Installing Delft3D FM on GRNETs HPC

[backeb]

Background:

10 September 2021

Hi @lorincmeszaros ,

Could you please provide us with more information about the software behind the HiSEA use case model running in HPC?

• Which are the software components that are needed? All of them that are described here https://oss.deltares.nl/web/delft3d/get-started#prerequisites or some of them? • Is there any software needed that is not defined there? • Are all of them or their dependencies open-source? • Could we register as an Organization to download them? Otherwise, on behalf of whom? • Could you also provide us with examples of what kind of tests/runs do you want to perform in the HPC?

PS: We are mostly concerned about the Linux OS installation.

Best Regards, @nikosT

13 September 2021

Hi @nikosT ,

Thank you for reaching out.

The modelling software to be used in the HISEA use case is Delft3D Flexible Mesh (https://oss.deltares.nl/web/delft3dfm / https://www.deltares.nl/en/software/delft3d-flexible-mesh-suite/ ). Please note the difference between the link you have in your email which points to Delft3D 4.0 (structured). In C-SCALE we will use the former one.

Delft3D FM is fully open source (GNU AGPL) but the procedure to obtain it as an “outsider” or as part of a project collaboration, such as C-SCALE, is different. Within C-SCALE you will certainly receive the latest version without problem and we will also work with you.

Let us internally discuss the procedure and nominate a point of contact from our software department who will assist you in the installation.

@Björn Backeberg @Anna van Gils @Sandra Gaytan Aguilar: Please share any other comments you may have and let’s coordinate and inform Kostas on who we can get the Delft3D FM installation done on HPC most efficiently.

Kind Regards,
@lorincmeszaros

15 September 2021

Hi all,

There is an initiative in Deltares to develop a Singularity container for Delft3D FM – I think this is an excellent use case to test it! @Dimitris Dellis and @Kostas Koumantaros does GRNET’s HPC support Singularity containers?

I will check about the status of the Singularity container and who the main contact point is, but I think it could be ready for deployment already.

Cheers @backeb

15 September 2021

Hi all. We support singularity, but this doesn't guarantee that any image can work. It depends on the software - mainly glibc - inside the container image if it can run. If the libc inside image is very recent, probably it will not work at all because recent versions require host kernel to be also recent. In case it works, for single node (i.e. run limited to a single machine) it is expected to work well. If it contains for example MPI for multiple nodes, obviously the MPI inside image has no idea about what network we have, which driver and so on. In this case the result in performance (after customization needed to make it run) may be seen in pages 16 and 42 of this public document : https://b2share.eudat.eu/api/files/acb2f772-47f4-4a44-85af-a83144bf9c9e/HPCE3_D12.6_BenchmarkingResults_v1.2.pdf

@ntellgrnet

22 September 2021

Dear @backeb and @lorincmeszaros

Could you please provide us with access to the latest Delft3D FM source code that is going to be used in the C-Scale project? Could you also include (or at least define) a representative problem size for the HiSEA use case? Additionally, are there any reports available with the scale of the HiSEA problem sizes and the execution time that they last on a typical PC? For example, a serial run on a commodity machine would be, let's say, a couple of hours? days?

@backeb, perhaps some of the questions/answers could be also added to the GitHub page too.

Thank you, @nikosT

cc @nikosT @lorincmeszaros @sandragaytan @kkoumantaros @ntellgrnet

[backeb]

Re Singularity The feedback I have about the Singularity container is the following:

Our current Singularity container is not thoroughly tested but works well for our experimental benchmarks. If you want to have that to test, we can make that available.

We intend to make a well tested Singularity container available in November.

@nikosT what is your preference, install directly on the HPC or via Singularity? I prefer the latter.

[nikosT]

Hi @backeb,

We would like to try both cases, since we want to test the performance of the native against the Singularity setup. (A native installation would probably hit better performance.) We would also appreciate it if you could make available the non-well-tested release.

[backeb]

@lorincmeszaros @avgils @nikosT @ntellgrnet

We have a Singularity container available internally at Deltares at p:\d-hydro\delft3dfm_containers\delft3dfm_2021.05

@lorincmeszaros can you arrange getting the source code for Delft3D FM.

The objectives being

1. Deploy the Singularity container
2. Install and compile Delft3D FM natively on the HPC
3. Compare performance

@ntellgrnet and @kkoumantaros how do we go about arranging access to the HPC, do we use the SRAM CO that @sebastian-luna-valero set up?

[sebastian-luna-valero]

Hi,

I think it would be ideal to test access via SRAM. Please see: https://github.com/c-scale-community/use-case-hisea/issues/10

Best regards, Sebastian

[ntellgrnet]

For GRNET HPC, as far the necessary data exist on ldap, we can get them, check for validity and create account if everything is OK. What if not (typical issues : invalid format of pub key, private ip addresses etc.) ?

[sebastian-luna-valero]

Good point, @ntellgrnet

I think for the moment we can address the initial issues on https://github.com/c-scale-community/use-case-hisea/issues/10

Later on we will create documentation to help users with well-known issues. After that we will discuss how to handle user support requests in C-SCALE.

[lorincmeszaros]

hi @nikosT @ntellgrnet (cc: @backeb @avgils),

We have discussed internally and we can share with you the singularity container upon signing the standard Delft3D FM Pre-release software licensing agreement (which includes both Docker and Singularity containers).

Please provide me the contact details of the person (name, address, email address) who can sign on behalf of GRNet at your earliest convenience. Upon receiving the details, I will send you the Agreement to be signed by GRNet. Immediatly after that we will send the container.

Let me know if you have any quesions regarding this.

[kkoumantaros]

can you please send us the template to fill it in with the appropriate details. cheers K.

[lorincmeszaros]

Yes, of course we share the template with you. Can we already pre-fill the contact person field with your name/email address and the address of GRNET? thanks!

[lorincmeszaros]

blank agreement was sent to @kkoumantaros

[backeb]

deprecated