Cheatsheets
This page will list cheat sheet for different HPC groups, you may use catalogs to find specific HPC
SciNet
Ceres
Login
| Method | Code/Link | Note |
|---|---|---|
| Login | ssh user.name@ceres.scinet.usda.gov |
Replace the user.name with your username in Scinet |
| DTN Login | ssh user.name@ceres-dtn.scinet.usda.gov |
DTN refer to data transfer node |
| GUI | Open Ondemand | Login tutorial and Usage |
Data Transfer
Note
Example to copy a directory from your local system to the HPC
Simply switch the order if you want transfer HPC --> local
| Method | Code/Link | Note |
|---|---|---|
| Windows | scp -r path\to\target user.name@ceres-dtn.scinet.usda.gov:/path/to/dest |
use " \ " on for windows path seperator, also if you are copying files instead of directory, remove -r |
| Linux | rsync -avz --no-p --no-g /path/to/target <user.name>@ceres-dtn.scinet.usda.gov:/path/to/dest |
|
| MacOS | rsync -avz --no-p --no-g /path/to/target <user.name>@ceres-dtn.scinet.usda.gov:/path/to/dest |
Use --iconv utf-8-mac if run into issue source |
| GUI | Globus | Instruction |
Compute
Warning
Do not run computational intensive job on login node, you need to allocate a computing node
| Method | Code/Link | Note |
|---|---|---|
| Allocate resource | salloc -n 2 -N 1 --mem 128G --cpus-per-task 8 -p short -t 01:00:00 |
Reserve -n 2 tasks in -N 1 Node with --mem=128GB memory under -p short partitions for -t 1 hour, Ceres gives you an interactive shell after allocated the resource |
| Job run | srun salloc -n 8 -N 1 --mem=128G -p=short -t 01:00:00 your_command |
Similiar with salloc but you can run your command use srun and specific the resource you need |
| Batch run | Batch script generator | Generally like to combine multiple srun together , check Tutorial for more detail |
| Check job | squeue -A |
|
| Cancel job | scancel jobID |
JobID can be obtained from squeue |
Software
| Method | Code/Link | Note |
|---|---|---|
| Check module availibility | module avail your_module |
your_module refer to the actual module name |
| load module | module load your_module |
If there are different versions for your_module, this will load the default version, use your_module/version_number to load the version you want |
| self install software | module load miniconda; conda install or pip install |
This will load Conda package manager and allow you to self-install package, check Toturial |
| Use container | module load apptainer; apptainer foo |
HPC environment cannot allow docker because of user privilege, apptainer is a great alternative |
Atlas
Access
| Method | Code/Link | Note |
|---|---|---|
| Login | ssh user.name@Atlas-login.hpc.msstate.edu |
Replace the user.name with your username in Scinet |
| DTN Login | ssh user.name@Atlas-dtn.hpc.msstate.edu |
DTN refer to data transfer node |
| GUI | Open Ondemand | login tutorial and Usage |
Data Transfer
Note
Example to copy a directory from your local system to the HPC
Simply switch the order if you want transfer HPC --> local
| Method | Code/Link | Note |
|---|---|---|
| Windows | scp -r path\to\target user.name@Atlas-dtn.hpc.msstate.edu:/path/to/dest |
use " \ " on windows path, also if you are copying files instead of directory, remove -r |
| Linux | rsync -avz --no-p --no-g /path/to/target <user.name>@Atlas-dtn.hpc.msstate.edu:/path/to/dest |
|
| MacOS | rsync -avz --no-p --no-g /path/to/target <user.name>@Atlas-dtn.hpc.msstate.edu:/path/to/dest |
Use --iconv utf-8-mac if run into issue source |
| GUI | Globus | Instruction |
Compute
Warning
Do not run computational intensive job on login node, you need to allocate a computing node
| Method | Code/Link | Note |
|---|---|---|
| Allocate resource | salloc -n 2 -N 1 --cpus-per-task 8 --mem 128G -p short -t 01:00:00 -A your_user_group |
Atlas does not excute interactive shell after use salloc and requires user group input, the user group typically is your project name, check Miscellaneous section in the cheat sheet for how to get your user group |
| Interactive | srun salloc -n 1 -N 1 --mem=128G -p=short -t 01:00:00 -A your_user_group --pty bash |
Get a shell on a compute job |
| job run | srun salloc -n 1 -N 1 --mem=128G -p=short -t 01:00:00 -A your_user_group your_command |
Similiar with salloc but you can run your command use srun and specific the resource you need |
| Batch run | Batch script generator | Generally like to combine multiple srun together , check Tutorial for more detail |
| Check job | squeue -A "Your user group" |
|
| Cancel job | scancel jobID |
JobID can be obtained from squeue |
Software
| Method | Code/Link | Note |
|---|---|---|
| Check module availibility | module avail your_module |
your_module refer to the actual module name |
| load module | module load your_module |
If there are different versions for your_module, this will load the default version, use your_module/version_number to load the version you want |
| self install software | module load miniconda; conda install or pip install |
This will load Conda package manager and allow you to self-install package, check Toturial |
| Use container | module load apptainer; apptainer foo |
HPC environment cannot allow docker because of user privilege, apptainer is a great alternative |
CSU
Cashew
Login
| Method | Code/Link | Note |
|---|---|---|
| Login | ssh user.name@cashew.engr.colostate.edu |
Replace the user.name with your username in Scinet |
| GUI | Open Ondemand |
Data Transfer
Note
Example to copy a directory from your local system to the HPC
Simply switch the order if you want transfer HPC --> local
| Method | Code/Link | Note |
|---|---|---|
| Windows | scp -r path\to\source user.name@cashew.engr.colostate.edu:/path/to/dest |
Use " \ " on windows path, also if you are copying files instead of directory, remove -r |
| Linux | rsync -avz --no-p --no-g /path/to/source user.name@cashew.engr.colostate.edu:/path/to/dest |
|
| MacOS | rsync -avz --no-p --no-g /path/to/source user.name@cashew.engr.colostate.edu:/path/to/dest |
Use --iconv utf-8-mac if run into issue source |
| GUI | open Ondemand | Under Files |
Compute
Warning
Do not run computational intensive job on login node, you need to allocate a computing node
| Method | Code/Link | Note |
|---|---|---|
| Check HPC | sinfo |
You may find availiable partition name, time limit to be useful |
| Interactive node | srun -n 1 -N 1 --mem 32GB --cpus-per-task 16 --gres=gpu:1 -p all -t 01:00:00 --pty bash |
Get an instance on compute node, -n 1 task -N 1 node --mem 32GB memory --cpus-per-task 16 cpus -gres=gpu:1 gpus -p all partition -t 01:00:00 hour --pty bash bash shell |
| job run | srun -n 1 -N 1 --mem 32GB --cpus-per-task 16 --gres=gpu:1 -p all -t 01:00:00 your_job_executable |
Job will be terminated when you close the terminal, if you want background processing use sbatch instead |
| Batch run | Copy Batch Script | use sbatch your_batch_file to submit batch jobs. More detail on cashew website |
| Check job | squeue -u your_user_name |
or just use squeue to check all running instances |
| Cancel job | scancel jobID |
JobID can be obtained from squeue |
Software
| Method | Code/Link | Note |
|---|---|---|
| Check module availibility | module avail your_module |
e.g. module avail git |
| load module | module load your_module |
To load specific version, e.g. module load git/2.46.0 |
| self install software | conda install or pip install |
Cashew will load conda and pip by default, you don't need to module load conda |
| Use container | Container env is not availiable on Cashew HPC |
Riviera
Login
| Method | Code/Link | Note |
|---|---|---|
| Login | ssh user.name@riviera.colostate.edu |
Replace the user.name with your username in Scinet |
| GUI | Riviera does not support OpenOnDemand |
Data Transfer
Note
Example to copy a directory from your local system to the HPC
Simply switch the order if you want transfer HPC --> local
| Method | Code/Link | Note |
|---|---|---|
| Windows | scp -r path\to\source user.name@riviera.colostate.edu:/path/to/dest |
Use " \ " on windows path, if you are copying files instead of directory, remove -r |
| Linux | rsync -avz --no-p --no-g /path/to/source user.name@riviera.colostate.edu:/path/to/dest |
|
| MacOS | rsync -avz --no-p --no-g /path/to/source user.name@riviera.colostate.edu:/path/to/dest |
Use --iconv utf-8-mac if run into issue source |
| GUI | Riviera does not support web GUI for data transfer, | User could use winSCP instead |
Compute
Warning
Do not run computational intensive job on login node, you need to allocate a computing node
Note
Riviera HPC does not load slurm by default, run module load slurm first to load slurm module
| Method | Code/Link | Note |
|---|---|---|
| Check HPC | sinfo |
You may find availiable partition name, time limit to be useful |
| Interactive node | srun -n 1 -N 1 --mem 32GB --cpus-per-task 16 --gres=gpu:1 -p day-long-gpu -t 01:00:00 --pty bash |
Get an instance on compute node, -n 1 task -N 1 node --mem 32GB memory --cpus-per-task 16 cpus -gres=gpu:1 gpus -p day-long-gpu partition -t 01:00:00 hour --pty bash bash shell |
| job run | srun -n 1 -N 1 --mem 32GB --cpus-per-task 16 --gres=gpu:1 -p day-long-gpu -t 01:00:00 your_job_executable |
Job will be terminated when you close the terminal, if you want background processing use sbatch instead |
| Batch run | Copy Batch Script | use sbatch your_batch_file to submit batch jobs. More detail on cashew website |
| Check job | squeue -u your_user_name |
or just use squeue to check all running instances |
| Cancel job | scancel jobID |
JobID can be obtained from squeue |
Software
| Method | Code/Link | Note |
|---|---|---|
| Check module availibility | module avail your_module |
e.g. module avail git |
| load module | module load your_module |
To load specific version, e.g. module load git/2.46.0 |
| self install software | conda install or pip install |
Riviera will load conda and pip by default, you don't need to module load conda |
| Use container | module load singularity |
Only Singularity availiable, apptainer is not supported |