On 20 Sep 2017, at 17:45, Kenneth Hoste
<[email protected]<mailto:[email protected]>> wrote:
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
Yep, get the issue. We are on lmod 6.4.3. Oh we. We tried 7.6 recently, ran
into issue and reverted to 6.4.3.
Thanks
Joachim
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
