---
tags:
  - Academic
catalog:
  name: Maestro
  description: Versatile drug discovery and materials modeling suite
  license_type: Academic
  disciplines:
    - Chemistry
    - Biosciences
  available_on:
    - web_interfaces:
        - Puhti
        - Mahti
    - Puhti
    - Mahti
    - Roihu
---

# Maestro

!!! info "Online Schrödinger certification courses offered by CSC"
    Users in scope of [CSC's Schrödinger license](#license) are eligible to
    apply for free-of-charge access to participate in online certification
    courses organized by Schrödinger. The offered *introductory* and
    *intermediate* online courses focus on a range of topics related to drug
    discovery and materials science.

    [Read more and apply here :material-open-in-new:](https://csc.fi/en/training-calendar/online-schrodinger-certification-courses-offered-by-csc-3/)

Schrödinger Maestro is a versatile molecular modeling environment. It has modules for
*drug design* and *materials science*. It can be used to build, edit, run and analyze
chemical model systems.

Schrödinger Maestro provides access to the
[Desmond molecular dynamics engine](https://video.csc.fi/media/t/0_3udcx6bk),
which runs **very well** on GPUs. We recommend watching the
[video below](#video-how-to-run-a-desmond-simulation-on-puhti)
on how to set up and run Desmond MD simulations on Puhti easily.

See also the [bottom of this page](#more-information) for links to further
self-learning materials.

[TOC]

## Available

* Roihu-CPU: 2025.1, 2025.2, 2025.3, 2025.4, 2026.1
* Puhti: 2024.2, 2024.3, 2024.4, 2025.1, 2025.2, 2025.3, 2025.4, 2026.1
* Mahti: 2024.2, 2024.3, 2024.4, 2025.1, 2025.2, 2025.3, 2025.4, 2026.1

A two-year cleaning cycle is applied on the Maestro modules on CSC supercomputers.
Specifically, this means that module versions older than two years will be removed.
This policy is enforced to free up disk space and encourage use of the latest versions
which tend to be more performant and have less bugs.

!!! warning "Desmond MD simulations cannot be run on Roihu!"
    Schrödinger only ships x86 builds of their software suite. This means that
    **any Schrödinger modules that require GPUs, most notably Desmond, cannot
    be run on Roihu**.

    CSC provides Maestro modules only on Roihu-CPU for purely CPU-based
    workloads such as virtual screening (Glide).

!!! info "Maestro versions older than 2023.1 will not work after 13.3.2025!"
    Schrödinger has taken into use a
    [new license manager](https://www.schrodinger.com/life-science/learn/white-paper/new-schrodinger-license-manager/),
    which does not support Maestro versions older than 2023.1. Consequently,
    **CSC's will no longer be able to provide a license for Maestro versions
    2022.4 and older after 13th of March 2025**. If not done already, please
    migrate to using versions 2023.1 or later as soon as possible!

    Please note that CSC's Schrödinger Maestro
    [license configuration instructions](https://wiki.eduuni.fi/pages/viewpage.action?pageId=130528861)
    have also been updated accordingly.
    [See more details below](#local-installation).

!!! info "Some notes about warnings"
    Maestro gives a warning for using a `schrodinger.hosts` file from your home
    directory. This is **not an issue**: that file cannot be made available in
    the installation directory, so please ignore the warning, but consider any
    others you may see.

    Similarly, warnings about missing graphics libraries should be harmless.
    However, don't hesitate to [contact CSC Service Desk](../support/contact.md)
    if you are unsure about any warning or error message you might get when
    using Maestro at CSC.

## License

Maestro is available for all academic users in Finland: staff and students, for academic
purposes. Please consult the [EULA](https://www.schrodinger.com/eula)
for the exact definition. Using Maestro means that you accept the EULA linked to above.
The Maestro license consists of floating licenses and tokens. If licenses run out, contact
us via [ServiceDesk](../support/contact.md).

## Usage

It is recommended to download and install Maestro on your own computer, see below.

### Local installation

Maestro can be installed on a Linux, Mac or Windows computer. Download the
appropriate files from [the Schrödinger website](https://www.schrodinger.com/).
You don't need a license to *download* the software, although you do need to
register at the Schrödinger website first. Note that getting access may take up
to 24 hours, so please be patient.

After you've downloaded and installed Maestro, you'll need to configure
licensing to be able to *run* the software.
[See these instructions on how to configure licensing](https://wiki.eduuni.fi/pages/viewpage.action?pageId=130528861)
(logging in to Eduuni requires Haka authentication). Accessing the license
requires that your computer is in the FUNET network, i.e. you're at the
university or connected to it via VPN from home.

!!! warning "Important note"
    Schrödinger version 2025.4 and later have the Job Server system enabled by
    default. Since this is not currently supported at CSC, users who rely on
    CSC-provided `schrodinger.hosts` files to write input files to be run on
    CSC supercomputers must configure their local installation to use the
    legacy Job Control system. Please do the following:

    === "Linux / macOS"

        1. Open a terminal and run:

            ```bash
            $SCHRODINGER/utilities/feature_flags -d JOB_SERVER
            ```

        2. Restart Maestro if you had the GUI open when running the command.

    === "Windows"
        
        1. Open the Schrödinger Command Prompt and run:

            ```bash
            featureflags off JOB_SERVER
            ```
        
        2. Restart Maestro if you had the GUI open when running the command.

### Standalone usage on Puhti

!!! info "Puhti vs. Mahti"
    Note that Mahti is mostly suitable for running Desmond MD simulations on GPUs.
    Most other jobs do not scale to full nodes, so please use Puhti instead for these.
    If in doubt, [contact us](../support/contact.md).

It is possible to run heavier computations on Puhti. Here, a brief overview is given.
Additional details and some diagnostics tips are explained in our [Maestro power usage
tutorial](../support/tutorials/power-maestro.md). See also the video below.

First, you need to [get a CSC account](../accounts/how-to-create-new-user-account.md)
and apply for [access to Puhti](../accounts/how-to-add-service-access-for-project.md).
Before you start the actual workflow below, you need to set up your Maestro environment
on Puhti.

These first four steps you only need to do once:

1. SSH to Puhti
     * `ssh <your username>@puhti.csc.fi`
2. Initialize Maestro with `module load maestro`
     * Make sure you use the same version as on your local computer
3. An error may appear on your screen. If it asks you to run a script to generate the hosts file,
   run it (copy paste it to the command line)
     * Now you have your own `schrodinger.hosts` file in your `$HOME` directory
4. Copy the HOST descriptions from the `schrodinger.hosts` file on Puhti to your local hosts
   file on your computer
     * Copy everything starting from `name: test` and paste it at the end of your local
       `schrodinger.hosts` file
     * This step may need administrator privileges

For actual simulations we recommend using Puhti as follows:

1. Set up your simulations on your local computer
2. Write the GUI-generated input files to disk
3. Copy them to Puhti with e.g. [`scp`](../data/moving/scp.md) or through the
   [Puhti web interface](../computing/webinterface/index.md)
4. If needed, edit the submission script (`your-jobname.sh`)
5. Run the script on the Puhti command line to submit the jobs to the queuing system
6. Copy the results back for analysis

!!! info "Note"

    Maestro jobs are not run via batch scripts like most other applications at CSC, but
    via Schrödinger binaries using options.

For example, a Desmond workflow could be run with the script:

```bash
"${SCHRODINGER}/utilities/multisim" -JOBNAME 2hhb_test -HOST gputest  \
-maxjob 1 -cpu 1 -m 2hhb_test.msj -c 2hhb_test.cfg -description "Molecular Dynamics" \
2hhb_test.cms -mode umbrella -set stage[1].set_family.md.jlaunch_opt=["-gpu"] \
-o 2hhb_test-out.cms -lic "DESMOND_GPGPU:16 -set "stage[1].set_family.md.jlaunch_opt=["\-LOCAL\"]" \
-LOCAL"
```

The scripts tend to be somewhat complicated, so it's best to write them out from the
Maestro GUI as explained above. Please also have a look at the [additional flags we
recommend to use](../support/tutorials/power-maestro.md).

To submit such a script in Puhti, you need to first load Maestro and then run the script

```bash
module load maestro
bash your_script_name.sh
```

!!! warning "Maestro GUI"
    We do **not** recommend running the Maestro GUI remotely on Puhti. It *can* be done via
    [the Puhti web interface remote desktop](../computing/webinterface/desktop.md), but
    the performance may be somewhat slow and submitted jobs may end up fizzled. Also,
    **no long/heavy tasks** should be done on the login nodes. Please consult the
    [Usage policy](../computing/usage-policy.md) page for more details.

!!! info "Note for Windows users"
    **Windows** users may need to edit the script created by the GUI a little.
    Replace the backslashes `\` with `/` in the path to the Maestro binary
    (right after `$SCHRODINGER` in the script).

#### Video: How to run a Desmond simulation on Puhti

The following tutorial video walks you through the process:

[![Maestro Standalone](http://img.youtube.com/vi/Aj205UDcWFE/0.jpg)](http://www.youtube.com/watch?v=Aj205UDcWFE "Maestro Standalone")

## References

Please cite the Maestro modules in all published work as described
in the Module manuals. Jaguar, for example, should be acknowledged with:

Jaguar, version 7.6, Schrödinger, LLC, New York, NY, 2009.

## More information

* [Tutorial and tips for power usage on Puhti](../support/tutorials/power-maestro.md)
* Manual including tutorials come with the Maestro GUI
* Schrödinger training materials overview
     * [Life science](https://www.schrodinger.com/life-science/learn/education/)
     * [Materials science](https://www.schrodinger.com/materials-science/learn/education/)
     * [Apply for free-of-charge online course seats](https://csc.fi/en/training-calendar/online-schrodinger-certification-courses-offered-by-csc-3/)
* Free learning resources at Schrödinger
     * [Life science](https://www.schrodinger.com/life-science/learn/education/free-learning-resources/)
     * [Materials science](https://www.schrodinger.com/materials-science/learn/education/free-learning-resources/)
* The [Schrödinger knowledge base](https://support.schrodinger.com/s/) has an
  extensive collection of articles, for example:
     * [How to restart a single Desmond simulation](https://www.schrodinger.com/kb/1883)
     * [How to restart a Desmond multisim workflow](https://www.schrodinger.com/kb/1896)
     * [Structure file formats compatible with Maestro](https://www.schrodinger.com/kb/1278)
* Video materials:
     * [Preparing, running and analyzing molecular dynamics simulations with Desmond](https://video.csc.fi/media/t/0_3udcx6bk)
     * [Getting Going with Maestro](https://learn.schrodinger.com/private/edu/release/current/Getting-Going-With-Video-Series/Maestro/Get-Going-Maestro-VS/Content/maestro/Page-Topics-m/01-Course-Intro-Get-Going.htm)
     * [Getting Going with Materials Science Maestro](https://learn.schrodinger.com/private/edu/release/current/Getting-Going-With-Video-Series/MS_Maestro/Get-Going-MS-VS/Content/maestro-ms/Page-Topics-ms/01-Course-Intro-Get-Going-ms.htm)
     * [Schrödinger YouTube channel](https://www.youtube.com/@SchrodingerTV)
* Issues on how to run Maestro in CSC environment: [contact CSC Service Desk](../support/contact.md)
* Scientific questions related to Maestro modules: [contact Schrödinger Support](https://support.schrodinger.com/s/contactsupport)
