change $LIBS in Ghostscript 9.27 easyconfig to include location of zlib library to link with by BenjaminHCCarr · Pull Request #11291 · easybuilders/easybuild-easyconfigs

BenjaminHCCarr · 2020-09-16T14:55:45Z

Ghostscript was not compiling due to failing on:
libpng/1.6.36-GCCcore-8.2.0/lib/libpng16.so.16: undefined reference to inflateValidate@ZLIB_1.2.9

needed to add -L$EBROOTZLIB/lib to the
preconfigopts += 'export LIBS="$LIBS -lz" && '
line

Ghostscript was not compiling due to failing on: `libpng/1.6.36-GCCcore-8.2.0/lib/libpng16.so.16: undefined reference to inflateValidate@ZLIB_1.2.9'` needed to add `-L$EBROOTZLIB/lib` to the `preconfigopts += 'export LIBS="$LIBS -lz" && '` line

Micket

lgtm

boegel · 2020-09-16T15:59:18Z

@boegelbot please test @ generoso

boegelbot · 2020-09-16T16:00:09Z

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=11291 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11291 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 7816

Test results coming soon (I hope)...

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Message to humans: this is just bookkeeping information for me,
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boegelbot · 2020-09-16T16:04:30Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
generoso-x-1 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/329f7b5c52d4323548efc9704be4d766 for a full test report.

sassy-crick · 2020-09-16T16:05:14Z

Test report by @sassy-crick
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
jon-Precision-Tower-7910 - Linux debian 10.5, x86_64, Intel(R) Xeon(R) CPU E5-2623 v3 @ 3.00GHz, Python 2.7.16
See https://gist.github.com/0a3b0c3b61ef5ec87bc71d72c6b16018 for a full test report.

Micket · 2020-09-16T16:08:13Z

Test report by @Micket
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
hebbe-c1 - Linux centos linux 7.8.2003, x86_64, Intel Core Processor (Haswell, no TSX), Python 2.7.5
See https://gist.github.com/e4b1dca59a8c0818bda526784c55713e for a full test report.

boegel · 2020-09-16T16:16:18Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node3407.kirlia.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz (cascadelake), Python 2.7.5
See https://gist.github.com/9b9cb674db988fc4c029b36f3d9aa428 for a full test report.

boegel · 2020-09-16T16:29:43Z

Going in, thanks @BenjaminHCCarr!

boegel · 2020-09-16T16:32:15Z

@BenjaminHCCarr I'm still a bit intriuged why this hasn't popped up for anyone else...

Can you share a bit more context about your EasyBuild configuration, which may help explain why you bumped into this but others haven't?

boegel · 2020-09-16T16:34:04Z

Could you also share which exact command was failing with the undefined reference error (so we can check works for installations that worked out fine for clues)?

BenjaminHCCarr · 2020-09-16T17:03:14Z

eb --version
This is EasyBuild 4.2.1 (framework: 4.2.1, easyblocks: 4.2.1)

Centos 7

   Static hostname: seskscpn080.prim.scp
         Icon name: computer-server
           Chassis: server
        Machine ID: 65113b1a0d2f6087d515e6a8cd0ee7ef
           Boot ID: 5a32347a99004bd7b9dd306f348a8a4d
  Operating System: CentOS Linux 7 (Core)
       CPE OS Name: cpe:/o:centos:centos:7
            Kernel: Linux 3.10.0-957.27.2.el7.x86_64
      Architecture: x86-64

building for Broadwell arch

Building Ghostscript 9.27 on GCCcore 8.2.0 received:

/opt/scp/software/binutils/2.31.1-GCCcore-8.2.0/bin/ld: /opt/scp/software/libpng/1.6.36-GCCcore-8.2.0/lib/libpng16.so.16: undefi
ned reference to `inflateValidate@ZLIB_1.2.9'
collect2: error: ld returned 1 exit status
make: *** [obj/aux/genconf] Error 1
make: *** Waiting for unfinished jobs....
/opt/scp/software/binutils/2.31.1-GCCcore-8.2.0/bin/ld: /opt/scp/software/libpng/1.6.36-GCCcore-8.2.0/lib/libpng16.so.16: undefi
ned reference to `inflateValidate@ZLIB_1.2.9'
collect2: error: ld returned 1 exit status
make: *** [obj/aux/genarch] Error 1
/opt/scp/software/binutils/2.31.1-GCCcore-8.2.0/bin/ld: /opt/scp/software/libpng/1.6.36-GCCcore-8.2.0/lib/libpng16.so.16: undefined reference to `inflateValidate@ZLIB_1.2.9'
collect2: error: ld returned 1 exit status
make: *** [obj/aux/echogs] Error 1
 (at easybuild/tools/run.py:533 in parse_cmd_output)

but:

seskscpg001:~/code/easybuild kkfp793$ grep -i zlib easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb
    # zlib is a runtime dep to avoid that it gets embedded in libbfd.so,
    ('zlib', '1.2.11'),
seskscpg001:~/code/easybuild kkfp793$ grep -i zlib easyconfigs/l/libpng/libpng-1.6.36-GCCcore-8.2.0.eb
    ('zlib', '1.2.11'),

it was pulling in system zlib which was 1.2.7

boegel · 2020-09-16T17:29:18Z

@BenjaminHCCarr Can you share the output of eb --show-config?

Also, which compiler command was triggering the failing ld? Can you maybe share a log file we can stare at?

terjekv · 2020-09-16T18:29:31Z

Test report by @terjekv
SUCCESS
Build succeeded for 49 out of 49 (1 easyconfigs in this PR)
arm1 - Linux ubuntu 18.04, AArch64, UNKNOWN (aarch64), Python 3.6.9
See https://gist.github.com/c9823ed1db0b8ce3b598184e7844aadf for a full test report.

LIBS change to fix Ghostscript ZLIB error

9244bb6

Ghostscript was not compiling due to failing on: `libpng/1.6.36-GCCcore-8.2.0/lib/libpng16.so.16: undefined reference to inflateValidate@ZLIB_1.2.9'` needed to add `-L$EBROOTZLIB/lib` to the `preconfigopts += 'export LIBS="$LIBS -lz" && '` line

BenjaminHCCarr changed the title ~~LIBS change to fix Ghostscript 9.27 - GCC 8.2.0 ZLIB error~~ {toos} Ghostscript 9.27 - GCC 8.2.0: LIBS change to fix ZLIB error Sep 16, 2020

BenjaminHCCarr changed the title ~~{toos} Ghostscript 9.27 - GCC 8.2.0: LIBS change to fix ZLIB error~~ {tools} Ghostscript 9.27 - GCC 8.2.0: LIBS change to fix ZLIB error Sep 16, 2020

BenjaminHCCarr changed the title ~~{tools} Ghostscript 9.27 - GCC 8.2.0: LIBS change to fix ZLIB error~~ {tools} [GCCcore/8.20] Ghostscript 9.27: LIBS change to fix ZLIB error Sep 16, 2020

Micket approved these changes Sep 16, 2020

View reviewed changes

boegel changed the title ~~{tools} [GCCcore/8.20] Ghostscript 9.27: LIBS change to fix ZLIB error~~ {tools} [GCCcore/8.2.0] Ghostscript 9.27: LIBS change to fix ZLIB error Sep 16, 2020

boegel added the bug fix label Sep 16, 2020

boegel added this to the next release (4.3.1) milestone Sep 16, 2020

boegel merged commit b3c955b into easybuilders:develop Sep 16, 2020

boegel changed the title ~~{tools} [GCCcore/8.2.0] Ghostscript 9.27: LIBS change to fix ZLIB error~~ change $LIBS in Ghostscript 9.27 easyconfig to include location of zlib library to link with Sep 16, 2020

BenjaminHCCarr deleted the patch-1 branch September 16, 2020 17:03

boegel mentioned this pull request Sep 22, 2020

make sure correct zlib is used in recent Ghostscript easyconfigs #11319

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