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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

  1. navigating into the directory in which it is installed
  2. typing bin/start
  3. 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 type app -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.

  • Can you provide the instructions you used to install the software? if 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 an ldconfig file or a modified LD_LIBRARY_PATH) – steeldriver Oct 1 '18 at 16:39
  • I realized I was unclear in the original post. After I saved the files onto my computer, I recall that the exact instructions for installing the software from the USB happened in the command line as a step-by-step process very much like a Windows installation Wizard. For the start-up instructions, those were found in the User Guide. I will add them in the original post. – phoenix Oct 1 '18 at 16:57
  • What does locate bin/Amira return? What does locate Amira-6.5.0/bin return? If you installed within the last 24 hours you have to use sudo updatedb before running locate command. – WinEunuuchs2Unix Oct 1 '18 at 22:59
  • locate bin/Amira returns /AmiraInstall/Amira-6.5.0/bin/Amira and locate 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. – phoenix Oct 2 '18 at 12:47
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Finally managed to install Amira. Ended up finding an older version of Amira on a previous user's account on the same computer. Wiped it. sudo apt-get install libjpeg62 and reinstalled Amira 6.5 on my account on a different hard-drive. It now opens when the commant bin/start is run and works fine with my license.

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