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SIENews

The newsletter of the SIE de Investigación y Enseñanza N. 66 - June 2021

Astronomical software support for macOS

Providing astronomical software support on macOS has proven to be more complicated and difficult than on Linux. This is due on one hand to the ever increasing security restrictions about what can run and how on macOS (for instance 32bit executables are no longer allowed on macOS Catalina and BigSur, and one needs to assign specific permissions to applications to enable access to some particular folders), on the other to the fact that many software packages do not come integrated in the OS repositories (as is the case for Linux distributions), but rely on third-party package managers like MacPorts, Homebrew, Nix or Conda.

We cannot provide support to all these different package managers, which, when installed alongside to one another, often produce incompatibilities and conflicts (with cryptic and hard-to-diagnose errors); nor can we support obsoleted versions of macOS.

As for the macOS version, we align with the (unpublished) Apple policy and will support the current plus the previous two versions, as done in other research centers (see for instance https://computing.cs.cmu.edu/desktop/os-lifecycle, or https://it.ucsf.edu/news/macos-1013-high-sierra-end-support). Among the package managers mentioned before, our experience of many years has led us to select MacPorts as the one we will provide support for, a decision also influenced by the fact the ESO uses MacPorts to build and release their instrument pipelines for macOS (https://www.eso.org/sci/software/pipelines/installation/macports.html). Of course do feel free to use HomeBrew or Conda (or any other package manager), but in case of trouble we won't be able to help.

Priority policy change in deimos and diva

The "deimos" and "diva" High Performance Computers were purchased in 2017 with the funds of three research lines of the Severo Ochoa (S.O.) Programme at IAC, which needed a HPC machine with hundreds of cores and a huge amount of shared memory, and GPU computing as well. For this reason, while any IAC researcher was able to use them, the members of these three research projects (Cosmology and Astroparticles, Formation and Evolution of Galaxies, Solar Physics) enjoyed higher priority in submitting and running their jobs.

After some discussion in the Research Area about the deimos and diva usage policy, it has been proposed that, after 4 years, the higher priority policy for the S.O. research teams should be discontinued. This change has already been implemented so that, from now on, the same priority is assigned to all diva and deimos users, regardless of which research group they belong to. Note though that in order to be able use SLURM (the Workload Manager), you still have to send a request to res_support@iac.es.

Removing "OLD" Intel and PGI compilers

Until last year, both the Intel and PGI compilers were subject to a yearly fee for the renewal of their license in order to use them on our Linux computers. However, two major changes took place last year: the PGI compilers became part of the NVIDIA HPC-SDK (High Performance Computing Software Development Kit), while Intel released the new oneAPI toolkit, presented in our March 2021 newsletter). The most important point is that both products are totally free and do not require any license or paid subscription.

Thus, we are going to remove soon the older installations of the Intel and PGI compilers, that is the ones which were enabled by the module load intel/2020_update4 and module load PGI/20.1 commands, and recommend using the compilers and associated libraries and tools of the NVIDIA HPC-SDK and Intel oneAPI suites. Just type module avail to find the exact module to load and use: the NVIDIA ones are found under the "/usr/local/share/modulefiles/compilers" heading and are prefixed by "nvhpc", while the oneAPI modules are gathered under the "/opt/intel/oneapi/modulefiles" heading.

Software update: python 3.8, astrometry.net, sextractor, R ...

The great advantage of using Ubuntu 18.04 LTS instead of Fedora is that it comes with 5-year Long Term Support. Note though that the LTS release includes updates for potential security problems and bugs, but not new versions of software. This means, for instance, that we cannot upgrade astrometry.net or R from the standard Ubuntu repositories: updates must be done either from Personal Package Archives (PPA), or by compiling and installing from source.

In the last few weeks we received requests to update Python (as the default 3.6 version is incompatible with the very latest releases of scipy, astropy, photutils and other packages), astrometry.net, R, sextractor and other related tools. Thus now Python v3.8, astrometry.net v0.85, R v4.0.5, sextractor v2.25.0, scamp v2.10.0 and swarp 2.41.5 are available on Ubuntu 18.04 desktops and burros. They can be used by loading first the corresponding module: type module avail to check them out. (The Environment Modules system is a tool to set or modify environment variables in the appropriate way for the software package you want to use. It avoids cluttering your environment, and allows selecting different versions of a same package.)

We'd also like to remind you that all old and new astronomical software packages work properly in a bash shell. If your default shell is still tcsh (check it with echo $SHELL), please send an email to CAU to have it changed to bash. Get in touch with the CAU or with us if you need help to migrate settings, variable definitions, aliases, etc. from tcsh to bash.

IAC cloud upgrade

Our "Servicios Informaticos" have recently changed the platform offering Cloud storage to IAC researchers from ownCloud to Nextcloud.

While the change should be mostly transparent to users, it improves the security by means of Two Factor Authentication (2FA), and provides additional functionalities, such as the ability to edit online documents, spreadsheets or presentations, and view video files online, alongside with other nice features.

The IAC Cloud service, similar in function to Google Drive, allows users to have their data available from anywhere and to share folders and files by giving read/edit permissions to outsiders. Everyone with an IAC account can use it, with the usual credentials. We initially offer 75 GB of storage to every user, but this can be increased if needed.

The service is available at https://cloud.iac.es/. Some documentation is also available in our intranet, at http://tiny.cc/iacCloudEs (spanish) and http://tiny.cc/iacCloudEn (english).

SIE de Investigación y Enseñanza :: N. 66 - June 2021 - Contact: