Nuestro pequeño cluster para cálculos de dinámica molecular en el CURE. Configurar este cluster fue una gran experiencia que amplió notablemente mis conocimientos previos de sysadmin con Undernet. Le saco poco cartel #cluster #moleculardynamics #cure #udelar #diy #physics #debian #slurm #openmpi

My head hurts. Doing a deep-dive into containerization/VM with #Jenkins. So many options. I think I'll give #LXD a shot. But frankly, since my #OpenMPI program is already containerized via #Apptainer, I'll just go ahead and build on the (fairly powerful) Jenkins host for now, just to get the pipeline built as a proof of concept.

Time for an adult beverage.

Finishing some runtime system work; decided to try a #deskpi #super6c cluster board.

An ITX form factor beowulf cluster is amazing.

#slurm & #nfs worked out of apt.

#ucx, #openmpi, #openshmem, #openpmix, #gasnet, & #hpx needed custom compilation.

@raspberrypi #arm #hpc #supercomputing

[FLISoL24] Avogadro: Un clúster de cálculo numérico con software libre (Santiago Roland)

https://tube.undernet.uy/w/pmL4BieQjo57BWfhWPK8MX

@kylewritescode Good morning Kyle.

I already had a productive morning. I finally figured out how to let my hybrid #Apptainer #OpenMPI container for our NASA code talk to #UKY's #HPC cluster’s InfiniBand backend. Now the code scales beautifully. Next up, getting it to run on our collaborators’ cluster at #UMN.

I think I’ll have my coffee now.

Hoy reinstalamos el cluster de dinamica molecular del CURE con Debian 12, 5 PCs con OpenMPI y un RAID-5 para almacenar los cálculos... el dios debianita debe estar orgulloso de mi y contento por la faena #cluster #cure #openmpi #slurm #debian #moleculardynamics #fisica #physics #dinamicamolecular

For @centos #Hyperscale users, we now have a fixed #pmux for CVE-2023-41915 and an upgraded #openmpi and rebuilt #slurm to go with it

https://nvd.nist.gov/vuln/detail/CVE-2023-41915

https://pagure.io/centos-sig-hyperscale/sig/issue/156

Instructions on enabling this if you are interested in trying it out

https://sigs.centos.org/hyperscale/content/repositories/main/

#CentOS
#CentOSStream
#CVE
#Hyperscalers
#SecurityUpdate

#OpenMPI 5.0 Ready To Say "Goodbye" To 32-Bit Support

https://www.phoronix.com/news/OpenMPI-5.0-Drops-32-bit

Original tweet : https://twitter.com/phoronix/status/1621470409144025090

@Santral pretty much the defacto standard in #HPC is #MPI or #OpenMPI on this topic many books are available https://mpitutorial.com/recommended-books

#openmp != #openmpi
#sapevatelo #themoreyouknow #parallel #api #mpi #multiprocessing #messageparsinginterface

#INT
#OpenMPI

https://explainshell.com/explain?cmd=gfortran+-fopenmp

> Enable the OpenMP extensions.

#OpenMPI
あるいはもしやnuma関係？ 弱小シングルプロセッサなのでそっち系の経験はないのだけど、numa関係でハマるとパフォーマンスがガク下がりときく(ethの割り込みの割り当てとか

https://www.open-mpi.org/projects/hwloc/tutorials/20140422-ComPAS-hwloc-tutorial.pdf

https://www.cc.kyushu-u.ac.jp/scp/support/faq/faq005.html

#INT
#OpenMPI
#setup

/usr/local/xxx_netcdf-4.4.4.1/gcc485/lib/libnetcdf.so.11

間違って他のディレクトリに入ったのか

#INT
#OpenMPI
#setup

$ mpicc
mpicc: error while loading shared libraries: libnetcdf.so.11: cannot open shared object file: No such file or directory

#openmpi

https://github.com/open-mpi/ompi/blob/master/README

このREADMEが
https://github.com/open-mpi/ompi/
のファイルと整合していない気はする

ユーザはどうしているのか?

あるいは、これは開発用であって、ユーザはやはりtar.gzファイルを取って作業する
ということなのかもしれない

(だからリポジトリ名をompiとしているのかも)

#INT
#openmpi
#setup

OpenMPI

v3.1.4: configureあり
v4.0.1: configureなし

v3.1.4でセットアップしていたか

v4.0.1は色々変わってそうで今回はパス

#INT
#OpenMPI
#setup

GitHubから取得したファイル
configureできない?

#INT
#centos
#setup
#module
#openmpi

OpenMPIのモジュールロード

Linux使用Moduler切换各种MPI环境
https://blog.csdn.net/kongxx/article/details/52253593

#INT
#centos
#setup
#OpenMPI

OpenMPIのセットアップは自分の記事を参考に
https://qiita.com/7of9/items/0dd38bfe6c9ed15622ac#open-mpi-v211

#INT
#openmpi
#version

v3.0とv3.1が別ものとしてアップデートされているのか

https://www-lb.open-mpi.org/software/ompi/v3.0/
https://www.open-mpi.org/software/ompi/v3.1/