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HighIander/..myNiceSmileiSetup

Last active September 11, 2020 13:01
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Sample smilei files
Raw
..myNiceSmileiSetup
use at your own risk!
Raw
.condaInit.sh
# >>> conda initialize >>>
# put this file somewhere in your home directory and source before working with conda, i.e. before sourcing the smilie.profile!
# you are adviced to auto-source it upon log-on, e.g. put "source ~/.condaInit.sh" in your .bashrc file
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/trinity/shared/pkg/devel/anaconda/2019.07/bin/conda' 'shell.bash' 'hook' 2\
> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/trinity/shared/pkg/devel/anaconda/2019.07/etc/profile.d/conda.sh" ]; then
. "/trinity/shared/pkg/devel/anaconda/2019.07/etc/profile.d/conda.sh"
else
export PATH="/trinity/shared/pkg/devel/anaconda/2019.07/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
Raw
jupyter.profile
#smilei python conda profile loader; put into the smilei profile directory to be auto-sourced by the smilei.profile
#on hemera4, you have to run the .condaInit first!
export PATH=$PATH:/home/kluget/picongpu-src/lib/python
# anaconda
export PATH="$HOME/anaconda3/bin:$PATH"
conda activate base # a clean profile, without any additional packages installed
conda activate --stack analysis # a profile for general python analysis stuff
conda activate --stack smilei # including happi
Raw
sbatch.sh
#!/bin/bash
#Sample sbatch.sh slurm submit script for smilei, on hemera; to be called from within the input file folder by smilei-submit script
#SBATCH --job-name=SmallCuLT94
#SBATCH --partition=intel # partition to be used (defq, gpu or intel)
#SBATCH --time=96:00:00 # walltime (up to 96 hours)
###SBATCH --nodes=2 # number of nodes
#SBATCH --ntasks=32 # number of tasks (i.e. parallel processes) to be started
#SBATCH --error=stderr
#SBATCH --output=stdout
mpiexec -n 32 src/smilei ./input.py
Raw
smilei-completion.bash
#/usr/bin/env bash
#WIP!
#use pic-edit to open the smilei input file in an editor and go the specified code block, this file provides autocompletion for the code blocks; put into smilei profile directory and use my smilei.profile to automatically source it
_smilei-edit()
{
local cur names
cur="${COMP_WORDS[COMP_CWORD]}"
#add auto completion words here:
names=$(echo "Vectorization";echo "vectorization";echo " ")
names=$names$(echo "Main"; echo "main";echo " ")
COMPREPLY=( $(compgen -W "${names}" -- ${cur}) )
return 0
}
complete -F _smilei-edit smilei-edit
Raw
smilei-edit
#/usr/bin/env bash
#open python input file and go to the specified code block; put path into PATH variable for convenience; put into smiley profile directory and use my smilei.profile to automatically have the dir in PATH
#we assume that the input file is always called *.py and only one py file is present!
#can auto complete with a number of blocks and automatically goes to the respective position in input.py
#currently, the editor has to be hardcoded, i.e. emacs -nw or vim
POSITION=""
if [ "$1" != "" ]
then
searchStr=$1"("
line=$(grep -i -n $searchStr *.py)
line=${line%%:*}
emacs -nw +$line *.py
else
emacs -nw *.py
fi
Raw
smilei-submit
#!/bin/bash
#submit script for smilei; put into smilei profile directory and use my smilei.profile in order to add automatically to PATH; submit inside the case-directory e.g. via qsub smilei-submit
homeDir=$(pwd)
force=False
verbose=False
batch=0
n=1
help=False
while [ "$1" != "" ]; do
case $1 in
-t | --target) export SIMPATH=$2
shift
;;
-f | --force ) force=True
;;
-s | --submitscript ) export SCRIPT=$2
shift
;;
-v | --verbose ) verbose=True
;;
-b | --batch ) export batch=$2
shift
;;
-n | --number ) export n=$2
shift
;;
-h | --help ) help=True
;;
esac
shift
done
if [ $help == True ]
then
echo "This script submits a Smilei simulation from the current directory"
echo "Usage: submit -t <target output directory> [options]"
echo "Options -s|--submitscript -f|--force -v|--verbose -h|--help:"
echo "-s: location of the submit submit script. Default: ./sbatch.sh"
echo "-f: force directory overwrite, if already existing"
echo "-v: verbose output"
echo "-b: if b>0: batch mode, starting with case b in batch.py"
echo "-n: if in batch mode, specifies the number of runs starting at b. Default is 1"
echo "-h: show this help"
exit
fi
if [ -d $SIMPATH ] && [ $force == False ]
then
echo '[Error!] Target directory' $SIMPATH 'already exists! Aborting.'
exit
else
if [ -d $SIMPATH ]
then
echo '[Warning!] Target directory' $SIMPATH 'already exists! Overwriting upon user request.'
# rm -rf $SIMPATH
fi
if [ $batch -gt 0 ]
then
if [ $verbose == True ]; then echo "Copying source from $PICSRC..."; fi
mkdir $SIMPATH
mkdir -p $SIMPATH/src
cp -r $PICSRC/* $SIMPATH/src
SIMPATHorig=$SIMPATH
a=$(($batch))
b=$(($batch+$n-1))
if [ $verbose == True ]; then echo "Submitting jobs in batch mode."; fi
for ((i=$a; i<=$b; i++))
do
if [ $verbose == True ]; then echo "---------------------------------"; fi
if [ $verbose == True ]; then echo "Job $i ($(($i-$a+1)) of $(($b-$a+1))):" ; fi
cd $homeDir
SIMPATH="${SIMPATHorig}/${i}"
mkdir $SIMPATH
echo "currentSim = ${i}" > $SIMPATH/current.py
if [ $verbose == True ]; then echo 'Copying input...'; fi
cp ./$PICINPUT $SIMPATH
cp ./$PICBATCH $SIMPATH
cp ./$PICSUBMITSCRIPT $SIMPATH
cd $SIMPATH
sed "/$PICNAME/s/$/$i/" $PICSUBMITSCRIPT > temp.sh && mv temp.sh $PICSUBMITSCRIPT
cat $PICBATCH $PICINPUT > temp && mv temp $PICINPUT
cat current.py input.py >temp && mv temp $PICINPUT
RES=$($PICSUBMIT $PICSUBMITSCRIPT)
echo 'qdel ' ${RES##* } >> "${SIMPATHorig}"/submittedJobIDs
if [ $verbose == True ]
then
echo "Submitted case $i using $PICSUBMITSCRIPT: ID ${RES##* }"
echo 'Please wait for the job to finish! Then, look for output in:'
echo ' '$SIMPATH
fi
done
if [ $verbose == True ]; then echo "---------------------------------"; fi
if [ $verbose == True ]; then echo "All job IDs can be found in ${SIMPATHorig}/submittedJobIDs"; fi
else
#not in batch mode
mkdir -p $SIMPATH/src
if [ $verbose == True ]; then echo 'Copying input and source...'; fi
cp ./$PICINPUT $SIMPATH/input.py
cp ./$PICSUBMITSCRIPT $SIMPATH
cp -r $PICSRC/* $SIMPATH/src
cd $SIMPATH
if [ $verbose == True ]
then
module list
echo "submitting job using $PICSUBMITSCRIPT ..."
echo ' '
fi
$PICSUBMIT $PICSUBMITSCRIPT
if [ $verbose == True ]
then
echo 'Please wait for the job to finish!'
echo 'Look for output in:'
echo ' '$SIMPATH
fi
fi
fi
Raw
smilei_hemera4.profile
#/usr/bin/env bash
#smilei profile for hemera @ hzdr
#put in a profile directory together with smilei-edit and smilei-completion.sh and jupyter.profile and smilei-submit for best convenience
#source .condaInit and this file before working with smilei
# User Information ################################# (edit the following lines)
# - automatically add your name and contact to output file meta data
# - send me a mail on batch system jobs: NONE, BEGIN, END, FAIL, REQUEUE, ALL,
# TIME_LIMIT, TIME_LIMIT_90, TIME_LIMIT_80 and/or TIME_LIMIT_50
export MY_MAILNOTIFY="NONE"
export MY_MAIL="[email protected]"
export MY_NAME="$(whoami) <$MY_MAIL>"
export PICPROFILES=$HOME/smilei-profiles
alias PICEDITOR="emacs -nw"
module purge
source $PICPROFILES/jupyter.profile
module load python/3.8.0
module load intel/19.0
module load openmpi/2.1.2
module load python/3.8.0
module load zlib/1.2.11
module load hdf5-parallel/1.8.20
module load ffmpeg/4.2.1
export PICSRC=$HOME/smilei-src
export PICINPUTS=$HOME/smilei-inputs
export PYTHONHOME=$PYTHON3_ROOT
export PATH=$PATH:$PICPROFILES
# Load autocompletion for PIConGPU commands
BASH_COMP_FILE=$PICPROFILES/smilei-completion.bash
if [ -f $BASH_COMP_FILE ] ; then
source $BASH_COMP_FILE
else
echo "bash completion file '$BASH_COMP_FILE' not found." >&2
fi
export PICINPUT=input.py
export PICBATCH=inputBatch.py
export PICSUBMITSCRIPT=sbatch.sh
export PICSUBMIT=sbatch
# how is the name of the simulation defined in the submit script
# for slurm, this is #SBATCH --job-name=
# needed to append the number of the current simulation to the name in bacth mode
export PICNAME='#SBATCH --job-name='
export PYTHONHOME=$PYTHON3_ROOT
export PATH=$PATH:$PICPROFILES
#Default threads
export OMP_NUM_THREADS=1
H5PY_DEFAULT_READONLY=1
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