At EAO we have a Starlink build working on Centos 7 at the moment. its
in a virtual machine though, so I'd guess we probably don't have a
system cfitsio library present. We haven't ran it in the last month,
but it doesn't look like Astro::FITS::CFITSIO has been updated since
october so I would hope it still works.
Is it possible that your build has built against one version but is
trying to load another? As a note, in my centos 7 build script I
explicitly do export LD_LIBRARY_PATH=$STARCONF_DEFAULT_STARLINK/lib
before building, although I can't remember if that's always necessary.
What do you get from running 'ldd' on the CFITSIO.so in your Perl
module build? (If it didn't install it should be some where in your
.cpanm/work directory -- see
/home/astro/phsaap/.cpanm/work/1546868621.14559/ based on your log
message.). Does the output change if you source the starlink setup
scripts?
Sarah
On Mon, 7 Jan 2019 at 04:11, Tom Marsh <[log in to unmask]> wrote:
>
> Hello, I thought I was going to manage to get through the whole starlink compilation without problem (on Centos 7) for the first time ever, but hit an issue during the perl module stage -- see below. I had a look at the CFITSIO.so library referred to, and there is indeed an undefined symbol there:
>
> nm CFITSIO.so | grep ffgsky
> 00000000000579f0 t XS_Astro__FITS__CFITSIO_ffgsky
> U ffgsky
>
>
> A quick google suggests a more recent cfitsio version is needed (3.39). Looking on the system here I see version 3.370, but I assumed starlink shipped its own version of cfitsio?
>
> Any suggestions on what I should do at this point? Perhaps not important from the point of view of making my PAMELA mod?
>
> Tom
>
> The output from the installation showing the problem:
>
> more /home/astro/phsaap/.cpanm/work/1546868621.14559/build.log
> cpanm (App::cpanminus) 1.7044 on perl 5.026001 built for x86_64-linux
> Work directory is /home/astro/phsaap/.cpanm/work/1546868621.14559
> You have make /usr/bin/make
> You have LWP 6.36
> You have /usr/bin/tar: tar (GNU tar) 1.26
> Copyright (C) 2011 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law.
>
> Written by John Gilmore and Jay Fenlason.
> You have /usr/bin/unzip
> Searching Astro::FITS::CFITSIO () on cpanmetadb ...
> --> Working on Astro::FITS::CFITSIO
> Fetching http://www.cpan.org/authors/id/P/PR/PRATZLAFF/Astro-FITS-CFITSIO-1.12.tar.gz
> -> OK
> Unpacking Astro-FITS-CFITSIO-1.12.tar.gz
> Entering Astro-FITS-CFITSIO-1.12
> Checking configure dependencies from META.json
> Checking if you have ExtUtils::MakeMaker 6.58 ... Yes (7.24)
> Configuring Astro-FITS-CFITSIO-1.12
> Running Makefile.PL
> Checking if your kit is complete...
> Looks good
> Generating a Unix-style Makefile
> Writing Makefile for Astro::FITS::CFITSIO
> Writing MYMETA.yml and MYMETA.json
> -> OK
> Checking dependencies from MYMETA.json ...
> Checking if you have ExtUtils::MakeMaker 0 ... Yes (7.24)
> Building and testing Astro-FITS-CFITSIO-1.12
> cp CFITSIO.pm blib/lib/Astro/FITS/CFITSIO.pm
> AutoSplitting blib/lib/Astro/FITS/CFITSIO.pm (blib/lib/auto/Astro/FITS/CFITSIO)
> Running Mkbootstrap for CFITSIO ()
> chmod 644 "CFITSIO.bs"
> "/storage/astro1/phsaap/software/star/Perl/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CFITSIO.bs blib/arch/auto/Astro/FITS/CFITSIO/CFIT
> SIO.bs 644
> "/storage/astro1/phsaap/software/star/Perl/bin/perl" "/storage/astro1/phsaap/software/star/Perl/lib/perl5/5.26.1/ExtUtils/xsubpp" -typemap '/stor
> age/astro1/phsaap/software/star/Perl/lib/perl5/5.26.1/ExtUtils/typemap' -typemap '/home/astro/phsaap/.cpanm/work/1546868621.14559/Astro-FITS-CFITS
> IO-1.12/typemap' CFITSIO.xs > CFITSIO.xsc
> mv CFITSIO.xsc CFITSIO.c
> gcc -c -I/storage/astro1/phsaap/software/star -I/storage/astro1/phsaap/software/star/include -fwrapv -fno-strict-aliasing -pipe -fstack-protector
> -strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -g -O2 -DVERSION=\"1.12\" -DXS_VERSION=\"1.12\" -fPI
> C "-I/storage/astro1/phsaap/software/star/Perl/lib/perl5/5.26.1/x86_64-linux/CORE" CFITSIO.c
> gcc -c -I/storage/astro1/phsaap/software/star -I/storage/astro1/phsaap/software/star/include -fwrapv -fno-strict-aliasing -pipe -fstack-protector
> -strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -g -O2 -DVERSION=\"1.12\" -DXS_VERSION=\"1.12\" -fPI
> C "-I/storage/astro1/phsaap/software/star/Perl/lib/perl5/5.26.1/x86_64-linux/CORE" util.c
> rm -f blib/arch/auto/Astro/FITS/CFITSIO/CFITSIO.so
> LD_RUN_PATH="/storage/astro1/phsaap/software/star/lib" gcc -shared -g -O2 -L/storage/astro1/phsaap/software/lib -L/usr/local/lib -fstack-protector-strong CFITSIO.o util.o -o blib/arch
> /auto/Astro/FITS/CFITSIO/CFITSIO.so \
> -L/storage/astro1/phsaap/software/star -L/storage/astro1/phsaap/software/star/lib -lcfitsio -lm \
>
> chmod 755 blib/arch/auto/Astro/FITS/CFITSIO/CFITSIO.so
> Manifying 1 pod document
> "/storage/astro1/phsaap/software/star/Perl/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CFITSIO.bs blib/arch/auto/Astro/FITS/CFITSIO/CFITSIO.bs 644
> PERL_DL_NONLAZY=1 "/storage/astro1/phsaap/software/star/Perl/bin/perl" "-Iblib/lib" "-Iblib/arch" test.pl
>
> Loading................................Can't load 'blib/arch/auto/Astro/FITS/CFITSIO/CFITSIO.so' for module Astro::FITS::CFITSIO: blib/arch/auto/Astro/FITS/CFITSIO/CFITSIO.so: undefined
> symbol: ffgsky at /storage/astro1/phsaap/software/star/Perl/lib/perl5/5.26.1/x86_64-linux/DynaLoader.pm line 193.
>
> Compilation failed in require at test.pl line 26.
> BEGIN failed--compilation aborted at test.pl line 26.
> make: *** [test_dynamic] Error 2
> -> FAIL Installing Astro::FITS::CFITSIO failed. See /home/astro/phsaap/.cpanm/work/1546868621.14559/build.log for details. Retry with --force to force install it.
> shika:perlmods>
>
> ########################################################################
>
> To unsubscribe from the STARDEV list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=STARDEV&A=1
--
Dr Sarah Graves
Scientific Programmer
East Asian Observatory/JCMT
[log in to unmask]
########################################################################
To unsubscribe from the STARDEV list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=STARDEV&A=1
|