Hi Joachim,
It's not entirely clear, but I *think* that Lmod itself gets broken by
the "module load jemalloc/4.1.0" that is being done when test loading
the generated MariaDB module.
Can you try and reproduce this outside of EasyBuild by:
module load intel/2016a
unset LD_LIBRARY_PATH
module load jemalloc/4.1.0
module list
The 'module list' will probably produce the same error "error while
loading shared libraries: libiomp5.so ...".
The problem is that the jemalloc module sets $LD_PRELOAD to a library
that requires libiomp5.so, but which is no longer available because
EasyBuild clears $LD_LIBRARY_PATH every time it runs a module command
(to try and avoid breaking Lmod, which is in this case backfiring).
Which Lmod version are you running here?
A recent version of Lmod should be robust enough not to suffer from this...
Based on https://github.com/TACC/Lmod/blob/master/README.md, Lmod 6.6 or
more recent should suffice.
regards,
Kenneth
On 20/09/2017 17:28, Joachim Hein wrote:
Attached as requested. Thanks for looking into this.
Best wishes
Joachim
On 20 Sep 2017, at 14:49, Kenneth Hoste <[email protected]
<mailto:[email protected]>> wrote:
Dear Joachim,
Can you send us the full debug log?
Are you running this installation in a clean environment (no modules
loaded)?
regards,
Kenneth
On 20/09/2017 12:36, Joachim Hein wrote:
Hi,
I am trying to build MariaDB-10.1.13-intel-2016a.eb and it fails the
sanity check in a way that I am lost on.
This is from the screen of the build:
== taking care of extensions...
== postprocessing...
== sanity checking...
== FAILED: Installation ended unsuccessfully (build directory:
/local/easybuild/build/MariaDB/10.1.13/intel-2016a): build failed
(first 300 chars): Sanity check failed: loading fake module failed:
'Module command \'module load MariaDB/10.1.13\' failed with exit
code 1; stderr: sh: error while loading shared libraries:
libiomp5.so: cannot open shared object file: No such file or
directory\nLmod has detected the following error: Failed to find \'
Looking into the logs I get:
<Screen Shot 2017-09-20 at 12.33.50.png>
There is a
/sw/easybuild/software/Core/ifort/2016.1.150-GCC-4.9.3-2.25/compilers_and_libraries_2016.1.150/linux/compiler/lib/intel64/
in that Library path and in there I get:
-bash-4.2$ ls
/sw/easybuild/software/Core/ifort/2016.1.150-GCC-4.9.3-2.25/compilers_and_libraries_2016.1.150/linux/compiler/lib/intel64/libiomp5.*
/sw/easybuild/software/Core/ifort/2016.1.150-GCC-4.9.3-2.25/compilers_and_libraries_2016.1.150/linux/compiler/lib/intel64/libiomp5.a
/sw/easybuild/software/Core/ifort/2016.1.150-GCC-4.9.3-2.25/compilers_and_libraries_2016.1.150/linux/compiler/lib/intel64/libiomp5.dbg
/sw/easybuild/software/Core/ifort/2016.1.150-GCC-4.9.3-2.25/compilers_and_libraries_2016.1.150/linux/compiler/lib/intel64/libiomp5.so
the intel openmp library. Anyone sees something I am missing?
Thanks
Joachim
