From d53e680698028a825882616483c6bd5c60ed59d3 Mon Sep 17 00:00:00 2001
From: Owain Kenway <o.kenway@ucl.ac.uk>
Date: Fri, 31 Jul 2020 13:22:47 +0100
Subject: [PATCH 1/3] Test scripts for Young.

---
 Applications/LAMMPS/at.young-thr.sh | 34 +++++++++++++++++++++++++++++
 Applications/LAMMPS/at.young.sh     | 30 +++++++++++++++++++++++++
 2 files changed, 64 insertions(+)
 create mode 100755 Applications/LAMMPS/at.young-thr.sh
 create mode 100755 Applications/LAMMPS/at.young.sh

diff --git a/Applications/LAMMPS/at.young-thr.sh b/Applications/LAMMPS/at.young-thr.sh
new file mode 100755
index 0000000..18170c6
--- /dev/null
+++ b/Applications/LAMMPS/at.young-thr.sh
@@ -0,0 +1,34 @@
+#!/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
diff --git a/Applications/LAMMPS/at.young.sh b/Applications/LAMMPS/at.young.sh
new file mode 100755
index 0000000..b91a4ac
--- /dev/null
+++ b/Applications/LAMMPS/at.young.sh
@@ -0,0 +1,30 @@
+#!/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

From 653ffeffecca32493023f631eb38a9a4eba58316 Mon Sep 17 00:00:00 2001
From: Owain Kenway <o.kenway@ucl.ac.uk>
Date: Fri, 31 Jul 2020 13:32:13 +0100
Subject: [PATCH 2/3] HECBioSim Script for Young.

---
 .../scripts/young-lammps-intel-80cores.sh         | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 Applications/LAMMPS/HECBioSim/scripts/young-lammps-intel-80cores.sh

diff --git a/Applications/LAMMPS/HECBioSim/scripts/young-lammps-intel-80cores.sh b/Applications/LAMMPS/HECBioSim/scripts/young-lammps-intel-80cores.sh
new file mode 100644
index 0000000..6326bd4
--- /dev/null
+++ b/Applications/LAMMPS/HECBioSim/scripts/young-lammps-intel-80cores.sh
@@ -0,0 +1,15 @@
+#!/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

From c8df68a4baa4abc08bfd2f499374325d6d60bc7e Mon Sep 17 00:00:00 2001
From: Owain Kenway <o.kenway@ucl.ac.uk>
Date: Tue, 2 Nov 2021 11:58:01 +0000
Subject: [PATCH 3/3] Git application test.

---
 Applications/git/README.md | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 Applications/git/README.md

diff --git a/Applications/git/README.md b/Applications/git/README.md
new file mode 100644
index 0000000..ab28a40
--- /dev/null
+++ b/Applications/git/README.md
@@ -0,0 +1,25 @@
+# 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.
\ No newline at end of file