Hi Tim, Malcolm,
I was wondering if you still have the source code for the 64 bit ECHOMOP? I think Malcolm worked on this last year - a student I was working with at the time, Gareth Smith, did some preliminary testing. Does the latest 2018A release contain the 64bit-translated code? It doesn't appear to work still - see below (using the Fedora 28 bit 2018A Starlink I just built). I am still using a 32 bit version on an old machine. Happy to try out any code/builds you might have....
Cheers,
John
$ echomop
----------- Initialising for ECHOMOP ------------
Echelle data reduction
Version 3.3-7
Type "echhelp echomop" for help
or "echhelp news" for news on changes
Type "echwww" to start hypertext documentation browser.
Type "echmenu" to start the monolith.
[jbarnes@pc-jrb 1]$ echmenu soft=xw
This is ECHOMOP Version 3.3-7
ECH_RDCTN - Reduction database /'ECH_RDCTN'/ > ech_testnew
DISPLAY - YES to overlay plots on images /NO/ > yes
DISPLAY is set to non-default value: YES.
!! There is no translation for environment variable "ADAM_USER"
Creating file: ech_testnew.
SOFT - Produce plots on screen /''/ > xw
Menu options containing a capitalised keyword may be
selected by typing the keyword or its first letter.
Any option can be selected by typing its number.
Use negative values to start parameter editing for an option.
For example, "-3" starts the parameter editor for option 3.
Main menu options:
0. HELP/HYPER (ASCII or hypertext help).
1. Start a reduction. 16. Check trace consistency.
2. Trace orders. 17. Post-trace Cosmic Ray locate.
3. Clip fitted traces. 18. Image cosmic ray pixels.
4. Determine dekker/object extent. 19. Quick-look Extraction.
5. Model flat field. 20. Check wavelength scales.
6. Model sky. 21. Scrunch and merge multiple.
7. Model object profile. 22. Model scattered light.
8. Extract orders 1-D. 23. ADJUST tuning parameters.
9. Locate arc line candidates. 24. Set single-order operations.
10. Identify features. 25. Set all-order operations.
11. Flatten order shape. 26. DISABLE an order.
12. Scrunch to linear scale. 27. PLOT reduction arrays.
13. Model/Extract orders 2-D. 28. Full MENU.
14. Save reduced data. 29. System ($) commands.
15. Plot order traces. 30. Output balance-factor frame.
31. EXIT (alias Q/E/QUIT/EXIT/99).
Use -nn to edit/view option parameters.
- Option number /'or Y for default=1'/ > 1
---------------------------------------------------------------------------
Starting processing task: Start a reduction. (ECH_LOCATE)
TRACIM - Frame for order tracing /''/ > testframe
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x7f827ce9235e in ???
#1 0x7f827ce91513 in ???
#2 0x7f827ff3422b in dtask_sighdlr
at /home/jbarnes/Build/starlink/libraries/pcs/dtask/dts_setsig.c:367
#3 0x7f827b895faf in ???
#4 0x7f827de2a635 in datFind_v4
at /home/jbarnes/Build/starlink/libext/hds-v4/datfinind.c:152
#5 0x7f827e058270 in datFind
at /home/jbarnes/Build/starlink/libraries/hds/hds_select.c:415
#6 0x7f827e275ff8 in dat_find_
at /home/jbarnes/Build/starlink/libraries/hds/fortran_interface.c:447
#7 0x7f827e272103 in cmp_shape_
at /home/jbarnes/Build/starlink/libraries/hds/cmp_shape.f:79
#8 0x41cada in ech_access_object_
at /home/jbarnes/Build/starlink/applications/echomop/ech_access_object.f:324
#9 0x4146f5 in ech_access_data_file_
at /home/jbarnes/Build/starlink/applications/echomop/ech_access_data_file.F:691
#10 0x40595b in ech_module_init_
at /home/jbarnes/Build/starlink/applications/echomop/ech_module_init.f:276
#11 0x43d412 in ech_echomop_option_
at /home/jbarnes/Build/starlink/applications/echomop/ech_echomop_option.f:1030
#12 0x41128f in echomop_
at /home/jbarnes/Build/starlink/applications/echomop/echomop.f:777
#13 0x4048f1 in echmono_
at /home/jbarnes/Build/starlink/applications/echomop/echmono.f:111
#14 0x4046e6 in dtask_applic_
at /home/jbarnes/Build/starlink/applications/echomop/dtask_applic.f:75
#15 0x7f827ff32d9c in dtask_obeydcl_
at /home/jbarnes/Build/starlink/libraries/pcs/dtask/dts_obeydcl.f:161
#16 0x7f827ff3176f in dtask_dcltask_
at /home/jbarnes/Build/starlink/libraries/pcs/dtask/dts_dcltask.f:153
#17 0x40454a in maintask
at /star/lib/dtask_main.f:143
#18 0x40454a in main
at /star/lib/dtask_main.f:165
________________________________
From: John.Barnes
Sent: 05 October 2018 15:39
To: [log in to unmask]
Cc: [log in to unmask]
Subject: Re: Starlink 2018A from source
Hi Tim, Malcolm,
I decided to try compling Starlink again with a new checkout of the 2018A branch. This time, the problem with FIGARO and the %LOC issue has gone away. I wonder if I installed a package at some stage since my last build attempt. I did remove libgfortran-static before building, so not sure if that was causing an issue (or indeed if there's been an update to some Fedora 28 packages since that fixed an issue somewhere).
I built with Fedora 28:
gcc-fortran / libgfortran 8.1.1-5.fc28
There are still a couple of other issues that I had to fix - I have detailed the problems I encountered and the fixes below. If you would like any more diagnostics or Fedora 28 package details from my build, let me know. I'd be happy to tar up and send the compilation directories and the build if useful - just let me know.
Thanks again for your help - it's very much appreciated.
Cheers,
John
1)
In starlink/applications/esp/ellpro.f
Declaration of arrays passed to subroutine:
CALL GJP_IDBVIP(MD,NCP,L,XV,YV,FV2,NOP,XI,YI,
: ZI,IWK,WK,IFAIL,STATUS)
have different dimensions from those in the subroutine definition
SUBROUTINE GJP_IDBVIP(md,ncp,ndp,xd,yd,zd,nip,xi,yi,zi,iwk,
: wk,istat,status)
Fedora 28 compiler didn't like this.
** SOLUTION: Make dimensions of arrays in initial declaration match those in the GJP_IDBVIP subroutine definition.
2)
cd thirdparty/kitware/vtk \
&& (make && make install) >make.log 2>make.log.err || { cat make.log.err; false; }
In file included from /usr/include/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/setup.h:173,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/cookie.c:81:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/setup.h:173,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/easy.c:24:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/setup.h:173,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/formdata.c:102:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/setup.h:173,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/getenv.c:24:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/setup.h:173,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/hash.c:24:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/setup.h:173,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/http.c:24:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/setup.h:173,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/if2ip.c:24:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/setup.h:173,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/mprintf.c:33:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/setup.h:173,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/multi.c:24:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/setup.h:173,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/sendf.c:24:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/setup.h:173,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/telnet.c:24:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/setup.h:173,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/transfer.c:24:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
In file included from /usr/include/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/setup.h:173,
from /home/jbarnes/Build/starlink/thirdparty/kitware/vtk/cmake/Utilities/cmcurl/url.c:26:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
# warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
^~~~~~~
CMake Error at CMake/vtkCompilerExtras.cmake:42 (if):
if given arguments:
"cc (GCC) 8.1.1 20180712 (Red Hat 8.1.1-5)
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software" " see the source for copying conditions. There is
NO
warranty" " not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.
" "VERSION_GREATER" "4.2.0" "AND" "BUILD_SHARED_LIBS" "AND"
"HAVE_GCC_VISIBILITY" "AND" "VTK_USE_GCC_VISIBILITY" "AND" "NOT" "MINGW"
"AND" "NOT" "CYGWIN"
Unknown arguments specified
Call Stack (most recent call first):
CMakeLists.txt:139 (include)
make[1]: *** [Makefile:677: all] Error 1
make: *** [Makefile.dependencies:3274: /star/manifests/vtk] Error 1
** SOLUTION: Get rid of check for gcc version on line 42 of ./VTK/CMake/vtkCompilerExtras.cmake as definitely > 4.2.0
and then again in ./VTK/CMake/GenerateExportHeader.cmake (i.e. ${_gcc_version} not working)
** SOLUTION: Comment out lines 178,179&180 of ./VTK/CMake/GenerateExportHeader.cmake as unnecessary
________________________________
From: Malcolm J. Currie <[log in to unmask]>
Sent: 04 October 2018 18:29
To: John.Barnes
Cc: [log in to unmask]
Subject: Re: Starlink 2018A from source
John,
> I was wondering if you could help with the problem I mentioned recently when compiling Starlink on Fedora 28.
I was hoping somebody else with Fedora could help with practical
tips.
> I have found that one of my workarounds has resulted in a problem - I detailed it below in 1) between then asterisks
Please could you send me the applications/figaro/config.log file.
Amongst a number of checks of features in the Fortran compiler, there
should be a test for LOC or %LOC. In mine on Mint the relevant part
reads:
configure:18083: checking whether gfortran has the %LOC extension
configure:18115: result: no
configure:18128: checking whether gfortran supports intrinsic LOC
configure:18147: result: yes
indicating that compiler supports the LOC() syntax.
> In addition to the problem with plotting I mentioned in 1), when I run
> FIGARO-isubset on and NDF file it doesn't actually work properly and
> prints
KAPPA:NDFCOPY is better. You can subset by pixels or world
co-ordinates, it's not limited to two dimensions, and it preserves the
WCS information.
> I think the # sections in the source code (See 1) below) are meant to
> be place holders or substituted into the code if necessary - rather
> than turned into print statements. It seems as though my build is
> failing the HAVE_PERCENTLOC and HAVE_INTRINSIC_LOC for some reason -
> maybe the line Do not have LOC or %LOC should never be reached. Any
> idea why that might be or what additional tests I might perform? I
> wonder if I am missing some devel file somewhere.
Yes, there is a preprocessor that edits the Fortran in these .F files.
The configure.ac has these lines to set the boolean HAVE_PERCENTLOC
and HAVE_INTRINSIC_LOC.
AC_FC_HAVE_PERCENTLOC()
AC_FC_CHECK_INTRINSICS(LOC)
If for some reason you have neither, then the error message you see
appears.
I'd still like to know all the extra packages that you needed to
install, so that I can update the main README in the source.
Malcolm
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