From: ive@msg.ucsf.edu Subject: Priism-IVE: Frequently Asked Questions (FAQ) Reply-To: ive@msg.ucsf.edu Organization: Macromolecular Structure Group, UC San Francisco Archive-name: priism-ive Last-modified: Tue Mar 26 18:00:00 PST 2002 URL: http://msg.ucsf.edu/IVE/FAQ.txt Priism-IVE: Frequently Asked Questions (FAQ) Topics covered in this FAQ: --------------------------- -1- CONFIGURATION -2- How do I change where the shared memory file is stored? -3- How do I change the user interface's colors? -4- How do I change the user interface's fonts? -5- TROUBLESHOOTING -6- Priism won't start; what can I do? -7- Priism won't exit; what can I do? -8- My decon job is taking forever. What's wrong? ------------------------------ Subject: -1- CONFIGURATION Date: 20 May 1999 18:00:00 PDT The answers to these questions discuss how to configure Priism. ------------------------------ Subject: -2- How do I change where the shared memory file is stored? Date: 20 May 1999 18:00:00 PDT Set the environment variable IVE_SHMDIR to the name of the directory where you want to store the file and restart Priism. You'll need write access to the directory; it's also preferable that you have fast access to the directory and plenty of space (the shared memory file and temporary files can be 200 to 300 megabytes for a typical session). ------------------------------ Subject: -3- How do I change the user interface's colors? Date: 21 May 1999 18:00:00 PDT In IVE 3.3, Priism uses the color scheme that's been selected for the SGI desktop. You can change this scheme by selecting Desktop->Customize->Color Schemes from the Toolchest menu. (If you don't know where that is you should consult the SGI Desktop User's Guide at Chapter 11 in particular has information on changing the desktop). Not all of the color schemes work equally well with Priism; typical problems are: help buttons and function buttons have the same or similar colors, read-only text is not distinguishable from editable text, or the small arrows on pulldown menus to indicate a nested pulldown aren't visible. Predefined schemes that avoid all of these problems are Arizona, IndigoMagic, Inverness, Milan, RedGreenSafe, and Vancouver. If you want to revert to the IVE 3 color scheme when running 3.3, set the environment variable IVE_OLD_LOOK to yes before running Priism. Other changes to how colors are used require editing X resource files. Changes for an individual user can be stored in the .Xdefaults file in his or her home directory; changes for all users of a system can be stored in the file, /usr/lib/X11/app-defaults/IVE. In either case, if the file does not exist, you'll have to create it before making the changes described below. There are three resources for IVE 3.3 that allow you to do things that can't be done by simply changing the color scheme. The first is IVE*useSchemes which you can use to tell Priism that it should not rely on the color schemes. To do this you would enter IVE*useSchemes: none in the resource file. The second is IVE*scheme which you can use to have Priism use a specific scheme without affecting the scheme used by other applications. For instance, if you wanted to use the scheme defined in /usr/lib/X11/schemes/Milan for Priism but not for other applications, you would put IVE*scheme: /usr/lib/X11/schemes/Milan in the resource file. The third resource controls which color from the color scheme is used on help buttons. By default, Priism acts as if IVE*form*helpButton*background: SGI_DYNAMIC AlternateBackground1 was specified in a resource file. If you like a scheme but not how the help buttons are colored, you might experiment with the other possible background colors; a scheme provides six different choices (AlternateBackground1 to AlternateBackground6). For both IVE 3 and IVE 3.3, you can use resources to set the colors for types of items in the menus; listed below are what the defaults are for IVE 3. IVE*background: pink IVE*form.background: pink IVE*form*textLabel*background: bisque IVE*form*textLabel*borderColor: bisque4 IVE*form*command*Background: bisque2 IVE*form*command*borderColor: grey IVE*form*helpButton*background: deepskyblue2 IVE*form*helpButton*foreground: black IVE*form*toggle*selectColor: black IVE*form*onoff*selectColor: red IVE*form*slide*background: SpringGreen3 IVE*form*confirm*background: deepskyblue2 IVE*form*confirm*foreground: black IVE*form*info*background: deepskyblue2 IVE*form*info*foreground: black IVE*form*error*background: yellow IVE*form*text*background: pink IVE*form*intField*background: lightblue IVE*form*floatField*background: lightblue IVE*form*charField*background: lightblue IVE*form*funcButton*background: SpringGreen3 IVE*form*arrow*background: SpringGreen3 IVE*form*toggle*background: SpringGreen3 IVE*form*menuBar*background: gold1 IVE*form*optionMenu*background: gold1 IVE*form*optionPane*background: gold1 IVE*form*draw.background: black IVE*form*scroll*background: springgreen3 IVE*form*scroll*rc*background: pink IVE*form*scroll*rc*funcButton*background: gold1 IVE*form*scroll*rc*helpButton*background: deepskyblue2 IVE*form*statusBar*background: gold1 IVE*form*radio_box*background: springgreen IVE*form*rcolumn*background: SpringGreen3 /usr/lib/X11/rgb.txt lists the color names that can be used for the above resources. ------------------------------ Subject: -4- How do I change the user interface's fonts? Date: 13 March 2002 18:00:00 PST To do this you will need to change an X resource file: either .Xdefaults in a user's home directory or /usr/lib/X11/app-defaults to make the change for all users of the system. The following resources set all the fonts used in the user interface: IVE*form*fontList, IVE*form*slide*fontList, IVE*form*onoffLabel*fontlist, IVE*form*textLabel*fontList, IVE*form*menuBar*fontList, IVE*form*optionMenu*fontList, IVE*confirm*fontList, IVE*error*fontList, and IVE*info*fontList. The first four set the fonts for buttons, fields, labels, and sliders in normal dialogs (in IVE 3 these were all set with IVE*form*fontList); the next two set the fonts for pulldown menus; the last three set the fonts used in simple popup message dialogs. The defaults for IVE 3.3 are (these are from the FixedWidthFont, ObliqueLabelFont, and PlainLabel and definitions for large fonts in /usr/lib/X11/schemes/Base/FontPalette; the small fonts are two points smaller): IVE*form*fontList: -*-screen-medium-r-normal--15-*-*-*-*-*-iso8859-1 IVE*form*slide*fontList: -*-screen-medium-r-normal--15-*-*-*-*-*-iso8859-1 IVE*form*onoffLabel*fontList: -*-screen-medium-r-normal--15-*-*-*-*-*-iso8859-1 IVE*form*textLabel*fontList: -*-screen-medium-r-normal--15-*-*-*-*-*-iso8859-1 IVE*form*menuBar*fontList: -*-helvetica-bold-o-normal-*-14-*-*-*-*-*-iso8859-1 IVE*form*optionMenu*fontList: -*-helvetica-bold-o-normal-*-14-*-*-*-*-*-iso8859-1 IVE*confirm*fontList: -*-helvetica-medium-r-normal--14-*-*-*-*-*-iso8859-1 IVE*error*fontList: -*-helvetica-medium-r-normal--14-*-*-*-*-*-iso8859-1 IVE*info*fontList: -*-helvetica-medium-r-normal--14-*-*-*-*-*-iso8859-1 In IVE3 the defaults are (IVE*form*fontList and IVE*error*fontList are not explicitly specified; what's listed is the value many people used in their .Xdefaults files) IVE*form*fontList: -sgi-screen-bold-*-*-*-16-*-*-*-*-*-*-* IVE*form*menuBar*fontList: -*-courier-bold-o-*--14-* IVE*form*optionMenu*fontList: -*-courier-bold-o-*--14-* IVE*error*fontList: -sgi-screen-bold-*-*-*-16-*-*-*-*-*-*-* The xlsfonts command can generate a list of the available font types on the system that can be used in lieu of the defaults. ------------------------------ Subject: -5- TROUBLESHOOTING Date: 21 May 1999 18:00:00 PDT These questions discuss what to do when Priism crashes, burns, or misbehaves in less drastic ways. ------------------------------ Subject: -6- Priism won't start; what can I do? Date: 2 Feb 2002 18:00:00 PDT There are a number of things to check depending on whether or not the system has told you anything about why it failed. The paragraphs that follow cover the more easily handled situations. If you see a message like "Priism: Command not found", the environment (specifically the PATH environment variable) is not correctly set so Priism can be found. A message like "rld: Fatal Error: Cannot Successfully map soname libIWL.so ..." is also a likely indicator that your environment (the LD_LIBRARY_PATH variable) is not set correctly. In either case you should talk to the person who installed Priism and ask him or her what you should do; if you are the person who installed Priism and you're using IVE 3.3, consult the Priism_setup file (it may not be present in older IVE3.3 versions or it may be called Priism3.3_setup) in the Priism directory for hints. The error from rld about being unable to find a library can also be caused if you have the LD_LIBRARYN32_PATH variable set. There are two workarounds: you can set LD_LIBRARYN32_PATH to include the Priism library directory (i.e., setenv LD_LIBRARYN32_PATH $(IVE_BASE)/LIB_IRIX:$(LD_LIBRARYN32_PATH) or modify the Prism_setup script to replace all occurrences of LD_LIBRARY_PATH with LD_LIBRARYN32_PATH. If you see the message "Killed" and the message "unix: Dynamic loader /usr/lib32/libc.so.1 not found" in the system logs when using IRIX 5.3, you're likely to be trying to run IVE 3.3 on a system that cannot support it. Use IVE 3 with IRIX 5.3 and 6.1; IRIX 6.2 or more recent versions of IRIX is needed for IVE 3.3. Another thing that can prevent Priism from starting is if a previous Priism session failed to delete its shared memory file. In IVE 3.3 (since February 1999) you can type ivekill to ensure that this file is deleted. Otherwise, type (if IVE_SHMDIR is not set, use HOME instead) ls -l $(IVE_SHMDIR)/IWL.SHM* If you see anything listed that's owned by you, you should delete it and attempt to restart Priism. ------------------------------ Subject: -7- Priism won't exit; what can I do? Date: 21 May 1999 18:00:00 PDT In IVE 3.3 (since February 1999) you can type ivekill at the command line to force Priism and the associated windows to exit. If the dialog for selecting Priism applications has disappeared but other Priism windows are still open, type "ivekill -f" instead. If ivekill is not available, here's a set of shell commands which will work in many cases (if IVE_SHMDIR is not set, use HOME instead): /etc/killall -g Priism /bin/rm -f $(IVE_SHMDIR)/IWL.SHM* /bin/rm -f $(IVE_SHMDIR)/.*3evitad* ------------------------------ Subject: -8- My decon job is taking forever. What's wrong? Date: 2 Jan 2001 18:00:00 PST Here are a couple of things to check: 1) Check the header for your input data (as one of the first things it does, decon writes a summary of the header to the log file). If the pixel spacings are invalid (not positive) or one of the wavelengths is invalid (not positive) that could be the cause. You should kill the decon job, use EditHeader to correct the input data, and restart the job. 2) The system could be spending most of its time paging chunks of memory to and from disk; this most frequently happens when deconvolving data sets which have large x, y, and z dimensions or when several memory intensive jobs are running at once. On IRIX, use osview and check the amount of free memory (under the System Memory category) and the Wait Ratio percentages, if the free memory is low and the wait ratio percentages are high, then the entire system is struggling because there is not enough physical memory available for the applications currently running. On Linux or OSF/1, you can use vmstat 10 10 (check memory statisics every 10 seconds over 10 intervals) and pay attention to the pin/pout (OSF/1) or si/so (Linux) columns. If these are high, then the system is paging. Depending on the situation, any of the following may be an appropriate solution: a) Run the job on a machine with more RAM. b) Run fewer jobs at once so that competition for memory is less fierce. c) In newer versions of decon, the decon dialog has an option (the Special Parameters->Use minimal amount toggle) which will cause decon to demand less memory (roughly a factor of 3) and use a scratch file instead. If the job is large enough to cause the machine to swap heavily, using this option can significantly improve the amount of time needed to perform the deconvolution. With older versions of decon, the same option could be turned on by including a -nomem option on the command-line for decon. ------------------------------ End of priism-ive Digest ******************************