1. Log in to the machine (with X term activated)

>$ ssh -X {username}@login.brazos.tamu.edu

2. Set up the environment to load Root (5.34) through miniconda, and to load Matlab 2015a. You must do this every time you log-in.

>$ export PATH=/home/hepxadmin/miniconda/bin:$PATH 
>$ export LD_LIBRARY_PATH=/home/hepxadmin/miniconda/lib 
>$ module load gcc/4.8.2 matlab/R2015a 

Note: This also sets up the path to the root libraries and the libblas libraries required by cdmstools (cdmsbats).

3. In your home area, create a designated folder for your analysis. This folder will contain cdmstools, the created matlab initialization files, and additional setup files (only a couple of them). It is recommended to keep all of them in the same location. And every time you start matlab for cdmstools analysis locate yourself there to load the startup scripts accurately.

 >$ mkdir cdms_matlab
 >$ cd cdms_matlab

4. Import the cdmstools repository. To do this you will have to set up a couple of variables, an ssh config file, and finally run cvs. For this you need to be able to log in to any of the stanford machines, alternatively you can get a cdmstools copy from another member of our group, and skip this part.

• Edit your ssh config file. If it doesn’t exist it will be created:
  

  >$ emacs ~/.ssh/config 

  – Append the following:

  Host neroHostname nero.stanford.edu
   port 26user {your-username}

  (Save the file and exit)

• Go to the directory where you want to locate the code in.
  – Check out the code:
  

  >$ git clone --recursive nero:/data/git/Analysis/MatCAP.git // or scdmstools_*.git

5. Run the following script (just type the following command). It will replace some make files, adding the paths to the libraries in miniconda, and libblas (makeCAP.mk, linalgebra/makeCAP.mk, CAP_auto_config.m), as well as adding a link to the boost c++ headers. It is important that you are in the location of cdmstools (but not inside it!).

>$ ~hepxadmin/matCAPgit_fixes/fix_brazosCAP.sh {your-abolute-path}/MatCAP 

6. In the cluster you need to request an interactive session, otherwise the load on the login node will exceed the quota and your session will stop working. Go to the Matlab and Interactive Sessions guide for more information about this. For now, just run an interactive session like this (this will open Matlab):

>$ srun -p interactive --pty --x11=first --mem 8000 matlab 

7. Matlab is open, now set up MatCAP. This will set up all the files and compile the code, it is only needed once, or if you make new calculated cuts and ‘update’ your CVS package. You should be in the directory created in step 2.

• The following are commands/input for Matlab:
  i. Go to the directory where the config files are located:
  

  >$ cd cdms_matlab/MatCAP/setup

  ii. You only need to run this once, next time you work MatCAP will already be set up and compiled! This will initialize the cdmstools configuration and compilation.
  

  >$ MatCAP_auto_config

• – You will be asked for input, choose (type) the following when prompted, some of them are ready for you to hit enter, some of them need to be re-defined as follows (replace {your-path} with the absolute path of the directory):
  • 
    
    • CAP directory:
      

      {your-path}/cdms_matlab/MatCAP

    • CAP_buffer directory:
      

      {your-path}/cdms_matlab/CAP_buffer

    • Default data directory (recommended):
      

      /fdata/hepx/store/user/cdms_data/

    • Default cal directory (recommended): Same as above
    • startup.m path (recommended):
      

      {your-path}/cdms_matlab // the same level as MatCAP directory

    • Then the CAP MEX files will be compiled.
    • You might see (orange) warnings, that’s ok, and messages indicating successful compilations. You should read:
      Done with compiling BatTools!
      Done with compiling cdmstools mex files!
      MatCAP_auto_config is now finished. You should be able to run CAP_init after restarting Matlab without any problems.
• iii. Exit Matlab
  

   >$ exit 

8. MatCAP is ready, you just need to load it upon starting Matlab. You are set! (Note: check the ~FCCS/ directory to make sure there are FCCS/root/data and FCCS/root/cuts directories under it. Create them if they are not here.)

• Open Matlab again, always open it where you put the startup.m file.
  

  >$ srun -p interactive --pty --x11=first --mem 8000 matlab

  • Again Matlab input:
    

    >$ CAP_init 

    This line initializes all the MatCAP tools once everything is compiled.

  • After the check is done, you will be prompted to load data. The first time, select independent files to create a .matlist file, or select all files within a path. The following times you don’t need to click on every dataset but instead in the saved filelist.
• For a MatCAP package that is already set up (i.e. if you have already followed all the steps above successfully), the only things you need to do after logging in are:
  

  >$ export PATH=/home/hepxadmin/miniconda/bin:$PATH 
  >$ export LD_LIBRARY_PATH=/home/hepxadmin/miniconda/lib 
  >$ module load gcc/4.8.2 matlab/R2015a 
  >$ cd {your-path}/cdms_matlab/
  >$ srun -p interactive --pty --x11=first --mem 8000 matlab(in MATLAB)>$ CAP_init