Scientific Applications under Big Sur: Update 5
General Issues with Big Sur
If you want an overview of Big Sur I'd recommend the excellent arstechnica review.
Apple has officially confirmed that the following Macs are compatible with Big Sur.
- MacBook (2015 or newer)
- MacBook Air (2013 or newer)
- MacBook Pro (Late 2013 or newer)
- Mac mini (2014 or newer)
- iMac (2014 or newer)
- iMac Pro (2017)
- Mac Pro (2013 and later)
In addition there is issue of the new Apple Silicon Macs with the new Apple M1 chip, if there is specific information about the new machines I've included it.
Snazzy Labs has an interesting commentary on the new Apple Silicon machines and promises a in depth technical review of all 3 models they have on order. The first reviews on Apple Silicon are now in
Scientific Applications
I've contacted all developers I know and their responses to date are shown below.
4-Peaks no known issues
Absoft Absoft Pro Fortran 2021 For macOS and OS X Fully compatible with macOS Big Sur (11.0)
alvaDesc We tested all our products and all of them work properly on MacOS Big Sur.
Amsterdam Modeling Suite As we only just finished our 2020 release our developers didn't dare switching to Big Sur yet. I can try on my own macbook shortly.
Anaconda seems to be working fine.
APE make sure you download the 64-bit version
Avogadro Been running Big Sur betas for a while - everything works. The next beta of Avogadro v2 will have some interface tweaks that are more noticeable on Big Sur (e.g., warning dialogs changed to be Mac-native). Don't yet have universal binaries, but working on it for Open Babel and Avogadro v2 betas (e.g. 1.94). Should still work fine on Apple Silicon computers.
BBEdit version 13 is compatible with macOS Big Sur. BBEdit 13.5 adds support for Apple Silicon
Brainsight macOS 11 Big Sur is coming out very soon, but do not upgrade your Mac yet, because Brainsight is not yet compatible with Big Sur
ChemAxon Most of our software in general requires Java, so as long as the appropriate Java version is installed, there should be no problem.
ChemDraw current version products (ChemDraw Professional 20.0.0.48 and ChemDraw Prime 20.0.0.48) supported with Mac OSX Catalina (v20.0 qualified with Mac OS 11.0 Beta)
ChemDoodle “The latest versions of ChemDoodle 2D (v11) and ChemDoodle 3D (v6) are fully supported on macOS Big Sur (macOS 10.16/11.0) and there are no known issues. In addition to supporting the operating system update, ARM based Macs (like those just released with the new Apple Silicon chip) are also fully supported for ChemDoodle 2D and ChemDoodle 3D with no known issues."
Conquest and Mercury from CCDC The full CSD software portfolio, including Mercury, ConQuest, Mogul, GOLD, CSD-CrossMiner, the CSD Python API and other components, has been tested and is not currently compatible with macOS Big Sur. Please note that our upcoming 2020.3 CSD Release will not be compatible with macOS Big Sur at point of release. We are working hard on a series of improvements to make our software portfolio compatible and fully supported, which we will make available to users as an update as soon as possible. In the meantime, a number of enhancements have been made to our products to simplify the configuration of and support specifically on macOS platforms. Examples are the removal of XQuartz as a dependency and removal of the need to run an X windows display for full use of the CSD Python API. These enhancements will be incorporated in future CSD software releases."
Cresset testing underway
CrystalMaker Works swimmingly! We’ve tested all our software on Big Sur - including a machine with Apple Silicon - and are happy to confirm full compatibility for CrystalMaker 10.5.5, SingleCrystal 4.1.0 and CrystalDiffract 6.8.5. Free updates to CrystalMaker 10.5.5 and SingleCrystal 4.1.0 were released yesterday morning and are recommended for anyone using “Big Sur”.
We are also very-pleased to announce the immediate availability of SingleCrystal 4.1 for Apple Silicon: this is our first Universal Binary and provides 100% native performance on the new Apple Silicon Macs, as well as 100% native performance on Intel.
As one of the vanishingly-few Mac science developers left, we’re proud of our reputation of developing genuine, native Mac apps. We’ve been doing this for over 25 years now and this is our fourth Mac hardware platform! (we’ve gone from Motorola 68K to PowerPC to Intel and now to Apple Silicon).
CYLView 1.0 does not work under Catalina.
DataWarrior Seems to be working fine.
Delta We are working on an update for Delta and will post it as soon as it is available.
DEVONthink version 3 is 64-bit compliant
EndNote We are in the process of testing and we will be updating our Compatibility page once our testing is complete.
EnzymeX no issues reported
Findings no issues reported
Gaussaian As far as we can tell so far, both of our current releases, Gaussian 16 rev. C.01 and GaussView 6.1.1 for macOS 64-bit Intel CPUs, run normally on macOS Big Sur. We do not have any reports of problems so far. We do not have a native port for Apple Silicon chips for either G16 or GaussView 6. However, for now, both of the Intel binaries that I mentioned above should run on Apple Silicon using Rosetta 2. We have not done full certification on the Apple Silicon at this point but Apple claims that Rosetta 2 should be capable of handling running existing binaries for Intel chips.
Highlights The PDF Reader for Research, updated for Big Sur with version 2020.3. Big Sur also fixes an annoying issue from PDFKit on Catalina where superscript text (e.g. citations) would break text selection.
Homebrew For most seems to work fine, remember to reinstall Xcode command line tools.
All the ICM products are compatible with Big Sur:
Other products that are compatible include:
Igor Pro Igor Pro 8.04 is the first version of Igor that is notarized and includes notarized WaveMetrics XOPs. We therefore recommend that you run Igor Pro 8.04 if you are using macOS 10.15 or macOS 11.0.
JalView Jalview works on macOS 11.0 Big Sur!
KNIME We are testing the upcoming version 4.3 of KNIME Analytics Platform against Big Sur and plan to have it supported by the time we do that release in the first week of December.
Manuscripts no issues reported
Matlab MATLAB is compatible with macOS 11 (Big Sur) from release R2020b onwards, support for Apple Silicon is in development
Mathematica no issues for latest version. testing on Apple Silicon underway
Mendeley no issues reported
Microsoft Office Microsoft has announced that Office 365 is ready for Big Sur - Apple Silicon M1 Macs will use Rosetta 2 for now
Mnova The current version of Mnova LiteCDE is compatible with MacOS Big Sur
NAG Fortran compiler Fortran compiler for Apple Silicon Macs now available to download
MOE Our initial tests showed no issues with this version.
Papers no issues reported
Parallels Parallels 16 is ready for Big Sur. Older Parallels Desktop versions only partially support working on macOS Big Sur due to technical reasons may experience issues depending on the configuration.
PYMOL On Intel Macs with macOS 11, PyMOL works fine, no known issues. We have not tested Apple Silicon (M1) yet.
Python Python 2.7 is no longer included - use Python 3 instead Python works fine on Apple Silicon and is "mad fast!".
QMForge 2.4 does not support Big Sur yet
R The front page of a CRAN site has a link ‘Download R for (Mac) OS X’. Click on that, then download the file R-4.0.3.pkg and install it. This runs on macOS 10.13 and later on Intel CPU20 (High Sierra, Mojave, Catalina, Big Sur, …).
RDKit All seems fine (Note: -Python 2.7 is no longer supported - use Python 3 instead)
Samson SAMSON 2020 R3 (the latest release) works on Big Sur.
Schrodinger Upgrading to macOS 11 will cause existing Schrödinger Suite releases to fail to run. We are hard at work to address this incompatibility and expect to extend support to macOS 11 in an upcoming Schrödinger Suite release
SeeSAR now updated to support Big Sur.
Sketch With version 70 release, we’re excited to introduce a UI redesign that fits right in with the new macOS Big Sur design language. It’s the same Sketch you know and love, but with every detail reconsidered — from a full-height sidebar, to a refreshed Inspector, and all-new iconography throughout the app.
Spartan Full testing on Big Sur has not been completed at this point expect to have a positive answer with regards to Big Sur by next week.
SPSS The current release IBM SPSS Statistics 27.0.1 and the current IBM SPSS Statistics Subscription release build 1.0.0.0.1447 will run on MAC OSX 11 Big Sur in translation mode.
Stardrop We haven't yet completed a full test cycle, but we have not seen any issues and don't anticipate any.
Swiss-PdbViewer Swiss-PdbViewer is a 32 bits application and will * NOT * run.
TensorFlow and TensorFlow Addons This pre-release delivers hardware-accelerated TensorFlow and TensorFlow Addons for macOS 11.0+. Native hardware acceleration is supported on Macs with M1 and Intel-based Macs through Apple’s ML Compute framework.
UCSF Chimera ChimeraX v1.1 does not work on MacOS 11.0 (Big Sur), but this problem has been fixed in v1.1.1 and the daily build.
VMD there interface issues under Big Sur
VMWare In preparation for the next major version of macOS 11.0 Big Sur, VMware has made full use of Apple’s hypervisor and other APIs, removing the need for kernel extensions and supporting macOS 11 as both host and guest.
Vortex Vortex works perfectly on Intel Macs under Big Sur, on Apple Silicon currently Elemental crashes.
Wizard In general works fine, some issue with older work books.
Xcode need to update to latest version. Remember to reinstall command line tools
XQuartz OpenGL and OpenCL are still here, even on Apple Silicon Macs
I’ll add more updates later, feel free to contact me and thanks for the comments to date.
Last update 26 November 2020
Open Chemical Sciences Workshops
The RSC CICAG Open Chemical Sciences meeting was a great success with attendees from around the world able to attend this online event. You can read more about the meeting on the CICAG website http://www.rsccicag.org/previous%20meetings.htm.
One component of the meeting was a series of workshops highlighting key Open-Source software applications for chemists. These sessions were recorded and are now available on the CICAG YouTube channel.
DataWarrior workshop by Isabelle Giraud DataWarrior combines dynamic graphical views and interactive row filtering with chemical intelligence. Scatter plots, box plots, bar charts and pie charts not only visualize numerical or category data, but also show trends of multiple scaffolds or compound substitution patterns. This workshop is an introductory tutorial, DataWarrior can be downloaded here http://www.openmolecules.org/datawarrior/download.html.
PyMOL workshop by Garrett Morris PyMOL is a comprehensive software package for rendering and animating 3D structures, in particular biomolecules. Website https://pymol.org/2/ You can install PyMOL via Conda: Conda: https://www.anaconda.com/distribution/ or Miniconda: https://docs.conda.io/en/latest/miniconda.html https://anaconda.org/psi4/pymol or https://omicx.cc/2019/05/26/install-pymol-windows/ or PyMOL from GitHub: https://github.com/schrodinger/pymol-open-source
UsingGoogleCoLab workshop by Jan Jensen Colaboratory, or "Colab" for short, allows you to write and execute Python in your browser, with Zero configuration required.
- Initial notebook: https://colab.research.google.com/drive/1t2ED9woH_cTOhCiiUZZzrTIUUfwsSds5?usp=sharing
- Final notebook: https://colab.research.google.com/drive/1rJOE6RNTCjByMqR-L3B7tZtwML3nIQVf?usp=sharing
ChEMBL workshop by Anna Gaulton ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.. This workshop is an introductory tutorial. Website https://www.ebi.ac.uk/chembl/
Fragalysis workshop by Rachel Skyner Fragalysis (fragment analysis) is a web-based platform for fragment-based drug discovery https://fragalysis.diamond.ac.uk/viewer/react/landing/). It’s initial use case is focussed around the fragment screening experiment at Diamond.. This workshop is an introductory tutorial.
Knime workshop by Greg Landrum KNIME Analytics Platform is the open source software for creating data science. Intuitive, open, and continuously integrating new developments, KNIME makes understanding data and designing data science workflows and reusable components accessible to everyone. This workshop is an introductory tutorial. Knime can be downloaded here https://www.knime.com/downloads. Data used in tutorial are here
SAMSON 2020 R3
A really interesting update to Samson
SAMSON is a software platform for computational nanoscience. Its generic, open architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. The SAMSON application and the SAMSON SDK are developed by the OneAngstrom led by Stephane Redon. SAMSON stands for "Software for Adaptive Modeling and Simulation Of Nanosystems".
One of the most exciting features of SAMSON 2020 R3 is the introduction of cloud computing capabilities. In many design situations, a local computer might have too little processing power to perform advanced calculations (e.g. high-throughput screening, some molecular dynamics simulations, etc.). The latest update introduces the possibility to perform cloud calculations directly from SAMSON.
From the users’ point of view, this means it will now be possible to use some cloud-enabled SAMSON extensions to perform calculations in the cloud with a unified, integrated approach, and focus on science. An obvious immediate advantage is the access to raw computing power (based on existing and upcoming computing hardware), the possibility to run many jobs in parallel, compare numerical experiments, perform long calculations while still being able to use your desktop/laptop.
The full release note are here.