Commit 0026b2b1 authored by root's avatar root

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
#!/bin/bash
#SBATCH --job-name FDS_example_job
#How many nodes/cores? FDS is MPI enabled and can operate across multiple nodes
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#What is the maximum time this job is expected to take? (Walltime)
#Format: Days-Hours:Minutes:Seconds
#SBATCH --time=1-24:00:00
module load FDS
fds inputfile.fds outputfile.fds
#!/bin/bash
# Name and partition
#SBATCH --job-name=FFTW-test.slurm
#SBATCH -p cloud
# Run on single CPU. This can run with MPI if you have a bit problem.
#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 FFTW/3.3.6-gompi-2017b
# Compile and execute
g++ -lfftw3 fftw_example.c -o fftw_example
./fftw_example > results.txt
# Example from : https://github.com/undees/fftw-example
#!/bin/bash
#SBATCH -p cloud
#SBATCH --ntasks=1
#SBATCH -t 0:15:00
module load FSL/5.0.9-centos6_64
# FSL needs to be sourced
source $FSLDIR/etc/fslconf/fsl.sh
srun bet /usr/local/common/FSL/intro/structural.nii.gz test1FSL -f 0.1
#!/bin/bash
#SBATCH -p cloud
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH -t 0:00:05
module load FSL/5.0.9-centos6_64
# FSL needs to be sourced
source $FSLDIR/etc/fslconf/fsl.sh
time bet /usr/local/common/FSL/intro/structural.nii.gz test1FSL -f 0.1
...@@ -2,7 +2,6 @@ ...@@ -2,7 +2,6 @@
# To give your job a name, replace "MyJob" with an appropriate name # To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=FreePascal-test.slurm #SBATCH --job-name=FreePascal-test.slurm
#SBATCH -p cloud
# Run on single CPU # Run on single CPU
#SBATCH --ntasks=1 #SBATCH --ntasks=1
...@@ -15,6 +14,8 @@ ...@@ -15,6 +14,8 @@
# SBATCH --mail-type=ALL # SBATCH --mail-type=ALL
# Load the environment variables # Load the environment variables
module purge
source /usr/local/module/spartan_old.sh
module load fpc/3.0.4 module load fpc/3.0.4
......
We have a FreePascal compiler on Spartan! # We have a FreePascal compiler on Spartan!
`module load fpc/3.0.4` module purge
/usr/local/module/spartan_old.sh
module load fpc/3.0.4
However, you will also need a fpc.cfg and a fp.cfg, for command-line and gui IDE. This includes PATHs to the various units etc. # However, you will also need a fpc.cfg and a fp.cfg, for command-line and gui IDE. This includes PATHs to the various units etc.
# These are all included in this directory, along with a simple "Hello World" program.
These are all included in this directory, along with a simple "Hello World" program. #
# Compile with
Compile with
`fpc hello.pas`
fpc hello.pas
#!/bin/bash #!/bin/bash
#SBATCH -p cloud
#SBATCH --ntasks=1 #SBATCH --ntasks=1
#SBATCH -t 00:15:00 #SBATCH -t 00:15:00
......
...@@ -2,7 +2,7 @@ We don't have the complete set of libraries installed (yet) on the compute nodes ...@@ -2,7 +2,7 @@ We don't have the complete set of libraries installed (yet) on the compute nodes
The following is an example session for visualisation. The following is an example session for visualisation.
[lev@cricetomys HPCshells]$ ssh spartan -Y [lev@cricetomys HPCshells]$ ssh spartan -X
.. ..
[lev@spartan ~]$ module load FreeSurfer/6.0.0-GCC-4.9.2-centos6_x86_64 [lev@spartan ~]$ module load FreeSurfer/6.0.0-GCC-4.9.2-centos6_x86_64
[lev@spartan ~]$ module load X11/20160819-GCC-4.9.2 [lev@spartan ~]$ module load X11/20160819-GCC-4.9.2
......
#!/bin/bash
# To give your job a name, replace "MyJob" with an appropriate name
#SBATCH --job-name=GAMESS-test.slurm
#SBATCH -p cloud
# Run on 1 cores
#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
# GAMESS likes memory!
#SBATCH --mem=64G
# Load the environment variables
module load GAMESS-US/20160708-GCC-4.9.2
rungms exam01.inp
# This is a directory for memory and program debugging and profiling.
# Launch an interactive job for these examples!
sinteractive --partition=physical --ntasks=2 --time=1:00:00
# Valgrind
# The test program valgrindtest.c is form Punit Guron. In this example the memory allocated to the pointer 'ptr' is never freed in the program.
# Load the module and compile with debugging symbols.
module load Valgrind/3.13.0-goolf-2015a
gcc -Wall -g valgrindtest.c -o valgrindtest
valgrind --leak-check=full ./valgrindtest 2> valgrind.out
# GDB
# Compile with debugging symbols. A good compiler will give a warning here, and run the program.
gcc -Wall -g gdbtest.c -o gdbtest
$ ./gdbtest
Enter the number: 3
The factorial of 3 is 0
# Load the GDB module e.g.,
module load GDB/7.8.2-goolf-2015a
# Launch GDB, set up a break point in the code, and execute
gbd gdbtest
..
(gdb) break 10
(gdb) run
(gdb) print j
# Basic commands in GDB
# run = run a program until end, signit, or breakpoint. Use Ctrl-C to stop
# break = set a breakpoint, either by linenumber, function etc. (shortcut b)
# list = list the code above and below where the program stopped (shortcut l)
# continue = restart execution of program where is stopped (shortcut c).
# print = print a variable (shortcut p)
# next, step = after using a signal or breakpoint use next and step to
# continue a progame line-by-line.
# NB: next will go 'over' the function call to the next line of code,
# step will go 'into' the function call (shortcut s)
#
# Variables can be temporarily modified with the `set` command
# e.g., set j=1
# The code will hit the breakpoint where you can interrogate the variables.
# Testing the variable 'j' will show it has not been initialised.
# Create a new file, initialise j to 1, and test again.
cp gdbtest.c gdbtest2.c
gcc -Wall -g gdbtest2.c -o gdbtest2
$ ./gdbtest
# There is still another bug! Can you find it? Use GDB to help.
# Once you have fixed the second bug, use diff and patch to fix the original.
# The -u option provides unified content for both files.
diff -u gdbtest.c gdbtest2.c > gdbpatch.patch
# The patch command will overwrite the source with the modifications
# specified in the destination. Test the original again!
patch gdbtest.c gdbpatch.patch
# For Gprof, instrumentation code is inserted with the `-pg` option when
# compiled.
#
# GPROF output consists of two parts; the flat profile and the call graph.
# The flat profile gives the total execution time spent in each function.
# The textual call graph, shows for each function;
# (a) who called it (parent) and (b) who it called (child subroutines).
#