TRANSP Production System for PPPL users

First time users see info on obtaining access to TRANSP data in MDSplus.
For details see Transp Unix Mdsplus Implementation
To setup your envirenment to run TRANSP on the unix cluster:
- On portals
  - module load ntcc
    See Setup for details.


Note: TRANSP runs are now stored in MDSplus Server TRANSPGRID.PPPL.GOV
      Tree = TRANSP_<TOK>

If you are on the unix cluster, runs are also in $ARCDIR/<TOK>/<yy>
IDL users see Accessing PPPL's TRANSP data in MDSplus with IDL

Getting a Proxy

Users can automatically renew their proxy at login by sourcing below scripts:

at PPPL

c-shell users add to:

$HOME/.cshrc:

if ($?TRANSP_LOCATION) then
   source $TRANSP_LOCATION/fusiongrid_proxypath.csh
endif

$HOME/.login:

 source $TRANSP_LOCATION/fusiongrid_access.csh

bash users add to:

$HOME/.bashrc:

. $TRANSP_LOCATION/fusiongrid_proxypath.sh

$HOME/.bash_profile:
```
. $TRANSP_LOCATION/fusiongrid_access.sh
```

GA
- define environment variable TRANSP_LOCATION = /c/source/ntcc/etc
- add /c/source/ntcc/bin and /c/source/ntcc/etc to your $PATH
- follow above examples for PPPL
other Sites
- install NTCC module tr_star or tr_client
- define environment variable TRANSP_LOCATION = $PREFIX/etc
- add $PREFIX/bin and $PREFIX/etc to your $PATH
  ($PREFIX is where you installed the software)
- follow above examples for PPPL
If your user name is different from your grid name
setenv FUSIONGRID_ACCESS_ARGS "--username=<gridname>"
For details see FusionGrid access scripts

Namelists

TR.DAT and TR.INF files are in $TRINF/<TOK>/<yy>

Basic Scripts

Note: tr_start and tr_send may be run from xtranspin

tr_start <runid>		
-----------------			
must be run from directory where Namelist is
creates MDSplus tree for input data
writes <runid>.REQUEST file
			
uses environments
  TR_EMAIL
  EDITOR

  MDS_TRANSP_SERVER    transpgrid.pppl.gov  (old PPPL Server)
                       _transpgrid.pppl.gov (FusionGrid Server)	

  MDS_TRANSP_TREE      (do NOT specify if PPPL user)

		
			
tr_send  <runid> [trdat] 
--------------------------			
must be run from same directory as tr_start
	queues run on petrel cluster
option: 
     trdat:   run trdat only

		
tr_cleanup <runid> <tok> 
-------------------------		
queues request to cleanup all traces of a run
if the run is still active, it will be aborted
		

tr_look <runid> [tok] [archive] 
---------------------------------		
writes interim MDSplus output into TRLOOK_<TOK> on transpgrid.pppl.gov

options: 
     archive:   for aborted and active runs
	        archive run "as is" on final destination
		if the run is still active, it will be aborted
     nomdsplus: generate CDF file only ( in $LOOKDIR/<TOK>)
	        If not PPPL: only use with archive

tr_halt <runid> <tok> [t <time>] 
---------------------------------------------		
suspend a run immediately, or at t = <time>

Steering a Run

It is now possible to halt and restart a TRANSP run under a new, or the same runid with modified input data.
The procedure for this is:

tr_halt <runid> <tok> [t <time>]
modify Namelist and/or Ufiles
rs_newrun
interactive program to verify, fixup Namelist
1. specify "old run"
  - at PPPL (non-globus)
    switch to "File Mode"
    enter $HALTDIR/<tok>/<runid> for "directory of old run"
  - Globus Users
    switch to "MDS Mode"
    enter Server, Tree and Runid
2. specify "new run"
  switch to "File Mode"
tr_start <runid>
tr_send <runid>
The Monitor will show the old runid under "steering".

Monitor Runs

Web Sites
Logfiles on disk
- completed runs:
  $LOGDIR/runlog/<TOK>/
- aborted runs:
  $RESULTDIR/<TOK>/<runid>/

Looking at Output

Interim output / Aborted runs

rplot t s transpgrid.pppl.gov t trlook_<tok> y <tok>.<yy> q <runid>
 or 
cd $LOOKDIR/<TOK>
rplot <runid>

Completed Runs

rplot  t  y  <tok>.<yy>  q  <runid>
  --or-- newer runs are on unix cluster in $ARCDIR
rplot  d  '$ARCDIR/<tok>/<yy>'  q  <runid>

Special Output (other then .CFD)

*.DATA* and *.XML files are in $ARCDIR/<TOK>/<yy>

Default Mdsplus Trees are:
- On Server transpgrid.pppl.gov
  - TRANSP_<TOK> for "temporary" runs
    these runs may be archived on demand (tr_save)
  - TRLOOK_<TOK> for "interim" output

To export a TRANSP run, you made at PPPL, to another Site, you run export_run to produce a tar file containing the mdsplus tree files, which you then can copy to the remote site. There will be site-specific rules, how to deal with it at the remote site. Very likely you need to assign a different runid/mdsplus-id. Currently this is only supported by GA.

At PPPL:

    export_run
    usage: export_run <runid> <tok> <year> [remote tree name]

    e.g: export_run 12345A01 d3d 94
         will produce /tmp/$USER/123450101.tar.gz

    e.g: export_run 12345A01 iter 06
         will produce /tmp/$USER/12e45A01.tar.gz

Copy the tar file to the remote site, using scp or globus-url-copy.
At remote site:
- At GA:
  Use the script archiverun, to generate a GA runid and add the run to the database.
  Unpack /u/aswath/archivetransprun.tar and follow the instructions in README.TXT

Import a Run

A TRANSP run made on another Site, that is accessible via MDSplus, can be imported to PPPL, but needs to be run from a privileged account.

as pshr#### with a proxy, run import_run
e.g: import_run 12345A01 _atlas.gat.com transp
import_run will
1. check if run already exists
2. extract input and output data from remote mdsplus Server
3. create a tree at PPPL
4. write all data into tree
5. instruct you how to run import_finish
as pshare, run import_finish

Scripts for Experts

To overwrite PPPL settings,e.g. to use globus, send input as tar file, etc. use below scripts.
See also Available PPPL Tools for Grid Users

tr_start.pl <server> <tree> <runid> [[<mdsid>, silent] [ nocreate | start_remote | nomdsplus | sendtree ][ R3 | R4 ]]
to run instead of tr_start
Examples:
- standard PPPL - pretend to be a grid user
  tr_start.pl _transpgrid.pppl.gov transp_tftr 12345A01
  will ask if you want a tar file
- without creating a mdsplus tree, for sending Ufiles, fetching tree
  tr_start.pl PPPL PPPL 12345A01 nocreate
- without creating a mdsplus tree, tree is created by TRANSP on remote client
  tr_start.pl _transpgrid.pppl.gov transp_tftr 12345A01 start_remote
- no MDSplus, for sending Ufiles, fetching output
  tr_start.pl NONE NONE 12345A01 nomdsplus
- create Tree, for sending tree files, receiving tree
  tr_start.p _transpgrid.pppl.gov transp_tftr 12345A01 sendtree
tr_send_pppl.pl <runid> <tok> [trdat] [FAST | SLOW],[ UFILE | CREATE | NOMDSPLUS | TREES]
to run instead of tr_send
Examples:
- pretend to be a grid user (standard or tar file)
  tr_send_pppl.pl 12345A01 tftr
- to send to transpcomp (instead of transpgrid)
  tr_send_pppl.pl 12345A01 tftr FAST
- NO tree was created by client, Tree will be created by PPPL on Client's Server
  tr_send_pppl.pl 12345A01 tftr UFILE
- NO tree was created, send Ufiles, PPPL creates local tree, to be fetched
  tr_send_pppl.pl 12345A01 tftr CREATE
- NO MDSPLUS, send Ufiles, fetch CDF & output
  tr_send_pppl.pl 12345A01 tftr NOMDSPLUS
- Send Tree Triplets to PPPL, to be returned with Output
  tr_send_pppl.pl 12345A01 tftr TREES
tr_send_cleanup <runid> <tok>
to run instead of tr_cleanup
submitting a run manually
See Submitting a Collaboratory Run