3. How to...

How to...


  • How to record a video of your screen on Windows 10:

    • press Win + Alt + R to start your recording

  • How to build an app with passthrough for the Oculus Quest 2


  • How to search for units in a specific building on domain.com.au:
    https://www.domain.com.au/sale/?excludeunderoffer=1&carspaces=1-any&street=70+mary+street

    How to search for units in a specific building on realestate.com.au:

    https://www.realestate.com.au/buy/in-70+mary+st,+brisbane+city,+qld+4000/list-1?numParkingSpaces=1&includeSurrounding=false&misc=ex-under-contract&activeSort=list-date&source=refinement

  • How to install sidewall flashing against weatherboard at an angle:
    https://www.youtube.com/watch?v=iPwAj5BCINI&t=358s


  • How to optimise Java heap size Xmx for GATK:
    https://ovarflow.readthedocs.io/en/latest/ResourceRequirements/Benchmarking/JavaXmx.html


  • How to do mixed reality capture with Oculus Quest 2


  • How to decide which hypothesis test to use:

    hypothesis testing flow diagram.jpg


  • %(#ffffff)[How to fix the desktop displaying as a black screen when using Oculus link with Windows 11:]

    • Go to Windows Settings -> Display -> Graphics -> "Custom options for apps"->"Add an app" ->"Desktop app". Click "Browse" and select:
    C:\Program Files\Oculus\Support\oculus-runtime\OVRServer_x64.exe

    • Click "Add". Select "Options" and set it to "Power saving", and click save.

    • Go into the oculus app on the desktop computer. Go to settings -> beta -> restart oculus.


  • How to transfer files to/from HPC tape storage:

    #To recall a file from tape you must have read access.
#dmget /apollo/dir1/dir2/file
#To migrate a file to tape and keep it on disk (i.e. dual state, state=DUL). You must have write access to file to migrate it.
#dmput /apollo/dir1/dir2/file
#To migrate a file to tape and remove it's disk blocks (i.e. offline, state=OFL)
#dmput -r /apollo/dir1/dir2/file
#To get detailed information about file's attributes.
#dmattr /apollo/dir1/dir2/file
#To determine a file's state, three letter code will be returned. States are listed below.
#dmattr -a state /apollo/dir1/dir2/file
#To determine a file's sitetag.
#dmattr -a sitetag /apollo/dir1/dir2/file
#To prevent file(s) being migrated to tape, set the sitetag to 16.
#dmtag -t 16 /apollo/dir1/dir2/file1 /apollo/dir1/dir2/file2
#alternatively:
#dmfind /apollo/dir/files | dmtag -t 16
#To allow file(s) to migrate to tape, set the sitetag back to 0.
#dmtag -t 0 /apollo/dir1/dir2/file1 /apollo/dir1/dir2/file2

  • How to recursively find all binary files in a folder and change their permission to executable with chmod in linux:

    find /path/of/desired/folder -type f -executable -exec sh -c "file -i '{}' | grep -q 'x-executable; charset=binary'" \; -print | xargs chmod +x

  • How to do 3D pooling of samples:
    Græsbøll 2016 how to do 3D pooling.pdf


  • How to recursively change the permissions of specific file types in a folder using chmod:

    find ./ -type f -iname "*.sh" -exec chmod +x {} \;

  • How to sort fastq files by their titles:

    cat file.fastq | paste - - - - | sort -k1,1 -t " " | tr "\t" "\n" > file_sorted.fastq

  • How to bypass paywalls:
    https://gitlab.com/magnolia1234/bypass-paywalls-chrome-clean


  • How to list all running processes in PBS-PRO

    qstat -rn1tw

  • How to find a best blast hit:

    https://www.biostars.org/p/144569/


  • How to generate pseudohaploid genome assemblies


  • How to calibrate an XYZ Printing da Vinci 2.0 A Duo 3D-printer:

    xyz calibrate.jpg


  • How to make the plastic stick to the base when 3d printing:

    https://www.youtube.com/watch?v=ShFaJ027pFs


  • How to install point-e on Windows 11:

    #in Windows Powershell note down the cuda version from this command:
nvidia-smi.exe

#look up the channel for your cuda version using this site:
#https://anaconda.org/nvidia/repo/installers?


#In Anaconda powershell:
conda update conda
conda update anaconda
conda update python
conda update --all
conda create --name point-e pip
#Now exit from the Powershell you are using and then open a new one before you activate the new "env".
conda activate point-e
#install cuda from the channel identified previously
conda install cuda --channel "nvidia/label/cuda-12.0"
#NB. there doesn't seem to be an option (yet) to use cud=12.0 in the code line below.  The line below is suggested when visiting https://pytorch.org/

conda install pytorch torchvision torchaudio pytorch-cuda=11.6 -c pytorch -c nvidia
#NB. I  found that the line below was necessary to get things to work
conda install cudatoolkit

conda install ipykernel jupyter

nvcc --version
conda install -c anaconda git
git clone https://github.com/openai/point-e.git
cd point-e
pip install -e .

jupyter notebook

#navigate to the notebook in Jupyter at:
#./point-e/point_e/examples/text2pointcloud.ipynb

#In the notebook add a cell at the beginning with the code below to test if the GPU is detectable:

import torch
print(f'PyTorch version: {torch.__version__}')
print('*'*10)
print(f'_CUDA version: ')
!nvcc --version
print('*'*10)
print(f'CUDNN version: {torch.backends.cudnn.version()}')
print(f'Available GPU devices: {torch.cuda.device_count()}')
print(f'Device Name: {torch.cuda.get_device_name()}')

#NB. I had an issue with the kernel crashing when plotting the pointclouds. 
#The error in the anaconda powershell was: 
#OMP: Error #15: Initializing libiomp5md.dll, but found libiomp5md.dll already initialized.
#The solution was to add a cell at the start of the script with the code:
import os
os.environ["KMP_DUPLICATE_LIB_OK"]="TRUE"
#NB. The above workaround apparently may cause crashes or silently produce incorrect results....
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