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              (superceded by setting in 3dmod preferences).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              Directory into which 3dmod should autosave the model (superceded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)