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Table of Contents

Current solution

It looks like (from user's perspective) we miss simplified way of choosing "dressed" Kepler and workflow that will be used to launch ETS. In fact, the same sort of issues will affect Python based workflows.

...

  • release of new FC2K (e.g.: version R4.2.6 this will be transparent for users - they don't need FC2K for day to day usage)
  • release of new Kepler  (e.g. version R5.0.16_v5.2.2)
  • release of all actors (based on tag, e.g.: v5.2.2)
  • release of supplementary components (e.g.: kplots - ETS_4.10b.10_v5.6.0/kplots)
  • release of workflow (e.g.: ETS_v5.2.2.xml)
  • release of autoGui (e.g.: 1.1)

...

User presses Y. Script performs upgrade of all tools installed for the user and starts most recent version of autoGui and most recent version of Kepler. Previous version of user's installation are preserved and it will be possible to go back to this version later.



Preliminary investigation

All the above solutions are keeping the current approach which requires user to have a sort of local install of Kepler (composed of links or of the full sources).

Before going in that direction, we want to check the technical feasibility of running a workflow with a Kepler that remains entirely in public place. 

...

Kepler 

We need to check that running Kepler in such mode is possible, it involves a few actions, mainly on Michal, but with help of others when/where needed:

System variables used by Kepler

At the moment, the way Kepler is executed, can be controlled by the set of environment variables and Java properties

Code Block
_JAVA_OPTIONS                  - this is the heaviest way of altering Java and Kepler. This option makes it possible to alter
                                 default settings of JVM. It overrides everything else.

KEPLER_JAVA_OPTIONS            - equivalent of _JAVA_OPTION however, this variable alters only Kepler
                                 example: setenv KEPLER_JAVA_OPTIONS "-Xss20m -Xms1g -Xmx4g -Dsun.java2d.xrender=false"
                               
KEPLER_DOT                     - points to root director where .kepler and KeplerData directories will be created

PTOLEMYII_DOT                  - points to root director where .ptolemyII directory will be created

KEPLER_WORK_DIR                - points to location where Kepler will be started. This way, it's possible to change
                                 location of current directory (instead of $KEPLER it will be pointed by $KEPLER_WORK_DIR)
                                 alternatively, this value can be passed via: -Dkepler.work.dir=....
                                 
-Duser.home=                   - This variable is passed to Kepler, this way it's possible to change user.home inside Kepler

-Duser.start.dir=              - This variable allows to pass information regarding current directory. It's possible to access
                                 this variable later on by calling System.getProperty("java.property.name")


Preparation for the test

To simulate the case where we run everything from the central installation I am working on a local copy with all the access rights set to read only

Code Block
> chmod a-w kepler

Test installation is here: /gss_efgw_work/work/g2michal/cpt/development/isolated_kepler/kepler 

Running from public installation

First test is related to running Kepler interactively from public install (can Kepler log be stored elsewhere) - I am using copy of: ETS_4.10b.10_v5.2.2 

We have first issue related to local changes inside KEPLER directory

Code Block
> ant run
...
...
  [compile] Compiling itm...

BUILD FAILED
/gss_efgw_work/work/g2michal/cpt/development/isolated_kepler/kepler/build-area/build.xml:56: java.io.FileNotFoundException: ./depcache/itm/dependencies.txt (Permission denied)

The above issue can be solved by running from the place where uses has access rights. For example, running it inside directory where user has write access will result in creating directory deepcache, and Kepler will start

Code Block
> pwd
/gss_efgw_work/work/g2michal/cpt/development/isolated_kepler
> ant -f ant -f kepler/build-area/build.xml run
> tree depcache
depcache
|-- actors
|   `-- dependencies.txt
|-- authentication
|   `-- dependencies.txt
|-- authentication-gui
|   `-- dependencies.txt
|-- component-library
|   `-- dependencies.txt
|-- configuration-manager
|   `-- dependencies.txt
|-- core
|   `-- dependencies.txt
|-- data-handling
|   `-- dependencies.txt
|-- dataone
|   `-- dependencies.txt
|-- dataturbine
|   `-- dependencies.txt
|-- display-redirect
|   `-- dependencies.txt
|-- ecogrid
|   `-- dependencies.txt
|-- event-state
|   `-- dependencies.txt
|-- gui
|   `-- dependencies.txt
|-- io
|   `-- dependencies.txt
|-- itm
|   `-- dependencies.txt
|-- job
|   `-- dependencies.txt
|-- loader
|   `-- dependencies.txt
|-- module-manager
|   `-- dependencies.txt
|-- module-manager-gui
|   `-- dependencies.txt
|-- opendap
|   `-- dependencies.txt
|-- r
|   `-- dependencies.txt
|-- repository
|   `-- dependencies.txt
|-- sms
|   `-- dependencies.txt
|-- ssh
|   `-- dependencies.txt
`-- util
    `-- dependencies.txt


Info
titleinstall_path.txt

There is an issue with install_path.txt  file. It can be solved by adding file use.keplerdata  inside Kepler  installation


There is, an issue with Log4J based logger

Code Block
[compile] Compiling itm...

run:
      [run] JVM Memory: min = 1g,  max = 4g, stack = 20m
      [run] log4j.properties found in CLASSPATH: /gss_efgw_work/work/g2michal/cpt/development/isolated_kepler/kepler/itm/resources/log4j.properties
      [run] log4j:ERROR setFile(null,true) call failed.
      [run] java.io.FileNotFoundException: keplerLog4J.log (Permission denied)

FIXED: I was able to overcome this issue (and at the same time changing work dir to different location) by implementing something like this inside file: kepler/build-area/src/org/kepler/build/Run.java 

Code Block
Java java = new Java();
java.setDir(new java.io.File(System.getenv("KEPLER_WORK_DIR")));

Kepler is started in two phases. First one, responsible for collecting modules and starting another one (workflow execution). This process is maintained by Ant. It is possible to overcome defaults and run the code in any directory (e.g. current one). At the moment, solution is little bit ugly (I am reading location - where Kepler is supposed to be started - from environment).

Running FC2K based actor inside Kepler

Running Kepler interactively with FC2K actors inside the workflow. We have to make sure that current directory can be set to any location outside of the Kepler. We run simple cases, then ETS-like ones, where some might read/write files in current directory

In order to run test case for ETS make sure to follow these steps:

Code Block
# prepare env.
> module load itmenv/ETS_4.10b.10_v5.6.0

# This is the place where your workflow will run.
# Just for a convenience I am creating new directory
# where all the files will be stored. However, it can be
# any location you like
# /tmp
# $ITMWORK
# $HOME
#
# for the whole scenario it really doesn't matter where you run the whole thing.
# However, note that after execution, inside your current directory you will find
# lots of small files. This is why it might be a good idea to start everything inside
# some separate directory - just to not pollute your $HOME

> mkdir $ITMWORK/isolated_kepler_test
> cd $ITMWORK/isolated_kepler_test

# This step is still required, but it may change in the future
> source $ITMSCRIPTDIR/ITMv2 jet

# Note that we are using "artificial" central installation.
# In the future, this location will be replaced with something like
# $SWITMDIR/kepler/trunk/ETS_4.10b.10_v5.6.1/kepler
> setenv KEPLER /gss_efgw_work/work/g2michal/cpt/development/isolated_kepler/ETS_4.10b.10_v5.6.1/kepler

# If you have these files somewhere else, this step is not required.
# If you want to make sure you are working with most recent release of ETS workflow
# I suggest you run this step anyway.
> svn co https://gforge6.eufus.eu/svn/keplerworkflows/tags/ETS_4.10b.10_v5.6.0

# do not go inside $KEPLER!
# This command starts Kepler and it will run it inside your
# current directory.
> $KEPLER/kepler.sh ETS_4.10b.10_v5.6.0/ETS_WORKFLOW.xml

# Once Kepler is opened and you can see the workflow in the canvas, simply execute the workflow

you should be able to execute the whole workflow and see the results as below

Image Added

In case actors create some files (e.g. for internal processing or as intermediate results), these files are no longer created inside $KEPLER. Instead, these are created in current directory - place where you have started Kepler

Code Block
> pwd
/gss_efgw_work/work/g2michal/isolated_kepler_test
> tree . -L 1 -a --charset=ascii
.
|-- EQDSK_COCOS_02_POS.OUT    - these are some files created by workflow (codes inside workflow)
|-- EQDSK_COCOS_13.OUT        -                             -"-
|-- EXPEQ_KEPLER.IN           -                             -"-
|-- EXPEQ.OUT                 -                             -"-
|-- EXPEQ.OUT.TOR             -                             -"-
|-- EXPTNZ.OUT                -                             -"-
|-- NOUT                      -                             -"-
|-- ETS_4.10b.10_v5.6.0       - This is the repository with ETS workflow, kplots, etc.
|-- kepler.log                - These are the logs of kepler.sh
|-- keplerLog4J.log           - These are the logs generated by Kepler via Log4J
|-- .kepler                   - This is the file you would normally find in $HOME
|-- KeplerData                -                     -"-
`-- .ptolemyII                -                     -"-


kepler.log file - one that contains log of Kepler's execution is also created in current directory.

No special actions are needed from user's side. Everything is set up inside kepler.sh script.

Standalone mode

Running these actors in standalone mode (checking the behaviour of the copy of sources/exec from initial place in Kepler to KEPLEREXECUTION/sandbox)

Debug mode

Running these actors in debug mode (checking the behaviour of the copy of sources/exec from initial place in Kepler to KEPLEREXECUTION/sandbox)

Batch mode

Running these actors in batch mode (checking the behaviour of the copy of sources/exec from initial place in Kepler to KEPLEREXECUTION/sandbox)

SBK based execution

Checking sbk execution - with simple workflow and then with ETS workflow

Default location of Kepler based cache files

We have agreed to make current working directory a place where all the local data used by Kepler will be stored.

Use-case - running two different sessions of Kepler

Let's say we want to run two, completely separate sessions of Kepler. In that case, user will do following

Info
titleWe are using already existing features


Code Block
KEPLER_DOT
PTOLEMYII_DOT
KEPLER_WORK_DIR



Code Block
> mkdir experiments
> cd experiments
> mkdir my_firs_experiment
> cd my_firs_experiment
> kepler.sh
... some things are happening ... workflow is started ... done ...
... at the end, user saves his own version of ETS workflow as "workflow.xml"
> cd ..
> mkdir my_second_experiment
> cd my_second_experiment
> kepler.sh
... some things are happening ... workflow is started ... done ...
... at the end, user saves his own version of ETS workflow as "workflow.xml"
> cd ../..
> tree experiments
experiments
|-- my_first_experiment
|   |-- KeplerData
|   |   `-- workflow.xml
|   |-- kepler.log
|   |-- keplerLog4J.log
|   |-- .local
|   |-- .ptolemyII
|   `-- SOME_FILE_CREATED_BY_PHYSICS_CODE
`-- my_second_experiment
    |-- KeplerData
    |   `-- workflow.xml
    |-- kepler.log
    |-- keplerLog4J.log
    |-- .local
    |-- .ptolemyII
    `-- SOME_FILE_CREATED_BY_PHYSICS_CODE

At the very end, all the local data end up in a location where Kepler was started. There are no references to $HOME or $KEPLER or some other locations. Everything is stored in the directory where Kepler was started.

...

First implementation of centrally protected Kepler release

This section contains very simple sample of dressed Kepler that is write protected. To get it running do following

Code Block
> mkdir -p ~/tmp/experiments/my_first_execution
> cd ~/tmp/experiments/my_first_execution

# This workflow simulates ETS workflow.
# It uses actor that is centrally installed.
> cp ~g2michal/public/nocpo_workflow.xml

> setenv KEPLER /gw/switm/kepler/trunk/R6.0.7/kepler
> $KEPLER/kepler.sh -cwd

# Open file ~/tmp/experiments/my_first_execution/nocpo_workflow.xml and run the workflow

Using centrally installed Kepler with sbk

sbk.sh was adapted to support centrally installed releases of Kepler. In order to use it one must do following:

Code Block
> module load itmenv
> setenv KEPLER /gw/switm/kepler/trunk/R6.0.7/kepler
> module switch scripts/R4

# /gss_efgw_work/work/g2michal/cpt/issues/batch_and_central_kepler/Test.xml
# contains sample workflow that we can use for testing

# $ITMSCRIPTDIR/batch_submission/wrapper-central.sh
# contains modified wrapper script that supports centrally installed Kepler
# it should be backward compatible with regular Kepler

> sbk.sh -name=test_batch_central \
 -file=/gss_efgw_work/work/g2michal/cpt/issues/batch_and_central_kepler/Test.xml \
 -marco:mem=10 \
 -marco:select=1 \
 -marco:cpus=1 \
 -marco:walltime=00:10:00 \
 -marco:block=false \
 -marco:queue=gw \
 -wrapper=$ITMSCRIPTDIR/batch_submission/wrapper-central.sh

Using centrally installed Kepler with sbk via ets module

Code Block
> module purge
> module load cineca
> module load ets

> sbk.sh -name=test_2 \
  -file=$ETS_HOME/ETS5.xml \
  -marco:mem=10 \
  -marco:select=1 \
  -marco:cpus=1 \
  -marco:walltime=00:10:00 \
  -marco:block=false \
  -marco:queue=gw


Kplots and other scripts 

We need to check that these scripts (currently copied within Kepler sources when Kepler is being dressed-up) can be stored outside Kepler (public place, versioned, and made available through module) and referenced from the workflow: kplots module will set up a KPLOTS_HOME which points to dir containing all the scripts, we need to check that reading this variable from the workflow will work correctly (getenv). Action on Olivier to create public install of kplots with modules, and on Dmitriy to update ETS workflow to link to Kplots scripts using the env variable set by module. These actions do no depend on Kepler actions above.


Info
titleAcknowledgement

This work has been carried out within the framework of the EUROfusion Consortium and has received funding from the Euratom research and training programme 2014-2018 under grant agreement No 633053.The scientific work is published for the realization of the international project co-financed by Polish Ministry of Science and Higher Education in 2019 and 2020 from financial resources of the program entitled "PMW"; Agreement No. 5040/H2020/Euratom/2019/2 and 5142/H2020-Euratom/2020/2”.