Thermodynamic laws

Three basic laws of thermodynamics

1) The first law of thermodynamics is a version of the law of conservation of energy, adapted for thermodynamic systems. The law of conservation of energy states that the total energy of an isolated system is constant; energy can be transformed from one form to another, but cannot be created or destroyed. The first law is often formulated by stating that the change in the internal energy of a closed system is equal to the amount of heat supplied to the system, minus the amount of work done by the system on its surroundings. Equivalently, perpetual motion machines of the first kind are impossible.

internal energy change of system   =   heat supplied to system

                                                                -  work done on ENV by system

2) The second law of thermodynamics states that

in every natural thermodynamic process the sum of the entropies of all participating bodies is increased.

In the limiting case, for reversible processes this sum remains unchanged.

The second law is an empirical finding that has been accepted as an axiom of thermodynamic theory. Statistical thermodynamics, classical or quantum, explains the law.

3) The third law of thermodynamics is sometimes stated as follows, regarding the properties of systems in equilibrium at absolute zero temperature:

The entropy of a perfect crystal at absolute zero is exactly equal to zero.

Entropy

In thermodynamics, entropy (usual symbol S) is a measure of the number of specific ways in which a thermodynamic system may be arranged, commonly understood as a measure of disorder.

According to the second law of thermodynamics the entropy of an isolated system never decreases; such a system will spontaneously proceed towards thermodynamic equilibrium, the configuration with maximum entropy.

Systems that are not isolated may decrease in entropy, provided they increase the entropy of their environment by at least that same amount.

Since entropy is a state function, the change in the entropy of a system is the same for any process that goes from a given initial state to a given final state, whether the process is reversible or irreversible. However, irreversible processes increase the combined entropy of the system and its environment.

Work

In physics, a force is said to do work if, when acting on a body, there is a displacement of the point of application in the direction of the force. For example, when a ball is held above the ground and then dropped, the work done on the ball as it falls is equal to the weight of the ball (a force) multiplied by the distance to the ground (a displacement).

MAG ecflow jobs

MAG ecflow job:

1. admin  ( /ecfmag/ecfnets/scripts/admin/mag )

JMAG_CKQUOTA @ wcoss (mag_ckquota.ecf @ ecf1)

export job="jmag_ckquota"

export pid=$$

export DATA=${DATAROOT}/${job}.${pid}

rm -rf $DATA

mkdir -p $DATA

cd $DATA

$SCRIPTSmag/exmag_checkquota.sh.ecf

If run on gyre :  

        $  /usr/lpp/mmfs/bin/mmlsquota    -j    nco-sib    gpfs-gd2

if run on tide :    

        $  /usr/lpp/mmfs/bin/mmlsquota    -j   nco-sib    gpfs-td2

cd /tmpnwprd1

rm -rf $DATA

log file : /nco/sib/magdev/com/output/prod/today/mag_ckquota.o%J

JMAG_CLEANUP @ wcoss (mag_cleanup.ecf @ ecf1)

export job="jmag_cleanup"

export pid=$$

export DATA=${DATAROOT}/${job}.${pid}

rm -rf $DATA

mkdir -p $DATA

cd $DATA

#1) clean up wcoss

$SCRIPTSmag/exmag_cleanup.sh.ecf

# Clean up GIF files : /nco/sib/magdev/com/mag/test/gifs

    find ./${i} -mindepth 1 -maxdepth 1 -mmin +1560 -type d

    find ./${i} -mindepth 1 -maxdepth 1 -mmin +1560 -type d -exec rm -rf '{}' ';'

# Clean up status files : /nco/sib/magdev/com/mag/test/status

    find ${LOG_DIR} -mindepth 1 -maxdepth 1 -mtime +3 -type d

    find ${LOG_DIR} -mindepth 1 -maxdepth 1 -mtime +3 -type d -exec rm -rf '{}' ';'

# Removing  log files : /nco/sib/magdev/com/output/prod/today

    find ${LOG_DIR} -mindepth 1 -maxdepth 1 -mtime +3 -type d

    find ${LOG_DIR} -mindepth 1 -maxdepth 1 -mtime +3 -type d -exec rm -rf '{}' ';'

# Clean up tmp dirs : /nco/sib/magdev/tmpnwprd1

    find ${TMP_DIR} -mindepth 1 -maxdepth 1 -mtime +3 -type d

    find ${TMP_DIR} -mindepth 1 -maxdepth 1 -mtime +3 -type d -exec rm -rf '{}' ';'

#2) clean up rzdm

/usr/bin/ssh -t -t  mag@ncorzdm.ncep.noaa.gov "bash /home/people/nco/mag/bin/exmag_cleanup_test.sh.ecf"

cd /tmpnwprd1

rm -rf $DATA

log file : /nco/sib/magdev/com/output/prod/today/mag_cleanup.o%J

JMAG_SETUP @ wcoss (ecmag_maintain.ecf  @ ecf1)

Purpose : Create sub-dir like 20150915 and create symbolic link "today" linked to the current day.

$ cd  /nco/sib/magdev/com/output/prod

$ ln   -vTsf   $out_dir/prod/$PDY $out_dir/prod/today

ln     [OPTION]...   [-T]     TARGET    LINK_NAME

-v : verbose, print name of each linked file

-T : treat  LINK_NAME  as a normal file

-s : make symbolic links instead of hard links

-f : force, remove destination files

export DATA=${NWROOT}/tmpnwprd1/JMAG_SETUP.${pid}

mkdir -p $DATA

cd $DATA

env

${NWROOT}/mag.${mag_ver}/scripts/exmag_setup.sh.ecf

${NWROOT}/mag.${mag_ver}/scripts/exMagDirClean.sh.ecf

cd ${NWROOT}/tmpnwprd1

rm -rf $DATA

exit

Log file :  /nco/sib/magdev/com/output/prod/today/ecmag_maintain.o%J

2. mag processor

( /ecfmag/ecfnets/scripts/mag/mag_processor/${model}/mag_${model}_processor.ecf  @ ecf1)

JMAG @ wcoss

export job=${job:-jmag.${MODEL}}

export pid=$$

export DATA=${DATAROOT}/${job}.${pid}

rm -rf $DATA

mkdir -p $DATA

cd $DATA

export jlogfile=${jlogfile:-$COMROOT/logs/jlogfiles/jlogfile.${job}.${pid}}

if [ "$hurr_model" == "yes" ]; then

mag_script=exmag_processor_hurr.pl

else

mag_script=exmag_processor.pl

fi

${SCRIPTSmag}/${mag_script}      ${MAGPROCPL_FLAGS}

msg="JOB $job ENDED NORMALLY."

postmsg $jlogfile "$msg"

rm -rf $DATA

date

Eg: /ecfmag/ecfnets/scripts/mag/mag_processor/gfs/mag_gfs_processor.ecf

export MODEL=gfs

export MP_CMDFILE=poe_script

export HOMEmag=$NWROOT/mag.$mag_ver

$HOMEmag/jobs/JMAG

3.  send2web

JSNDMAG2WEB

export job=${job:-jmag.${MODEL}}

export pid=$$

export DATA=${DATAROOT}/${job}.${pid}

rm -rf $DATA

mkdir -p $DATA

cd $DATA

export jlogfile=${jlogfile:-$COMROOT/logs/jlogfiles/jlogfile.${job}.${pid}}

$SCRIPTSmag/exsendmag2web.sh.ecf   $MODEL   $TABLEDIR/$TABLE   $transfer_file   $yyyymmdd $cycle

if [ "${MAG_TRANSFER}" = "ON" ]; then        # If this is not running in development...

$HOMEmag/scripts/exmag_status_sync.sh.ecf

fi

cd ${BASE_DIR}/tmpnwprd1

rm -rf $DATA

Eg: /ecfmag/ecfnets/scripts/mag/mag_send2web/gfs/ecmag_sync_gfs.ecf

export MODEL=GFS

export TABLE=MAG_sync_table.tbl

export ncorzdm_username=mag;

export HOMEmag=$NWROOT/mag.$mag_ver;

$HOMEmag/jobs/JSNDMAG2WEB

rsync in exsendmag2web.sh.ecf :

/usr/bin/rsync -v -v   --rsh="/usr/bin/ssh -c arcfour128,aes128-cbc,arcfour,aes128-ctr,blowfish-cbc -o macs=hmac-md5,hmac-md5-96 -o compression=yes"     --stats   --timeout=30     --update  /nco/sib/magdev/com/mag/test/gifs/gfs/20151001/12/{allow.cfg,index.php}     mag@ncorzdm:/home/www/nco_mag/test_data/gfs/20151001/12

rsync flag description:

-v : increase verbosity, the more -v given, the more info will be printed.

--rsh : specify remote shell to use.

--stats : give some file transfer status

--update : force rsync to skip any files which exist  on the destination and have a modified time newer than source file.

/nco/sib/magdev/nwtest/mag.trunk_726/scripts/exsendmag2web.sh.ecf    

GFS

/nco/sib/magdev/nwtest/mag.trunk_726/fix/MAG_sync_table.tbl

/nco/sib/magdev/com/mag/test/status/transfer/gfs_2015100112_69_133_153.transfer

20151001

12

How to switch host where ecflow submit jobs to?

1. $  ssh -Y   Deyong.Xu@cpecflow1.ncep.noaa.gov
2. $  ecflowview &
3. from the ecFlow viewer:
1. halt   (right-click on MAG, choose halt)
2. wait for jobs to bleed off and go to 4. Or proceed with c and d
3. set to complete (right-click on each, choose set complete):
1. ecmaintain
2. rsync_requeue
3. mag_cleanup
4. Kill all the jobs on tide / gyre as mag.dev account.
1. $  sudo  -u mag.dev -i
2. $  bjobs  -u mag.dev
3. $  bjobs  -u mag.dev | grep devhigh | awk '{print "bkill", $1}'
4. (Now, cut and paste the results of step iii. to actually kill the jobs)

1. $  sudo -u mag.dev -i  ( sudo to mag.dev account on cpecflow1 server )
2. $  vi  /home/mag.dev/etc/prodmachinefile    and switch the order of the wcoss host names (the development machine should be the first one)
3. from the ecFlow viewer:

1. restart (right-click on MAG, choose restart)
2. check each task, verify that it is queue, and the next time to run is after the current time (click on task, click on “i” icon on upper right bar, choose tab “Why”, and examine TASK line)

How make hidden transfer file into visible and trigger processing event in ecflow?

-----------------------------------------

 “exmag_processor.pl”    

-----------------------------------------

$transfer_file_hidden="${Config::status_dir}/transfer/.${model}_${date}${cycle}_${job}_${main::transfer_seq}_${random}.transfer";

if (! open ($trans_filehandle, "> $transfer_file_hidden")) {

    logmsg($Config::fatal, "Error opening transfer file: $transfer_file_hidden: $!");

    return 1;

}

 logmsg($Config::info, "Poe job completed successfully, so make the transfer file ${transfer_file} visible:");

 if (! rename    $transfer_file_hidden,    $transfer_file) {

      logmsg($Config::fatal, "Error renaming the hidden transfer file to visible name:  

                  ${transfer_file}");

        return 1;

 }

if (! $main::development_mode) {   # when not running at the command prompt

       # dxu : set the event “processing” to be true in the corresponding model *.ecf .

        `ecflow_client    --event     processing`;  

 }

Event and Trigger

Event:

The event keyword assigns an event to the task currently being defined. Only tasks can have events and they can be considered as an attribute of a task. There can be many events and they are displayed as nodes.

An event has a number and possibly a name. If it is only defined as a number, its name is the text representation of the number without leading zeroes. For example, event 007 can be accessed as event 7 or as event 007. Event's numbers must be positive and their name can contain only letters and digits. The use of letters is optional; the event name can consist simply of digits.

eg:

task x

event 1                 # Can only be referred to as x:1

event 2  prepok  # Can only be referred to as x:prepok

event 3  99           # This is asking for trouble!

real MAG example:

family ghm

task mag_ghm_full_processor

 event   1    processing         # dxu:  1 is useless ;   processing = false

 time 00:02 23:52 00:10

Trigger:

The purpose of an event is to signal partial completion of a task and to be able to trigger another job which is waiting this partial completion.

eg:

suite x

family f

task t1

event  foo

task t2

trigger  t1:foo == set   # foo = set ; foo=true

                                    #t1:foo is relative path.  

Three steps to combine event and trigger :

1) Assign an event to a task.

task   create_a_file

    event      event_A         # event name : event_A ,    event_A = false .

2) Modify the task to change the event value to true.

 In  task  create_a_file,

        ecflow_client    --event    event_A   # command "ecflow_client  --event" sets  

                                                                 # event_A = true

3) Task  copy_a_file  checks value of event_A of task create_a_file and will run if event_A = true.

task copy_a_file

       trigger   create_a_file: event_A          # check event_A’s value.

ecflow system:  cpecflow1.ncep.noaa.gov

/ecfmag/ecfnets/defs

1. Directory structure:

(note : use “admin” for demo. )

admin.def

Purpose:

1. set ENV variables using keyword edit.
2. set cron schedule.

suite admin

 repeat day 1

 edit ECF_HOME '/ecfmag/ecfnets/scripts'

 edit ECF_INCLUDE '/ecfmag/ecfnets/scripts'

 edit ECF_OUT '/ecfmag/ecfnets/output'

 edit ECF_TRIES '1'

 edit ECF_FILES '/ecfmag/ecfnets/scripts'

 edit ECF_JOB_CMD '%ECF_JOB% 1> %ECF_JOBOUT% 2>&1'

 family mag

    task mag_requeue

     cron 00:14 23:49 00:10

##    task rsync_requeue

##      time 00:14 23:49 00:10

    task mag_cleanup

     edit ECF_JOB_CMD '/ecfmag/ecfutils/unixsubmit %ECF_JOB% %ECF_JOBOUT% ibmsp'

     edit ECF_PASS 'FREE'

     time 00:14

    task ecmag_maintain

    edit ECF_JOB_CMD '/ecfmag/ecfutils/unixsubmit %ECF_JOB% %ECF_JOBOUT% ibmsp'

    edit ECF_PASS 'FREE'

    time 00:07

    task mag_ckquota

     edit ECF_JOB_CMD '/ecfmag/ecfutils/unixsubmit %ECF_JOB% %ECF_JOBOUT% ibmsp'

     edit ECF_PASS 'FREE'

     cron 00:05 23:49 01:00

 endfamily

endsuite

mag_requeue.ecf

…..

python ${pythondir}/node_status.py | grep complete  >${magout}/mag_list

for model in `cat ${magout}/mag_list | awk -F" " '{print $1}'`

do

  echo

  echo "JOB IS COMPLETE - REQUEUE-ING TASK: $model"

  echo

  ecflow_client --requeue force $model

  export err=$?

  if [ $err -ne '0' ]

  then

    ecflow_client --abort="ecflow_client --force FAILED: $model NOT requeued"

  fi

done

if [ -s ${magout}/mag_list ]

then

  echo

  echo "THE FOLLOWING HAVE BEEN REQUEUED:"

  cat ${magout}/mag_list

  echo

fi

rm -f ${magout}/mag_list

date

if test $err -eq '0'

then

  ecflow_client --complete

else

  ecflow_client --abort

fi