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1. Profile should be established this umask  will be required later in the stack install as will the ulimit  settings
   

   Code Block
   language shell
   # .bash_profile umask 0022 ulimit -S -s unlimited if [[ ~/.bashrc ]]; then . ~/.bashrc fi cd ~

   
   
2. Follow the instructions for Prerequisites for Ubuntu (one-off):  https://spack-stack.readthedocs.io/en/latest/NewSiteConfigs.html#prerequisites-ubuntu-one-off 
   1. When installing the gcc compilers, if you would like to make sure you install version 13
      

      Code Block
      language shell
      # Compilers apt install -y gcc-13 g++-13 gfortran-13 gdb

3. Follow the instructions for creating a new environment:   https://spack-stack.readthedocs.io/en/latest/NewSiteConfigs.html#newsiteconfigs-linux-createenv 
   1. Step 1: For now use the 1.9.0 release branch when cloning spack-stack (Place the spack-stack clone in you home directory.)
      

      Code Block
      language shell
      git clone -b release/1.9.0 --recurse-submodules https://github.com/jcsda/spack-stack.git cd spack-stack # Sources Spack from submodule and sets ${SPACK_STACK_DIR} source setup.sh

   2. Step 2: Create a unified-dev environment - complete step following newsiteconfigs 
      

      Code Block
      language shell
      spack stack create env --site linux.default --template unified-dev --name unified-env.gcc --compiler=gcc cd envs/unified-env.gcc/ spack env activate [-p] .

   3. Step 3: follow newsiteconfigs 
   4. Step 4: follow newsiteconfigs 
   5. Step 5: Check that “spack compiler find --scope system” reports version 13.x)
   6. Step 6: follow newsiteconfigs 
   7. Step 7:  Use openmpi 5.0.5, can skip  add of mpich.  

      1. 1. Code Block
            language shell
            gcc --version # insert your gcc version here (example 13.3.0) spack config add "packages:all:compiler:[gcc@13.3.0]"

         2. Code Block
            language shell
            # openmpi v5.0.5 skip mpich install spack config add "packages:all:providers:mpi:[openmpi@5.0.5]"

   8. Step 8: follow newsiteconfigs 
   9. Step 9: skip - if new Orbstack 
   10. Step 10: skip - if new Orbstack
   11. Step 11: concretize and install: follow newsiteconfigs 
   12. Step 12 - 14: follow newsiteconfigs 

Building jedi-bundle and running skylab

1. Follow instructions in the JEDI documentation
   1. HOST=localhost
   2. COMPILER=gnu
   3. And uncomment/modify the module command lines so they look like
      1. module purge
      2. module use /home/steveherbener/spack-stack/envs/ue-gcc/install/modulefiles/Core
      3. module load stack-gcc/13.3.0
      4. module load stack-openmpi/5.0.5
      5. module load stack-python/3.11.7
   4. https://jointcenterforsatellitedataassimilation-jedi-docs.readthedocs-hosted.com/en/latest/using/running_skylab/running_skylab.html
   5. In the jedi-tools provided setup.sh script, set:
2. You will need to setup the mysql and r2d2 localhost. I followed the instructions in the R2D2 repo.
   1. sudo su
   2. mysql -u root
   3.   use mysql;
   4.   alter user ‘root’@’localhost’ identified with mysql_native_password by ‘’;
   5.   flush privileges;
   6.   exit;   # exit mysql
   7. exit  # exit sudo
   8. https://github.com/JCSDA-internal/r2d2/blob/develop/TUTORIAL.md#prerequisites-for-hpc-macos-and-aws-single-nodes
   9. To start the mysql server use: sudo service mysql start
   10. I had trouble getting the local database setup script to run due to permission problems with logging into the mysql server as ‘root’@’localhost’. I had to do the following to get this working. What this does is remove the password on the root user in the mysql server.
3. Initially, I could not get the ecflow UI to connect to the mac display. I had to follow the instructions here to get this working :
   1. Step 2 in these instructions didn’t work for me. What you want to do is simply copy the contents of the ~/.ssh/id_rsa.pub file on your mac home directory into the ~/.ssh/authorized_keys file on your OrbStack (ubuntu) home directory.
https://github.com/orbstack/orbstack/
4. (https://github.com/orbstack/orbstack/issues/139#issuecomment-1595364746
Take note in Step 5 of the manner in which you connect to the OrbStack machine from the mac. Every time you access the OrbStack machine you will need to open a terminal on the mac (not through ObsStack) and run the given ssh command (ssh -Y -p 2222 127.0.0.1).
5. ):
   Let's transcribe these specifically for our environment:
   
   
   1. step 0: install Xquartz (desktop app or brew)
   2. step 1: make sure you've created an orb machine (such as the Ubuntu example)
   3. Step 2: copy the contents of the ~/.ssh/id_rsa.pub file on your mac home directory into the ~/.ssh/authorized_keys file on your OrbStack (ubuntu) home directory.
      

      Code Block
      language shell
      cat /mnt/mac/Users/$USER/.ssh/id_rsa.pub > ~/.ssh/authorized_keys chmod 600 ~/.ssh/authorized_keys

   4. Step 3: install SSH server
      

      Code Block
      language shell
      sudo apt-get update sudo apt install openssh-server # change ListenStream from 22 to 2222 sudo vim /lib/systemd/system/ssh.socket

      
      
   5. Step 4: restart the machine:
      

      Code Block
      language shell
      # exit orb machine exit # from Mac restart orb machine orbctl restart <name>

      
      
   6. Step 5: Every time you access OrbStack machine and wish to use X11 forwarding you will need to use a terminal on the Mac and run the given ssh command (ssh -Y -p 2222 127.0.0.1).
      

      Code Block
      language shell
      # from Mac access X11 enabled Orb ssh -Y -p 2222 127.0.0.1 # if you want these utilities and to test xclock (optional) sudo apt-get install -y x11-apps

      
      

Changes for running skylab with R2D2 V3

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