Index of /ProgramDocuments/Mosflm

If you really have to go straight to the installation, it's later in this document. However, be prepared to come back here if you run into trouble!

Installing MOSFLM on most UNIX computers is really very easy; for several systems you can pick up a gzip'd binary, which once it has been gunzip'd will run straight away; you should really pick up the mosflm.hlp at the same time from the same directory; this contains the on-line help which you use when running mosflm. The file mosflm_user_guide.doc is a plain-text version of the new HTML document mosflm_user_guide.html.

You should also be prepared to read the files README_610.html README_600.html which contain much that applies to v6.11 as well. However, where there is a conflict, the advice here should be followed.

There are specific notes on the following;

• Graphics problems on Linux machines and Compaq Alphas with 4D60T graphics cards.
• Linux
• SGI
• Existing users of REFIX with MOSFLM
• CCP4 Libraries

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  The program has been built successfully on the following machines and operating systems; however there are a number of caveats of which you should be aware (but see below for these).

  If your login shell is csh or tcsh, the Makefile in the top directory has checks for the environment variables PWD and HOSTTYPE; the different builds are all included in files in sub-directories according to the host type. You shouldn't need to touch the Makefiles at all, I hope (problems to the usual address...).

  The build has not been tested for the login shell bash (or any other variant of sh). I believe that the HOSTTYPE environment variable is often different for these shells than for csh or tcsh, in which case the build may not work straightforwardly.

  
    Build Platform                      O/S             
  Compaq Alpha 500MHz, 4Gb         Compaq Tru64 UNIX
  SGI 200MHz R4010/4400, 64Mb      Irix 5.3 
  SGI 175MHz R10000/R10010, 192Mb  Irix 6.2 
  SGI 400MHz R12000/R12010, 512Mb  Irix 6.5
  PC 233MHz Pentium, 128Mb         Red Hat Linux (gcc 2.7.2.3, g77 egcs-2.90.29)
  PC 800MHz Athlon, 256Mb          Red Hat Linux (gcc,g77 version 2.95.1) 
  Apple Powerbook G3 500MHz, 128Mb LinuxPPC 2000 (gcc,g77 version 2.95.3)
  

  The build will involve a lot of paging if your machine has limited RAM, as will running the program. The executable is ~3.0 - 3.6Mb, and integrating a single 8Mb image uses up to around 16Mb, so I'd guess that 32Mb RAM is about the minimum you'd want to use. MOSFLM will not run on a PC with less than 20Mb of RAM.

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  • Graphics problems on Linux machines and Compaq Alphas with 4D60T graphics cards

    1. The XDL_VIEW libraries from the CCP4 distribution 4-4.1 are slightly broken but have been fixed in a recent (this was written on 02-Mar-2001) patch. If you do not have this fixed version, then you will need to apply these patches.

       Copy the file xdl_patches to the directory $CCP4/x-windows/xdl_view/src,

       cd to that directory, then issue the following command;

       patch < patches

       This assumes that you have the patch utility installed on your system! Then rebuild and install the xdl_view libraries on your system.

    2. The colour depth problems in earlier releases are fixed by these modifications.

       I believe that the problems with the 4D60T graphics card installed in some Alphas have also been fixed, so patches for xdl_view libraries are no longer distributed with MOSFLM. If you have problems, contact me directly so that I can address the issue.

  • Linux

    1. Optimization for PC Linux (not PowerPC) might be improved by making the following change in include.i386-linux , but some versions of gcc and g77 are over aggressive in their optimizations; this can lead to unexpected run-time errors, but seems to work with older versions of the compilers (e.g. gcc version 2.7.2.3 and g77 using gcc version egcs-2.90.29).

       setenv MOSFLAGS "-O1 -fno-second-underscore -fno-globals -w ${DEBUG}"

       becomes

       setenv MOSFLAGS "-O2 -fno-second-underscore -fno-globals -w ${DEBUG}"

    2. You can try to improve the optimization of the subroutine control (by changing MCFLAGS, but all versions of g77 seem to be too aggressive. I wouldn't recommend doing it!

  • SGI only:

    1. Optimization for 32 bit binaries may be improved by making the following change in include.iris4d

       setenv MOSFLAGS "-O2 -w -Nn18000 -Nq12000"

       becomes

       setenv MOSFLAGS "-O2 -w -Nn18000 -Nq12000 -Olimit 11400"

       in mosflm/Makefile.iris4d -Olimit 11400 might increase performance, but compilation takes forever. The line's there if you want to uncomment it, but my guess is that you'll lose more in the compilation than you'll ever gain in performance.

  • Existing users of REFIX with MOSFLM

    The script for adding REFIX autoindexing to the build-it-yourself distribution is the same as for v6.10.

  • CCP4 Libraries

    It is necessary that your CCP4 libraries (i.e. the two files libccp4.a and libxdl_view.a) are in a directory with the environment variable $CCP4_LIB; releases of MOSFLM prior to v6.xx have assumed that the variable is $CLIB, which is contrary to current CCP4 practice. However, if $CCP4_LIB has not been defined, the build procedure will assign it the current value of $CLIB.

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  INSTALLATION

  The simplest way to install for most users will be to copy the appropriate pre-built binary from ftp.mrc-lmb.cam.ac.uk/pub/mosflm/ver611/pre-built, and put it in your exection path. These executables include both DPS and REFIX indexing.

  Note well, however; these versions will not process images which are more than 4000 pixels in each direction (and thus need only 32Mb virtual memory to run). The default build-it-yourself version can cope with 8000 pixels in each direction (and hence needs 128Mb virtual memory).

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  • MOSFLM 6.11 will not build correctly with versions of the CCP4 library before 4-4.1. If you have an earlier version, you should seriously consider updating!

    If you have not installed the latest updates (dated after 02-Mar-2001) to the xdl_view libraries, you should do so before attempting to build MOSFLM 6.11, or apply the patches as described above.

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  • If you have the old-style autoindexing routines (REFIX), you need to do the following before building the program. There are several routines at the end of the file mosflm/mosflm_all_ip_inc.for which need to be removed and the REFIX files added (while in the mosflm subdirectory) with the script is included in the file add_refix.com.

  • If you haven't defined CCP4_LIB in your normal login setup, you might want to edit the line in the top-directory Makefile

    	#define CCP4_LIB ${CLIB}
    

    to suit your local conditions.

  • Some sites have not defined the PWD environment variable, which is used in the build procedure. You can either define this to be the top directory of the distribution before you start the build, or you can edit the top-level Makefile and change the line

    	DPS        = ${PWD}
    

    to suit.
  • In the distribution's top-level directory, type

    	./build
    

    The script should determine your HOSTTYPE and then build and install mosflm in its bin directory.

    Alternatively, you can type

    	source include.$HOSTTYPE
    	make
    

    and that should work too.

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  If you are a new user of MOSFLM and would like the option of using REFIX with the build-it-yourself version, you should e-mail Andrew Leslie and ask for it.

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  Harry Powell, MRC-LMB, MRC Centre, Hills Road, Cambridge, U.K. CB2 2QH harry@mrc-lmb.cam.ac.uk
  Last modified: Mon Mar 5 14:54:15 GMT 2001