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For each resource it shows a map of the OS-visible processorsthat correspond to the specified resources, with '*' representing theapplicable processors. For example, on a 4-core system, a line in thecache output with a map of shared by cores 3 and 4.
All of the IMOD programs are available via the IMOD Download Page. The distribution is bundled together using the tar program with gzip compression, then placed in a file after a shellscript that can extract and install the programs. For Windows andMac,there is an executable installer than runs this script; for Linuxyou need to run the script yourself at the command line. If you are willing to install to the default location in the system and set up the IMOD environment for all users in the default way, then you can use the installers onWindows and Mac, and install on Linux simply by running thescript, e.g., sh imod_4.11.1_RHEL6.sh(In this guide, the specific filenames with \"4.11.1\" are used as anexample; you should always substitute the full name of the file that you areinstalling for the one shown here.)You cannot click on the .sh file toinstall it. This command will not work on Windows unless the Cygwin toolkit is installed. The executable installer for Windows (with extension .exe) does work by clicking on it to install (either with or without Cygwin). If you have followed our recommended installation procedures in the past, you will be able to upgrade using the same method. If you want to install to a location other than the default, you can specify the desired location inside of which the IMOD directory will be placed, e.g., sh imod_4.11.1_RHEL6.sh -dir /optOlder versions will be renamed, and at the end the installation script will offer to remove them for you.
Download a JRE or JDK from the Adoptium releases page. If you start at the Adoptium home page, press the \"Other platforms\" button to get to this page; the \"Latest Release\" button on the home page downloads a Java software development kit (JDK) that is considerably larger and is not needed. You can choose the latest release or one of the releases marked as LTS (long term support); they are all compatible with Etomo and all are being maintained with security updates. Keep the default selection of the JVM, the HotSpot. Download a JRE for your operating system, or a JDK if a JRE is not available. Windows. Click on the installer to run it and take the default options, in particular the one to put Java on the path. Mac OS. Click on the installer to run it. It will install to /Library/Java/JavaVirtualMachines. By some mysterious means, running /usr/bin/java should end up running the highest version in this directory (or the most recent installation, if there is both a JRE and a JDK of that version). To verify that it is running the intended version, enter java -version In IMOD 4.11, the Etomo startup script in these packages will look for the latest directory in /Library/Java/JavaVirtualMachines and run the Java there. If this fails or is not running the right version, there are two options: Set the environment variable IMOD_JAVADIR to the directory in the package containing the bin directory, for example export IMOD_JAVADIR=/Library/Java/JavaVirtualMachines/adoptopenjdk-12.jre/Contents/Home To set this on a system-wide basis, you can make a file IMOD.sh in /usr/local/ImodCalib with this line; or you can add the line to /etc/profile and /etc/zprofile in the place where the IMOD environment is set. Put the bin directory in the package on your path, for example export PATH=\"/Library/Java/JavaVirtualMachines/adoptopenjdk-12.jre/Contents/Home/bin:$PATH\" To do this on a system-wide basis, make either of the two changes described for option 2. Linux. If your distribution does not provide OpenJDK packages, see if you can use the RPM or DEB install packages from AdoptOpenJDK and follow the instructions there for installation. Otherwise, you will need to get one of their .tar.gz packages and untar in a location of your choice. Then you have two options: set the environment variable IMOD_JAVADIR to the top Java directory; or add the bin directory that it contains to your PATH. To do either of these on a system-wide basis, you can put the appropriate line in files IMOD.sh and/or IMOD.csh in /usr/local/ImodCalib. Java is notoriously insecure when run in browsers and requires frequent updating if a browser is enabled to run Java. The frequency of security vulnerabilities when using it just to run a program like Etomo is less clear; but it is a good idea to keep it up to date.
NVIDIA installation. Installing NVIDIA drivers is straightforward on some systems, but here are some instructions that may be helpful for older Fedora and for Red Hat/Centos throughversion 7. The latest versions of the drivers change the Driver line in /etc/X11/xorg.conf from \"nv\" to \"nvidia\" if you accept their offer to modify the file. For recent Fedora, search for \"Install NVIDIA driversFedora xx\", where xx is your version number, and study thevarious instructions that you find. On Ubuntu, the automatic installation through Synaptic Package Manager or its current equivalent should be adequate. However, onlaptops, it is important to know whether the NVIDIA card has Optimustechnology for switching between the card and built-in graphics. If itdoes, the regular methods will probably not work, but one solution is toinstall bumblebee (search on bumblebee and the Linux distribution namefor specific instructions). Bumblebee allows you to control whichgraphics device programs use. At least as of a few years ago, you coulddirect a program to access the NVIDIA graphics by starting it with athe optirun command. Thus, if you simply start a newshell, e.g., with optirun bash and run IMOD commands fromthis shell, you should find that 3dmod uses the NVIDIA graphics and thatthe GPU is available for reconstruction.
Rosetta2 for M1 Macs. To install IMOD 4.11 on an M1-based Mac, Rosetta2 must be installed. IMOD 4.11 currently runs only through this emulator, but a package compiled for M1 is available in IMOD 4.12 beta. Python for OS 12. The default installation in OS 12.3 no longer includes Python. You must install a Python first to install IMOD. The recommended option is a package from python.org; here is aPython 3.9.11 universal installer package that runs on Intel and M1 processors. Installed, this package takes about 180 MB if documentation is omitted. Another option is to install Python through homebrew. The third option is to install the Apple Developer Command Line Tools, which the system will offer to install if you enter \"python3\" at the command line. This package takes 2.2 GB. The IMOD installer will recognize all of these Pythons regardless of whether they are on the search path, and if you install some other Python, it needs to be on the search path and you will probably need to use the command-line self-installing package instead of the clickable installer.Installing IMOD The clickable installer (ending in \".pkg\") will install to /Applications and will place appropriate source commands in /etc/profile, /etc/zprofile, and /etc/csh.login. You will need administrative privileges to use this installer.
After installing on OS 11 or 12, the Launchpad (multiple icon display) will show IMOD with two tempting icons inside, 3dmod and Qt Assistant. It will not work to click on 3dmod or Qt Assistant. The package built under OS 10.14 is fully signed and the system should not object when you try to install it in OS 10.14, 10.15 or 11.0. If for some reason you need to install a package built on an earlier OS, there are two options. You can click on the question mark in the upper right of the message that you get when you try to run the package; it will direct you to open the Settings - Security and Privacy - Private tab where you can confirm the installation after dismissing the installer message. Or, you can use the command-line package described next. The command-line self-installing package (ending in \".sh\") will install to /Applications or to an alternate location with the -dir option. The \".sh\" file will not work by clicking on it, only by running it at the command line. It will place appropriate \"source\" commands for defining the user environment in /etc/profile, /etc/profile, and/etc/csh.login. You need to be able to use sudo. Open a terminal window (under Applications-Utilities), change directory to the place where the package is located, and enter, e.g.: sudo sh imod_4.11.1_osx10.11_CUDA8.0.sh You will need to exit and restart Terminal for changes from theinstallation to take effect, or you can just source /etc/profile (if you arerunning bash), /etc/zprofile (if you are running zsh) or /etc/csh.login (if you are running tcsh). If you are upgrading IMOD with the default installation procedures and your previous installation used another method of setting environment variables, then you may need to remove \"source\" or other environment-setting commands from various files, such as /etc/profile, /etc/csh.login, or users' .bashrc, .profile,or .cshrc files. Fixing an IMOD Installation after a System Update. On OS 11 or 12, system updates may replace the files in /etc that source the IMOD environment-setting commands, and IMOD will stop working. To recover from this without reinstalling IMOD, run the command sudo /Applications/IMOD/fixMacInstall or if IMOD is installed elsewhere, run sudo pathToIMOD/fixMacInstall where pathToIMOD is the full path to the IMOD directory. If this command fails with \"Command not found\", it is probably because there is no Python runnable as \"python\" on the path, in which case this should work: sudo /Applications/IMOD/pythonLink/python /Applications/IMOD/fixMacInstall
Once the links are made, test that 3dmod will start by finding it in the IMOD/bin and clicking on it. Installing Java. To check whether you have Java installed, you can try to start Etomo by entering etomo, or just enter java-version in a terminal. If it is not installed, you will get amessage from the operating system offering to take you to theOracle site. Ignore this message and see 1.1 Installing Java for Etomo..Using a 3-button Mouse. The one-button mouse on the Mac can be used in 3dmod with some keyboard modifiers, but this is painful. Just get a 3-button mouse. It may just work when you plug it in, so try it in 3dmodbefore installing drivers. Installing Logitech and some other drivers may actually make it stop working, and the solution is to uninstall the drivers.Manual Install. To install manually from the tar file that you can get by running the self-installing file with the -extract option, you have two alternatives. To do it from the command line, open a Terminal window and: 153554b96e
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