imodenv(1) imodenv(1) NAME Description of IMOD environment variables DESCRIPTION This page describes all of the environment variables that can be set for use with IMOD programs. User-level variables AUTODOC_DIR Alternative directory to search for an autodoc file when a program uses PIP for input. ETOMO_LOG_DIR Directory into which eTomo will place error log files named by date and time, instead of into $HOME/.etomologs. Set this to a non-existent name (e.g., stuffAndNonsense) to have sequentially numbered error logs kept in the directory from which eTomo was started. ETOMO_LOGS_TO_RETAIN Set this to the number of log files named by date and time to retain in the directory where they are kept. The default is 31 if this variable is not set. ETOMO_MEM_LIM Memory limit for running etomo. Define this as a number of megabytes followed by the letter "m". The default of 128m is set in the etomo startup script. Larger values will allow larger final alignment logs to be displayed. IMOD_AUTOSAVE Interval at which 3dmod should autosave the model, in minutes (superceded by setting in 3dmod preferences). IMOD_AUTOSAVE_DIR Directory into which 3dmod should autosave the model (superceded by setting in 3dmod preferences). IMOD_BRIEF_HEADER If this variable is set, all Fortran programs except header will output a brief header with the dimensions, pixel size, mode, minimum, maximum, and mean value, and the first and last title. IMOD_CALIB_DIR Directory in which IMOD-related information can live, unaffected by upgrading the main IMOD directory. Set by startup scripts to /usr/local/ImodCalib. IMOD_CSHELL Variable specifying a command to use when running csh/tcsh on a script. Used by Bead Fixer and could be used elsewhere. This variable can contain a path to the C shell executable plus flags. The -f flag is always added. IMOD_DIR The path to the top IMOD directory; set by startup scripts, or can be set before startup script is run. IMOD_DUMP_FSCACHE Makes 3dmod tell the system to dismiss the file system cache while loading a file on Linux. This behavior was originally the default because, on early 64-bit systems with files bigger than about half of the system memory capacity, the system would swap out data within 3dmod while loading. This bad system behavior is no longer observed in testing on FC4, RHEL4 and RHEL5. Set this variable (no value needed) for working on systems that show this problem. IMOD_JAVADIR Location of Java to be used to run eTomo; $IMOD_JAVADIR/bin is put on the front of the path in the etomo startup script. IMOD_NO_IMAGE_BACKUP If this variable is set (no value needed), virtually all programs that create image files will no longer back up an existing file by adding ~ to the name. Instead, they will overwrite the file. IMOD_PLUGIN_DIR Main directory for IMOD plugins; set by startup scripts to be inside IMOD. IMOD_PROCESSORS Number of processors in the computer; used by slicer to decide how many threads to run in parallel. Also used to create a parallel processing table when cpu.adoc is not found. IMOD_PS_FONT Name of a font (instead of Helvetica) to use in the Postscript output from various graphics programs; Arial is good for going to Illustrator. IMOD_QTLIBDIR Directory in which IMOD's copy of Qt lives, if any. Set by IMOD startup scripts. IMOD_STEREO_COMMAND When using hardware stereo, system command for switching the monitor to display left and right buffers in overlapping fashion. IMOD_STEREO_RESTORE System command for switching the monitor back to normal mode. IMOD_STEREO_TBOFFSET Default value of vertical offset when using top/bottom stereo display. IMOD_TMPDIR Path for temporary directory used by scripts. On Windows, this should be in Cygwin format, not in Windows format. IMOD_USE_GPU This variable will tell the Tilt program (and eventually perhaps other programs) to use the GPU on a CUDA-capable NVIDIA graphics card. Set the variable to 0 to use the best available GPU, or to a positive number to specify the GPU to use. If there is only one GPU, 0 and 1 have the same effect. This setting is overridden by the UseGPU entry to Tilt, if any. PIP_PRINT_ENTRIES Set this variable to 1 to enable printing of all options entered into a program using PIP input or 0 to disable it. The variable is automatically set to 1 when running programs through command files (i.e., vmstocsh and vmstopy both add lines to their output to set the variable to 1). Thus, if you leave the variable unset in your environment, entries will be printed in programs run through "subm" but not when programs are run at the command line. If you want the output when running at the command line, set the variable to 1 in your environment. To avoid this output when running a command file, add a line $setenv PIP_PRINT_ENTRIES 0 at the beginning of the file. PLAX_REDRAWS If there is trouble with the "plax" window used by Fortran graphics programs not updating properly, set this variable to the number of times for it be drawn (try 2 or 3). These programs include nda, sda, mtk, genhstplt, mtoverlap, mtpairing, avgstatplot, and filterplot. RAPTOR_BIN Directory where alternative RAPTOR executables are located; leave this undefined to run the executables in IMOD. READ_MODE0_SIGNED Set this variable non-zero to override the default for whether an MRC file in mode 0 should be read as signed or unsigned bytes. Potential values are: -2 to read all mode 0 files as unsigned, even ones with an IMOD stamp -1 to read mode 0 files lacking an IMOD stamp as unsigned 1 to read mode 0 files lacking an IMOD stamp as signed -2 to read all mode 0 files as signed, even ones with an IMOD stamp The values of -1 and 1 could be useful if a file header has incorrect entries for the minimum and maximum. Values of -2 or 2 would be needed if other software changed the representation of bytes in a file without modifying the IMOD stamp and flag values. RUNCMD_VERBOSE Set this variable to 1 to have the runcmd function called by Python programs print each command, input to the command, and the output of the command unless the output was already printed on standard out. WRITE_MODE0_SIGNED Set this variable to 1 to have all MRC files in mode 0 written as signed bytes. In some future IMOD version, this may be the default behavior, and then the variable can be set to 0 to have files written as unsigned bytes. Build and Test Variables CUDA_DIR Directory with CUDA toolkit, must be defined to enable building with CUDA. CUDA_BIN_PATH On Windows, this must be defined as the location of CUDA binaries if they are not in $CUDA_DIR/bin CUDA_LIB_PATH On Windows, this must be defined as the location of CUDA libraries if they are not in $CUDA_DIR/lib IMOD_TEST_SECTION This is passed to the uitest script when running eTomo tests. It is used to choose one of the tests in uitest.adoc. IMOD_UITEST_DATA When running eTomo tests, the root directory for data files. IMOD_UITEST_SCRIPT This is used in uitest.make. It should be set to the location of the uitest script IMOD_UITEST_SOURCE When running eTomo tests, the location of the uitest.adoc and all autodocs it refers to. JAVA_DIR Location of Java SDK to be used by the IMOD build and test script. MSVCREDIST Location of Microsoft Visual C redistributable run-time libraries that are to be copied when building a distribution. When this is defined, manifests are also added to all executables. QTDIR Location of Qt, or at least of Qt bin directory if include is elsewhere. BL3DEMC 4.3.7 imodenv(1)