Spatkin - Revision history

Redaktor at 18:18, 28 June 2023

2023-06-28T18:18:16Z

← Older revision		Revision as of 20:18, 28 June 2023
Line 35:		Line 35:
	* Dockerfile to build a Docker container image:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-Dockerfile spatkin-1.0.0-Dockerfile]		* Dockerfile to build a Docker container image:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-Dockerfile spatkin-1.0.0-Dockerfile]
	* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]		* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]
	* Setup instructions <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/>BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">export LC_ALL=C<br/>singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div>		* Setup instructions <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/><br/>BUILDING a Singularity container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">$ singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within the sinfularity container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">export LC_ALL=C<br/>$ singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div><br/><br/>BUILDING a Docker container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">$ docker build --build-arg user=$USER --build-arg uid=$(id -u) --build-arg gid=$(id -g) -t spatkin .</span></div><br/>RUNNING the Docker container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">$ xauth nlist $DISPLAY \| sed -e 's/^..../ffff/' \| xauth -f /tmp/.docker.xauth nmerge -<br/>$ docker run -e DISPLAY=unix$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix -v /tmp/.docker.xauth:/tmp/.docker.xauth:rw -e XAUTHORITY=/tmp/.docker.xauth -v $HOME:$HOME spatkin </span></div><br/>

	<br/>		<br/>
	====Documentation====		====Documentation====

Redaktor at 09:20, 9 June 2023

2023-06-09T09:20:27Z

← Older revision		Revision as of 11:20, 9 June 2023
Line 33:		Line 33:
	<br/>		<br/>
	====[<b>new</b>] Containers====		====[<b>new</b>] Containers====
	* Dockerfile to build a Docker container image:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0~~-singularity~~-Dockerfile spatkin-1.0.0-Dockerfile]		* Dockerfile to build a Docker container image:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-Dockerfile spatkin-1.0.0-Dockerfile]
	* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]		* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]
	* Setup instructions <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/>BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">export LC_ALL=C<br/>singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div>		* Setup instructions <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/>BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">export LC_ALL=C<br/>singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div>

Redaktor at 09:20, 9 June 2023

2023-06-09T09:20:10Z

← Older revision		Revision as of 11:20, 9 June 2023
Line 33:		Line 33:
	<br/>		<br/>
	====[<b>new</b>] Containers====		====[<b>new</b>] Containers====
	* Dockerfile to build a Docker container image:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity~~.recipe~~ spatkin-1.0.0-Dockerfile]		* Dockerfile to build a Docker container image:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity-Dockerfile spatkin-1.0.0-Dockerfile]
	* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]		* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]
	* Setup instructions <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/>BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">export LC_ALL=C<br/>singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div>		* Setup instructions <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/>BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">export LC_ALL=C<br/>singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div>

Redaktor at 09:19, 9 June 2023

2023-06-09T09:19:28Z

← Older revision		Revision as of 11:19, 9 June 2023
Line 33:		Line 33:
	<br/>		<br/>
	====[<b>new</b>] Containers====		====[<b>new</b>] Containers====
			* Dockerfile to build a Docker container image:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-Dockerfile]
	* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]		* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]
	* Setup instructions <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/>BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">export LC_ALL=C<br/>singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div>		* Setup instructions <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/>BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">export LC_ALL=C<br/>singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div>

Redaktor at 12:20, 27 May 2023

2023-05-27T12:20:21Z

← Older revision		Revision as of 14:20, 27 May 2023
Line 34:		Line 34:
	====[<b>new</b>] Containers====		====[<b>new</b>] Containers====
	* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]		* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]
	* Setup instructions <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/>BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">export LC_ALL=C<br/>singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div~~></accordion~~>		* Setup instructions <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/>BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">export LC_ALL=C<br/>singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div>
	<br/>		<br/>
	====Documentation====		====Documentation====

Redaktor: Accordion to collapsible

2023-05-08T18:09:04Z

Accordion to collapsible

← Older revision		Revision as of 20:09, 8 May 2023
Line 19:		Line 19:
	====Source code====		====Source code====
	* C++ source code:   [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-source.tar.gz spatkin-1.0.0-source.tar.gz]		* C++ source code:   [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-source.tar.gz spatkin-1.0.0-source.tar.gz]
	<~~accordion parent~~="~~accordion~~" ~~heading~~="~~How to compile~~">Compilation on Linux, Mac, and Windows is managed by [http://www.cmake.org/ CMake] – see file COMPILING.txt in the source code for building instructions.</~~accordion~~>		* Compilation instructions <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/>Compilation on Linux, Mac, and Windows is managed by [http://www.cmake.org/ CMake] – see file COMPILING.txt in the source code for detailed building instructions.</div></div>
	<br/>		<br/>
	====Stand-alone executables====		====Stand-alone executables====
	* ~~Mac~~ application bundle (zipped "app"):   [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-x86_64-darwin16.zip spatkin-1.0.0-x86_64-darwin16.zip]<~~accordion parent~~="~~accordion~~" ~~heading~~="~~How to verify and run~~">COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.12 (Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted spatkin-1.0.0-x86_64-darwin16.zip is b841ced9da16a6cff9ab2f25654c9334<br/><br/>EXAMPLES:  Example S<span style="font-variant:small-caps">patkin</span> input files can be found inside Spatkin.app, in folder Documentation. Independently, they can be downloaded [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-examples.zip here].</~~accordion~~>		* macOS: application bundle (zipped "app"):   [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-x86_64-darwin16.zip spatkin-1.0.0-x86_64-darwin16.zip]
			* macOS: verification and running <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/>COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.12 (Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted spatkin-1.0.0-x86_64-darwin16.zip is b841ced9da16a6cff9ab2f25654c9334<br/><br/>EXAMPLES:  Example S<span style="font-variant:small-caps">patkin</span> input files can be found inside Spatkin.app, in folder Documentation. Independently, they can be downloaded [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-examples.zip here].</div></div>

	* Windows 64-bit installer:   [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-x86_win64-setup.exe spatkin-1.0.0-x86_win64-setup.exe]<~~accordion parent~~="~~accordion~~" ~~heading~~="~~How to verify and run~~">COMPATIBILITY:  This software was built with MSYS2/MinGW64 on Windows 10, and tested on Windows 10 and Windows 8.<br/><br/>SECURITY:  The downloadable installer is not signed with a certificate (so in windows terms it comes from an "unknown publisher") but its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted spatkin-1.0.0-x86_win64-setup.exe is e3 27 16 0b 5a 0e a1 b7 f8 b8 e7 7b 46 c0 26 ec<br/><br/>EXAMPLES:  After installation, example S<span style="font-variant:small-caps">patkin</span> input files can be found in the windows user directory Documents/SpatkinModels. (There is a new set of examples; installer asks whether the previously installed set of examples should be removed; it's recommended to remove previous examples.) Independently, the same set of examples can be downloaded [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-examples.zip here].</~~accordion~~>		* Windows 64-bit: installer:   [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-x86_win64-setup.exe spatkin-1.0.0-x86_win64-setup.exe]
			* Windows 64-bit: verification and running <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/>COMPATIBILITY:  This software was built with MSYS2/MinGW64 on Windows 10, and tested on Windows 10 and Windows 8.<br/><br/>SECURITY:  The downloadable installer is not signed with a certificate (so in windows terms it comes from an "unknown publisher") but its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted spatkin-1.0.0-x86_win64-setup.exe is:<br/>e3 27 16 0b 5a 0e a1 b7 f8 b8 e7 7b 46 c0 26 ec<br/><br/>EXAMPLES:  After installation, example S<span style="font-variant:small-caps">patkin</span> input files can be found in the windows user directory Documents/SpatkinModels. (There is a new set of examples; installer asks whether the previously installed set of examples should be removed; it's recommended to remove previous examples.) Independently, the same set of examples can be downloaded [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-examples.zip here].</div></div>
	<br/>		<br/>
	====Virtual machines with pre-installed S<span style="font-variant:small-caps">patkin</span>====		====Virtual machines with pre-installed S<span style="font-variant:small-caps">patkin</span>====
	* Virtual machine hosting Ubuntu Linux: [{{SERVER}}/software/spatkin/release/Virtual_machine_with_spatkin.7z Virtual_machine_with_spatkin.7z]<~~accordion parent~~="~~accordion~~" ~~heading~~="~~How to set up and run~~">The [http://www.7-zip.org 7-zip] archive contains a configured virtual machine that was created under VirtualBox 5.1.22. Virtual disk format is VMDK; the guest operating system installed on the disk should thus run not only under VirtualBox but also under VMWare, QEMU, and other virtualization solutions. The machine hosts Ubuntu Linux 16.04.2 LTS.<br/><br/>PLATFORM:  VirtualBox for the major operating systems (as hosts) can be downloaded free of charge from [http://www.virtualbox.org/wiki/Downloads http://www.virtualbox.org/wiki/Downloads].<br/><br/>LAUNCHING:  After downloading, the archive should be decompressed (command-line: 7z x Virtual_machine_with_spatkin.7z). In Oracle VirtualBox Manager, one should choose from the menu Machine -> Add and point to the SpatkinLinuxBox.vbox file. In the guest Linux system, the default user is ubuntu (password: ubuntu); this user is automatically logged after startup. S<span style="font-variant:small-caps">patkin</span> can be launched via a desktop shortcut or by opening terminal and typing <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">spatkin</span>.<br/><br/>EXAMPLES:  Example SPATKIN input files can be found in /home/ubuntu/local/spatkin/share/doc. Independently, they can be retrieved, most easily, using wget in Terminal:<br/><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">wget {{SERVER}}/software/spatkin/release/spatkin-1.0.0-examples.zip</span><br/><br/>POSSIBLE ISSUES:  An issue that often arises when launching a virtual machine within VirtualBox for the first time is the lack of hardware-accelerated virtualization technologies such as VT-x or AMD-V. Please note that you may need to enable this feature by changing advanced CPU settings in BIOS of your computer (support for virtualization is often disabled by default).</~~accordion~~>		* Virtual machine hosting Ubuntu Linux: [{{SERVER}}/software/spatkin/release/Virtual_machine_with_spatkin.7z Virtual_machine_with_spatkin.7z]
			* Setup instructions <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/>The [http://www.7-zip.org 7-zip] archive contains a configured virtual machine that was created under VirtualBox 5.1.22. Virtual disk format is VMDK; the guest operating system installed on the disk should thus run not only under VirtualBox but also under VMWare, QEMU, and other virtualization solutions. The machine hosts Ubuntu Linux 16.04.2 LTS.<br/><br/>PLATFORM:  VirtualBox for the major operating systems (as hosts) can be downloaded free of charge from [http://www.virtualbox.org/wiki/Downloads http://www.virtualbox.org/wiki/Downloads].<br/><br/>LAUNCHING:  After downloading, the archive should be decompressed (command-line: 7z x Virtual_machine_with_spatkin.7z). In Oracle VirtualBox Manager, one should choose from the menu Machine -> Add and point to the SpatkinLinuxBox.vbox file. In the guest Linux system, the default user is ubuntu (password: ubuntu); this user is automatically logged after startup. S<span style="font-variant:small-caps">patkin</span> can be launched via a desktop shortcut or by opening terminal and typing <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">spatkin</span>.<br/><br/>EXAMPLES:  Example SPATKIN input files can be found in /home/ubuntu/local/spatkin/share/doc. Independently, they can be retrieved, most easily, using wget in Terminal:<br/><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">wget {{SERVER}}/software/spatkin/release/spatkin-1.0.0-examples.zip</span><br/><br/>POSSIBLE ISSUES:  An issue that often arises when launching a virtual machine within VirtualBox for the first time is the lack of hardware-accelerated virtualization technologies such as VT-x or AMD-V. Please note that you may need to enable this feature by changing advanced CPU settings in BIOS of your computer (support for virtualization is often disabled by default).</div></div>
	<br/>		<br/>
	====[<b>new</b>] Containers====		====[<b>new</b>] Containers====
	* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]<~~accordion parent~~="~~accordion~~" ~~heading~~="~~How to set up and run~~">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">export LC_ALL=C<br/>singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div></accordion>		* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]
			* Setup instructions <div class="toccolors mw-collapsible mw-collapsed"><div class="mw-collapsible-content"><br/>BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">export LC_ALL=C<br/>singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div></accordion>
	<br/>		<br/>
	====Documentation====		====Documentation====

Redaktor at 11:10, 5 December 2019

2019-12-05T11:10:56Z

← Older revision		Revision as of 13:10, 5 December 2019
Line 30:		Line 30:
	<br/>		<br/>
	====[<b>new</b>] Containers====		====[<b>new</b>] Containers====
	* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]<accordion parent="accordion" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div></accordion>		* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]<accordion parent="accordion" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">export LC_ALL=C<br/>singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div></accordion>
	<br/>		<br/>
	====Documentation====		====Documentation====

Redaktor at 22:20, 19 November 2018

2018-11-19T22:20:23Z

← Older revision		Revision as of 00:20, 20 November 2018
Line 22:		Line 22:
	<br/>		<br/>
	====Stand-alone executables====		====Stand-alone executables====
	* Mac application bundle (zipped "app"):   [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-x86_64-darwin16.zip spatkin-1.0.0-x86_64-darwin16.zip]<accordion parent="accordion" heading="How to verify and run">COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.12 (Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,~~Inconsolatam~~,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted spatkin-1.0.0-x86_64-darwin16.zip is b841ced9da16a6cff9ab2f25654c9334<br/><br/>EXAMPLES:  Example S<span style="font-variant:small-caps">patkin</span> input files can be found inside Spatkin.app, in folder Documentation. Independently, they can be downloaded [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-examples.zip here].</accordion>		* Mac application bundle (zipped "app"):   [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-x86_64-darwin16.zip spatkin-1.0.0-x86_64-darwin16.zip]<accordion parent="accordion" heading="How to verify and run">COMPATIBILITY:  This software was built with XCode 8 and tested under macOS 10.12 (Sierra). It is likely incompatible with previous Mac operating system releases.<br/><br/>SECURITY:  MD5 sum of the downloadable ZIP archive can be checked in Terminal:<div align="center"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">md5 <i>path_to_zip</i></span></div>MD5 sum of untainted spatkin-1.0.0-x86_64-darwin16.zip is b841ced9da16a6cff9ab2f25654c9334<br/><br/>EXAMPLES:  Example S<span style="font-variant:small-caps">patkin</span> input files can be found inside Spatkin.app, in folder Documentation. Independently, they can be downloaded [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-examples.zip here].</accordion>

	* Windows 64-bit installer:   [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-x86_win64-setup.exe spatkin-1.0.0-x86_win64-setup.exe]<accordion parent="accordion" heading="How to verify and run">COMPATIBILITY:  This software was built with MSYS2/MinGW64 on Windows 10, and tested on Windows 10 and Windows 8.<br/><br/>SECURITY:  The downloadable installer is not signed with a certificate (so in windows terms it comes from an "unknown publisher") but its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,~~Inconsolatam~~,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted spatkin-1.0.0-x86_win64-setup.exe is e3 27 16 0b 5a 0e a1 b7 f8 b8 e7 7b 46 c0 26 ec<br/><br/>EXAMPLES:  After installation, example S<span style="font-variant:small-caps">patkin</span> input files can be found in the windows user directory Documents/SpatkinModels. (There is a new set of examples; installer asks whether the previously installed set of examples should be removed; it's recommended to remove previous examples.) Independently, the same set of examples can be downloaded [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-examples.zip here].</accordion>		* Windows 64-bit installer:   [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-x86_win64-setup.exe spatkin-1.0.0-x86_win64-setup.exe]<accordion parent="accordion" heading="How to verify and run">COMPATIBILITY:  This software was built with MSYS2/MinGW64 on Windows 10, and tested on Windows 10 and Windows 8.<br/><br/>SECURITY:  The downloadable installer is not signed with a certificate (so in windows terms it comes from an "unknown publisher") but its integrity can be checked manually in command line using a Windows pre-installed utility:<br/><div align="center"><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">certUtil -hashfile <i>path_to_installer</i> MD5</span></div>MD5 sum of untainted spatkin-1.0.0-x86_win64-setup.exe is e3 27 16 0b 5a 0e a1 b7 f8 b8 e7 7b 46 c0 26 ec<br/><br/>EXAMPLES:  After installation, example S<span style="font-variant:small-caps">patkin</span> input files can be found in the windows user directory Documents/SpatkinModels. (There is a new set of examples; installer asks whether the previously installed set of examples should be removed; it's recommended to remove previous examples.) Independently, the same set of examples can be downloaded [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-examples.zip here].</accordion>
	<br/>		<br/>
	====Virtual machines with pre-installed S<span style="font-variant:small-caps">patkin</span>====		====Virtual machines with pre-installed S<span style="font-variant:small-caps">patkin</span>====
	* Virtual machine hosting Ubuntu Linux: [{{SERVER}}/software/spatkin/release/Virtual_machine_with_spatkin.7z Virtual_machine_with_spatkin.7z]<accordion parent="accordion" heading="How to set up and run">The [http://www.7-zip.org 7-zip] archive contains a configured virtual machine that was created under VirtualBox 5.1.22. Virtual disk format is VMDK; the guest operating system installed on the disk should thus run not only under VirtualBox but also under VMWare, QEMU, and other virtualization solutions. The machine hosts Ubuntu Linux 16.04.2 LTS.<br/><br/>PLATFORM:  VirtualBox for the major operating systems (as hosts) can be downloaded free of charge from [http://www.virtualbox.org/wiki/Downloads http://www.virtualbox.org/wiki/Downloads].<br/><br/>LAUNCHING:  After downloading, the archive should be decompressed (command-line: 7z x Virtual_machine_with_spatkin.7z). In Oracle VirtualBox Manager, one should choose from the menu Machine -> Add and point to the SpatkinLinuxBox.vbox file. In the guest Linux system, the default user is ubuntu (password: ubuntu); this user is automatically logged after startup. S<span style="font-variant:small-caps">patkin</span> can be launched via a desktop shortcut or by opening terminal and typing <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,~~Inconsolatam~~,monospace;">spatkin</span>.<br/><br/>EXAMPLES:  Example SPATKIN input files can be found in /home/ubuntu/local/spatkin/share/doc. Independently, they can be retrieved, most easily, using wget in Terminal:<br/><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,~~Inconsolatam~~,monospace;">wget {{SERVER}}/software/spatkin/release/spatkin-1.0.0-examples.zip</span><br/><br/>POSSIBLE ISSUES:  An issue that often arises when launching a virtual machine within VirtualBox for the first time is the lack of hardware-accelerated virtualization technologies such as VT-x or AMD-V. Please note that you may need to enable this feature by changing advanced CPU settings in BIOS of your computer (support for virtualization is often disabled by default).</accordion>		* Virtual machine hosting Ubuntu Linux: [{{SERVER}}/software/spatkin/release/Virtual_machine_with_spatkin.7z Virtual_machine_with_spatkin.7z]<accordion parent="accordion" heading="How to set up and run">The [http://www.7-zip.org 7-zip] archive contains a configured virtual machine that was created under VirtualBox 5.1.22. Virtual disk format is VMDK; the guest operating system installed on the disk should thus run not only under VirtualBox but also under VMWare, QEMU, and other virtualization solutions. The machine hosts Ubuntu Linux 16.04.2 LTS.<br/><br/>PLATFORM:  VirtualBox for the major operating systems (as hosts) can be downloaded free of charge from [http://www.virtualbox.org/wiki/Downloads http://www.virtualbox.org/wiki/Downloads].<br/><br/>LAUNCHING:  After downloading, the archive should be decompressed (command-line: 7z x Virtual_machine_with_spatkin.7z). In Oracle VirtualBox Manager, one should choose from the menu Machine -> Add and point to the SpatkinLinuxBox.vbox file. In the guest Linux system, the default user is ubuntu (password: ubuntu); this user is automatically logged after startup. S<span style="font-variant:small-caps">patkin</span> can be launched via a desktop shortcut or by opening terminal and typing <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">spatkin</span>.<br/><br/>EXAMPLES:  Example SPATKIN input files can be found in /home/ubuntu/local/spatkin/share/doc. Independently, they can be retrieved, most easily, using wget in Terminal:<br/><span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">wget {{SERVER}}/software/spatkin/release/spatkin-1.0.0-examples.zip</span><br/><br/>POSSIBLE ISSUES:  An issue that often arises when launching a virtual machine within VirtualBox for the first time is the lack of hardware-accelerated virtualization technologies such as VT-x or AMD-V. Please note that you may need to enable this feature by changing advanced CPU settings in BIOS of your computer (support for virtualization is often disabled by default).</accordion>
	<br/>		<br/>
	====[<b>new</b>] Containers====		====[<b>new</b>] Containers====
	* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]<accordion parent="accordion" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,~~Inconsolatam~~,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,~~Inconsolatam~~,monospace;">singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div></accordion>		* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]<accordion parent="accordion" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolata,monospace;">singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div></accordion>
	<br/>		<br/>
	====Documentation====		====Documentation====

Redaktor at 12:52, 7 November 2018

2018-11-07T12:52:23Z

← Older revision		Revision as of 14:52, 7 November 2018
Line 30:		Line 30:
	<br/>		<br/>
	====[<b>new</b>] Containers====		====[<b>new</b>] Containers====
	* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]<accordion parent="accordion" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolatam,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator ~~with~~ a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolatam,monospace;">singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div></accordion>		* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]<accordion parent="accordion" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolatam,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator within a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolatam,monospace;">singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div></accordion>
	<br/>		<br/>
	====Documentation====		====Documentation====

Redaktor at 12:51, 7 November 2018

2018-11-07T12:51:57Z

← Older revision		Revision as of 14:51, 7 November 2018
Line 30:		Line 30:
	<br/>		<br/>
	====[<b>new</b>] Containers====		====[<b>new</b>] Containers====
	* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]<accordion parent="accordion" heading="How to set up and run">BUILDING a container:<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolatam,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator with a container:<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolatam,monospace;">singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div></accordion>		* A docker-based recipe for a singularity container:  [{{SERVER}}/software/spatkin/release/spatkin-1.0.0-singularity.recipe spatkin-1.0.0-singularity.recipe]<accordion parent="accordion" heading="How to set up and run">BUILDING a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolatam,monospace;">singularity build spatkin.simg spatkin-1.0.0-singularity.recipe </span></div><br/>LAUNCHING the simulator with a container (in terminal):<div align="left"> <span style="font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera Sans Mono,Consolas,Inconsolatam,monospace;">singularity exec spatkin.simg /opt/local/bin/Spatkin</span></div></accordion>
	<br/>		<br/>
	====Documentation====		====Documentation====