Well after my last post about Swift and Jupyter a reader sent me link to the use of both Julia and Fortran programming languages in a Jupyter Notebook.
More information in this lecture Project Jupyter: Architecture and Evolution of an Open Platform for Modern Data Science by Fernando Perez.
Project Jupyter, evolved from the IPython environment, provides a platform for interactive computing that is widely used today in research, education, journalism and industry. The core premise of the Jupyter architecture is to provide tools for human-in-the-loop interactive computing. It provides protocols, file formats, libraries and user-facing tools optimized for the task of humans interactively exploring problems with the aid of a computer, combining natural and programming languages in a common computational narrative.
Amber is a suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active develpment community
Amber 18 ajor new features include:
- Free energy calculations on GPUs
- GPU support for 12-6-4 ion potentials
- Domain decomposition for CPU-parallelism
- Nudged elastic band calculations for pmemd (CPU and partial GPU implementation)
- Constant redox potential calculations, to supplement constant pH simulations
- Support and significant performance improvements for the latest Maxwell, Pascal and Volta GPUs from NVIDIA.
- New pmemd.gem code for advanced force fields, including AMOEB
AmberTools 18 new features include
- CUDA-enabled pbsa solver; extensions for membrane modeling with PB *lambda-dynamics method for constant pH simulations *packmol_memgen tool for building lipids and bilayers *New ("middle") integration algorithms in sander *Build tools based on CMake *Continued updates and extensions to cpptraj: *ability to obtain energies from snapshots of PME simulations *Pairlist and other speedups *improved scripting abilities
Instructions for installing Amber under Mac OSX are here http://ambermd.org/Installation.php
You will need to install gfortran, whilst you can download the binary it might be worth considering using Homebrew as described here
First let me say I’m not a big Fortran user but any blog posts about Fortran always seem to be very popular, and I do get asked regularly about how to compile Fortran applications.
So I've decided to gather together all the Fortran news, tips and resources onto a dedicated Fortran on a Mac page.
If you know of anything else it would be useful to include please let me know.
I just came across Simply Fortran includes the GNU Fortran compiler, an advanced development environment including project management, and an integrated debugger for fast and easy installation.
Simply Fortran is tested on OSX Snow Leopard through macOS Sierra.
Added to the Fortran on a Mac page.
Everytime I mention Fortran there is an uptick in the site views so I know there are plenty of readers with an interest in Fortran on a Mac.
There is an interesting post on the NextMove Software blog, Just what you wanted for Christmas – a compiler for Gaussian.
This package provides a “pgf77” script that emulates the Portland Group’s PGI fortran 77 compiler, instead using the Free Software Foundation’s GNU gfortran compiler instead. This emulation is sufficient to allow packages such as Gaussian03, that would otherwise require a commercial compiler, to be built using open source tools. In addition, this package also allows Gaussian03 to be built on a case-insensitive file system (such as when using Mac OS X, cygwin or a FAT32 drive) by overriding the behaviour of “cp” and “gau-cpp” such that they don’t cause problems when used by Gaussian’s build scripts on non case-sensitive file systems.
gXXforrtran is available on GitHub In theory, it should work for a standard Linux or Mac system.
However, as they don’t have access to the Gaussian source code they can't check it. Anyone out there care to try it?
I’m not a Fortran user but overtime I mention it there is a sharp uptick in page views so there are obviously a significant number of users who might be interested in this workshop.
Date: 24 - 25 August 2016. Time: 09:30 - 17:30. Location: Learning Resource and Development Centre (Library), E building, Culham Centre for Fusion Energy, Culham Science Centre, Abingdon, OX14 3DB
TOPICS WILL INCLUDE:
- Software engineering for computational science;
- Modern Fortran standards and how to write optimized and efficient Fortran;
- NetCDF and HDF5 scientific file formats for data sharing in Fortran;
- GNU Automake to automate the build process;
- pFUnit unit testing framework for testing Fortran codes;
- Doxygen for Fortran code documentation;
- Git version control for collaborative code development;
- In-memory visualisation using PLplot in Fortran;
- IEEE Floating Point Exception Handling
- Software verification and portability using the NAG Fortran compiler
- Fortran interoperability with C, Python and R;
- Introduction to parallelism for Fortran.
There is a page of Fortran Resources here.
Any posts on Fortran always seem to attract attention so I thought I'd flag this opportunity.
Larry Zottarelli, the last original Voyager engineer still on the project, is retiring after a long and storied history at JPL. While there are still a few hands around who worked on the original project, now the job of keeping this now-interstellar spacecraft going will fall to someone else. And that someone needs to have some very specific skills …Know Cobol? Can you breeze through Fortran? Remember your Algol
More details here
First let me say I’m not a big Fortran user but any blog posts about Fortran always seem to be very popular, and I do get asked regularly about how to compile Fortran applications. So when I saw that the NNSA, national labs team with Nvidia to develop open-source Fortran compiler technology to integrate into LLVM I thought I'd mention it.
LLVM is a collection of reusable compiler and tool chain technologies with a modular design that facilitates support for a wide variety of programming languages and processor architectures.The Fortran front-end module created through this project will be derived from NVIDIA’s PGI Fortran compiler, which has been used in production across a variety of high performance computing systems for more than 25 years. PGI® software is a leading supplier of software compilers and tools for parallel computing.
I've compiled a list of Fortran resources for the Mac here.
Fortran has a long history with scientific programming and so it is perhaps not surprising that overtime I mention Fortran there is an uptick in readers. FTranProjectBuilder is the only IDE specifically designed for Fortran programming on the Mac and has recently been updated to version 2.0.
This update brings improvements to the interface, context sensitive autocompletes, and in addition derived type, Intrinsic procedure, module and procedure popovers
In addition the Nocturnal Aviation Software has been updated with screenshots of the updated FTranProjectBuilder, Mac Fortran Blog and a section of free Fortran code snippets.
A while back I compiled a list of resources for Fortran on a Mac.
Last month I compiled a page of Fortran resources for the Mac. At the time I was hoping it would be a useful resource but thought it would draw a limited audience. In fact it turned out to very popular, the page has been accessed nearly 1000 times with readers spending between 3 and 4 minutes on the page. I've also been contacted by a couple of fortran developers who have suggested additional resources and tips for compiling.
Chargemol program performs atomic population analysis to determine DDEC net atomic charges, atomic spin moments, and effective bond orders. Because the DDEC net atomic charges are simultaneously optimized to reproduce atomic chemical states and the electrostatic potential surrounding a material, they are well-suited for constructing force-fields used in atomistic simulations (e.g., classical molecular dynamics or monte carlo simulations) and for quantifying electron transfer between atoms in complex materials and during chemical reactions
The DDEC method is described in the following publication and references therein.
Thomas A. Manz and David S. Sholl, "Improved Atoms-in-Molecule Charge Partitioning Functional for Simultaneously Reproducing the Electrostatic Potential and Chemical States in Periodic and Non-Periodic Materials", J. Chem. Theory Comput., Vol. 8 (2012) 2844-2867. DOI
The program can be run using either Matlab or Fortran source codes, which yield identical numbers. The Fortran code is parallelized with OpenMP and runs much faster than the Matlab code.
First let me say I’m not a big Fortran user but any blog posts about Fortran always seem to be very popular, and I do get asked regularly about how to compile Fortran applications. So I’ve put together a page summarising all the resources that I’m aware of, together with some installation instructions.
If you know of anything I’ve missed feel free to email me or add them to the comments.
Whenever I post anything about Fortran there is a noticeable uptick to page views so I thought I’d post a link to this review on Ars Technica
Scientific computing’s future: Can any coding language top a 1950s behemoth?. This is a very interesting review and discussion on scientific programming and it is no surprise that for the more computationally intensive number crunching applications Fortran still rules.
“I don't know what the language of the year 2000 will look like, but I know it will be called Fortran.” —Tony Hoare, winner of the 1980 Turing Award, in 1982.
I’ve just been told that the Absoft Pro Fortran 2014 v14 Compiler Suite For Mac OS X is available.
Pro Fortran 2014 v14 - A few of the new features for this release are: AWE-Chart, AWE-Plot, AWE-Form & Enhanced AVX Instruction set performance. Pro Fortran 2014 builds faster code with Absoft's Exclusive Dynamic AP Load Balancing Technology, OpenMP 3.0 support, SMP Analyzer, Tools Plug-in, New HPC Scientific & Engineering Math Library and more.
The Absoft IDE is the only commercial Fortran/C++ development environment designed by Fortran experts. It includes: programmer's editor, Absoft's SMP and Vector analyzer, Fx3 graphical debugger, SMP and MPI control features, optimized math libraries and 2D/3D graphics.
I know that Fortran is still very important in scientific computing so this may be of interest.
CLFORTRAN is an open source (LGPL) Fortran module, designed to provide direct access to GPU, CPU and accelerator based computing resources available by the OpenCL standard.
Added to the GPU Science page.
I’ve just updated the listing of Scientific Applications under Mavericks and I thought I’d highlight one application. The page I have on Tools for Fortran Programmers is consistently one of the top accessed Blog entries. I’m sure one of the reasons for this popularity is FTranProjectBuilder the only Mac-native Fortran development environment (IDE) it works with the gfortran, g95, ifort, Absoft Pro Fortran, NAG nagfor and PGI pgfortran compilers. Since I mentioned it last FTranProjectbuilder has been updated six more times, in April, May, July, August and October with new features like the ability to build static libraries, trackpad interaction and compiler errors now being marked in the source code. Full details are in the project notes on the Nocturnal Aviation Software website , and yes, all of the tools, including FTranProjectbuilder are compatible with 10.6.8+, and run fine on 10.9 Mavericks.
Fortran still has a significant user base in the scientific community where the speed, portability, array handling and access to shared memory make it a very powerful option.
There is a nice comparison of programming languages from the viewpoint of scientists here
I’m not a Fortran programmer so I’ve perhaps not as close an eye on this as other areas, however looking at the Fortran IDE FTranProjectBuilder release notes it seems there have been 17 updates in the last 12 months. FTranProjectBuilder is now up to version 1.15 with new features being added at a steady rate. Of note for scientists FTranProjectBuilder has support for two of the most common parallel processing libraries. If your program is coded for MPI using OpenMPI or OpenMP and you have them installed, you can use FTranProjectBuilder to run on multiple processors.
These sites might also be useful
News for all you Fortran programmers out there.
Absoft Corporation announced immediate availability of new Pro Fortran 2013 for Mac OS
Primary new features of Absoft Pro Fortran 2013 include: - Compatible with Mountain Lion and X code command line toolset - New AVX optimizations improve application speed up to 10% - Many additional F2008 extension supported - Upgraded ATools/GUI environment simplifies application development - New AWE (Absoft Window Environment) spreadsheet feature allows graphical display of 2D arrays - Absoft HPC Scientific and Engineering numerical library included at no additional charge - Compatible with IMSL v7.0, & 6.0 and NAG 23 numerical libraries - Additional product details http://www.absoft.com/AbsoftMacIntelCompiler.htm
Pricing: $299 academic, $699 commercial. IMSL 32/64-bit bundle an available option
I known there are a number of Fortran users so I thought I’d highlight this message
The Absoft Pro Fortran 2012 for Mac OS currently shipping is compatible with Mountain Lion. Absoft Pro Fortran 2012 Mac OS customers who purchased earlier than June 2012 who want to run on Mountain Lion will need to download the Service Pack v11.5.2 which can be done at no charge from the Absoft site: http://www.absoft.com/download/downloads.html
Pro Fortran versions prior to 2012 are not compatible with Mountain Lion and will require an upgrade.
I’m not a Fortran user myself but I know a lot of scientists swear by it for high performance code, so I thought I’d mention Nocturnal Aviation Software the creators of FTranProjectBuilder the only Mac-native Fortran development environment (IDE) it works with the gfortran, g95, ifort, Absoft Pro Fortran, NAG nagfor and PGI pgfortran compilers.
FTranProjectBuilder is for scientists, engineers and students. It's useful for large, complex projects, but makes even simple programs easy to manage. To speed up program development it has:
- Single window interface
- Editor, console and notes views
- Project wide search
- Execution input from console or file
- Execution timer
- Errors and search results organized by file in outline view
- Add files by drag and drop, or import an existing makefile
FTranProjectBuilder manages the dependencies, object and module files, program executable and a standard makefile for you. You spend your time working on your code. FTranprojectBuilder does the rest.
Absoft Corporation, today announced general availability of a new Xcode 4.3 Compatibility Pack for Absoft Pro Fortran 2012 customers running Mac OS X. The Compatibility Pack is available (only) as part of Absoft's new Service Pack v11.5.1 for Pro Fortran 2012 Mac OS customers.
The Compatibility Pack allows installation of Pro Fortran 2012 with Xcode 4.3 and is compatible with Apple's reorganized directory structure.
The Service Pack v11.5.1 which includes the Compatibility Pack for Mac OS X can be downloaded at NO CHARGE by current Absoft Pro Fortran 2012 Mac OS X customers from:http://www.absoft.com/download/downloads.html