HEAsoft v6.23 - Known Issues

If you are using HEASOFT v6.22.1 and don't want to upgrade to v6.23 just yet, see the HEASOFT 6.22.1 Issues List.

Several packages track issues separately from this page:

• Swift
• CALDB
• XSPEC
• XSTAR
• XIMAGE
• XRONOS

The following is a list of known issues in v6.23 of HEAsoft not covered by the above pages.

• Ubuntu 16.10, 17.04 & 17.10, and Debian 9:

  Several HEASoft tasks (including extractor, ximage, et al.) suffer memory faults under newer Debian-based operating systems (including Ubuntu 16.10, 17.04, 17.10, and Debian 9).

  Another HEASoft release that supports the default compilers these systems is forthcoming prior to the release of the 18.04 LTS operating system in April 2018. Until that time, users are advised to do one of the following:

  
    - Delay updating beyond Ubuntu 16.04.x (or Debian 8.x)
  
    - Use the pre-compiled HEASoft binaries for Ubuntu (built in 16.04)
  
      or
  
    - Build HEASoft 6.23 using the compilers from the "gcc-4.8" package,
      i.e. prior to running configure, set up your environment as follows:
  
      $ sudo apt-get -y install gcc-4.8
  
      $ setenv CC gcc-4.8                 or  $ export CC=gcc-4.8
      $ setenv CXX g++-4.8                or  $ export CXX=g++-4.8
      $ setenv FC gfortran-4.8            or  $ export FC=gfortran-4.8
  
  




• Mac "configure failed..." Fortran compiler issue:

  The configure script may generate an error ("Configure failed in the AST package!") resulting from a MacPorts assembler (as) under /opt/local/bin being ahead of the default Apple /usr/bin/as in a user's PATH (which may result from an automated change made to .profile during a MacPorts installation). To get past this issue, put /usr/bin at the front of your PATH:

     export PATH="/usr/bin:$PATH"
  

• MacPorts "unexpected token" linker issue:

  If you are using MacPorts compilers in your build, 'make' may fail when building the HEASoft source code distribution with an error referring to a new Xcode linker ("ld") format ("tbd"), e.g.:

  ld: in '/System/Library/PrivateFrameworks/CoreEmoji.framework/Versions/A/CoreEmoji.tbd', unexpected token: !tapi-tbd-v2 ...
  

  The underlying issue is discussed here and here; it appears that when new versions of the XCode command line tools are released, problems such as this may affect MacPorts compilers until they catch up with Apple's changes. Users should be able to get around the error in our build by installing the MacPorts 'xcode' variant of the linker ld64 as a temporary measure:

  
      sudo port install ld64 +ld64_xcode
  
  

  and when MacPorts eventually supports the latest XCode command line tools, you can switch back to the latest ld64 with the following:

  
      sudo port install ld64 +ld64_latest
  
  

• Mac "suffix or operands invalid for 'movq'" Fortran compiler issue:

  When using the gnu.org gfortran binaries note their recommendation that when installing new versions of the compiler you should remove the previous gfortran installation first:

     $ sudo rm -r /usr/local/gfortran /usr/local/bin/gfortran
  

  Failure to do so may result in a corrupted compiler installation, leading to the "suffix or operands invalid for 'movq'" error.



• Ubuntu ds9 & HEASoft:

  After initializing HEASoft on Ubuntu Linux, the ds9 GUI (if installed) may fail to start up (saying "can't find package xml" or "can't find package uri 1.1"). This results from incompatibilities between the Tcl/Tk included with HEASoft and the Ubuntu system libraries. Until a more elegant solution can be devised, we recommend that users try one of the following options, depending on the file type of your ds9 (shell script or compiled executable - check the output from "file `which ds9`" to determine which it is):

  
  1) If ds9 is the shell script version, edit it to change the line
  
       exec wish8.6 -f ${DS(_HOME-/usr/share/saods9}/library/ds9.tcl $*
  
     to
  
       exec /usr/bin/env -u LD_LIBRARY_PATH /usr/bin/wish8.6 -f ${DS9_HOME-/usr/share/saods9}/library/ds9.tcl $*
  
  or
  
  2) If ds9 is the compiled executable version, create a new file
     "$HEADAS/bin/ds9" containing the following lines:
  
       #!/bin/sh
       exec /usr/bin/env -u LD_LIBRARY_PATH /usr/bin/ds9 "$@"
  
     (Note this assumes that `which ds9` = /usr/bin/ds9)
  
     To make the new script executable, run the following command:
  
       $ chmod +x $HEADAS/bin/ds9
  
     Then, as long as $HEADAS/bin is ahead of /usr/bin in your PATH, you
     should now be able to successfully run ds9 from the command line:
  
       $ rehash
       $ ds9
  
  




• Apple XCode vs. MacPorts gcc/g++:
  
  Some HEASoft tasks may fail with memory errors on Mac OS X when compiled with the MacPorts gcc/g++, so we continue to recommend that users build HEASoft only with the Apple XCode (Clang/LLVM) gcc/g++ compilers (and the XCode perl and python interpreters as well). This may be ensured by setting the relevant environment variables prior to running the configure script:

  
   In C-shell variants (tcsh/csh):       In Bourne shell variants (bash/sh):
  
      % setenv CC /usr/bin/gcc              % export CC=/usr/bin/gcc
      % setenv CXX /usr/bin/g++             % export CXX=/usr/bin/g++
      % setenv PERL /usr/bin/perl           % export PERL=/usr/bin/perl
      % setenv PYTHON /usr/bin/python       % export PYTHON=/usr/bin/python
  
  

  As Apple does not provide a Fortran compiler, you will need to use one installed from MacPorts (or elsewhere), so for example:

  
      % setenv FC /opt/local/bin/g95            % export FC=/opt/local/bin/g95
   or
      % setenv FC /opt/local/bin/gfortran-mp-5  % export % FC=/opt/local/bin/gfortran-mp-5
   or
      % setenv FC /usr/local/bin/gfortran       % export FC=/usr/local/bin/gfortran
  
  

  We stress that you avoid using /opt/local/bin/gcc-* and /opt/local/bin/g++-* when building HEASoft from the source code distribution.



• "relocation R_X86_64_32 against `.rodata' can not be used when making a shared object":
  
  Users building HEASoft from the source code distribution may run into this error which refers to a "Bad value" in the file heacore/wcslib/C/cel.o, from which the linker "could not read symbols". It also suggests that you "recompile with -fPIC". This situation most likely occurrs when users perform a re-build after a previously unsuccessful build attempt. To get past this issue, try the following:

  
     $ cd heasoft-6.23/BUILD_DIR
     $ make distclean
  
  

  When that finishes, restart the build procedure beginning with "./configure", then "make", and let us know if this does not resolve the problem.



• fv - XPA_METHOD:
  
  Some users of the fv GUI may experience long delays at startup, or error messages of the type "XPA$WARNING: xpans needs to be running on this machine", or "XPA$ERROR: invalid host name specified: $host:$port" (when using the ds9 display device). These issues tend to occur on Macs with customized firewall settings, or on machines without valid IP addresses. This can be resolved by setting the XPA_METHOD environment variable to the value "local" (to use local/UNIX sockets instead of inet sockets):

  
          export XPA_METHOD=local          # Bourne shell (bash/sh)
  or
          setenv XPA_METHOD local          # C-shell (csh/tcsh)
  
  

• Perl version mismatch::
  
  Pre-compiled Perl libraries used extensively by mission software (Swift, Suzaku, NuSTAR) and other packages are not especially portable, so we generally recommend building HEASoft from the source code distribution.



• xspec / PLT - wenv, whead, wdata:
  
  Some GNU Fortran compilers (gfortran 4.4.x, 4.0.x, 4.1.x) appear to have internal issues which prevent the PLT commands wenv, whead and wdata from working unless an output file is specified; i.e. attempts at producing terminal output may fail with "Fortran runtime error: Invalid argument". To get around this, provide an output file name when using these commands, for example:

       wenv myFile1.qdp
       whead myFile2.qdp
       wdata myFile3.qdp
  




• HEASoft and other software packages (CIAO, XMM-SAS):
  
  

  Please note:

  Users may wish to download and run our hwrap script to create an alternate runtime environment for HEASOFT to help avoid conflicts with other software packages, but if not, please take note of the potential pitfalls below:
  
  
  • CIAO:
    
    Please see the following notes at the CXC website regarding the potential dangers of using CIAO and HEASOFT together in the same session:
    
    
    • FTOOLS & CIAO
      
    • Parameter file conflicts
  
  
  
  • XMM:
    
    When the XMM-SAS is initialized after HEASoft (when both are used in the same session), the SAS setup changes the value of the environment variable PGPLOT_FONT with the result that plots in e.g. Xspec may (or may not, depending on the software distributions in use) have no axis labels or values. Users can fix this by resetting PGPLOT_FONT to point to the HEASoft location:

         C-shell:
    
             setenv PGPLOT_FONT $HEADAS/lib/grfont.dat
    
         Bourne shell:
    
             export PGPLOT_FONT=$HEADAS/lib/grfont.dat
    
      

    or by simply re-initializing HEASoft:

         C-shell:
    
             source $HEADAS/headas-init.csh
    
         Bourne shell:
    
             . $HEADAS/headas-init.sh
      

    This may in turn have consequences for plotting in XMM-SAS, in which case users may need to return PGPLOT_FONT to the SAS setting when using it for data analysis.

Web page maintained by: Bryan K. Irby