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- Use bash as your shell
- Go to https://conda.io/miniconda/.html
- Install the Python 2.7 64 bit bash installer (unless your OS is 32 bit but it most likely will not be)
- Find the installed file Miniconda3Miniconda2-latest-Linux-x86_64.sh
- It will probably be in Downloads, so do cd Downloads
- Run it with bash Miniconda3 bash Miniconda2-latest-Linux-x86_64.sh
- Add miniconda2 to PATH
- The installation will automatically add the bin subdirectory of the installation to PATH in your .bashrc file
- Close and reopen terminal and check by typing conda list which will print out the installed packages
- If conda is not found, follow step 5, else skip to step 6
- If not already created, create a .bash_profile file in your home directory
Add the following script to it. This checks for the .bashrc and will run it on start up
Code Block language bash #!/bin/bash if [ -f $HOME/.bashrc ]; then source $HOME/.bashrc fi
Run conda update -y conda to update miniconda
Install psana conda with conda install -y --channel lcls-rhel<num> psana-conda where <num> is the the RHEL version
- The following dependencies will be picked up from the channel used above:
- hdf5
- openmpi
- mpi4py
- h5py
- tables
- To use one's own build of one of these dependencies, install them first with conda install.
- Visit the psana meta.yaml file to view the version requirements for psana. These versions must be included in the environment.
- The following dependencies will be picked up from the channel used above:
Copy the experiment database from /reg/g/psdm/data/ExpNameDb/experiment-db.dat
Make a directory in the home directory with mkdir -p psdm/data/ExpNameDb
Copy the database
With rsync: rsync -t psexport:/reg/gpsdm/data/ExpNameDb/experiment-db.dat ~psdm/data/ExpNameDb/
With SCP: scp -p psexport:/reg/g/psdm/data/ExpNameDb/experiment-db.dat ~psdm/dataExpNameDb/
Copy the experiment data that will be used for analysis. This step requires patience if many runs will be copied
- For example, downloading run 54 from the experiment xpptut15, the following steps were taken:
- First create the required directories with mkdir -p psdm/xpp/xpptut15/
- Then these files were copied
From /reg/d/psdm/xpp/xpptut15/xtc to ~/psdm/xpp/xpptut15/xtc:
Code Block language bash -bash-4.2$ ls /reg/d/psdm/xpp/xpptut15/xtc/ | grep 54 e665-r0054-s00-c00.xtc e665-r0054-s01-c00.xtc e665-r0054-s02-c00.xtc e665-r0054-s03-c00.xtc e665-r0054-s04-c00.xtc e665-r0054-s05-c00.xtc
From /reg/d/psdm/xpp/xpptut15/xtc/index to ~/psdm/xpp/xpptut15/xtc/index:
Code Block language bash -bash-4.2$ ls /reg/d/psdm/xpp/xpptut15/xtc/index | grep 54 e665-r0054-s00-c00.xtc.idx e665-r0054-s01-c00.xtc.idx e665-r0054-s02-c00.xtc.idx e665-r0054-s03-c00.xtc.idx e665-r0054-s04-c00.xtc.idx e665-r0054-s05-c00.xtc.idx
From /reg/d/psdm/xpp/xpptut15/xtc/smalldata to ~/psdm/xpp/xpptut15/xtc/smalldata:
Code Block language bash -bash-4.2$ ls /reg/d/psdm/xpp/xpptut15/xtc/smalldata | grep 54 e665-r0054-s00-c00.smd.xtc e665-r0054-s01-c00.smd.xtc e665-r0054-s02-c00.smd.xtc e665-r0054-s03-c00.smd.xtc e665-r0054-s04-c00.smd.xtc e665-r0054-s05-c00.smd.xtc
- And the entire directory /reg/d/psdm/xpp/xpptut15/calib to ~/psdm/xpp/xpptut15/calib
- Copy using either rsync or SCP. SCP may be simpler in this case because it copies the data of a symbolic link which is what is desired.
- For example, downloading run 54 from the experiment xpptut15, the following steps were taken:
- Two environment variables must be set, SIT_DATA and SIT_PSDM_DATA by adding the following commands to the .bash_profile file
- export SIT_DATA=$HOME/psdm/data
- export SIT_PSDM_DATA=$HOME/psdm
- If step 5 was not done, create a .bash_profile file instead and begin it with #!/bin/bash
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