Update for 20/12

.gitignore

+ABAQUS/Door.odb
+AFNI/ARzs_data.tgz
+Beast/Dengue4.env.trees
 BLAST/dbs
 BLAST/rat-ests
 Cufflinks/sample.bam
+Delft3D/*
+!Delft3D/Delft3D-test.slurm
+!Delft3D/run_all_examples.sh
+!Delft3D/run_all_examples_sp.sh
+!Delft3D/sed_in_file.tcl
 digits/digits.img
 FreeSurfer/buckner_data
 FreeSurfer/buckner_data-tutorial_subjs.tar.gz

Delft3D/Delft3D-test.slurm

+#!/bin/bash
+
+# Name and Partition
+#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 purge
+module load Delft3D/7545-intel-2016.u3
+
+./run_all_examples.sh

Delft3D/run_all_examples.sh

+#!/bin/bash
+
+
+echo "Running testcase 01_standard ..."
+cd 01_standard
+./run_flow2d3d.sh >screen.log 2>&1
+
+
+echo "Running testcase 01_standard parallel ..."
+./run_flow2d3d_parallel.sh >screen_parallel.log 2>&1
+cd ..
+
+
+echo "Running testcase 02_domaindecomposition ..."
+cd 02_domaindecomposition
+./run_flow2d3d.sh >screen.log 2>&1
+cd ..
+
+
+echo "Running testcase 03_flow-wave ..."
+cd 03_flow-wave
+./run_flow2d3d.sh >screen.log 2>&1
+
+
+echo "Running testcase 03_flow-wave parallel ..."
+./run_flow2d3d_parallel_wave.sh >screen_parallel.log 2>&1
+cd ..
+
+
+echo "Running testcase 04_fluidmud ..."
+cd 04_fluidmud
+./run_flow2d3d_flm.sh >screen.log 2>&1
+cd ..
+
+
+echo "Running testcase 05_mormerge ..."
+cd 05_mormerge/merge
+./run_flow2d3d_wave_mormerge.sh >screen.log 2>&1
+cd ../..
+
+
+echo "Running testcase 06_delwaq ..."
+cd 06_delwaq
+./run_delwaq.sh >screen.log 2>&1
+cd ..
+
+
+echo "Running testcase 07_wave ..."
+cd 07_wave
+./run_wave.sh >screen.log 2>&1
+cd ..
+
+
+echo "Running testcase 08_part-tracer ..."
+cd 08_part-tracer
+./run_part.sh >screen.log 2>&1
+cd ..
+
+
+echo "Running testcase 09_part-oil ..."
+cd 09_part-oil
+./run_part.sh >screen.log 2>&1
+cd ..
+
+
+echo "Running testcase 10_delwaq-part-tracer ..."
+cd 10_delwaq-part-tracer
+./run_delwaq_part.sh >screen.log 2>&1
+cd ..
+
+
+echo "Running testcase 11_standard_netcdf ..."
+cd 11_standard_netcdf
+./run_flow2d3d.sh >screen.log 2>&1
+cd ..
+
+
+echo ...finished
+

Delft3D/run_all_examples_sp.sh

+#!/bin/bash
+
+
+echo "Running testcase 01_standard (sp) ..."
+cd 01_standard
+../sed_in_file.tcl config_d_hydro.xml "<library>flow2d3d" "<library>flow2d3d_sp"
+./run_flow2d3d.sh >screen.log 2>&1
+
+
+echo "Running testcase 01_standard parallel (sp) ..."
+./run_flow2d3d_parallel.sh >screen_parallel.log 2>&1
+   # Undo changes
+../sed_in_file.tcl config_d_hydro.xml "<library>flow2d3d_sp" "<library>flow2d3d"
+cd ..
+
+
+echo "Running testcase 02_domaindecomposition (sp) ..."
+cd 02_domaindecomposition
+../sed_in_file.tcl config_d_hydro.xml "<library>flow2d3d" "<library>flow2d3d_sp"
+./run_flow2d3d.sh >screen.log 2>&1
+../sed_in_file.tcl config_d_hydro.xml "<library>flow2d3d_sp" "<library>flow2d3d"
+cd ..
+
+
+echo "Running testcase 03_flow-wave (sp) ..."
+cd 03_flow-wave
+../sed_in_file.tcl config_d_hydro.xml "<library>flow2d3d" "<library>flow2d3d_sp"
+./run_flow2d3d.sh >screen.log 2>&1
+
+
+echo "Running testcase 03_flow-wave parallel (sp) ..."
+./run_flow2d3d_parallel_wave.sh >screen_parallel.log 2>&1
+../sed_in_file.tcl config_d_hydro.xml "<library>flow2d3d_sp" "<library>flow2d3d"
+cd ..
+
+
+echo "Running testcase 04_fluidmud (sp) ..."
+cd 04_fluidmud
+../sed_in_file.tcl config_d_hydro_mud.xml "<library>flow2d3d" "<library>flow2d3d_sp"
+../sed_in_file.tcl config_d_hydro_sed.xml "<library>flow2d3d" "<library>flow2d3d_sp"
+./run_flow2d3d_flm.sh >screen.log 2>&1
+../sed_in_file.tcl config_d_hydro_mud.xml "<library>flow2d3d_sp" "<library>flow2d3d"
+../sed_in_file.tcl config_d_hydro_sed.xml "<library>flow2d3d_sp" "<library>flow2d3d"
+cd ..
+
+
+echo "Running testcase 05_mormerge (sp) ..."
+cd 05_mormerge/input
+../../sed_in_file.tcl config_d_hydro.xml "<library>flow2d3d" "<library>flow2d3d_sp"
+cd ../merge
+./run_flow2d3d_wave_mormerge.sh >screen.log 2>&1
+cd ../input
+../../sed_in_file.tcl config_d_hydro.xml "<library>flow2d3d_sp" "<library>flow2d3d"
+cd ../..
+
+
+echo "Skipping testcases 06_delwaq, 07_wave, 08_part-tracer, 09_part-oil, and 10_delwaq-part-tracer (no sp variant)"
+
+
+echo "Running testcase 11_standard_netcdf (sp) ..."
+cd 11_standard_netcdf
+../sed_in_file.tcl config_d_hydro.xml "<library>flow2d3d" "<library>flow2d3d_sp"
+./run_flow2d3d.sh >screen.log 2>&1
+../sed_in_file.tcl config_d_hydro.xml "<library>flow2d3d_sp" "<library>flow2d3d"
+cd ..
+
+
+echo ...finished
+

Delft3D/sed_in_file.tcl

+#! /usr/bin/tclsh
+
+global argv
+
+set filename [lindex $argv 0]
+set searchstring  [lindex $argv 1]
+set replacestring  [lindex $argv 2]
+
+set infile [open $filename]
+set wholefile [read $infile]
+close $infile
+set newfile {}
+foreach line [split $wholefile "\n"] {
+   regsub -all -- "$searchstring" $line "$replacestring" line
+   lappend newfile $line
+}
+set outfile [open $filename "w"]
+puts -nonewline $outfile [join $newfile "\n"] 
+close $outfile
+

SQLite/SQLite-test.slurm

+#!/bin/bash
+
+# Job and partition
+#SBATCH --job-name=SQLite-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 purge
+module load SQLite/3.27.2-spartan_gcc-8.1.0
+
+# SQLite has "dot commands" which you can use for file operations and
+# database commands.
+
+sqlite3 earthquake.db < commands.sql

SQLite/commands.sql

+create table richter(one varchar(10), two smallint, three vachar(50));
+insert into richter values('Micro',1,'Cannot be felt');
+insert into richter values('Minor',3,'Often felt');
+insert into richter values('Moderate',5,'Felt. Light objects damaged');
+insert into richter values('Major',7,'Heavy items damaged, large area');
+insert into richter values('Massive',9,'Intense damage, buildings toppled, cracks in ground');
+.save earthquake.db
+.mode list
+.separator |
+.output textdump.txt
+select * from richter;
+.exit

SQLite/earthquake.sql

+.read file.sql
+.separator ","
+.import quakes.csv table
+.headers on
+.separator "|"
+SELECT EVENT_ID, Latitude FROM table WHERE Latitude < -45 ;
+SELECT count(*) FROM table;

Valgrind/README

+# This is a directory for memory 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

Valgrind/valgrindtest.c

+#include<stdio.h>
+#include<string.h>
+#include<stdlib.h>
+
+int main(void)
+{
+    char *ptr = (char*)malloc(10);
+    memset(ptr, 0, 10);
+
+    strncpy(ptr, "Linux", strlen("Linux"));
+
+    printf("\n ptr = [%s]\n", ptr);
+    ptr[0] = 'a';
+    printf("\n ptr = [%s]\n", ptr);
+
+    return 0;
+}
+