TRANSP Production System

All users need a PPPL transp account in addition to a user account.
First time users see info on obtaining access to TRANSP data in MDSplus.
For details on MDSplus access see Transp Unix Mdsplus Implementation
At PPPL
- PPPL users do NOT need a Grid Proxy.
- To setup your envirenment to access TRANSP output or submit runs:
  - On portals
    - module load intel/2015.u1
    - module load ntcc/tshare
      See Setup for details.
- TRANSP runs are stored on the
  - 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
Off Site
- At GA
  - To get PPPL tools:
    source /c/transp/etc/transp_setup.csh
- At MIT
  - To get PPPL tools:
    - bash users
      - export NTCCHOME=/usr/local/cmod/codes/transp/pppl_tools
      - source $NTCCHOME/transp_setup.bash
    - tcsh users
      - setenv NTCCHOME /usr/local/cmod/codes/transp/pppl_tools
      - source $NTCCHOME/transp_setup.csh
Index to Details
Getting a Proxy

PPPL users do not need a Grid Proxy.

Users can automatically renew their proxy at login by sourcing below scripts:
- off-site users
  - tcsh users add to the end of:
    - $HOME/.cshrc:
```
if ($?TRANSP_LOCATION) then
   source $TRANSP_LOCATION/fusiongrid_proxypath.csh
endif
```
    - $HOME/.login:
```
 source $TRANSP_LOCATION/fusiongrid_access.csh
```
  - bash users add to the end of:
    - $HOME/.bash_profile:
```
if [ -f $TRANSP_LOCATION/fusiongrid_access.sh ]; then
   . $TRANSP_LOCATION/fusiongrid_access.sh
fi
```
    - $HOME/.bashrc:
```
. $TRANSP_LOCATION/fusiongrid_proxypath.sh
```
- at GA
  - tcsh users:
    - source /c/transp/etc/transp_setup.csh
    - follow above instructions for off-site users
- other Sites
  - If you installed NTCC module tr_start 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)
  - You can download the scripts here
    then extract scripts into $TRANSP_LOCATION.
  - follow above examples for off-site users

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> [tshare] [<pbs-queue>] 		
-----------------			
must be run from directory where Namelist is
creates MDSplus tree for input data
writes <runid>.REQUEST file
			
uses environments
  TR_EMAIL	       Your e-mail address	

  EDITOR	       Your favourite editor

  MDS_TRANSP_SERVER    transpgrid.pppl.gov  (for PPPL Users)
                       NONE (for non-PPPL if not using mdsplus)
  
  MDS_TRANSP_TREE      (do NOT specify if PPPL user or nomdsplus)

		
			
tr_send  <runid> 
--------------------------			
must be run from same directory as tr_start
	submits run to pppl pbs queue
	(for non-PPPL via globus-job-submit)


For non-PPPL, if not using mdsplus:
tr_send_pppl.pl  <runid> <TOK> NOMDSPLUS 

		
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

This is disabled.

Monitor Runs

Web Sites
- PPPL Grid Monitor
- logfile / tail of active run
Logfiles on disk
- completed runs:
  $LOGDIR/<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-- at PPPL reading from disk:
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] [xtar | noxtar | nocreate | nomdsplus | sendtree] [ -nbi_np <np> ] [ -alt <username> | tshare ] [-q <pbs-queue>]
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.pl transpgrid.pppl.gov transp_tftr 12345A01 sendtree
tr_send_pppl.pl <runid> <tok> [ -s ] [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) (disabled)
  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