Commit 2f8c1efb authored by root's avatar root

Fix email addresses and remove module load spartan_2019

parent 737b9070
......@@ -43,3 +43,4 @@ Trimmomatic/.backup
*.odb
*.csv
*.data
*.inp
......@@ -10,7 +10,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
......@@ -10,7 +10,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
......@@ -10,7 +10,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
......@@ -10,7 +10,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
......@@ -11,7 +11,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
......@@ -11,7 +11,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
......@@ -10,7 +10,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
......@@ -10,7 +10,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
#!/bin/bash
#SBATCH --job-name="2015ANSYS2dstress"
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < 2dstress.inp > 2dstress.out
#!/bin/bash
#SBATCH --job-name="2015ANSYS2drtuss"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < 2dtruss.inp > 2dtruss.out
#!/bin/bash
#SBATCH --job-name="2015ANSYS3dbike"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < 3dbike.inp > 3dbike.out
#!/bin/bash
#SBATCH --job-name="2015ANSYSArray"
#SBATCH --time=0:15:00
#SBATCH --array=1-2
echo "Starting task $SLURM_ARRAY_TASK_ID"
DIR=$(sed -n "${SLURM_ARRAY_TASK_ID}p" ansysdirs)
cd $DIR
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
# Place the code to execute here
input=*.inp
output=$(echo $input | cut -d'.' -f 1)
ansys190 -b < $input > ${output}.out
../2dtruss
../3dbike
#!/bin/bash
#SBATCH --job-name="2015ANSYSAxisymmetry"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < Axisymmetry.inp > Axisymmetry.out
#!/bin/bash
#SBATCH --job-name="2015ANSYSbeam"
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < beamsolid.inp > beamsolid.db
#!/bin/bash
#SBATCH --job-name="2015ansysBuckling"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < Buckling1.inp > Buckling1.out
#!/bin/bash
#SBATCH --job-name="2015ansysBuckling"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < Buckling2.inp > Buckling2.out
#!/bin/bash
#SBATCH --job-name="2015ansysDistLoad"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < DistLoad.inp > DistLoad.out
#!/bin/bash
#SBATCH --job-name="2015ansysDynamicHarmonic"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < DynamicHarmonic.inp > DynamicHarmonic.out
#!/bin/bash
#SBATCH --job-name="2015ansysDynamicModal"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < DynamicModal.inp > DynamicModal.out
#!/bin/bash
#SBATCH --job-name="2015ansysDynamicTransient"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < DynamicTransient.inp > DynamicTransient.out
#!/bin/bash
#SBATCH --job-name="2015ansysNonLinearA"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < NonLinearA.inp > NonLinearA.out
#!/bin/bash
#SBATCH --job-name="2015ansysNonLinearB"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < NonLinearB.inp > NonLinearB.out
This source diff could not be displayed because it is too large. You can view the blob instead.
#!/bin/bash
#SBATCH --job-name="2015ANSYStest"
#SBATCH --job-name="2015ANSYSplate"
# Note this order has to be kept. It's horrible, but it works.
module purge
......
This diff is collapsed.
#!/bin/bash
# job name:
#PBS -N ansys_benchmark
# how many cpus?
#PBS -l nodes=1:ppn=2
# How long to run the job? (hours:minutes:seconds)
# You will almost certainly need to change this.
#PBS -l walltime=00:15:00
# Wait for license file
# Please leave this as it is, makes it a lot safer.
# PBS -W x=gres:aa_r+1
#PBS -W x=GRES:aa_r+1%aa_r_hpc+2
# Environmental varibles to make it work:
module load ansys/145
cd $PBS_O_WORKDIR
# Launching the job!
NODES=$(cat $PBS_NODEFILE | sort | uniq -c | awk '{print $2 "*" $1}' | tr '\n' ',' | sed 's/,$//')
echo "This job is allocated on $NODES"
cfx5solve -def Benchmark.def -parallel -par-dist $NODES
#!/bin/bash
# ------------------------------------
# ANSYS - CFX FSI script.
# All you need change is wall time and name of input files.
# And possibly the job name.
# -----------------------------------
# pbs launching script example for ANSYS job:
# job name: --- Change this if you like
#PBS -N ansys_job_01
# how many cpus? --- Probably best choice.
#PBS -l nodes=8
# How long to run the job? (hours:minutes:seconds)
# You will almost certainly need to change this.
#PBS -l walltime=00:30:00
# Name of output file:
# PBS -o ansys_test_job_02.txt
# Wait for license file
# Please leave this as it is, makes it a lot safer.
# PBS -l software=aa_r+1
#PBS -W x=GRES:aa_r+1%aa_r_hpc+2
# For CFX use only
# PBS -l software=cfx_par_proc+8
# Environmental varibles to make it work:
module load ansys/145
cd $PBS_O_WORKDIR
# Launching the job!
NODES=$(cat $PBS_NODEFILE | sort | uniq -c | awk '{print $2 "*" $1}' | tr '\n' ',' | sed 's/,$//')
echo "This job is allocated on $NODES"
cfx5solve -def OscillatingPlate.def -ansys-input OscillatingPlate.inp -parallel -par-dist $NODES
Please note that this tutorial is not complete yet!
# ANSYS Job Submission Examples
## Introduction
All the examples here use the old build system and ANSYS_CFD v19.0 (2019).
The example OscillatingPlate is a classic from ANSYS involving a plate in a Fluid-Structure Interaction (FSI). The original example for High
Performance Computing was from the Victorian Partnership for Advanced Computing (2015) using TORQUE PBS and then ported to the Univeristy of
Melbourne using the Slurm Workload Manager.
All other examples come from the rather impressive ANSYS tutorial collection from the University of Alberta
(https://sites.ualberta.ca/~wmoussa/AnsysTutorial/index.html). As should be evident from these, only part of ANSYS (the computation side for
solving) is represented in batch processing. Interactive visualisation and post-processing interpretation requires a different approach.
## Directory Listing
The directories are as follows:
2dtruss: Basic functions will be shown to provide you with a general knowledge of command line codes.
3dbike: Intermediate ANSYS functions will be shown in detail to provide you with a more general understanding of how to use ANSYS.
2dstress: Boolean operations, plane stress and uniform pressure loading will be introduced in the creation and analysis of this 2-Dimensional
object.
Solid: This tutorial will introduce techniques such as filleting, extrusion, copying and working plane orienation to create 3-Dimensional
objects.
SelfWeight: Incorporating the weight of an object into the finite element analysis is shown in this simple cantilever beam example.
DistLoad: The application of distributed loads and the use of element tables to extract datal.
NonLinearA: A large moment is applied to the end of a cantilever beam to explore Geometric Nonlinear behaviour (large deformations).
BucklingE: Use both Eigenvalue and Nonlinear methods are used to solve a simple buckling problem.
BucklingN: Use both Eigenvalue and Nonlinear methods are used to solve a simple buckling problem.
NonLinearB: How to include material nonlinearities in an ANSYS model.
DynamicModal: Explore the modal analyis capabilities of ANSYS.
DynamicHarmonic: Explore the harmonic analyis capabilities of ANSYS.
DynamicTransient: Explore the transient analyis capabilities of ANSYS.
ThermalPure: Analysis of a pure conduction boundary condition example.
ThermalMix: Analysis of a Mixed Convection/Conduction/Insulated boundary condition example.
ThermalTrans: Analysis of heat conduction over time.
Axisymmetry: Utilizing axisymmetry to model a 3-D structure in 2-D to reduce computational time.
Again, it is re-iterated, these are not complete tutorials for ANSYS, just batch examples for the solver computation portion of the various
tasks. See the University of Alberta website for complete tutorials.
## Array
A sample directory-driven job array is provided that takes a list of ANSYS directories and runs the jobs simultaneously. This will save you a
lot of time!
## Note for admins.
There will be changes to dependent software due to change in toolchain. Attempts to use a more consistent toolchain for X11 with GCC/4.9.2
result in libXp.so.6 shared object file not found. The modules we have in these examples, whilst truly ugly, does work.
Last update: LL20210216
#!/bin/bash
#SBATCH --job-name="2015ANSYSSelfWeight"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < SelfWeight.inp > SelfWeight.out
#!/bin/bash
#SBATCH --job-name="2015ANSYSolid"
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < solid.inp > solid.out
#!/bin/bash
#SBATCH --job-name="2015ThermalMix"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < ThermalMix.inp > ThermalMix.out
#!/bin/bash
#SBATCH --job-name="2015ThermalPure"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < ThermalPure.inp > ThermalPure.out
#!/bin/bash
#SBATCH --job-name="2015ThermalTrans"
#SBATCH --time=0:15:00
# Note this order has to be kept. It's horrible, but it works.
module purge
source /usr/local/module/spartan_old.sh
module load X11/20190311-spartan_gcc-6.2.0
module load motif/2.3.5-goolf-2015a
module load libXpm/3.5.11-goolf-2015a
module load ANSYS_CFD/19.0
ansys190 -b < ThermalTrans.inp > ThermalTrans.out
......@@ -7,7 +7,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
......@@ -13,11 +13,24 @@ As with all Slurm directives, the SBATCH command can be applied within the batch
To convert a directory of files to include an array ID see the following example:
```
$ touch aaa.fastq.gz bbb.fastq.gz ccc.fastq.gz ddd.fastq.gz
$ ls
aaa.fastq.gz bbb.fastq.gz ccc.fastq.gz ddd.fastq.gz
$ n=1; for f in *fastq.gz; do mv "$f" "$((n++))$f"; done
$ ls
1aaa.fastq.gz 2bbb.fastq.gz 3ccc.fastq.gz 4ddd.fastq.gz
```
See also the Octave array example in /usr/local/common/Octave.
An alternative would be to read in the files using sed. Insert the following into the job submission script immediately after the Slurm
directives. For example;
```
item=$(ls *.fastq.gz | sed -n ${SLURM_ARRAY_TASK_ID}p)
```
The example "folders" illustrates the use of datasets in separate folders. This example is derived from Compute/Calcul Canada.
See also the Octave array example in /usr/local/common/Octave for the use of multiple files or scripts as an array.
See also the Array directory in /usr/local/common/ANSYS/Array and /usr/local/common/R/Array for the use of folders as an array.
pacific2016
pacific2017
atlantic2016
atlantic2017
#!/bin/bash
#SBATCH --array=1-4
echo "Starting task $SLURM_ARRAY_TASK_ID"
DIR=$(sed -n "${SLURM_ARRAY_TASK_ID}p" case_list)
cd $DIR
# Place the code to execute here
pwd
ls
......@@ -10,7 +10,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Speciation-extinction analyses
......
......@@ -10,7 +10,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Speciation-extinction analyses
......
......@@ -10,7 +10,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
......@@ -10,7 +10,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
......@@ -7,7 +7,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
......@@ -7,7 +7,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
......@@ -10,7 +10,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
......@@ -10,7 +10,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......
......@@ -10,7 +10,7 @@
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-user=youremailaddress@unimelb.edu.au
# SBATCH --mail-type=ALL
# Load the environment variables
......