How to...



  • 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 list all running processes in PBS-PRO

    qstat -rn1tw
    


  • How to find a best blast hit:

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





  • 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....
    
    
    




  • How to create threaded replies in NodeBB:

    https://github.com/NodeBB/NodeBB/issues/7319



  • How to negotiate a better home loan rate with your bank (from Barefoot Investor SCOTT PAPE):

    You: Hello, my account number is ______. I’ve been with you for ___ years, but I’ve applied to refinance with UBank. Their rate is ____ per cent, which is a full ___ per cent cheaper than you’re charging me. Given our longstanding relationship, I’d like you to match the offer — or send me the forms I need to switch to UBank.

    Bank rep: One moment, please.

    (You’re bluffing, of course. However, the bank’s sales team have strict targets, backed by incentives, that they have to meet — one of which is giving profitable customers discounts to stop them leaving.)

    Bank rep: We can’t match the rate you have quoted. However, we understand you are a valuable customer, so we would like to offer you a 0.15 per cent discount.

    You: That’s not good enough. I’ve already got conditional approval … so in order to stay I need at least a 0.5 per cent discount. Could you please speak to your supervisor? I’m happy to wait.

    Bank rep (a full six minutes later): On reviewing your case, we can offer you that 0.5 per cent discount on your current rate.

    You: Brilliant! Please send me an email confirming the new rate and confirming that it will be applied as of start of business tomorrow.



  • How to fix the error "FATAL: container creation failed:" "error: can't mount image " "failed to mount squashfs filesystem: input/output error":

    #This occurs when you try to run a singularity container within a VM and it is located on a mounted ntfs filesystem. The solution is to transfer the container to a different filesystem eg. ext3.
    

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