HEASoft v6.34 - Known Issues
If you are using HEASoft v6.33 and don't want to upgrade to v6.34 just yet,
see the HEASoft 6.33 Issues List.
Several packages track issues separately from this page:
The following is a list of known issues in HEASoft not covered
by the above pages.
Last modified Thursday, 03-Oct-2024 10:47:15 EDT
- nupipeline:
In NuSTARDAS v2.1.4. the nupipeline task may fail with an
error
nupipeline_0.4.12: Metrology System: input files not found
for users of QuickLook ToO products while looking for
files in an event_cl/ directory that does not yet exist.
Running nupipeline with check_metsim_files=no, or running
the command
pset nupipeline check_metsim_files=no
prior to running nupipeline fixes the issue. The
6.34 downloads have been udpated (to "nustardas_16Sep24_v2.1.4a") with
this fix on 16 September.
- numetrology:
The NuSTARDAS task numetrology may fail when built with the
default Apple C compiler (clang) - e.g., while running
nupipeline - with an error
nupipeline_0.4.9: Error: running 'numetrology'
Tests suggest that this error can be resolved by rebuilding numetrology
with compiler optimization turned off, which may be accomplished in the
following way: first, initialize heasoft and then edit the file
heasoft-6.34/nustar/BUILD_DIR/hmakerc
to change COPT (line 88) from "-O2" to "", then:
cd nustar/tasks/numetrology
hmake clean
hmake all
hmake install
- SAOImage DS9 on MacOS:
As noted on the SAOImage download page, please be aware that the
DS9 Aqua application does not allow for runtime command line
options, as required by e.g., xselect, so we recommend installing
the Darwin X11 version of ds9 instead.
- Xspec on older Macs:
Compilation of Xspec may fail under older macOS with the error:
'timespec_get' was not declared in this scope
Users should be able to get past this by editing lines 47-51 of
heasoft-6.33.2/Xspec/src/XSutil/Utils/TimeUtility.cxx
to change this code block:
# if defined(__APPLE__)
timespec_get(&tnow, TIME_UTC);
#else
clock_gettime(CLOCK_REALTIME, &tnow);
#endif
To just this:
clock_gettime(CLOCK_REALTIME, &tnow);
- Ubuntu (22.04) and pip version 22.0.2:
When running "make install" on Ubuntu (22.04 only?), users may need to update the default pip version (22.0.2) to avoid errors installing HEASoftPy:
Building wheels for collected packages: UNKNOWN
...
HEASoftPy not found under heasoft-6.34/heacore/heasoftpy/build
To update pip to a newer version (e.g., 24.0):
sudo pip install --upgrade pip
- FV in Virtual Machines:
When used on Virtual Desktops (e.g. VirtualBox), FV windows may appear blank. This issue may be mitigated by disabling "3D acceleration" in the display options.
- IXPE & MatPlotLib:
The IXPE task ixpeplot_polarization may fail with a cryptic and
unhelpful error message when using MatPlotLib older than version
3.7.0. To fix this issue, update to version 3.7.0 (or newer).
- IXPE & AstroPy:
Due to a bug in certain 5.x versions of AstroPy, some files
(such as the IXPE Level 1 event files) containing variable-length
arrays may trigger in several IXPE tools a "ValueError" with the
message "the heapsize limit for 'P' format has been reached. Please
consider using the 'Q' format for your file.", even if the file is
already formatted with the "Q" format.
Affected versions of AstroPy appear to be
5.0.5, 5.0.6, 5.1.1, 5.2, 5.2.1, and 5.2.2,
so users encountering this issue are advised to update to v5.3.0
or newer.
- Mac "Configure failed":
The HEASoft configure script may fail with
"C compiler cannot create executables",
"Configure failed in the AST package!", or
"configure failed for heacore component fftw!",
and one of the config.logs may show
ld: library not found for -lSystem
This error typically implies that third-party compiler suites (e.g.
Homebrew or MacPorts, needed in order to provide a Fortran compiler)
are out-of-synch with the Apple (XCode) Command Line Tools (CLT),
for example if you updated the CLT but did not reinstall MacPorts or
Homebrew after doing so. Since these third-party compilers use the
CLT, they must typically be rebuilt/reinstalled whenever XCode/CLT
are updated.
For example, some users have worked their way past this by
uninstalling
the CLT and then
reinstalling
the CLT, then uninstalling and reinstalling the Homebrew compilers.
Other compiler-related failures during the configure stage
can typically be resolved by putting /usr/bin at the
front of your PATH environment variable (as recommended in
our Mac installation guide), e.g. to
put the Apple assembler and other system utilities ahead of third-party
versions in order of preference.
- WSL and Windows PATH variables:
Some users of WSL on Windows may have PATH environment variables that
contain directory paths containing double quotes ("). The HEASoft
initialization will fail as a result, so users need to modify their
PATH variable to remove the offending characters.
- CentOS 7.x compilers:
Note for users of CentOS 7.x: On CentOS 7, the default GNU
compiler suite is v4.8, which is not supported for building HEASoft.
CentOS 7 users may install a newer 'devtoolset' compiler suite for use
in building HEASoft, in the following way (for example):
sudo yum -y install devtoolset-9
scl enable devtoolset-9 bash
Locate the devtoolset-9 installed directories:
gcc -print-search-dirs
/opt/rh/devtoolset-9/root/usr/lib/gcc/x86_64-redhat-linux/9
In the next step, set the compiler variables accordingly (for example):
export CC=/opt/rh/devtoolset-9/root/usr/bin/gcc
export CXX=/opt/rh/devtoolset-9/root/usr/bin/g++
export FC= /opt/rh/devtoolset-9/root/usr/bin/gfortran
You will likely also need to update your LD_LIBRARY_PATH to include
the path to the libraries needed by these compilers (for example):
export LD_LIBRARY_PATH=/opt/rh/devtoolset-9/root/usr/lib
- Using "sudo" or "screen":
Since configuring HEASoft typically works best when setting environment
variables to point to specific compilers, using sudo at the
configure stage is not recommended since sudo spawns a new shell that
does not automatically inherit current environment settings. The sudo
command should not be needed for configuring in any case; it should
only be necessary when running "make install", and only then if you
are writing to a root-protected area (e.g. /usr/local or /Applications).
Similarly, the screen command does not inherit all environment
variables, so if you spawn a screen session before running the
configure script, be sure to check or set environment variables
after starting the screen utility.
- "Developer cannot be verified" or "unidentified developer" error on Macs:
Some Mac users have reported problems configuring and/or running
pre-compiled HEASoft binaries. To free HEASoft binaries from
the Apple quarantine, use the xattr utility, e.g.:
$ cd heasoft-6.31.1/x86_64-apple-darwin20.6.0
$ xattr -r -d com.apple.quarantine BUILD_DIR/configure lib/* bin/*
- Fortran compiler requirements:
HEASoft now includes a new dependency on the FGSL library which
requires a Fortran 2008 feature (c_loc for targeted arrays); therefore
GNU Fortran compilers older than version ~5.x are unsupported.
- Perl symbol lookup error, "undefined symbol: Perl_Gthr_key_ptr":
If running a HEASoft Perl script generates an error similar to the above,
it may result from a Perl version incompatibility
(common when using the pre-compiled binaries), but it may also occur if
you have the VERSIONER_PERL_PREFER_32_BIT environment variable set
to "yes". If "echo VERSIONER_PERL_PREFER_32_BIT" returns "yes", then
unset it:
unset VERSIONER_PERL_PREFER_32_BIT
or, in C-shell:
unsetenv VERSIONER_PERL_PREFER_32_BIT
- 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 (mentioning "can't find package xml", "can't find package uri 1.1", or "package require base64"").
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 ${DS9_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
- "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-6.31.1/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:
- XMM-SAS:
The XMM-SAS setup typically adjusts your LD_LIBRARY_PATH
environment variable (or DYLD_LIBRARY_PATH on macOS) to include
the SAS library folders, one of which includes a copy of the C++ compiler
library (libstdc++). This can cause problems building HEASoft,
so we recommend that HEASoft be built in a
session in which the SAS has not been initialized, or at least one in
which your [DY]LD_LIBRARY_PATH is either empty or otherwise does
not include the installed SAS directories.
Similarly, after both SAS and HEASoft are installed, if they are
initialized in the same session (terminal), C++-based tasks
such as XSPEC may suffer runtime problems if the XMM-SAS library
directories precede the one needed by XSPEC in [DY]LD_LIBRARY_PATH
(as is the case if the SAS is initialized after HEASoft.
As an example, if you compiled HEASoft on a Mac using the Homebrew
compilers, XSPEC will need to have the Homebrew library path ahead of
the SAS library directories in your DYLD_LIBRARY_PATH:
For example:
C-shell:
setenv DYLD_LIBRARY_PATH "/usr/local/opt/gcc/lib/gcc/10:${DYLD_LIBRARY_PATH}
Bourne shell:
export DYLD_LIBRARY_PATH="/usr/local/opt/gcc/lib/gcc/10:${DYLD_LIBRARY_PATH}
Additionally, when both the SAS & HEASoft are used in the same session
and the SAS was initialized after HEASoft, 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.
If you have any questions about the information above, please write to
us at the FTOOLS help desk.
HEASoft / FTOOLS Help Desk
If FTOOLS has been useful in your research, please reference this
site (https://heasarc.gsfc.nasa.gov/ftools) and use the
ASCL reference for HEASoft
[ascl:1408.004] or the
ASCL reference for the original FTOOLs paper
[ascl:9912.002]:
Blackburn, J. K. 1995, in ASP Conf. Ser., Vol. 77, Astronomical
Data Analysis Software and Systems IV, ed. R. A. Shaw, H. E. Payne,
and J. J. E. Hayes (San Francisco: ASP), 367.
Web page maintained by:
Bryan K. Irby
HEASARC Home |
Observatories |
Archive |
Calibration |
Software |
Tools |
Students/Teachers/Public
Last modified: Thursday, 03-Oct-2024 10:47:15 EDT
The Astrophysics Science Division (ASD) at NASA's Goddard Space Flight Center (GSFC) seeks a creative, innovative individual with strong teamwork and leadership skills to serve as Director of the High Energy Astrophysics Science Archive Research Center (HEASARC). This will be a permanent civil servant position. + Learn more.
|