Installation problems

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Installation Problems

If you have installed from source and have seen a line such as

  installed 304/344 programs

something really bad has happened. Most likely during building or linking a common error occured for each problem. You can look in the logfiles in $MIR/tmp or try and compile a program to see it directly on the screen:

  mir.subs fitsio
  mir.prog itemize

and see if any of the common problems below fit the description:

Compiler problem

If you get the not-too-uncommon error

 g77: command not found

you obviously don't have the right fortran compiler. Check if your system came with gfortran instead of g77. If so, add the


command line argument to the install.miriad or test_a_new_miriad_cvs script. If not, did you really read the requirements page?

Runtime problem

A common problem is with SELinux, which requires shared libraries to be given extra permission. The error message you might see is:

  xxx: error while loading shared libraries: $MIRLIB/ cannot restore segment prot after reloc: Permission denied. Two solution:

1) edit /etc/selinux/config (as root, or use a GUI system tool) and disable SELinux. Reboot is needed :-(

2) use the chcon command to enable a shared library,e.g.

   chcon -t texrel_shlib_t $MIRLIB/

Missing header files problem

Many workstation installation of linux and mac will install runtime libraries, but skip over the development version of these packages. In order to compile them, you will need them.

  xpanel.c:89:25: error: X11/Xaw/Box.h: No such file or directory

will need

  fedora 9:     libXaw-devel
  ubuntu 8.10:  libaw7-dev

Commands like rpm -qf `locate X11/Xaw/Box.h` on an RPM based system, and ... on a DEB based system will help you find out what package a particular file belongs to.

PGPLOT problems

  • A common problem is a missing driver. Here is a recipe to enable a driver that you know will work:
 edit $MIRLIB/drivers.list                <--- (un)comment the drivers you want to include/exclude
 mir.install pgplot

When shared libraries are used, this is usually enough, all programs that use PGPLOT should now know about the new driver set. Use device=\? to view the active list.

  • another common problem is that the X development files (include files such as Xos.h etc.) were not installed on your system. This is covered elsewhere on this page. You will most likely see that MIRIAD programs do not compile and complain about a missing -lpgplot
  • on 64bit machines some drivers (notably the GIF driver) do not work. If you installation produces a seg fault, do the following:
 cd $MIR/borrow/pgplot/drivers
 mir.install pgplot

and your shared library is updated. If you don't use shared libraries, all programs would have to be relinked as well (normally not needed)

 mir.install prog
  • on one particular Mac 10.5 machine strange linking problems went away when this user was using a FINK based version of pgplot in the following way:
 rm $MIRLIB/libpgplot.*
 cd $MIR
 install/install.miriad pgplot=0

hkmiriad problems

hkmiriad is a hacked mostly-C based set of miriad programs that you can find in $MIR/src/spec/hkmiriad. It has been written by Jin Koda (caltech).

The old style install essentially uses this:

 cd $MIR/borrow/zeno
 make miriad_install
 cd $MIR/src/spec/hkmiriad
 cp  Makefile
 make miriad_install

A common problem is the linking of fortran and C. If you have used the old-style install, there will be a Makefile in $MIR/install that contains the FLIBS= macro. Edit the Makefile in $MIR/src/spec/hkmiriad and replace the simple value for FLIBS (-lg2c) to be the more complex one. An example could be something like

  FLIBS = -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../.. -L/lib/../lib64 -L/usr/lib/../lib64 -lfrtbegin -lg2c -lm -lgcc_s

Currently there is no support to install this in the new build system.

Common Problems

If you install from source, two of the most common problems for failure are:

  • a missing or wrong fortran compiler. As of this writing g77 is still the default, but newer versions of gfortran now know how to build pgplot and no patching is needed anymore (except the keyword gfortran=1 to the install.miriad script). Different distros will hide the fortran compiler in perhaps not the most logical places (not to mention package names can change):
    • fedora: compat-gcc-34-g77 or gcc-gfortran
  • missing (X11) development packages. On linux your package manager should be queried for these. Unfortunately not each linux distribution (or version) will use the exact same name for this. A common example is the X11 development package. For example pgplot will need a file /usr/include/X11/Xos.h (it could also live somewhere else).
    • fedora 7: xorg-x11-proto-devel-7.2-9.fc7
    • ubuntu 8.04: x11proto-core-dev, libx11-dev
    • mandrive 2008: libxorg-x11-devel
    • mandrake 10.1: libxorg-x11-devel-6.8.2-0.5mdk
  • on 64bit ubuntu8.04 here's a report on how to fix the system, where the libXaw library was 'missing', and also includes an example of installing some missing system tools.
  cd /usr/lib  ;  ln -s
  apt-get install gfortran
  apt-get install g++
  cd /usr/local/miriad_cvs
  ./configure --prefix=`pwd`/build F77=gfortran
  make install
  • the new build system has not been thoroughly tested. A common problem is with that results in a make that ends disappointingly as follows:
 make[1]: *** No rule to make target `install'.  Stop.
 make[1]: Leaving directory `/algol1/teuben/miriad/auto/miriad/borrow/pgplot'
 make: *** [install-recursive] Error 1
  • the new build system may fail on latex building the manuals. If so, use 'make -i' instead.
  • if you try to compile a program and you see some error message like this:
  /usr/bin/ld: cannot find -lpgplot

most likely you have missing components on your system. Missing header file you might see. It means you did not install the development software for X11 on your system. It's one of the requirements. If this happens on a mac, go install Xcode. On linux you'll need to install the X develpment packages, as describe earlier on this page.

  • Missing files: what package does it belong to?

This is a common situation. You might see a compiler complain about a missing header file, but your friend has this file, but not you... Depending on the type of Linux distro (sorry, for Mac you're SOL here) here's a neat trick:

  rpm -qf  /usr/include/X11/Xos.h       (for Redhat, Fedora, Suse etc.)
  dpkg -S  /usr/include/X11/Xos.h       (for Debian, Ubuntu etc.)

after you have identified the package name, they can be installed via the appropriate GUI tool, or on the commandline

 yum install xorg-x11-proto-devel       (for a Redhat derivative)
 dpkg -i x11proto-core-dev              (for a Debian derivative)

Mac OS X

Although the modern Mac is running a "unix" variant, there are some issues you should be aware of. Certainly make sure your requirements are met (i.e. you have compilers installed, some developer tools are present, etc.etc.). Here are some helpful notes if you get stuck building from source:

Unsolved problems

  • [SOLVED] some linker issue on Ubuntu 7? The same error also occurs on Ubuntu 8.04 and 9.04 !!
  % mir.prog itemize
  /usr/bin/ld: /home/ijlee/miriad/bin/linux/itemize: hidden symbol `__stack_chk_fail_local' in /usr/lib/libc_nonshared.a(stack_chk_fail_local.oS) is referenced by DSO
  /usr/bin/ld: final link failed: Nonrepresentable section on output
  collect2: ld returned 1 exit status

The problem appears to be that g77 (a gcc3 derived product) is linked with gcc4. Although this is not a problem on e.g. Fedora, on Ubuntu it is. Solution is to use gfortran instead. In the old-style install, simply pass gfortran=1 to the install script, viz.

  install/install.miriad gfortran=1
  • in debug compile mode (setenv MIRDEBUG 1) on a mac you can get linking errors (can't find atom for N_GSYM stabs...).
  • the new build cannot be easily relocated using the install/make_miriad_starts script

If you are activating the new build, i.e.

  ln -s build_new build
  source miriad_start.csh

there are variables in automiriad.csh that have an absolute path and are not derived from $MIR. You will have to fix these manually. That includes a reference to PGPLOT variables in the pgplot-config.csh file.

  • on a mac (10.5.6) all programs with uvio are now doing bus error. (reported: Bolatto May 2009)
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