+
+if PY3:
+    text_type = str
+else:
+    text_type = unicode
+
+
+def force_text(s, encoding='utf-8', errors='strict'):
+    if isinstance(s, text_type):
+        return s
+    return s.decode(encoding, errors)
+
+
+class Pygtail(object):
+    """
+    Creates an iterable object that returns only unread lines.
+
+    Keyword arguments:
+    offset_file   File to which offset data is written (default: <logfile>.offset).
+    paranoid      Update the offset file every time we read a line (as opposed to
+                  only when we reach the end of the file (default: False))
+    every_n       Update the offset file every n'th line (as opposed to only when
+                  we reach the end of the file (default: 0))
+    on_update     Execute this function when offset data is written (default False)
+    copytruncate  Support copytruncate-style log rotation (default: True)
+    """
+    def __init__(self, filename, offset_file=None, paranoid=False, copytruncate=True,
+                 every_n=0, on_update=False):
+        self.filename = filename
+        self.paranoid = paranoid
+        self.every_n = every_n
+        self.on_update = on_update
+        self.copytruncate = copytruncate
+        self._offset_file = offset_file or "%s.offset" % self.filename
+        self._offset_file_inode = 0
+        self._offset = 0
+        self._since_update = 0
+        self._fh = None
+        self._rotated_logfile = None
+
+        # if offset file exists and non-empty, open and parse it
+        if exists(self._offset_file) and getsize(self._offset_file):
+            offset_fh = open(self._offset_file, "r")
+            (self._offset_file_inode, self._offset) = \
+                [int(line.strip()) for line in offset_fh]
+            offset_fh.close()
+            if self._offset_file_inode != stat(self.filename).st_ino or \
+                    stat(self.filename).st_size < self._offset:
+                # The inode has changed or filesize has reduced so the file
+                # might have been rotated.
+                # Look for the rotated file and process that if we find it.
+                self._rotated_logfile = self._determine_rotated_logfile()
+
+    def __del__(self):
+        if self._filehandle():
+            self._filehandle().close()
+
+    def __iter__(self):
+        return self
+
+    def next(self):
+        """
+        Return the next line in the file, updating the offset.
+        """
+        try:
+            line = self._get_next_line()
+        except StopIteration:
+            # we've reached the end of the file; if we're processing the
+            # rotated log file, we can continue with the actual file; otherwise
+            # update the offset file
+            if self._rotated_logfile:
+                self._rotated_logfile = None
+                self._fh.close()
+                self._offset = 0
+                # open up current logfile and continue
+                try:
+                    line = self._get_next_line()
+                except StopIteration:  # oops, empty file
+                    self._update_offset_file()
+                    raise
+            else:
+                self._update_offset_file()
+                raise
+
+        if self.paranoid:
+            self._update_offset_file()
+        elif self.every_n and self.every_n <= self._since_update:
+            self._update_offset_file()
+
+        return line
+
+    def __next__(self):
+        """`__next__` is the Python 3 version of `next`"""
+        return self.next()
+
+    def readlines(self):
+        """
+        Read in all unread lines and return them as a list.
+        """
+        return [line for line in self]
+
+    def read(self):
+        """
+        Read in all unread lines and return them as a single string.
+        """
+        lines = self.readlines()
+        if lines:
+            try:
+                return ''.join(lines)
+            except TypeError:
+                return ''.join(force_text(line) for line in lines)
+        else:
+            return None
+
+    def _is_closed(self):
+        if not self._fh:
+            return True
+        try:
+            return self._fh.closed
+        except AttributeError:
+            if isinstance(self._fh, gzip.GzipFile):
+                # python 2.6
+                return self._fh.fileobj is None
+            else:
+                raise
+
+    def _filehandle(self):
+        """
+        Return a filehandle to the file being tailed, with the position set
+        to the current offset.
+        """
+        if not self._fh or self._is_closed():
+            filename = self._rotated_logfile or self.filename
+            if filename.endswith('.gz'):
+                self._fh = gzip.open(filename, 'r')
+            else:
+                self._fh = open(filename, "r", 1)
+            self._fh.seek(self._offset)
+
+        return self._fh
+
+    def _update_offset_file(self):
+        """
+        Update the offset file with the current inode and offset.
+        """
+        if self.on_update:
+            self.on_update()
+        offset = self._filehandle().tell()
+        inode = stat(self.filename).st_ino
+        fh = open(self._offset_file, "w")
+        fh.write("%s\n%s\n" % (inode, offset))
+        fh.close()
+        self._since_update = 0
+
+    def _determine_rotated_logfile(self):
+        """
+        We suspect the logfile has been rotated, so try to guess what the
+        rotated filename is, and return it.
+        """
+        rotated_filename = self._check_rotated_filename_candidates()
+        if rotated_filename and exists(rotated_filename):
+            if stat(rotated_filename).st_ino == self._offset_file_inode:
+                return rotated_filename
+
+            # if the inode hasn't changed, then the file shrank; this is expected with copytruncate,
+            # otherwise print a warning
+            if stat(self.filename).st_ino == self._offset_file_inode:
+                if self.copytruncate:
+                    return rotated_filename
+                else:
+                    sys.stderr.write(
+                        "[pygtail] [WARN] file size of %s shrank, and copytruncate support is "
+                        "disabled (expected at least %d bytes, was %d bytes).\n" %
+                        (self.filename, self._offset, stat(self.filename).st_size))
+
+        return None
+
+    def _check_rotated_filename_candidates(self):
+        """
+        Check for various rotated logfile filename patterns and return the first
+        match we find.
+        """
+        # savelog(8)
+        candidate = "%s.0" % self.filename
+        if (exists(candidate) and exists("%s.1.gz" % self.filename) and
+            (stat(candidate).st_mtime > stat("%s.1.gz" % self.filename).st_mtime)):
+            return candidate
+
+        # logrotate(8)
+        # with delaycompress
+        candidate = "%s.1" % self.filename
+        if exists(candidate):
+            return candidate
+
+        # without delaycompress
+        candidate = "%s.1.gz" % self.filename
+        if exists(candidate):
+            return candidate
+
+        rotated_filename_patterns = (
+            # logrotate dateext rotation scheme - `dateformat -%Y%m%d` + with `delaycompress`
+            "-[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]",
+            # logrotate dateext rotation scheme - `dateformat -%Y%m%d` + without `delaycompress`
+            "-[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9].gz",
+            # logrotate dateext rotation scheme - `dateformat -%Y%m%d-%s` + with `delaycompress`
+            "-[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]-[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]",
+            # logrotate dateext rotation scheme - `dateformat -%Y%m%d-%s` + without `delaycompress`
+            "-[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]-[0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9].gz",
+            # for TimedRotatingFileHandler
+            ".[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]",
+            # chainRename pattern
+            "_[0-9][0-9]"
+        )
+        for rotated_filename_pattern in rotated_filename_patterns:
+            candidates = glob.glob(self.filename + rotated_filename_pattern)
+            if candidates:
+                candidates.sort()
+                return candidates[-1]  # return most recent
+
+        # no match
+        return None
+
+    def _get_next_line(self):
+        line = self._filehandle().readline()
+        if not line:
+            raise StopIteration
+        self._since_update += 1
+        return line
+
+
+def main():
+    # command-line parsing
+    cmdline = OptionParser(usage="usage: %prog [options] logfile",
+        description="Print log file lines that have not been read.")
+    cmdline.add_option("--offset-file", "-o", action="store",
+        help="File to which offset data is written (default: <logfile>.offset).")
+    cmdline.add_option("--paranoid", "-p", action="store_true",
+        help="Update the offset file every time we read a line (as opposed to"
+             " only when we reach the end of the file).")
+    cmdline.add_option("--every-n", "-n", action="store",
+        help="Update the offset file every n'th time we read a line (as opposed to"
+             " only when we reach the end of the file).")
+    cmdline.add_option("--no-copytruncate", action="store_true",
+        help="Don't support copytruncate-style log rotation. Instead, if the log file"
+             " shrinks, print a warning.")
+    cmdline.add_option("--version", action="store_true",
+        help="Print version and exit.")
+
+    options, args = cmdline.parse_args()
+
+    if options.version:
+        print("pygtail version", __version__)
+        sys.exit(0)
+
+    if (len(args) != 1):
+        cmdline.error("Please provide a logfile to read.")
+
+    if options.every_n:
+        options.every_n = int(options.every_n)
+    pygtail = Pygtail(args[0],