I installed Amira (ThermoFisher Scientific) on my Linux machine (Ubuntu 16.04.5 LTS) by following the Linux Installation Guide in the Amira User Guide. I have the floating license for it. I meet all of the specifications for the program in terms of computer specs and it can run on Linux (though it was made specifically for Red Hat and I don't know if that will have any bearing on its usability). Visually, in both ls view from the terminal and the GUI file explorer, it appears that all files have downloaded correctly off of the USB and nothing appears to be missing.
The instructions said to start Amira in command-line by:
In brief
- navigating into the directory in which it is installed
- typing
bin/start
- then it should run and open
In depth (from user manual)
In general, on Unix systems, Amira is started via the start script located in the subdirectory bin. Usually, this script will be linked to /usr/local/bin/Amira or something similar. Alternatively, the user may define an alias Amira pointing to bin/start.
On Windows systems, Amira is usually started via the start menu or via a desk-top icon. Nevertheless, the Amira executable may also be invoked directly by calling bin/arch-Win64VC12-Optimize/Amira.exe. In this case, the same command line options as on a Unix system are understood.
The syntax of Amira is as follows:
Amira [options] [files ...] Data files specified in the command line will be loaded automatically. In addition to data files, script files can also be specified. These scripts will be executed when the program starts.
The following options are supported:
•
-help
Prints a short summary of command line options.•
-version
Prints the version string of Amira.•
-no stencils
Tells Amira not to ask for a stencil buffer in its 3D graphics windows. This option can be set to exploit hardware acceleration on some low-end PC graphics boards.•
-no overlays
Tells Amira not to use overlay planes in its 3D graphics windows. Use this option if you expe- rience problems when redirecting Amira on a remote display.•
-no gui
Starts up Amira without opening any windows. This option is useful for executing a script in batch mode.•
-logfile filename
Causes any messages printed in the console window also to be written into the specified log file. Useful especially in conjunction with the -no gui option.•
-depth number
This option is only supported on Linux systems. It specifies the preferred depth of the depth buffer. The default on Linux systems is 16-bit.•
-style={windows | motif | cde}
This option sets the display style of Amira’s Qt user interface.•
-debug
This options applies to the developer version only. It causes local packages to be executed in Amira Start-Up 467debug version. By default, optimized code will be used.•
-cmd
command [-host hostname] [-port port] Send Tcl command to a running Amira application. Optionally the host name and the port number can be specified. You must typeapp -listen
in the console window of Amira before commands can be received.•
-clusterdaemon
Start as VR daemon, on a cluster slave node (Amira XScreen Extension). This may be replaced by a service. See the online documentation for more information.•
-tclcmd
command Executes the Tcl command in the starting application.
However, after hitting enter, I get the message:
using arch-LinuxAMD64-Optimize ...
using embedded libudev.so.0
using embedded libgfortran.so.1
using embedded libicudata.so.42
using embedded libXm.so.4
/AmiraInstall/Amira-6.5.0/bin/arch-LinuxAMD64-Optimize/Amira: error while loading shared libraries: libMeshVizDataMapping.so: cannot open shared object file: No such file or directory
The same error message is given for ./Amira
After extensive googling online, it seems that an alternative way of opening Amira is to simply enter Amira
in the Terminal. That seems to me as being a shortcut added in the bashrc file. And once implemented, yields
No command 'Amira' found, did you mean:
Command 'mira' from package 'mira-assembler' (universe)
Amira: command not found
There really doesn't seem to be much documentation online and I would appreciate any thoughts, solutions, or ideas on how to get this program running.
Thank you.
libMeshVizDataMapping.so
is provided by the vendor but is not installed into a "system" loader path, you may need to take extra steps (such as providing anldconfig
file or a modifiedLD_LIBRARY_PATH
)locate bin/Amira
return? What doeslocate Amira-6.5.0/bin
return? If you installed within the last 24 hours you have to usesudo updatedb
before runninglocate
command.locate bin/Amira
returns/AmiraInstall/Amira-6.5.0/bin/Amira
andlocate Amira-6.5.0/bin
returns the locations of all of the libraries including the one it cannot access. However, when I added a path towards it, the same initial error occurred.