This page is currently being updated to include examples of submission and configuration commands that can be used on CTBP resources.
It should be noted that this example assumes the use of only one GPU per task and requests an equal amount of memory and CPU resources based on the total resources of each node. The amount of CPU and RAM memory utilized can be increased or decreased based on the user's experience with their system.
Requesting access
To request access to the clusters please use the following form:
https://www.crc.rice.edu/app/rice_signup.php
Slurm configuration
To obtain information about the number of nodes, number of CPUS, memory and number of GPUs in each cluster use the following command:
sinfo -o "%N %c %m %f %G " -p your_partition
NOTS (commons)
This partition includes 16 volta GPU nodes, each equipped with 80 CPUs and 182GB of RAM. In addition, each node includes 2 NVIDIA GPUs.
#SBATCH --account=commons #SBATCH --partition=commons #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=40 #SBATCH --mem=90G #SBATCH --gres=gpu:1 ml gomkl/2021a OpenMM/7.7.0-CUDA-11.4.2
NOTS (ctbp-common)
This partition includes two ampere GPU nodes, each equipped with an AMD EPYC chip featuring 16 CPUs and 512GB of RAM. In addition, each node includes 8 NVIDIA A40 GPUs with 48GB of memory.
#SBATCH --account=ctbp-common #SBATCH --partition=ctbp-common #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=2 #SBATCH --mem=64G #SBATCH --gres=gpu:1 ml gomkl/2021a OpenMM/7.7.0-CUDA-11.4.2
NOTS (ctbp-onuchic)
This partition includes one GPU node, equipped with an AMD EPYC chip featuring 16 CPUs and 512GB of RAM. In addition, each node includes 8 NVIDIA A40 GPUs with 48GB of memory.
#SBATCH --account=ctbp-onuchic #SBATCH --partition=ctbp-onuchic #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=2 #SBATCH --mem=64G #SBATCH --gres=gpu:1 ml gomkl/2021a OpenMM/7.7.0-CUDA-11.4.2
OpenMM on NOTS
You can deploy and run you own version of OpenMM via conda environment. For that, first install the OpenMM inside a conda environment requesting the modules already installed on NOTS. Note that in order to run with Nvidia GPUs, it has to be complicated with CUDA/<version>.
# Load conda and gpu modules module load Anaconda3/2022.05 CUDA/11.4.2 # Create the openmm environment conda create --prefix $HOME/openmm # Activate the new env. source /opt/apps/software/Anaconda3/2022.05/bin/activate conda activate $HOME/openmm # Then install OpenMM. You can also follow by installing your favorite MD wrapper conda install -c conda-forge openmm cudatoolkit=11.4.2 h5py openmichrom opensmog
This would be an example of a running slurm script.
#!/bin/bash -l #SBATCH --account=ctbp-common #SBATCH --partition=ctbp-common #SBATCH --job-name=Template-OPENMM #SBATCH --ntasks=1 #SBATCH --threads-per-core=1 #SBATCH --cpus-per-task=1 #SBATCH --mem-per-cpu=2G #SBATCH --gres=gpu:1 #SBATCH --time=00:05:00 #SBATCH --export=ALL module purge module load Anaconda3/2022.05 CUDA/11.4.2 source /opt/apps/software/Anaconda3/2022.05/bin/activate conda activate $HOME/openmm python your_script.py
ARIES
This partition includes 22 GPU nodes and 2 High Memory CPU nodes:
- 19 x MI50 Nodes (gn01-gn19): 1x AMD EPYC 7642 processor (96 CPUs), 512GB RAM, 2TB storage, HDR Infiniband, 8x AMD Radeon Instinct MI50 32GB GPUs.
- 3x MI100 Nodes (gn20-gn22): 2x AMD EPYC 7V13 processors (128 CPUs), 512GB RAM, 2TB storage, HDR Infiniband, 8x AMD Radeon Instinct MI100 32GB GPUs
- 2x Large Memory Nodes (hm01-02): 2x AMD EPYC 7302 processors (64 CPUs), 4TB RAM, 4TB storage, HDR Infiniband.
To submit a job to GPU queue, it is necessary to launch 8 processes in parallel, each with a similar runtime to minimize waiting time. This ensures that all of the GPUs are used efficiently.
#SBATCH --account=commons #SBATCH --partition=commons #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --export=ALL #SBATCH --time=06:00:00 #SBATCH --gres=gpu:8 module load foss/2020b OpenMM
*Alternative if running 8 jobs in parallel
#SBATCH --account=commons #SBATCH --partition=commons #SBATCH --ntasks=8 #SBATCH --cpus-per-task=6 #SBATCH --threads-per-core=1 #SBATCH --mem-per-cpu=3G #SBATCH --gres=gpu:8 #SBATCH --time=06:00:00 #SBATCH --export=ALL module load foss/2020b OpenMM
Checking usage
In order to determine if your process is running correctly, in each cluster you can connect directly to each compute server while you are running the file with ssh. Then use the command top to check the CPU and memory usage, rocm-smi to check the GPU usage for AMD/RADEON GPUs and nvidia-smi to check the GPU usage for NVIDIA GPUs,
Remote access to the clusters
To access the servers from outside of Rice it is recommended to connect to them through the gw.crc.rice.edu server. Here we will show how to create a passwordless ssh tunnel that will allow you to securely connect to a remote machine without having to enter a password everytime you connect.
Generate the keys
First generate a pair of public and private keys on your local machine. Open a terminal and enter the following command:
ssh-keygen -t rsa
Save the key in the default key and leave the passphrase empty. This will generate a pair of public and private keys, with the default file names id_rsa and id_rsa.pub. Don't share or expose your private key.
Copy the keys to the gateway server
Copy the public key to the remote machine (The gw.crc.rice.edu server). Enter the following command in your terminal, replacing user with the correct rice user id:
ssh-copy-id user@gw.crc.rice.edu
This will copy your public key, id_rsa.pub, to the remote machine and add it to the authorized_keys file on the remote machine.
Test the connection. Enter the following command in your terminal to connect to the remote machine:
ssh user@gw.crc.rice.edu
You should be able to connect to the remote machine without being prompted for a password. Exit to your local machine using Ctrl+D
Create a ssh config file
To make it easier to connect to the remote machine in the future, you can create or edit your ssh config file in ~/.ssh/config. This file allows you to specify connection settings and aliases for different remote machines. To create an ssh config file, open the ~/.ssh/config file in a text editor and enter the following information, replacing user_id with your username on the remote machine:
Host crc
User user_id
HostName gw.crc.rice.edu
IdentityFile ~/.ssh/id_rsa
Host aries
User user_id
HostName aries.rice.edu
ProxyJump crc
Port 22
IdentityFile ~/.ssh/id_rsa
Host nots
User user_id
HostName nots.rice.edu
ProxyJump crc
Port 22
IdentityFile ~/.ssh/id_rsa
Test the connection from you local machine to the remote machine using the alias. The gateway will be accessible without a password. You should be able to connect to the gateway enter the following command in your terminal:
ssh crc
Exit to your local machine with Ctrl+D
Copy the keys to the compute servers
To add the keys to the compute servers add the keys from your local machine to ~/.ssh/authorized_keys in the compute machine. For that in your local machine get the public key by executing the following command:
cat ~/.ssh/id_rsa.pub
Connect from your local machine to the compute servers using the settings and alias specified in the ssh config file with the following command:
ssh nots
You will be prompted for a password. Once you have entered it, you can edit or create the ~/.ssh/authorized_keys file on the compute server using a text editor like vi. Make sure to create the folder .ssh first if it doesn't exist:
mkdir .ssh vi ~/.ssh/authorized_keys
Add the contents of your local machine's ~/.ssh/id_rsa.pub file to a new line in the authorized_keys file. Save the file exit the text editor (:wq) and then exit to your local machine with Ctrl+D.
To test the connection. Enter the following command in your terminal to connect to the remote machine:
ssh nots
You should now be able to connect to the compute server without being prompted for a password.
Repeat these steps for each additional compute server you want to connect to.
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