Use Schrodinger to calculate molecular structure - Elastic High Performance Computing

This topic uses Schrodinger as an example to describe how to calculate molecular structure by using an Elastic High Performance Computing (E-HPC) cluster.

Background information

Schrodinger provides a physics-based computational platform that integrates differentiated solutions for predictive modeling and data analysis to facilitate the exploration of the chemical space. The platform can be used in drug discovery and materials science in various fields, such as aerospace, energy, semiconductors, and electronic displays. For more information, see the official website of Schrodinger.

Preparations

Create an E-HPC cluster. For more information, see Create a cluster by using the wizard.

Configure the following parameters.

Parameter	Description
Hardware settings	Deploy a standard cluster, which consists of two management nodes, one compute node, and one logon node. Select GPU-accelerated instance types for compute nods. In this example, ecs.gn5-c4g1.xlarge is used.
Software settings	Deploy a CentOS 7.6 public image and the Slurm scheduler. Turn on VNC.

Create a cluster user. For more information, see Create a user.
The user is used to log on to the cluster, compile LAMMPS, and submit jobs. In this example, the following information is used to create the user:
- Username: testuser
- User group: sudo permission group
Install the VMD software. For more information, see Install software:
Download and install the Schrodinger software.
Schrodinger is paid software. For more information about how to purchase, download, install, and use Schrodinger software, see the official website of Schrodinger.
Download and install the CUDA driver on the compute nodes.
For more information about how to download and install the CUDA driver, see NVIDIA CUDA.

Step 1: Configure Schrodinger

Before you start to use Schrodinger for the first time, you need to configure the environment.

Log on to the cluster as the root user. For more information, see Log on to an E-HPC cluster.
Modify the configuration file of the Slurm scheduler.
```
vim /opt/schrodinger/queues/SLURM2.1/config 
```
In the configuration file, specify REMOTE_LICENSE_SERVER=${ehpcname} to the server that you set when you register the license for the Slurm scheduler. Example:
```
QPATH=/usr/bin
QPROFILE=
QSUB=sbatch
QDEL=scancel
QSTAT=squeue
LICENSE_CHECKING=yes
REMOTE_LICENSE_SERVER=schrodinge_ehpc-test
```

Configure the hosts file of Schrodinger.

vim /opt/schrodinger/schrodinger.hosts

Sample content:

name: comp-gpu
queue: SLURM2.1
qargs: --partition=comp --nodes=1  --ntasks=%NPROC% --mem=3G  --gres=gpu:%NPROC%
host: manager
processors: 4
gpgpu: 0, NVIDIA P100

Step 2: Submit a job

Log on to the cluster as the cluster user. In this example, testuser is used. For more information, see Log on to an E-HPC cluster.

Run the following commands to download and decompress the sample file:

wget https://public-ehpc-package.oss-cn-hangzhou.aliyuncs.com/desmond_md_job_10-GPU.tar.gz
tar xf desmond_md_job_10-GPU.tar.gz

Run the following commands to submit the job:
```
cd desmond_md_job_10
./desmond_md_job_10.sh
```
The following example response indicates that the generated job ID is manager-0-646496c8.
```
JobId: manager-0-646496c8
```

Step 3: View the job result

Run the following command to view the job execution status:
```
squeue
```
The job information is displayed in the response. An R in the ST column indicates that the job is running.
```
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
                 3      comp desmond_ testuser  R       1:27      1 compute000
```
Note
- The job takes about 10 minutes to run. After the job is run, you can run the sacct command to check whether the job is completed.
- The job result is exported to the desmond_md_job_10-out.cms.
Use VNC to view the result of the job.
1. Enable VNC.
  1. In the left-side navigation pane of the E-HPC console, click Cluster.
  2. On the Cluster page, select a cluster. Choose More > VNC.
  3. Use VNC to remotely connect to a visualization service. For more information, see Use VNC to manage a visualization service.
2. In the Virtualization Service dialog box of the cloud desktop, choose Application > System Tools > Terminal.
3. Run the /opt/vmd/1.9.3/vmd to open Visual Molecular Dynamics (VMD).
4. On the VMD Main page, choose File > New Molecule....
5. Click Browse... at the Filename to select the result file named desmond_md_job_10-out.cms.
  In this example, testuser is used as the user. The path of the job result file is /home/testuser/desmond_md_job_10/desmond_md_job_10-out.cms.
6. Click Load. You can view the result of the job in the VMD 1.9.3 OpenGL Display window.