Merge pull request #2 from owainkenwayucl/master

Include git application test

Applications/LAMMPS/HECBioSim/scripts/young-lammps-intel-80cores.sh

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+#!/bin/bash -l
+
+#$ -l h_rt=6:00:00
+#$ -l mem=4000M
+#$ -cwd
+#$ -pe mpi 80
+
+#$ -A Test_allocation
+#$ -P Free
+
+module load default-modules/2018
+module load lammps/7Aug19/userintel/intel-2018
+
+export KMP_BLOCKTIME=0
+gerun `which lmp_default` -pk intel 0 omp 1 -sf intel -in benchmark.in.intel

Applications/LAMMPS/at.young-thr.sh

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+#!/bin/bash -l
+
+# Job script for running LAMMPS as an acceptance test on UCL software stack.
+# Owain Kenway
+
+#$ -S /bin/bash
+
+#$ -l h_rt=12:0:0
+
+#$ -l mem=1G
+
+#$ -N lammps-12hr
+
+#$ -cwd
+
+# Modify following according to what is suitable for this architecture.
+#$ -pe mpi 160
+
+#$ -l threads=1
+
+# You need to amend the next two lines for your account.
+#$ -A Test_allocation 
+#$ -P Free
+
+module load rcps-core/1.0.0
+module load compilers/intel/2018
+module load mpi/intel/2018
+# module load lammps/7Aug19/userintel/intel-2018
+module load lammps/7Aug19/userintel/intel-2018 # Intel optimised alternative
+
+export OMP_NUM_THREADS=2
+
+#gerun  lmp_default -in in.rhodo.at.kathleen -log log.at.$JOB_ID
+gerun  lmp_default -sf intel -in in.rhodo.at.kathleen -log log.at.$JOB_ID # Intel optimised alternative

Applications/LAMMPS/at.young.sh

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+#!/bin/bash -l
+
+# Job script for running LAMMPS as an acceptance test on UCL software stack.
+# Owain Kenway
+
+#$ -S /bin/bash
+
+#$ -l h_rt=12:0:0
+
+#$ -l mem=1G
+
+#$ -N lammps-12hr
+
+#$ -cwd
+
+# Modify following according to what is suitable for this architecture.
+#$ -pe mpi 80
+
+# You need to amend the next two lines for your account.
+#$ -A Test_allocation 
+#$ -P Free
+
+module load rcps-core/1.0.0
+module load compilers/intel/2018
+module load mpi/intel/2018
+#module load lammps/7Aug19/basic/intel-2018
+module load lammps/7Aug19/userintel/intel-2018 # Intel optimised alternative
+
+#gerun  lmp_default -in in.rhodo.at.kathleen -log log.at.$JOB_ID
+gerun  lmp_default -sf intel -in in.rhodo.at.thomas -log log.at.$JOB_ID # Intel optimised alternative

Applications/git/README.md

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+# Git Application test
+
+This test tests a file-system's performance creating and manipulating small files by cloning the Spack repository.
+
+Slow file-systems time out while doing this.  
+
+The test is simple:
+
+```console
+$ time git clone https://github.com/spack/spack.git
+Cloning into 'spack'...
+remote: Enumerating objects: 325196, done.
+remote: Counting objects: 100% (525/525), done.
+remote: Compressing objects: 100% (321/321), done.
+remote: Total 325196 (delta 207), reused 376 (delta 120), pack-reused 324671
+Receiving objects: 100% (325196/325196), 134.56 MiB | 3.37 MiB/s, done.
+Resolving deltas: 100% (140857/140857), done.
+Updating files: 100% (8707/8707), done.
+
+real	11m42.167s
+user	0m27.791s
+sys	0m7.893s
+```
+
+This test is pass/fail.