Commit 7584a2f4 authored by root's avatar root

Update for 20/12

parent 0427871f
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
......
This diff is collapsed.
#!/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
#!/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
#!/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
#! /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
#!/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
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
.read file.sql
.separator ","
.import quakes.csv table
.headers on
.separator "|"
SELECT EVENT_ID, Latitude FROM table WHERE Latitude < -45 ;
SELECT count(*) FROM table;
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# 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
#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;
}
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