July 2020 - firedrake - imperial.ac.uk

Re: [firedrake] trying to install Firedrake on the LSU HPC cluster
by Ham, David A 24 Jul '20

24 Jul '20

Dear Shawn, The install instructions on the website are more directed at workstation/laptop users than supercomputers. Automation of dependency installation on supercomputers isn’t really possible because we need to use the compiler toolchains and MPI that the system specifies. I would, however, note that the comments that the sysadmin made about Firedrake being specifically geared towards Ubuntu and MacOS are not correct. Rather, we provide automatic upstream dependency installation on those platforms for the benefit of novice users. Running ./firedrake-install --show-dependencies will list the core external dependencies. All of these are probably already available, possibly by loading the correct set of modules. This is the output: ************************************************ The following dependencies need to be installed: ************************************************ * A C and C++ compiler (for example gcc/g++ or clang), GNU make * A Fortran compiler (for PETSc) * Blas and Lapack * Boost * Git * Python version >=3.6 * The Python headers * autoconf, automake, libtool * CMake You’re also likely to need to tell the installer something about your toolchain, and in particular what the MPI compilers and launch command are. Another frequent source of issues on supercomputers are less than fully functional Python installs – either because missing pip or lacking ssl certificates. Sometimes users end up building Python from source in order to get a fully working Python. A couple of recent examples of scripts which people have written to install Firedrake on supercomputers are at: https://github.com/firedrakeproject/firedrake-archer/blob/master/install_fi… https://github.com/firedrakeproject/isambard/blob/master/install_firedrake_… Finally, if you have issues, then posting an issue on GitHub including the firedrake-install.log is usually the best thing to do. Regards, David -- Dr David Ham Department of Mathematics Imperial College London https://www.imperial.ac.uk/people/david.ham From: <firedrake-bounces(a)imperial.ac.uk> on behalf of Shawn W Walker <walker(a)lsu.edu> Date: Thursday, 23 July 2020 at 19:23 To: firedrake <firedrake(a)imperial.ac.uk> Subject: [firedrake] trying to install Firedrake on the LSU HPC cluster Hello Firedrake people. The IT staff here at LSU are having some trouble installing firedrake on our clusters. I’m forwarding the email below detailing those difficulties for your information. If you have any suggestions, please let me know. -Shawn From: LONI Systems Support [mailto:sys-help@loni.org] Sent: Thursday, July 23, 2020 11:58 AM To: Shawn W Walker <walker(a)lsu.edu> Subject: Re: [Sys-help#20200716106172] FW: firedrake on LSU HPC? Hi Shawn, Another update: 1. Native installation wasn't successful, yet. The installation script states "Any required system packages are installed using brew (MacOS) or apt (Ubuntu and similar Linux systems). On a Linux system without apt, the installation will fail if a dependency is not found." Since we run Redhat, taking care of all dependencies will take some time. 2. I was able to build a working container image on a box running Fedora, but the same image fails on the cluster with the issue reported here: https://github.com/firedrakeproject/firedrake/issues/1712<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.co…> It's supposed to be fixed last month, but I'm still getting it on the cluster. 3. Overall it's not very friendly with clusters. For one, it's specifically geared towards Ubuntu, but I don't think there are many clusters running Ubuntu. The difficulties are summarized in the issue report here: https://github.com/firedrakeproject/firedrake/issues/1779<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.co…> Cheers, Le -- LONI/LSU HPC Support staff sys-help(a)loni.org<mailto:sys-help@loni.org> Help Line: +1 (225) 578-0900 http://www.loni.org/ -- Helpful Documentation: http://www.hpc.lsu.edu/docs/faq/index.php http://www.hpc.lsu.edu/users/help.php http://hpc.loni.org/ 07/20/2020 18:35 - Shawn W Walker wrote: Thanks Le. -Shawn From: LONI Systems Support [mailto:sys-help@loni.org] Sent: Monday, July 20, 2020 4:50 PM To: Shawn W Walker <walker(a)lsu.edu<mailto:walker@lsu.edu>> Subject: Re: [Sys-help#20200716106172] FW: firedrake on LSU HPC? Hi Shawn, Just a quick update: I was able to build a container for it, but ran into errors running the example on their website, most likely due to permission issues in the container as well as how MPI is set up. I may need to install it from source. I'll get back to you as soon as possible. Cheers, Le -- LONI/LSU HPC Support staff sys-help(a)loni.org<mailto:sys-help@loni.org> Help Line: +1 (225) 578-0900 http://www.loni.org/ -- Helpful Documentation: http://www.hpc.lsu.edu/docs/faq/index.php http://www.hpc.lsu.edu/users/help.php http://hpc.loni.org/ 07/16/2020 15:42 - LONI Systems Support wrote: Hi Shawn, Let me take a look and get back to you. Cheers, Le -- LONI/LSU HPC Support staff sys-help(a)loni.org<mailto:sys-help@loni.org> Help Line: +1 (225) 578-0900 http://www.loni.org/ -- Helpful Documentation: http://www.hpc.lsu.edu/docs/faq/index.php http://www.hpc.lsu.edu/users/help.php http://hpc.loni.org/ 07/16/2020 15:37 - Shawn W Walker wrote: Hello. I would like to get Firedrake up and running on the HPC system. Can you help? -Shawn From: Le Yan Sent: Thursday, July 16, 2020 3:28 PM To: Shawn W Walker <walker(a)lsu.edu<mailto:walker@lsu.edu>> Subject: Re: firedrake on LSU HPC? Hi Shawn, I just took a look at it and it seems to have Docker images available, so we could try to create a Singularity container image. I'll get back to you. Could you please forward the email to sys-help(a)loni.org<mailto:sys-help@loni.org> so we will have a record? And I assume either SuperMIC or Super Mike 2 should be fine, right? Cheers, Le ----------------------------------------- Le Yan, PhD Assistant Director High Performance Computing Information Technology Services Louisiana State University 343 Frey Computing Services Building, Baton Rouge, LA 70808 office 225-578-7524 | fax 225-578-6400 lsu.edu<http://www.lsu.edu/> | hpc.lsu.edu<http://hpc.lsu.edu/> ________________________________ From: Shawn W Walker <walker(a)lsu.edu<mailto:walker@lsu.edu>> Sent: Thursday, July 16, 2020 3:16 PM To: Le Yan <lyan1(a)lsu.edu<mailto:lyan1@lsu.edu>> Subject: firedrake on LSU HPC? Hello Le. Do you know if this software can be “easily” installed on the HPC system: https://www.firedrakeproject.org/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fired…> It is similar to FEniCS. The main issue is whether PETSC is configured properly for Firedrake. -Shawn

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trying to install Firedrake on the LSU HPC cluster
by Shawn W Walker 23 Jul '20

23 Jul '20

Hello Firedrake people. The IT staff here at LSU are having some trouble installing firedrake on our clusters. I’m forwarding the email below detailing those difficulties for your information. If you have any suggestions, please let me know. -Shawn From: LONI Systems Support [mailto:sys-help@loni.org] Sent: Thursday, July 23, 2020 11:58 AM To: Shawn W Walker <walker(a)lsu.edu> Subject: Re: [Sys-help#20200716106172] FW: firedrake on LSU HPC? Hi Shawn, Another update: 1. Native installation wasn't successful, yet. The installation script states "Any required system packages are installed using brew (MacOS) or apt (Ubuntu and similar Linux systems). On a Linux system without apt, the installation will fail if a dependency is not found." Since we run Redhat, taking care of all dependencies will take some time. 2. I was able to build a working container image on a box running Fedora, but the same image fails on the cluster with the issue reported here: https://github.com/firedrakeproject/firedrake/issues/1712<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.co…> It's supposed to be fixed last month, but I'm still getting it on the cluster. 3. Overall it's not very friendly with clusters. For one, it's specifically geared towards Ubuntu, but I don't think there are many clusters running Ubuntu. The difficulties are summarized in the issue report here: https://github.com/firedrakeproject/firedrake/issues/1779<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.co…> Cheers, Le -- LONI/LSU HPC Support staff sys-help(a)loni.org<mailto:sys-help@loni.org> Help Line: +1 (225) 578-0900 http://www.loni.org/ -- Helpful Documentation: http://www.hpc.lsu.edu/docs/faq/index.php http://www.hpc.lsu.edu/users/help.php http://hpc.loni.org/ 07/20/2020 18:35 - Shawn W Walker wrote: Thanks Le. -Shawn From: LONI Systems Support [mailto:sys-help@loni.org] Sent: Monday, July 20, 2020 4:50 PM To: Shawn W Walker <walker(a)lsu.edu<mailto:walker@lsu.edu>> Subject: Re: [Sys-help#20200716106172] FW: firedrake on LSU HPC? Hi Shawn, Just a quick update: I was able to build a container for it, but ran into errors running the example on their website, most likely due to permission issues in the container as well as how MPI is set up. I may need to install it from source. I'll get back to you as soon as possible. Cheers, Le -- LONI/LSU HPC Support staff sys-help(a)loni.org<mailto:sys-help@loni.org> Help Line: +1 (225) 578-0900 http://www.loni.org/ -- Helpful Documentation: http://www.hpc.lsu.edu/docs/faq/index.php http://www.hpc.lsu.edu/users/help.php http://hpc.loni.org/ 07/16/2020 15:42 - LONI Systems Support wrote: Hi Shawn, Let me take a look and get back to you. Cheers, Le -- LONI/LSU HPC Support staff sys-help(a)loni.org<mailto:sys-help@loni.org> Help Line: +1 (225) 578-0900 http://www.loni.org/ -- Helpful Documentation: http://www.hpc.lsu.edu/docs/faq/index.php http://www.hpc.lsu.edu/users/help.php http://hpc.loni.org/ 07/16/2020 15:37 - Shawn W Walker wrote: Hello. I would like to get Firedrake up and running on the HPC system. Can you help? -Shawn From: Le Yan Sent: Thursday, July 16, 2020 3:28 PM To: Shawn W Walker <walker(a)lsu.edu<mailto:walker@lsu.edu>> Subject: Re: firedrake on LSU HPC? Hi Shawn, I just took a look at it and it seems to have Docker images available, so we could try to create a Singularity container image. I'll get back to you. Could you please forward the email to sys-help(a)loni.org<mailto:sys-help@loni.org> so we will have a record? And I assume either SuperMIC or Super Mike 2 should be fine, right? Cheers, Le ----------------------------------------- Le Yan, PhD Assistant Director High Performance Computing Information Technology Services Louisiana State University 343 Frey Computing Services Building, Baton Rouge, LA 70808 office 225-578-7524 | fax 225-578-6400 lsu.edu<http://www.lsu.edu/> | hpc.lsu.edu<http://hpc.lsu.edu/> ________________________________ From: Shawn W Walker <walker(a)lsu.edu<mailto:walker@lsu.edu>> Sent: Thursday, July 16, 2020 3:16 PM To: Le Yan <lyan1(a)lsu.edu<mailto:lyan1@lsu.edu>> Subject: firedrake on LSU HPC? Hello Le. Do you know if this software can be “easily” installed on the HPC system: https://www.firedrakeproject.org/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fired…> It is similar to FEniCS. The main issue is whether PETSC is configured properly for Firedrake. -Shawn

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MatNest and blockSize
by Karin&NiKo 12 Jul '20

12 Jul '20

Dear Firedrakers, I am solving a 3 fields coupled problem with Firedrake. I would like to use a multiplicative block-preconditioner but PETSc complains about a local size not being correct. [0] Arguments are incompatible [0] Local size 9 not compatible with block size 2 I have noticed that the use of a MatAij solves the problem (see comment in line 132) but I am afraid this is just a side effect. Am I missing something? Thanks in advance, Nicolas

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plea for images
by Cotter, Colin J 07 Jul '20

07 Jul '20

Dear Firedrakers, Firedrake is partially supported by the Platform for Research in Simulation Methods (an EPSRC grant at Imperial College) [yes I know PRISM is an unfortunate acronym!]. We are looking for some new images for the PRISM website prism.ac.uk. If you have a flashy image from your Firedrake-based work that you don't mind being used to promote Firedrake through the prism.ac.uk website please can you send it to me offlist and I will pass it on. all the best --cjc Professor Colin Cotter (he/him) Department of Mathematics 755, Huxley Building Imperial College London South Kensington Campus United Kingdom of Great Britain and Northern Ireland +44 2075943468

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