Using the shell

Standard commands

• ssh kitzeslab@<robin's URL>
• pwd - print working directory. This is the directory, aka the "folder", that you're issuing commands from.
• ls - list contents of the current working directory
• ls /Volumes/seagate1/ - list the contents of the directory /Volumes/seagate1/
• ls -lh - list the files with more information: l = long list, h = human-readable file sizes
• cd - change directories into your home directory
• cd .. - go up one directory, e.g. from /Volumes/seagate1/ to /Volumes/.
• cd seagate1/ - change directories into seagate1/. This is a relative path, i.e. the shell attempts to change into a directory contained within the current working directory.
• cd /Volumes/seagate1 - change directories into /Volumes/seagate1/. This is an absolute path, i.e. you can do this from any working directory
• mkdir hello - make a directory called hello within the current directory
• mkdir /Users/tessa/Recordings/MSD-0001 - make the directory MSD-0001 within preexisting directory /Users/tessa/Recordings/.
• scp kitzeslab@<robin's URL>:/Volumes/seagate1/data/field-data/<date folder>/<card folder>/<filename>.WAV . - copy a file into your current working directory (specified by .).
• scp kitzeslab@<robin's URL>:/Volumes/seagate1/data/field-data/<date folder>/<card folder>/<filename>.WAV /Users/<username>/Recordings - copy a file into the directory /Users/<username>/Recordings.

Helpful programs

Watch your processor usage: htop

Run long programs: tmux

This package allows you run programs in the background. Use this for long programs that you'd like to keep running, even if you leave, exit your SSH session, etc.

• New tmux session: tmux new -s <descriptive-session-name>
• Detach from session: ^B then D
• View sessions: tmux ls
• Reattach to session: tmux attach -t <descriptive-session-name>

MongoDB

Working data for our analyses, e.g., statistics, generated spectrograms, etc. are stored in MongoDB. Mongo is a nesting structure: many collections can lie within a single database. Mongo can be investigated from within the mongo shell (accessed by typing mongo) or from within the Bash shell.

Mongo shell

$ mongo
> help # help for large-scale Mongo methods
> db.help() # help for methods to manage DBs
> show dbs # view all databases
> use <db name> # use a databse
> db.getCollectionNames() # get collection names while using a database
> db.<collection name>.drop() # drop a collection while using a database
> db.dropDatabase() # drop an entire database

Mongo in bash

Move a collection

Dump a collection into the current directory:

$ mongodump -d <db_name> -c <collection_name>

Dump will be stored in ./dump/<db name>/<collection name>.

Compress the dump to move it easily: (naming convention: <db>-<collection>-<date>)

$ tar cvf <name>.tar.gz dump

Load/restore a collection

Will automatically try to load to a database & collection with the same name as the one it came from. (Or you can specify a new collection name using -d and -c). If the collection already exists, the mongorestore will fail.

$ mongorestore -d <new name of database> -c <new name of collection> <.bson file to restore from>

CRC & slurm

Get onto the cluster with

ssh h2p.crc.pitt.edu

For software shared between nodes: module spider python

Other helpful commands:

• module load
• module list
• module unload
• module purge
• which python