Singularity: Slurm plugin missing header

[gdolle]

When trying to compile the slurm plugin --with-slurm, I get an error with a missing header:

singularity.c:32:29: fatal error: lib/singularity.h: No such file or directory  #include "lib/singularity.h"

Maybe this include should be removed ? (like here https://github.com/singularityware/singularity/commit/e699be95cdb7c2352f22dfa844c2cec301e0adfe)

Version of Singularity:

Release 2.3.0

[moskalenko]

Same here, full error:

Making all in slurm
make[3]: Entering directory singularity-2.3/src/slurm' depbase=echo singularity.lo | sed 's|[^/]$|.deps/&|;s|.lo$||';\ /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -I/opt/slurm/include -MT singularity.lo -MD -MP -MF $depbase.Tpo -c -o singularity.lo singularity.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -I/opt/slurm/include -MT singularity.lo -MD -MP -MF .deps/singularity.Tpo -c singularity.c -fPIC -DPIC -o .libs/singularity.o singularity.c:32:29: error: lib/singularity.h: No such file or directory singularity.c: In function ‘setup_container_environment’: singularity.c:66: warning: incompatible implicit declaration of built-in function ‘snprintf’ singularity.c: In function ‘setup_container_cwd’: singularity.c:130: warning: initialization makes pointer from integer without a cast singularity.c: In function ‘setup_container’: singularity.c:148: warning: incompatible implicit declaration of built-in function ‘printf’ singularity.c:172: error: redeclaration of ‘image’ with no linkage singularity.c:145: note: previous declaration of ‘image’ was here singularity.c:173: warning: assignment makes pointer from integer without a cast make[3]: *** [singularity.lo] Error 1 make[3]: Leaving directorysingularity-2.3/src/slurm'
make[2]: [all-recursive] Error 1
make[2]: Leaving directory singularity-2.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directorysingularity-2.3/src'
make: * [all-recursive] Error 1

However, just patching those includes out is not sufficient as it doesn't address re-declaration of image.

singularity.c: In function ‘setup_container_environment’:
singularity.c:65: warning: incompatible implicit declaration of built-in function ‘snprintf’
singularity.c: In function ‘setup_container_cwd’:
singularity.c:129: warning: initialization makes pointer from integer without a cast
singularity.c: In function ‘setup_container’:
singularity.c:147: warning: incompatible implicit declaration of built-in function ‘printf’
singularity.c:171: error: redeclaration of ‘image’ with no linkage
singularity.c:144: note: previous declaration of ‘image’ was here
singularity.c:172: warning: assignment makes pointer from integer without a cast

[gmkurtzer]

I can take a stab at this, but the SLURM plugin does need to be updated and @bbockelm (who "owns" that component), has been focused on other things. If anyone wants to try and get to this before I can, it would be greatly appreciated!

Thank you!

[hsteininger]

Hi, are there any news about a patch to fix missing header for Slurm Integration PlugIn.

Thanks.

[mbrt]

This issue prevents us from upgrading to 2.3.1, because we need the --with-slurm and definitely the security fix. Are there any workarounds?

[votavap]

I have a patch for the build, but wanted to test the plugin before I submit a pull request. I will see if I can get to it later today or tomorrow unless this is urgent and somebody wants to give it a try.

[mbrt]

I'd be happy to test your patch, if this can help to speedup the process

Il 29 giu 2017 20:07, "votavap" [e-mail] ha scritto:

I have a patch for the build, but wanted to test the plugin before I
submit a pull request. I will see if I can get to it later today or
tomorrow unless this is urgent and somebody wants to give it a try.

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[votavap]

@mbrt That would be great!!
https://github.com/votavap/singularity/
It's a fork from the main repo and there is a slurm-plugin-patch-devel branch from the development branch and (if needed) slurm-plugin-patch branch from the master. I managed to build both on CentOS7.3 using gcc 4.8.5.

[mbrt]

@votavap the build worked fine for RHEL 7 and the basic singularity functionality is there. I'll now test the slurm functionality. I think the patch is good

[votavap]

@mbrt Thank you for testing this!

[votavap]

@gmkurtzer I believe this issue can now be closed.

[votavap]

@gmkurtzer Or perhaps not till it gets merged to the mater at some point in the future, jumped the gun here a bit ;-) Same with #811

[gmkurtzer]

OK, that sounds good. I'll leave this open until it gets merged into master. Thanks!

[kav2k]

This can now be closed; it landed in 2.4

[vsoch]

Great, thanks @kav2k , closing issue.