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*Qs 1: How do I cite or mention the cluster in papers? or what is the preferred method?
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You could try a trace. cmake --trace . 2>&1 | tee /tmp/cmakeOut.txt You may have to explicitly mention the path, For example: cmake . -DLAPACK_LIBRARIES=/sw/library/lapack/lapack-3.6.0/3.6.0/lib64/liblapack.so -DBLAS_LIBRARIES=/sw/library/blas/CBLAS/lib/cblas_LINUX.so OR: cmake . -DLAPACK_LIBRARIES=/sw/library/lapack/lapack-3.6.0/3.6.0/lib64/liblapack.so -DBLAS_LIBRARIES=/sw/library/blas/CBLAS/lib/cblas_LINUX.so -DCMAKE_INSTALL_PREFIX=/sw/simbody/353 |
Qs28: How do I check number of CPUs my job is using
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You can find out on which compute node your job is running: qstat -1an|grep snumber >>>>>>>>>>>>>>>>>>> e.g: qstat -1an|grep s2761086 4598354.pbsserv s2761086 workq DT_k-e_04 21795 1 1 10gb 99999 R 523:2 n010/0 Here you see it is running on n010 Then you can do this: ssh nodename -t "htop" or ssh nodename -t "htop -u username" e.g.ssh n010 -t "htop -u s2761086" Press <F2> key, go to "Columns", and add PROCESSOR under "Available Columns". The currently used CPU ID of each process will appear under "CPU" column. |
Qs29: How to customize an environmental variable using modules
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Qs 31: Multi Cores are requested and allocated by PBs but job runs only on 1 core. Why is that?
This contribution is from Nicholas Dhal and is acknowledged. Nick is an active Grifith HPC user.
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Qs 32: How to check the remaining licenses on the license server
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e.g scp -r /export/home/s5284664/folder n061:/lscratch/s5284664/
Qs.56: NCMAS process and application
NCMAS facilities overview and who should apply
https://youtu.be/7ZZVk4HtdDY
NCMAS process and application 2021
https://youtu.be/hmV_j5GFgI0
Qs 57: What kind of storage and compute is available on Griffith HPC
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Additionally and in parallel, you can also apply directly when the application opens
Please note that projects will be given a fixed allocation which is given per quarter on a use it or loose it basis. Allocations cannot be carried forward or backward into other quarters. Standard disk space per project is 75GB in /scratch and if a project needs more you will need to contact help@nci.org.au.
Students cannot be a lead CI on an NCI project however, for the QCIF share postdocs can be. For NCMAS the lead CI is required to have an ARC or NHMRC grant or equivalent which is why larger groups apply for NCMAS. A grant is not required for a project under QCIF. However, the QCIF allocations are small, around 20-50 thousand per quarter. Larger allocations are only available through NCMAS.
Some applications like Mathematica and Matlab are licensed software. Mathematica is only available to ANU researchers on NCI. For Matlab, Griffith will need to get in contact with NCI to set up their institutional license. At the moment this is not available so one cannot use it. Unless you have your own license. But also in that case you would need to get in touch with NCI first to see if you can use Matlab on Gadi or not.
In general, allocations are given in service units SUs. 1 core hour is charged at 2 SUs. So if you have a calculation running using 4 cores and taking 48 hours then you will be charged 4*48*2=384 SUs for that calculation.
If a larger disk space (e.g 300GB) is needed, you would need to talk to NCI to increase the space in /scratch to accommodate this. If a larger RAM (e.g 400GB ), then you would need to make sure you run in a queue that supports that ram request. They could be charged more than 2 SUs per core hour though, so you would need to factor that in.
But talk to NCI, help@nci.org.au, first to see if you could use the application (e.g Matlab) onNCI before you even consider applying for an allocation on NCI.
Qs69: How to install bioinformatics software in your home directory
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The login or head node of each cluster is a resource that is shared by many users. Running a GUI job on the login node is prohibited and may adversely affect other users. X11 Forwarding is only possible for interactive jobs.
Please note that there is a performance penalty when running a GUI job on the compute nodes using the method outlined below.
Set up X11 forwarding
To use X11 port forwarding, Install Xming X Server on Windows laptop/desktop first. Install the xming fonts package as well.
See instructions here: https://griffith.atlassian.net/wiki/spaces/GHCD/pages/4035477/xming
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- http://mobaxterm.mobatek.net/download-home-edition.html
- putty
- Filezillia
- Windows WSL system lets you run the linux versions of ssh under windows.wsl --installThis should get you command line: ssh, scp, and sftp;
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To transfer from remote to locally: scp -r remotehostname:/export/home/snumber/FolderName ~/
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Minimal docker images are kept here: /sw/Containers/docker mkdir -p /export/home/snumber/sw/Containers cd /export/home/snumber/sw/Containers Convert the tarball to a Singularity image. module load singularity/4.1.3 singularity build --sandbox pytorch docker-archive:///sw/Containers/docker/pytorchnew.tar (it takes quite sometimes to create the sandbox. Please be patient. You only have to do this once!) for testing: singularity shell -e -B /scratch/snumber:/scratch/snumber -B /export/home/snumber:/export/home/snumber /export/home/snumber/sw/Containers/pytorch e.g: Singularity> python Python 3.10.12 (main, Nov 20 2023, 15:14:05) [GCC 11.4.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import torch >>> torch.cuda.is_available() True So we see it works! So now you need to integrate this into a slurm or pbs script. PBS examples are here Slurm would be like this: create a run script: mkdir /export/home/snumber/slurm/data create a file /export/home/snumber/slurm/data/myrun1.sh cat /export/home/snumber/slurm/data/myrun1.sh >>>>>>>>> cd /export/home/snumber/slurm/data python /export/home/snumber/slurm/data/isCuda.py >>>>>>>>>> make it executable: chmod +x /export/home/snumber/slurm/data/myrun1.sh Here is the content of the slurm.01 file >>>>cat slurm.02 >>>>>>>>>>>>> #!/bin/bash ####SBATCH --account=def-yoursnumber #SBATCH --job-name=helloWord #SBATCH --cpus-per-task=1 #SBATCH --mem-per-cpu=1500MB #SBATCH --gres=gpu:a100:1 ###SBATCH --qos=work #SBATCH --qos=work ###SBATCH --mem=4000M # memory per node #SBATCH --time=0-03:00 module load singularity/4.1.3 ##./program # you can use 'nvidia-smi' for a test singularity exec -e -B /scratch:/scratch -B /export/home/snumber:/export/home/snumber /export/home/snumber/sw/Containers/pytorch "data/myrun1.sh" >>>>>>>>>>> To submit the slurm job: sbatch slurm.02 Alternatively, to run interactively: srun --export=PATH,TERM,HOME,LANG --job-name=hello_word --cpus-per-task=1 --mem-per-cpu=1500MB --time=1:00:00 --qos=work --gres=gpu:a100:1 --pty /bin/bash -l singularity shell -e -B /scratch/snumber:/scratch/snumber -B /export/home/snumber:/export/home/snumber /export/home/snumber/sw/Containers/pytorch cd data sh myrun1.sh >>>Some errors you can ignore while building the sandbox>>> INFO: Starting build... INFO: Fetching OCI image... INFO: Extracting OCI image... 2024/05/20 12:37:31 warn rootless{usr/local/nvm/versions/node/v16.20.2/bin/corepack} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2024/05/20 12:37:32 warn rootless{usr/local/nvm/versions/node/v16.20.2/bin/npm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2024/05/20 12:37:32 warn rootless{usr/local/nvm/versions/node/v16.20.2/bin/npx} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2024/05/20 12:38:17 warn rootless{usr/lib/libarrow.so} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2024/05/20 12:38:17 warn rootless{usr/lib/libarrow.so.1400} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2024/05/20 12:38:17 warn rootless{usr/lib/libarrow_acero.so} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2024/05/20 12:38:17 warn rootless{usr/lib/libarrow_acero.so.1400} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2024/05/20 12:38:17 warn rootless{usr/lib/libarrow_dataset.so} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2024/05/20 12:38:17 warn rootless{usr/lib/libarrow_dataset.so.1400} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2024/05/20 12:38:34 warn rootless{usr/lib/libparquet.so} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" 2024/05/20 12:38:34 warn rootless{usr/lib/libparquet.so.1400} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers" INFO: Inserting Singularity configuration... INFO: Creating sandbox directory... INFO: Build complete: pytorch >>>> |
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