bashrc_common

#!/bin/bash
# This set of commands gets called by all big environments
# Structure reintroduced: 05/06/2022
#
# state what's going on
echo $bufferstring
echo "Executing $envdir/bashrc_common"

# start by clearing all aliases
#unalias -a

# Make prompt show current working directory
# But only if bashrc_common hasn't been sourced already
if ! [ sourced_common_already ]; then
    PS1='\w$ '
fi

# Extra appendages to PATH to allow 
# programs to be installed locally
export PATH=$PATH:$HOME/bin
export PATH=$PATH:$HOME/usr/bin

#####################
#DIRECTORY STRUCTURES
#####################

# Python startup file
export PYTHONSTARTUP=$HOME/environment/python_startup.py
# Note: on Pleaides, there is also /etc/pythonstart, should I worry about this?

# Main folders
export doc=$HOME/Documents
export down=$HOME/Downloads
export desk=$HOME/Desktop

# universal Desktop subdirs (mostly on Mac)
export notes=$desk/Research_Notes
export pubrev=$desk/Publication_Review
export thesis=$desk/Thesis
export pres=$desk/Presentations
export cv=$desk/CV
export papers=$desk/Paper_Library
export pub=$desk/Publications
export tachletter=$pub/Tacho_Letter
export tachletterplots=$pub/Tacho_Letter_Plots_Part2
export tachapj=$pub/Tacho_ApJ
export tachapjplots=$pub/Tacho_ApJ_Plots

export prop=$desk/Proposals
export solartw=$desk/Solar_Thermal_Wind

export proprsr=$doc/Proposal_to_Recruit_Support_Retain_UrMs_APS
export fin=$doc/Financial

# Rayleigh environent
export ra=$HOME/rayleigh
export racode=$ra/code
export rapp=$racode/post_processing

export raRyan=$HOME/rayleigh_Ryan
export racodeRyan=$raRyan/code
export rappRyan=$racodeRyan/post_processing

export rau=$ra/utils
export raco=$rau/compute # /usr/bin/co is a command
export rapl=$rau/plot # /usr/bin/plot is a command
export raleg=$rau/zz_legacy # /usr/bin/plot is a command
export idref=$raco/hydro_ideal_reference_state

# Pleiades directory shortcuts

# Rayleigh simulation root directories on Pleiades
export nb=/nobackup/lmatilsk
export nbnick=/nobackup/nfeather
export tach=$nb/00_Tacho_Letter
export boulder=$nb/00_Boulder_Survey
export check=$nb/00_Rayleigh_Checkpoints

export postdoc=$nb/00_Summer_Postdoc
export casem=$tach/case_M
export caseh=$tach/case_H

# LCD  hard-disk shortcuts
export alt=/altair/loma3853
export pol=/pollux/loma3853
export cast=/castor/loma3853 #/usr/bin/cas is a program on Freyr
export sarg=/sargas/loma3853 # /usr/sbin/sargas is a program on Freyr
export miz=/mizar/loma3853

export postdoclcd=$alt/00_Summer_Postdoc-fresh

# LCD ssh shortcuts
export hyp=hyperion
export fre=freyr
export bac=bacchus
export tel=tellus
export hyd=hydra
export hyd2=hydra2
export scy=scylla

# other command aliases
alias fn='find `pwd` -name ' # fn for "full name"
alias gt='gnome-terminal'

# Get disk usage
get_du() {
    du -hsc * >> $(date +%F)_du
}

get_du_app() {
    du -hsc --apparent-size * >> $(date +%F)_du_app
}

# Source global definitions
if [ -f /etc/bashrc ]; then
    echo $bufferstring
    echo "Executing /etc/bashrc"
    . /etc/bashrc 
fi

# always ssh with display privileges
alias ssh='ssh -X'
alias less='less -MN' # make less show line numbers and  filename in status bar

# sym links
alias linkra='ln -s $racode/bin/rayleigh.opt'
alias linkdbg='ln -s $racode/bin/rayleigh.dbg'
alias linkmain='rm rayleigh.*; ln -s $racode/bin/main/rayleigh.* .'
alias linkmods='rm rayleigh.*; ln -s $racode/bin/allmods/rayleigh.* .'
alias linkcustom='rm rayleigh.*; ln -s $racode/bin/custom/rayleigh.* .'
alias linkperfcond='rm rayleigh.*; ln -s $racode/bin/perfcond/rayleigh.* .'
alias linkmulti='rm rayleigh.*; ln -s $racode/bin/multi/rayleigh.* .'
alias linkrome='rm rayleigh.*; ln -s /home4/nfeather/software/Rayleigh-Rome-2.28/bin/* .'

alias linknobinrz='rm rayleigh.*; ln -s $racode/bin/noBinRZ/rayleigh.* .'
alias linktraceback='rm rayleigh.*; ln -s $racode/bin/traceback/rayleigh.* .'

# post processing
alias runra='mpiexec -np 16 ./rayleigh.opt -nprow 4 -npcol 4'
alias runra1="./rayleigh.opt -nprow 1 -npcol 1"

# Configure rayleigh with .muck extension
alias configmuck='EXT=".muck" ./configure'

# Tar up some sample output (G_Avgs, Shell_Avgs, AZ_Avgs,
# Equatorial_Slices, Meridional_Slices, Shell_Slices, Shell_Spectra)
# as well as main_input, reference, transport, and grid_info for
# a given Rayleigh run directory
alias make_sample='tar -cvfh datasample.tar $(find AZ_Avgs/ | sort | tail -n 3) $(find Equatorial_Slices/ | sort | tail -n 3) $(find G_Avgs/ | sort | tail -n 3)  $(find Meridional_Slices/ | sort | tail -n 3) $(find Shell_Avgs/ | sort | tail -n 3) $(find Shell_Slices/ | sort | tail -n 3) $(find Shell_Spectra/ | sort | tail -n 3) main_input equation_coefficients grid_info jobinfo.txt'

alias make_sample_data='tar -cvf datasample.tar $(find AZ_Avgs/ | sort | tail -n 3) $(find Equatorial_Slices/ | sort | tail -n 3) $(find G_Avgs/ | sort | tail -n 3)  $(find Meridional_Slices/ | sort | tail -n 3) $(find Shell_Avgs/ | sort | tail -n 3) $(find Shell_Slices/ | sort | tail -n 3) $(find Shell_Spectra/ | sort | tail -n 3) main_input equation_coefficients grid_info jobinfo.txt data/'

alias make_sample_data_and_plots='tar -cvfh datasample.tar $(find AZ_Avgs/ | sort | tail -n 3) $(find Equatorial_Slices/ | sort | tail -n 3) $(find G_Avgs/ | sort | tail -n 3)  $(find Meridional_Slices/ | sort | tail -n 3) $(find Shell_Avgs/ | sort | tail -n 3) $(find Shell_Slices/ | sort | tail -n 3) $(find Shell_Spectra/ | sort | tail -n 3) main_input equation_coefficients grid_info jobinfo.txt data/ plots/'

# Rayleigh routines

# parallel
# set default nproc based on hostname
host=`hostname`
#if [[ "$host" == *"$ldanst"* ]] || [[ "$host" == *"$nodest"* ]]; then
if [[ "$host" == "lfe"* ]] || [[ "$host" == "pfe"* ]]; then
    nproc=1 # process in serial on the lfes and pfes
elif [[ "$host" == "lorensMac"* ]] || [[ "$host" == "cu-genvpn"* ]] || [[ "$host" == *"eduroam"* ]]; then
    nproc=2
else
    nproc=`nproc --all` # by default, use max number of processes
fi
# ppc for "python parallel call"
#export ppc="mpiexec -n $nproc --oversubscribe python -u"
export ppc="mpiexec -n $nproc python -u"
source $HOME/environment/bashrc_ra_routines

setnproc() {
    nproc=$1
    #export ppc="mpiexec -n $nproc --oversubscribe python -u"
    export ppc="mpiexec -n $nproc python -u"
    source $HOME/environment/bashrc_ra_routines
}

# count lines in a directory
# usage: countlines directory/ \*.[extension]
# NOTE: must include "\" before "*" so the wildcard doesn't get expanded
# when passed to the function ("\*" passes the asterisk verbatim in $2)
# Example:
# countlines compute/ \*py [note final slash is irrelevant; could use "compute"]
countlines() {
    find $1 -name "$2" -type f | xargs wc -l
}

countfiles() {
    find $1 -type f | wc -l
}

# sequentialize images in directory
alias sequence="python $raco/sequentialize_images.py"
# ffmpeg shortcut for making movies form img????.png files
alias ffm="ffmpeg3 -framerate 30 -i img%04d.png -qscale 5 movie.mp4"

# BASH SHORTCUTS
alias rmsslice="bash $rau/bash/rm_sslice.sh"
alias rmtexaux="rm *aux *bbl *blg *log *out *synctex.gz"

alias mvbashrc="mv ~/.bashrc ~/.bashrc-bak; mv ~/.bash_profile ~/.bash_profile-bak"
alias mvbashrcbak="mv ~/.bashrc-bak ~/.bashrc; mv ~/.bash_profile-bak ~/.bash_profile"

# say now we've sourced common
sourced_common_already=1