Schrodinger Installation & Settings

This documents helps you to install and set the schrodinger settings to be able to run schrodinger from your PC.

Important Notes

The hostname and schrodinger path may need to be updated based on HPC Resource View and the versions of the schrodinger and its license path. Check it out with "module display schrodinger"
Edit the options on "qargs" field based on the need for your job.

Windows

Open setup.exe
Follow the guided installation which basically involves a few next clicks
You may be prompted to automatically install Microsoft Visual C++ Runtime
Replace the schrodinger.hosts file in your installation directory (C:/<Schrodinger-version> or C:/Program Files/<Schrodinger-version> with the following content. We need to update the values in <>.

schrodinger: C:\<Schrodinger-path>

# cluster

#Schrodinger Path in the cluster; check with "module display schrodinger" in HPC

schrodinger: /usr/local/schrodinger/2017-3

# Include the HPC login node (check HPC Resource View )

Host: rider.case.edu

# Use your CaseID

user: <YOUR_CASE_ID>

Queue: SLURM2.1

# Below we are requesting 36 hrs of wall clock time, 1 node, two CPUs, 150gb of memory in a smp queue.

# If you don't have high memory requirement, use batch partition instead of smp to decrease the queue time

qargs: --time=36:00:00,--nodes=1,--ntasks=1,--cpus-per-task=2,--mem=150gb,--partition=smp

# Set the environments based on "module display schrodinger" in HPC

env: SCHRODINGER=/usr/local/schrodinger/2017-3

env: SCHRODINGER_THIRDPARTY=/usr/local/schrodinger/2017-3/thirdparty

env: SCHROD_LICENSE_FILE=27008@hpcmaster.case.edu

env: MAESTRO_TEMP=/scratch/schrodinger

Processors: 40

Setting up the Environment variable and ssh without password on your local machine...

- Right-click My Computer, select Properties
- Click Advanced System Settings -> Environment Variables
- In the User variables flap, add the following:
- Variable Name: SCHROD_LICENSE_FILE
- Variable Value: 27008@hpcmaster.case.edu
- Run Schrodinger->Remote Login->Generate Keys
- Click Initialize Host Access and if there is no entry, add: rider.case.edu,and your case id in the panel that has host and username.
- Click Initialize and enter case password if asked
- Run Maestro

Linux/Mac

Open Terminal (see HPC Quick Guide)

sudo su

Untar the downloaded tar file

tar -xvf <schrodinger>.tar

Go to Schrodinger directory and run the Install command

cd <schrodinger-dir>

./INSTALL

Choose the Preferred Installation location as : /usr/local/schrodinger/<version>

When prompted for installing all the available modules or third party, say y

Select scratch: /tmp

Edit the schrodinger.hosts file as showed below:

tmpdir: /tmp

# Slurm Cluster

Name: Rider-SMP

queue: SLURM2.1

#Schrodinger Path in the cluster; check with "module display schrodinger" in HPC

schrodinger:/usr/local/schrodinger/2017-3

# Below we are requesting 100 hrs of wall clock time, 1 node, 4 CPUs, 150gb of memory in a smp queue.

# If you don't have high memory requirement, use batch partition instead of smp to decrease the queue time

qargs: -N 1 -c 4 --time=4-04:00:00 --mem=150gb --partition=smp

# Include the HPC login node (check HPC Resource View )

Host: rider.case.edu

# Use your CaseID

User: <CaseID>

# Set the environments based on "module display schrodinger" in HPC

env: SCHRODINGER=/usr/local/schrodinger/2017-3

env: SCHRODINGER_THIRDPARTY=/usr/local/schrodinger/2017-3/thirdparty

env: MAESTRO_TEMP_LOCATION=/scratch/schrodinger

env: SCHROD_LICENSE_FILE=27008@hpcmaster.case.edu

Processors: 40

tmpdir: /scratch/schrodinger

Setting up the Environment variable and ssh without password on your local machine...

At the terminal, type:

ssh-keygen

Use the following command:

ssh-copy-id ~/.ssh/id_rsa.pub <CaseID>@rider.case.edu

Go to the terminal and create a file run_schrod with following content:

export SCHROD_LICENSE_FILE=27008@hpcmaster.case.edu

/usr/local/schrodinger/<version>/maestro

Run Maestro by typing:

sh run_schrod