title: ‘DDT on pinklady’ date: 2022-05-22 permalink: /posts/2022/05/DDT on Pinklady/

• To connect pinklady, the user should type “ssh libi292@pinklady.pnl.gov” in terminal.

I have installed the (master) development version of ATS on pinklady along with DDT as a debugger (the trial license is good through June 24). We must run the master branch as the linkage to PFLOTRAN actually runs (though I have yet to verify that it is correct). Please update all input decks to use it.

To run ats:

• ssh to pinklady
• cd /software/hamm495
• (alt ats-master env_ats_master.sh lib)
• source env_ats_master.sh
• 

If you can not do source with an error source: not found. Please check the shell you used by env | grep SHELL. Sometime, it will be sh not bash. Therefore, you need to swith sh to bash. or create a new file for sh.

• chsh -s /bin/bash libi292
• which mpirun
• ensure that the output from which mpirun prints “/software/hamm495/alt/bin/mpirun”

• navigate to the directory with the input file ats –xml_file=filename.xml

• Download ats-regression-tests-master.zip and unzip it on pinklady

• To debug ats through DDT:

• V1. Install VcXsrv (https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fvcxsrv%2F&data=05%7C01%7Cbing.li%40pnnl.gov%7C3c5e1effa41c4fd8ce4708da3440c77b%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637879750065872906%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8OdFdF%2BHpedsiULh0CvgDBv1Fa9tNEg1ot%2FDFIBxFRs%3D&reserved=0) on your Window machine; Xming will not work) (It did not work for my case)
• V2. download Mobaxterm (https://mobaxterm.mobatek.net/download.html)
• Start the VcXsrv xserver
• ssh to pinklady cd /software/hamm495
• source env_ats_master.sh
• which mpirun
• ensure that the output from which mpirun prints “/software/hamm495/alt/bin/mpirun”
• navigate to the directory with the input file ddt & # Click on ‘Run’
• Specify the location of the executable in the “Application” field (e.g. /software/hamm495/ats-master/amanzi-install-master-Debug/bin/ats)
• Specify the command line arguments in the “Arguments:” field (e.g. –xml_file=filename.xml) # Ensure that the checkbox to the left of Runtime is checked (this enables MPI)
• Click Run

Please let me know if there are mistakes in these instructions or questions. You must source the env_ats_master.sh file as it sets correct environment variables.