sigblog

Rescale is pleased to announce the availability and latest release of the Amber (2014) molecular dynamics and modeling suite for CPUs and GPUs. I will go over the process for requesting and receiving access to run your Amber simulations. Then, I will share the results of a typical job with timings over a range of processor counts and on the GPU.

Running Amber on Rescale first requires purchasing an Amber license; steps to purchase a license can be found on www.ambermd.org. Once you have purchased a license, you can request access to the Amber software package on Rescale by taking the following steps:

  1. Sign in to https://platform.rescale.com on your browser of choice
  2. Select +New Job in the top left corner of the page
    Intro
  3. Click Software in the workflow diagram or Software Settings in the workflow checklist at the right of the screen
    SoftwareSettings
  4. Find Amber in the list of available software. Software is listed alphabetically, however there are two additional ways available to find software:
    1. Type the name directly in the search box
    2. Click the Life Sciences icon to filter codes by Industry
      Select
  5. Notice that Amber is greyed-out; selecting Amber will bring up a dialog box to send a request for access; click Send
    Request
  6. A Rescale representative will then contact you to verify license ownership
  7. Rescale will then enable access for you to run your Amber simulations on Rescale
  8. At your next login, you should see that Amber is no longer greyed-out.
  9. Select Amber to continue setting up your first Amber job. Note there are additional hardware charges to run Amber on Rescale.

Now that you have access to Amber, you can setup and run your first Amber simulation. Here is a help page that explains how to do this. You can also click on any of the Results links in the table below to see jobs that have already run on the Rescale platform. It is then a simple matter to clone the job and run it yourself to familiarize yourself with running jobs on Rescale.

Finally, I will show the results of timings for running a model of lysozyme with a toluene ligand, a standard benchmark, on multiple processor counts, and also on a GPU provided with the Jade core type. These are not formal benchmarks but still provide reasonable estimates of the performance you can expect to achieve on Rescale. If you have any questions or need help getting started running your Amber simulations on Rescale, send an email to support@rescale.com. Happy simulating!

Lysozyme with toluene – 29,074 atoms, including 8802 explicit waters – Nickel core type
#CPUs ns/day relative scaling
1 1.63 1.0 results
4 5.54 0.85 results
16 14.98 0.21 results
#GPUs ns/day speedup (rel. 4 CPUs)
1 55.54 10.0X results

This article was written by Sidney Elmer.

San Francisco, CARescale, a leading cloud platform provider of simulation software and high performance computing (HPC) solutions, today announced that Zack Smocha has joined the company as Vice President of Product Marketing, bringing two decades of experience in cloud and enterprise software marketing to his new role. As a member of the Rescale executive team, Smocha will play a key role in supporting Rescale’s mission to provide the leading cloud based high performance computing (HPC) and simulation platform empowering the world’s engineers, scientists, developers and IT professionals to design innovative products and transform IT into unified, agile environments.

“Zack is an ideal choice to drive Rescale’s awareness, product strategy and enable the sales growth in the simulation software and high performance computing (HPC) solutions” said Joris Poort, CEO of Rescale. “In the last year we’ve had over 300% growth and made significant investments in our core products, including the release of ScaleX Enterprise. Zack will play a critical role in further defining the leading high performance computing simulation platform and bringing it to market.”

Previously, Smocha spent four years at Coverity (acquired by Synopsys) and one year at the software integrity group at Synopsys, providing software quality and security testing solutions, where he led the demand generation, product marketing, product management and business development for their commercial and cloud open source solutions. Prior to that, Smocha held leadership roles in product marketing and product management at Sauce labs, Athoc and Mercury.

“With the explosion of cloud and the demand for robust and fast engineering innovation, to gain competitive edge IT organizations must transform their stagnant, on-premise resources into an agile, optimized cloud HPC platform.  I am enormously excited to work with Rescale’s customers that are the leaders and innovators in aerospace, automotive, energy, etc.” said Zack Smocha, Vice President of Product Marketing, Rescale.

About Rescale:
Rescale is the world’s leading cloud platform provider of simulation software and high performance computing (HPC) solutions. Rescale’s platform solutions are deployed securely and seamlessly to enterprises via a web-based application environment powered by preeminent simulation software providers and backed by the largest commercially available HPC infrastructure. Headquartered in San Francisco, CA, Rescale’s customers include global Fortune 500 companies in the aerospace, automotive, life sciences, marine, consumer products, and energy sectors. For more information on Rescale products and services, visit www.rescale.com.

This article was written by Rescale.

andrasblog2

Introduction
Computer simulations are often used to examine how a system behaves for a variety of different conditions, such as Computational Fluid Dynamics (CFD) simulations of a wing operating at a range of Mach numbers or a jet engine compressor at varying pressure ratios. These simulations are computationally expensive and can take anywhere from a few hours to a few days to perform. One strategy to reduce the time to solution is to use a better initial condition to start the simulation. By providing the solver an initial condition that is “closer” to the final solution, fewer iterations are required and the computation time is reduced. Providing an appropriate initial condition can also improve simulation stability, especially at operating points with complex physics such as wing stall.

In this post, we will simulate the turbulent flow around a wing for a range of Mach numbers from 0.5 to 0.9 at an Angle of Attack of approximately 3 degrees, and the results of the previous computation will be used as the initial condition for the next (e.g. the results for Mach 0.5 will be used to initialize the Mach 0.6 computation). The turbulent ONERA M6 tutorial for the open-source Stanford University Unstructured (SU2) CFD solver serves as the basis for these computations. The mesh and configuration files used here come from the SU2 Github repository. While using a previous solution as an input to the next computation has always been possible using the Rescale interface, the new “custom optimization” Python SDK allows users to do this programmatically and within a single job.

You can use the following links to clone or view the job and follow along:
Clone Job
View Job

Python Script Development
The first step is to develop the Python script to run the computations and modify the SU2 configuration file for the task. A similar concept of “templating” used in Design of Experiment jobs will be used here. Several lines of the configuration file input-template.cfg are modified to allow values to be populated by the Python script (as below to set the Mach number). The full configuration file template can be found in the job.

The Python script used to run the computations is given below in full. We will then discuss each of the parts, pointing out important concepts and providing suggestions. Note that a SU2 computation produces a specific “restart” file for the purposes of starting another computation. This restart file contains the values of the solution primitives at each node point.

Starting with the first block,

Here we are importing the Python modules os and shutil which are useful for file operations. More importantly, however, is the Rescale optimization SDK which is used to submit runs. This module will be placed automatically on the Python path when running a custom optimization job. The file names of the configuration template and mesh are also declared.

In this block we first define a list of Mach numbers, representing each of the operating points, and a global run count is defined (rescale_run). This run count is not required, however, it is useful for tracking purposes. We then enter a for loop to run each of the operating points. A run specific configuration file is made and populated with the desired Mach number. Next, we define a list of input file names for the run, namely the configuration file and the mesh file. These files will be transferred from the optimizer node to the compute node(s). Finally, the resulting “restart” file from the computation is named restart_file_.dat and set in the configuration file. This restart file is added to a list of output files which will be transferred back from the compute node(s) to the optimizer node after the run is finished.

Note that the remaining blocks all are within the for loop defined above.

Here we setup the initial condition for the solver. If it is not the first run, there is a restart file available to set the initial condition. In this case, the configuration file is set to use the restart file from the previous run and this restart file is added to the list of input files. If it is the first run, no restart file is available, and this is set in the configuration file.

The command to run the computation is defined next. The parallel_computation.py is a Python wrapper script provided by SU2 to perform multi-core calculations. Note the use of $RESCALE_CORES_PER_SLOT to define the number of cores. This environment variable is automatically created for you based on your hardware settings. The run is then submitted, specifying the command to be run, the input and output files, and finally the variable values for this run (in this case just the Mach number).

In the final block, we instruct the script to wait for the run to complete before continuing the for loop and incrementing the run count. The restart file from the run is automatically transferred from the compute node(s) back to the optimizer node as we declared it an output file.

Running the Job on Rescale
Having developed the Python script, we turn now to running the job on the Rescale platform. The “Job Type” is set to “Optimization” and a zip file MachOpPoints.zip containing the Python script, mesh file, and configuration template file is uploaded as an input file.

input-files
Under “Optimizer Settings,” the “Custom” option and the command is set to run the Python script (python runOpPoints.py). SU2 has also been selected as the software for this job.

optimizer-settings

Finally, we select 4 Nickel cores per slot and a single slot (as the computations are run one after another) on the “Hardware Settings” page. We are now ready to submit the job!

hardware-settings

Each of the operating points will appear as a “child run” of run 1 (labelled 1.1, 1.2…). You can live tail the files of each of the computations. In the image below we are examining the process_output.log file, which contains the residual information from SU2, for the third computation (Mach 0.7)

live-tail

The job takes about an hour to complete. Once completed, the “Results” tab will appear as below and the 5 runs can be seen.

results-window-all

Clicking the second run 1.2, the files specific to that job are seen.

run2-results

We see the input-2.cfg configuration file produced by the Python script as well as the restart file restart_file_1.dat from the previous run. Examining the process_output.log file, we see the line:

confirming that the computation was started using the initial condition from the restart file.

If you’re interested in more information about Rescale’s platform, please contact us at info@rescale.com.

This article was written by Andras Kiss.

Comsol-PR (2)

San Francisco, CA – Rescale is excited to announce the availability of COMSOL Multiphysics® software on Rescale simulation platforms through a collaboration with COMSOL, creators of the robust, physics-based modeling and simulation software.

COMSOL Multiphysics® is an all-inclusive modeling software, based on powerful numerical methods, for simulating physics-based problems. With COMSOL Multiphysics® users are able to account for coupled or multiphysics phenomena. The simulation suite is further expandable with more than 30 add-on products for simulating electrical, mechanical, fluid flow, and chemical applications allowing for unlimited multiphysics combinations.

Simulation experts can use the Application Builder within COMSOL Multiphysics® to create specialized simulation apps that can be run by engineers and others not well versed in simulation. These apps are hosted and run on the COMSOL Server™ software, which is also available on Rescale’s cloud.

Now COMSOL Multiphysics® users can run computationally demanding analyses on high-end hardware that matches the power and flexibility of their solvers. Users submit simulations using their existing COMSOL Multiphysics® licenses with on-demand high performance computing (HPC) hardware, making use of the software’s automatic and sophisticated parallel processing capabilities. The new Rescale and COMSOL collaboration allows users to accelerate their COMSOL Multiphysics® analyses using Rescale’s diverse and dynamic pay-per-use HPC platforms, leveraging built-in administration and collaboration tools designed to improve and speed-up the simulation process.

“This important initiative with Rescale allows our users to take full advantage of both the COMSOL Multiphysics® software and Rescale’s secure and flexible simulation environments,” says Phil Kinnane, COMSOL’s VP of Business Development. “Now internal hardware capabilities are no longer a limiting simulation factor for our customers.”

“We’re very excited to be partnering with COMSOL to offer their unique software on our platforms. COMSOL Multiphysics® is a critical tool for many engineers and scientists worldwide and an excellent addition to our suite of available software packages” said Rescale’s Vice President of Sales, Tony Spagnuolo.

For users interested in taking advantage of COMSOL Multiphysics® in the cloud using Rescale’s platforms, you can contact Rescale and COMSOL using the resources below. To begin running COMSOL Multiphysics® immediately, you can create a free Rescale account by going to www.rescale.com/signup.

COMSOL
Email: info@comsol.com
Phone: +1 781 273 3322

Rescale
Email: info@rescale.com
Phone: +1 415 589 0530

About COMSOL:
COMSOL is a global provider of simulation software for product design and research to technical enterprises, research labs, and universities. Its COMSOL Multiphysics® product is an integrated software environment for creating physics-based models and simulation apps. A particular strength is its ability to account for coupled or multiphysics phenomena. Add-on products expand the simulation platform for electrical, mechanical, fluid flow, and chemical applications. Interfacing tools enable the integration of COMSOL Multiphysics® simulations with all major technical computing and CAD tools on the CAE market. Simulation experts rely on the COMSOL Server™ product to deploy apps to their design teams, manufacturing departments, test laboratories, and customers throughout the world. Founded in 1986, COMSOL employs more than 450 people in 22 offices worldwide and extends its reach with a network of distributors.

About Rescale:
Rescale is the world’s leading cloud platform provider of simulation software and high performance computing (HPC) solutions. Rescale’s platform solutions are deployed securely and seamlessly to enterprises via a web-based application environment powered by preeminent simulation software providers and backed by the largest commercially available HPC infrastructure. Headquartered in San Francisco, CA, Rescale’s customers include global Fortune 500 companies in the aerospace, automotive, life sciences, marine, consumer products, and energy sectors. For more information on Rescale products and services, visit www.rescale.com.

Read COMSOL’s announcement here.

This article was written by Rescale.