Commit ba741e1b authored by Femi Kadri's avatar Femi Kadri

changes to LST batch scripts

parent 9f5fc66a
#!/bin/bash
#
# schooner_finalize_LST.sh
#
# This example batch script is intended for running pure MPI
# parallel programs only (not hybrid MPI/OpenMP or hybrid
# MPI/pthreads).
#
# last modified by OSCER 2016-06-08 10:40
#
# Also, please note that lines that begin with pound-SBATCH (#SBATCH)
# are batch scheduler directives, so they are absolutely crucial.
# DON'T REMOVE THE pound sign (#) from before the SBATCH!!!!
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
# NOTE: If you create any file of human-readable text on a Windows PC,
# you *MUST* perform the following command on it:
#
# dos2unix filename
#
# where you replace "filename" with the name of the file; for example:
#
# dos2unix /home/yourusername/input_directory/input_filename.txt
#
# This is because virtually all text editors in Windows embed hidden
# special characters in text files (for example, font information),
# and these hidden special characters cause Unix/Linux programs to
# choke.
#
# To submit a batch job:
#
# sbatch jobname.sh
#
# Note that there is no "<" sign in the above command.
#
#
# To see what batch jobs you personally have in the scheduler:
#
# squeue -u yourusername
#
# To see what batch jobs everyone has in your partitions:
#
# squeue
#
# To kill a batch job (replace JOBID with the batch job ID number):
#
# scancel JOBID
#
# but again replacing JOBID with the batch job identifer.
#
###
#
# The SBATCH directive below says the name of the partition to be used.
# In most cases, you should use the queue named normal.
#
#SBATCH --partition=normal
#
# The SBATCH directive below says to request exclusive access on the
# participating compute nodes, so that other batch jobs (for example,
# those submitted by other users) don't run on the same compute nodes
# as this batch job, and therefore don't interfere with it.
#
#SBATCH --exclusive
#
# Use 40 MPI processes at 20 MPI processes per node, which is to
# say 2 nodes in the case of the normal partition.
#
# Please use the following pattern for nodes in the normal partition:
# -- For ntasks <= 20, please use ntasks-per-node equal to n unless
# you have a very good reason to do otherwise.
# -- For ntasks >= 20, please use ntasks-per-node equal to 20 unless
# you have a very good reason to do otherwise.
#
# This is because each compute node has 2 chips and each chip
# has 10 cores, for a total of 20 cores per node. We recommend
# using the same number of MPI processes per node as cores,
# unless you've benchmarked your code's performance and found
# that you take fewer node hours by using fewer than 20 per node.
#
# NOTE: You are encouraged to change these to numbers that are
# appropriate for you.
#
#SBATCH --ntasks=20
#SBATCH --ntasks-per-node=10
#
# STDOUT is the output that normally would go to the terminal screen.
# STDERR is like STDOUT, except that it contains error messages instead
# of regular output.
#
# The SBATCH directive below says, send STDOUT and STDERR to the filenames
# listed below.
#
# Note that, in these filenames, %J will be replaced by the batch job ID
# number
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
#SBATCH --output=/scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git/LST_finalize_%J_stdout.txt
#SBATCH --error=/scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git/LST_finalize_%J_stderr.txt
#
# The SBATCH directive below says to run for up to 12 hours (and zero
# minutes and zero seconds) of "wall clock" time (time experienced in
# real life).
# Currently, the maximum allowable wall clock time per batch job is
# 48:00 hours.
# Acceptable time formats include "minutes", "minutes:seconds",
# "hours:minutes:seconds", "days-hours", "days-hours:minutes" and
# "days-hours:minutes:seconds".
#
#SBATCH --time=06:00:00
#
# The SBATCH directive below says the name of the batch job, as it
# will appear in the batch partition when you do an squeue command.
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
#SBATCH --job-name=LST_finalize
#
# The SBATCH directive below says the e-mail address to send
# notifications to, which should be changed to your e-mail address.
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
#SBATCH --mail-user=phemykadri@gmail.com
#
# The SBATCH directive below says to e-mail a notification when the
# batch job either completes or fails.
#
# If you only want e-mails when when a batch job fails, then delete
# the SBATCH directive below.
#
#SBATCH --mail-type=ALL
#
# Change to the directory that you want to run in.
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
#SBATCH --workdir=/scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git
#
#################################################
# If you like, you may uncomment the following line
# to display your working directory in your output,
# to make sure that you're in the correct directory.
# pwd
pwd
# If your job requires any "module load" commands,
# then please insert them here, without a pound sign (#).
# Typically, if your program required a
# module to compile it, then include the same module
# here to run your program. In particular, if you do not
# already load an application module that includes an mpi
# toolchain, then explicitly load an mpi toolchain here.
# For example:
# module load mpi/intel
#module load pgi/16.1
module load intel/2016a
# Run the executable, redirecting input from the given file.
# The date commands and the time command help track runtime
# and performance.
#
# NOTE: The line with a "<" sign, immediately before the
# second date command, redirects standard input
# (typically a user typing at the keyboard) from a file of
# human readable text.
# If your program uses no input, or if for all input your program
# explicitly opens its files inside the program (for example, via
# an OPEN statement in Fortran or an fopen command in C), then you
# don't need that line, so DELETE IT.
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
# Here, also CHANGE executable_directory to the directory where your
# executable resides, CHANGE executable_filename to the name of the
# executable file, CHANGE input_directory to the directory where your
# standard input file resides, and CHANGE input_filename.txt to the
# name of your standard input file (that is, the file that you want
# to use for standard input, instead of a user typing live at the
# keyboard, which isn't possible for a batch job).
date
time \
mpirun \
/scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git/lbm \
< /scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git/input.txt \
&& date
#!/bin/bash
#
# schooner_initial_LST.sh
#
# This example batch script is intended for running pure MPI
# parallel programs only (not hybrid MPI/OpenMP or hybrid
# MPI/pthreads).
#
# last modified by OSCER 2016-06-08 10:40
#
# Also, please note that lines that begin with pound-SBATCH (#SBATCH)
# are batch scheduler directives, so they are absolutely crucial.
# DON'T REMOVE THE pound sign (#) from before the SBATCH!!!!
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
# NOTE: If you create any file of human-readable text on a Windows PC,
# you *MUST* perform the following command on it:
#
# dos2unix filename
#
# where you replace "filename" with the name of the file; for example:
#
# dos2unix /home/yourusername/input_directory/input_filename.txt
#
# This is because virtually all text editors in Windows embed hidden
# special characters in text files (for example, font information),
# and these hidden special characters cause Unix/Linux programs to
# choke.
#
# To submit a batch job:
#
# sbatch jobname.sh
#
# Note that there is no "<" sign in the above command.
#
#
# To see what batch jobs you personally have in the scheduler:
#
# squeue -u yourusername
#
# To see what batch jobs everyone has in your partitions:
#
# squeue
#
# To kill a batch job (replace JOBID with the batch job ID number):
#
# scancel JOBID
#
# but again replacing JOBID with the batch job identifer.
#
###
#
# The SBATCH directive below says the name of the partition to be used.
# In most cases, you should use the queue named normal.
#
#SBATCH --partition=normal
#
# The SBATCH directive below says to request exclusive access on the
# participating compute nodes, so that other batch jobs (for example,
# those submitted by other users) don't run on the same compute nodes
# as this batch job, and therefore don't interfere with it.
#
#SBATCH --exclusive
#
# Use 40 MPI processes at 20 MPI processes per node, which is to
# say 2 nodes in the case of the normal partition.
#
# Please use the following pattern for nodes in the normal partition:
# -- For ntasks <= 20, please use ntasks-per-node equal to n unless
# you have a very good reason to do otherwise.
# -- For ntasks >= 20, please use ntasks-per-node equal to 20 unless
# you have a very good reason to do otherwise.
#
# This is because each compute node has 2 chips and each chip
# has 10 cores, for a total of 20 cores per node. We recommend
# using the same number of MPI processes per node as cores,
# unless you've benchmarked your code's performance and found
# that you take fewer node hours by using fewer than 20 per node.
#
# NOTE: You are encouraged to change these to numbers that are
# appropriate for you.
#
#SBATCH --ntasks=20
#SBATCH --ntasks-per-node=10
#
# STDOUT is the output that normally would go to the terminal screen.
# STDERR is like STDOUT, except that it contains error messages instead
# of regular output.
#
# The SBATCH directive below says, send STDOUT and STDERR to the filenames
# listed below.
#
# Note that, in these filenames, %J will be replaced by the batch job ID
# number
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
#SBATCH --output=/scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git/LST_initial_%J_stdout.txt
#SBATCH --error=/scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git/LST_initial_%J_stderr.txt
#
# The SBATCH directive below says to run for up to 12 hours (and zero
# minutes and zero seconds) of "wall clock" time (time experienced in
# real life).
# Currently, the maximum allowable wall clock time per batch job is
# 48:00 hours.
# Acceptable time formats include "minutes", "minutes:seconds",
# "hours:minutes:seconds", "days-hours", "days-hours:minutes" and
# "days-hours:minutes:seconds".
#
#SBATCH --time=04:00:00
#
# The SBATCH directive below says the name of the batch job, as it
# will appear in the batch partition when you do an squeue command.
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
#SBATCH --job-name=LST_initial
#
# The SBATCH directive below says the e-mail address to send
# notifications to, which should be changed to your e-mail address.
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
#SBATCH --mail-user=phemykadri@gmail.com
#
# The SBATCH directive below says to e-mail a notification when the
# batch job either completes or fails.
#
# If you only want e-mails when when a batch job fails, then delete
# the SBATCH directive below.
#
#SBATCH --mail-type=ALL
#
# Change to the directory that you want to run in.
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
#SBATCH --workdir=/scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git
#
#################################################
# If you like, you may uncomment the following line
# to display your working directory in your output,
# to make sure that you're in the correct directory.
# pwd
pwd
# If your job requires any "module load" commands,
# then please insert them here, without a pound sign (#).
# Typically, if your program required a
# module to compile it, then include the same module
# here to run your program. In particular, if you do not
# already load an application module that includes an mpi
# toolchain, then explicitly load an mpi toolchain here.
# For example:
# module load mpi/intel
#module load pgi/16.1
module load intel/2016a
# Run the executable, redirecting input from the given file.
# The date commands and the time command help track runtime
# and performance.
#
# NOTE: The line with a "<" sign, immediately before the
# second date command, redirects standard input
# (typically a user typing at the keyboard) from a file of
# human readable text.
# If your program uses no input, or if for all input your program
# explicitly opens its files inside the program (for example, via
# an OPEN statement in Fortran or an fopen command in C), then you
# don't need that line, so DELETE IT.
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
# Here, also CHANGE executable_directory to the directory where your
# executable resides, CHANGE executable_filename to the name of the
# executable file, CHANGE input_directory to the directory where your
# standard input file resides, and CHANGE input_filename.txt to the
# name of your standard input file (that is, the file that you want
# to use for standard input, instead of a user typing live at the
# keyboard, which isn't possible for a batch job).
date
time \
mpirun \
/scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git/lbm \
< /scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git/input.txt \
&& date
#!/bin/bash
#
# schooner_resume_LST.sh
#
# This example batch script is intended for running pure MPI
# parallel programs only (not hybrid MPI/OpenMP or hybrid
# MPI/pthreads).
#
# last modified by OSCER 2016-06-08 10:40
#
# Also, please note that lines that begin with pound-SBATCH (#SBATCH)
# are batch scheduler directives, so they are absolutely crucial.
# DON'T REMOVE THE pound sign (#) from before the SBATCH!!!!
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
# NOTE: If you create any file of human-readable text on a Windows PC,
# you *MUST* perform the following command on it:
#
# dos2unix filename
#
# where you replace "filename" with the name of the file; for example:
#
# dos2unix /home/yourusername/input_directory/input_filename.txt
#
# This is because virtually all text editors in Windows embed hidden
# special characters in text files (for example, font information),
# and these hidden special characters cause Unix/Linux programs to
# choke.
#
# To submit a batch job:
#
# sbatch jobname.sh
#
# Note that there is no "<" sign in the above command.
#
#
# To see what batch jobs you personally have in the scheduler:
#
# squeue -u yourusername
#
# To see what batch jobs everyone has in your partitions:
#
# squeue
#
# To kill a batch job (replace JOBID with the batch job ID number):
#
# scancel JOBID
#
# but again replacing JOBID with the batch job identifer.
#
###
#
# The SBATCH directive below says the name of the partition to be used.
# In most cases, you should use the queue named normal.
#
#SBATCH --partition=normal
#
# The SBATCH directive below says to request exclusive access on the
# participating compute nodes, so that other batch jobs (for example,
# those submitted by other users) don't run on the same compute nodes
# as this batch job, and therefore don't interfere with it.
#
#SBATCH --exclusive
#
# Use 40 MPI processes at 20 MPI processes per node, which is to
# say 2 nodes in the case of the normal partition.
#
# Please use the following pattern for nodes in the normal partition:
# -- For ntasks <= 20, please use ntasks-per-node equal to n unless
# you have a very good reason to do otherwise.
# -- For ntasks >= 20, please use ntasks-per-node equal to 20 unless
# you have a very good reason to do otherwise.
#
# This is because each compute node has 2 chips and each chip
# has 10 cores, for a total of 20 cores per node. We recommend
# using the same number of MPI processes per node as cores,
# unless you've benchmarked your code's performance and found
# that you take fewer node hours by using fewer than 20 per node.
#
# NOTE: You are encouraged to change these to numbers that are
# appropriate for you.
#
#SBATCH --ntasks=20
#SBATCH --ntasks-per-node=10
#
# STDOUT is the output that normally would go to the terminal screen.
# STDERR is like STDOUT, except that it contains error messages instead
# of regular output.
#
# The SBATCH directive below says, send STDOUT and STDERR to the filenames
# listed below.
#
# Note that, in these filenames, %J will be replaced by the batch job ID
# number
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
#SBATCH --output=/scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git/LST_resume_%J_stdout.txt
#SBATCH --error=/scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git/LST_resume_%J_stderr.txt
#
# The SBATCH directive below says to run for up to 12 hours (and zero
# minutes and zero seconds) of "wall clock" time (time experienced in
# real life).
# Currently, the maximum allowable wall clock time per batch job is
# 48:00 hours.
# Acceptable time formats include "minutes", "minutes:seconds",
# "hours:minutes:seconds", "days-hours", "days-hours:minutes" and
# "days-hours:minutes:seconds".
#
#SBATCH --time=06:00:00
#
# The SBATCH directive below says the name of the batch job, as it
# will appear in the batch partition when you do an squeue command.
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
#SBATCH --job-name=LST_resume
#
# The SBATCH directive below says the e-mail address to send
# notifications to, which should be changed to your e-mail address.
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
#SBATCH --mail-user=phemykadri@gmail.com
#
# The SBATCH directive below says to e-mail a notification when the
# batch job either completes or fails.
#
# If you only want e-mails when when a batch job fails, then delete
# the SBATCH directive below.
#
#SBATCH --mail-type=ALL
#
# Change to the directory that you want to run in.
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
#SBATCH --workdir=/scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git
#
#################################################
# If you like, you may uncomment the following line
# to display your working directory in your output,
# to make sure that you're in the correct directory.
# pwd
pwd
# If your job requires any "module load" commands,
# then please insert them here, without a pound sign (#).
# Typically, if your program required a
# module to compile it, then include the same module
# here to run your program. In particular, if you do not
# already load an application module that includes an mpi
# toolchain, then explicitly load an mpi toolchain here.
# For example:
# module load mpi/intel
#module load pgi/16.1
module load intel/2016a
# Run the executable, redirecting input from the given file.
# The date commands and the time command help track runtime
# and performance.
#
# NOTE: The line with a "<" sign, immediately before the
# second date command, redirects standard input
# (typically a user typing at the keyboard) from a file of
# human readable text.
# If your program uses no input, or if for all input your program
# explicitly opens its files inside the program (for example, via
# an OPEN statement in Fortran or an fopen command in C), then you
# don't need that line, so DELETE IT.
#
# Everywhere throughout this batch script file:
# * CHANGE yourusername to your username;
# * CHANGE youremailaddress@yourinstitution.edu to your e-mail address;
# * CHANGE directory_to_run_in to the directory you want to run in;
# * CHANGE jobname to your preferred name for this batch job.
#
# Here, also CHANGE executable_directory to the directory where your
# executable resides, CHANGE executable_filename to the name of the
# executable file, CHANGE input_directory to the directory where your
# standard input file resides, and CHANGE input_filename.txt to the
# name of your standard input file (that is, the file that you want
# to use for standard input, instead of a user typing live at the
# keyboard, which isn't possible for a batch job).
date
time \
mpirun \
/scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git/lbm \
< /scratch/kasperone1/lbm/lbm2/lbm_scaff10/lbm.git/input.txt \
&& date
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