Commit 0026b2b1 authored by root's avatar root
Browse files

2020/07/22 update

parent 7584a2f4
Current Error
=============
so: undefined symbol: __intel_avx_rep_memcpy
Instructions
============
Abaqus example modified from Lev Lafayette, "Supercomputing with Linux", Victorian Partnership for Advanced Computing, 2015 Abaqus example modified from Lev Lafayette, "Supercomputing with Linux", Victorian Partnership for Advanced Computing, 2015
The Abaqus FEA suite is commonly used in automatic engineering problems using a common model data structure and integrated solver technology. As licensed software it requires a number of license tokens based on the number of cores required, which can be calculated by the simple formula int(5 x N^0.422), where N is the number of cores. Device Analytics offers an online calculator at http://deviceanalytics.com/abaqus-token-calculator . The Abaqus FEA suite is commonly used in automatic engineering problems using a common model data structure and integrated solver technology. As licensed software it requires a number of license tokens based on the number of cores required, which can be calculated by the simple formula int(5 x N^0.422), where N is the number of cores. Device Analytics offers an online calculator at http://deviceanalytics.com/abaqus-token-calculator .
......
#!/bin/bash
#SBATCH --ntasts=1
#SBATCH --time=0:05:00
#SBATCH --GRES=abaqus+5
module load ABAQUS/6.14.2-linux-x86_64
# Run the job 'Door'
abaqus job=Door
#!/bin/bash
#SBATCH --partition=physical
#SBATCH --time=1:00:00
#SBATCH --ntasks=8
module load ABINIT/8.0.8b-intel-2016.u3
abinit < tbase1_x.files >& log
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=ABRicate-test.slurm
#SBATCH -p cloud
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module load ABRicate/0.8.7-spartan_intel-2017.u2
# The command to actually run the job
abricate ecoli_rel606.fasta
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=ABySS-test.slurm
#SBATCH -p cloud
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module load ABySS/2.0.2-goolf-2015a
# Assemble a small synthetic data set
tar xzvf test-data.tar.gz
sleep 20
abyss-pe k=25 name=test in='test-data/reads1.fastq test-data/reads2.fastq'
# Calculate assembly contiguity statistics
abyss-fac test-unitigs.fa
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=ADMIXTURE-test.slurm
#SBATCH -p cloud
# Run with two threads
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module load ADMIXTURE/1.3.0
# Untar sample files, run application
# See admixture --help for options.
tar xvf hapmap3-files.tar.gz
admixture -j2 hapmap3.bed 1
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=AFNI-test.slurm
#SBATCH -p cloud
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module load AFNI/linux_openmp_64-spartan_intel-2017.u2-20190219
# Untar dataset and run script
tar xvf ARzs_data.tgz
./@ARzs_analyze
#!/bin/bash
# SBATCH --account=punim0396
# SBATCH --partition=punim0396
#SBATCH --job-name="ANSYS test"
#SBATCH --partition=physical-cx4
#SBATCH --ntasks=1
#SBATCH --time=0-00:10:00
#SBATCH --gres=aa_r+1%aa_r_hpc+12
module load ansys/19.0-intel-2017.u2
ansys19 -b < OscillatingPlate.inp > OscillatingPlate.db
#!/bin/bash
# Job name and partition
#SBATCH --job-name=ARAGORN-test.slurm
#SBATCH -p cloud
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module load ARAGORN/1.2.36-GCC-4.9.2
# Run the application
aragorn -o results sample.fa
#!/bin/bash
# Add your project account details here.
# SBATCH --account=XXXX
#SBATCH --partition=gpgpu
#SBATCH --ntasks=4
#SBATCH --time=1:00:00
module load Amber/16-gompi-2017b-CUDA-mpi
mpiexec /usr/local/easybuild/software/Amber/16-gompi-2017b-CUDA-mpi/amber16/bin/pmemd.cuda_DPFP.MPI -O -i mdin -o mdout -inf mdinfo -x mdcrd -r restrt
#!/bin/bash
# Job name and partition
#SBATCH --job-name=BAMM-test.slurm
#SBATCH -p cloud
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Speciation-extinction analyses
# You must have an ultrametric phylogenetic tree.
# Load the environment variables
module load BAMM/2.5.0-spartan_intel-2017.u2
# Example from: `http://bamm-project.org/quickstart.html`
# To run bamm you must specify a control file.
# The following is for diversification.
# You may wish to use traits instead
# bamm -c template_trait.txt
bamm -c template_diversification.txt
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=ABySS-test.slurm
#SBATCH -p cloud
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module load BBMap/36.62-intel-2016.u3-Java-1.8.0_71
# See examples at:
# http://seqanswers.com/forums/showthread.php?t=58221
reformat.sh in=sample1.fq out=processed.fq
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=BEDTools-test.slurm
#SBATCH -p cloud
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module load BEDTools/2.28.0-spartan_intel-2017.u2
# BEDTools has an extensive test suite; but the tests assumes the wrong
# location for the application!
# So all these tests need to be be modified to include:
# BT=$(which bedtools)
cp -r /usr/local/easybuild/software/BEDTools/2.27.1-intel-2017.u2/test/* .
find ./ -type f -exec sed -i -e 's/${BT-..\/..\/bin\/bedtools}/$(which bedtools)/g' {} \;
sh test.sh
# Specific example commands available here:
# https://bedtools.readthedocs.io/en/latest/content/example-usage.html#bedtools-intersect
# Calculate assembly contiguity statistics
abyss-fac test-unitigs.fa
#!/bin/bash
# Set the partition
#SBATCH -p cloud
# Set the number of processors that will be used.
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
# Set the walltime (10 hrs)
#SBATCH --time=10:00:00
# Load the environment variables
module load BLAST/2.2.26-Linux_x86_64
# Run the job
blastall -i ./rat-ests/rn_est -d ./dbs/rat.1.rna.fna -p blastn -e 0.05 -v 5 -b 5 -T F -m 9 -o rat_blast_tab.txt -a 8
#!/bin/bash
#SBATCH --partition=cloud
#SBATCH --time=2:00:00
#SBATCH --ntasks=1
mkdir -p data/ref_genome
curl -L -o data/ref_genome/ecoli_rel606.fasta.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/017/985/GCA_000017985.1_ASM1798v1/GCA_000017985.1_ASM1798v1_genomic.fna.gz
sleep 30
gunzip data/ref_genome/ecoli_rel606.fasta.gz
curl -L -o sub.tar.gz https://downloader.figshare.com/files/14418248
sleep 60
tar xvf sub.tar.gz
mv sub/ data/trimmed_fastq_small
mkdir -p results/sam results/bam results/bcf results/vcf
module load BWA/0.7.17-intel-2017.u2
bwa index data/ref_genome/ecoli_rel606.fasta
bwa mem data/ref_genome/ecoli_rel606.fasta data/trimmed_fastq_small/SRR2584866_1.trim.sub.fastq data/trimmed_fastq_small/SRR2584866_2.trim.sub.fastq > results/sam/SRR2584866.aligned.sam
samtools view -S -b results/sam/SRR2584866.aligned.sam > results/bam/SRR2584866.aligned.bam
samtools sort -o results/bam/SRR2584866.aligned.sorted.bam results/bam/SRR2584866.aligned.bam
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=BEAST-test.slurm
#SBATCH -p cloud
# Run on 4 cores
#SBATCH --ntasks=4
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module load Beast/2.3.1-intel-2016.u3
beast Dengue4.env.xml
#!/bin/bash
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
# You might need an external license file
# export LM_LICENSE_FILE=port@licenseserver
module load COMSOL/5.2
# Example batch command from csiro.org.au
comsol batch -inputfile mymodel.mph -outputfile mymodelresult.mph -batchlog mybatch.log -j b1 -np 8 -mpmode owner
#!/bin/bash
# Name and Partition
#SBATCH --job-name=CPMD-test.slurm
#SBATCH -p cloud
# Run on two cores
#SBATCH --ntasks=2
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module load CPMD/4.3-intel-2018.u4
# Example taken from Axek Kohlmeyer's classic tutorial
# http://www.theochem.ruhr-uni-bochum.de/~legacy.akohlmey/cpmd-tutor/index.html
mpiexec -np 2 cpmd.x 1-h2-wave.inp > 1-h2-wave.out
#!/bin/bash
#SBATCH --job-name=Cufflinks-test.slurm
#SBATCH -p cloud
# Multicore
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=2
# set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 1:00:00
# Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu
# SBATCH --mail-type=ALL
# Load the environment variables
module purge
module load Cufflinks/2.2.1-GCC-4.9.2
# Set the Cufflinks environment
CUFFLINKS_OUTPUT="${PWD}"
cufflinks --quiet --num-threads $SLURM_NTASKS --output-dir $CUFFLINKS_OUTPUT sample.bam
#!/bin/bash #!/bin/bash
# Name and Partition # Name and Partition
#SBATCH --job-name=ABySS-test.slurm #SBATCH --job-name=Deflt3D-test.slurm
#SBATCH -p cloud
# Run on single CPU
#SBATCH --ntasks=1
# set your minimum acceptable walltime=days-hours:minutes:seconds # set your minimum acceptable walltime=days-hours:minutes:seconds
#SBATCH -t 0:15:00 #SBATCH -t 1:00:00
# Specify your email address to be notified of progress. # Specify your email address to be notified of progress.
# SBATCH --mail-user=youreamiladdress@unimelb.edu # SBATCH --mail-user=youreamiladdress@unimelb.edu
...@@ -16,6 +12,7 @@ ...@@ -16,6 +12,7 @@
# Load the environment variables # Load the environment variables
module purge module purge
source /usr/local/module/spartan_old.sh
module load Delft3D/7545-intel-2016.u3 module load Delft3D/7545-intel-2016.u3
./run_all_examples.sh ./run_all_examples.sh
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment