Hi Tim,
OK, I didn't take into account that the toolchain support for OpenMPI
(implemented in easybuild/toolchains/mpi/openmpi.py, which is where the
crash is occuring) may be depending on MPI_MODULE_NAME being non-empty...
Try including this in your toolchain definition as well (indented
properly to be part of the PicGompi class):
def _set_mpi_compiler_variables(self):
"""Define MPI wrapper commands."""
# version-dependent, see
http://www.open-mpi.org/faq/?category=mpi-apps#override-wrappers-after-v1.0
# assumption here is that OpenMPI version being used is recent
enough (>= 1.7) to provide mpifort
self.MPI_COMPILER_MPIF77 = 'mpifort'
self.MPI_COMPILER_MPIF90 = 'mpifort'
self.MPI_COMPILER_MPIFC = 'mpifort'
# this needs to be done first, otherwise e.g., CC is set to
MPICC if the usempi toolchain option is enabled
for var, _ in COMPILER_VARIABLES:
self.variables.nappend('OMPI_%s' % var,
str(self.variables[var].get_first()), var_class=CommandFlagList)
super(PicGompi, self)._set_mpi_compiler_variables()
This will effectively override the implementation of
_set_mpi_compiler_variables in openmpi.py, which should hopefully solve
your problem...
Do note that I'm assuming that the OpenMPI version provided by your
external module is sufficiently recent...
The underlying issue is indeed that get_software_version is not taking
into account that the module could be an external module.
Can you try and reproduce the problem you had with using your external
module name in MPI_MODULE_NAME?
I'll open an issue to try and get this fixed then...
regards,
Kenneth
On 08/09/16 02:27, Tim Slauson wrote:
Hi Kenneth,
Thanks for the MPI_MODULE_NAME suggestion. I had earlier tried setting
that to my external module name, but ran into different errors and
just gave up.
When I set MPI_MODULE_NAME to an empty list, the OpenMPI toolchain
module hits an IndexError when trying to retrieve a software version
(see traceback below). Since I'm specifying that information in an
external module metadata file, shouldn't the software version be taken
from there?
Thanks,
Tim
ERROR: Traceback (most recent call last):
File
"/import/usrlocal/easybuild/2.8.2/software/EasyBuild/2.8.2/lib/python2.6/site-packages/easybuild_framework-2.8.2-py2.6.egg/easybuild/main.py",
line 114, in build_and_install_software
(ec_res['success'], app_log, err) = build_and_install_one(ec,
init_env)
File
"/import/usrlocal/easybuild/2.8.2/software/EasyBuild/2.8.2/lib/python2.6/site-packages/easybuild_framework-2.8.2-py2.6.egg/easybuild/framework/easyblock.py",
line 2363, in build_and_install_one
result = app.run_all_steps(run_test_cases=run_test_cases)
File
"/import/usrlocal/easybuild/2.8.2/software/EasyBuild/2.8.2/lib/python2.6/site-packages/easybuild_framework-2.8.2-py2.6.egg/easybuild/framework/easyblock.py",
line 2279, in run_all_steps
self.run_step(step_name, step_methods)
File
"/import/usrlocal/easybuild/2.8.2/software/EasyBuild/2.8.2/lib/python2.6/site-packages/easybuild_framework-2.8.2-py2.6.egg/easybuild/framework/easyblock.py",
line 2158, in run_step
step_method(self)()
File
"/import/usrlocal/easybuild/2.8.2/software/EasyBuild/2.8.2/lib/python2.6/site-packages/easybuild_framework-2.8.2-py2.6.egg/easybuild/framework/easyblock.py",
line 1554, in prepare_step
self.toolchain.prepare(self.cf <http://self.cf>g['onlytcmod'],
silent=self.silent)
File
"/import/usrlocal/easybuild/2.8.2/software/EasyBuild/2.8.2/lib/python2.6/site-packages/easybuild_framework-2.8.2-py2.6.egg/easybuild/tools/toolchain/toolchain.py",
line 608, in prepare
self.set_variables()
File
"/import/usrlocal/easybuild/2.8.2/software/EasyBuild/2.8.2/lib/python2.6/site-packages/easybuild_framework-2.8.2-py2.6.egg/easybuild/tools/toolchain/compiler.py",
line 154, in set_variables
super(Compiler, self).set_variables()
File
"/import/usrlocal/easybuild/2.8.2/software/EasyBuild/2.8.2/lib/python2.6/site-packages/easybuild_framework-2.8.2-py2.6.egg/easybuild/tools/toolchain/mpi.py",
line 94, in set_variables
self._set_mpi_compiler_variables()
File
"/import/usrlocal/easybuild/2.8.2/software/EasyBuild/2.8.2/lib/python2.6/site-packages/easybuild_framework-2.8.2-py2.6.egg/easybuild/toolchains/mpi/openmpi.py",
line 62, in _set_mpi_compiler_variables
ompi_ver = self.get_software_version(self.MPI_MODULE_NAME)[0]
IndexError: list index out of range
On Wed, Sep 7, 2016 at 3:32 AM, Kenneth Hoste <[email protected]
<mailto:[email protected]>> wrote:
Hi Tim,
Welcome to the wonderful world of EasyBuild!
On 07/09/16 01:29, Tim Slauson wrote:
Hello EasyBuilders,
I'm trying out EasyBuild for the first time (version 2.8.2),
and am having trouble hooking in the vendor-provided MPI
modules on one of our clusters. The modules all follow the
same naming convention of name/compiler/ver (e.g.
openmpi/gnu/1.10.2, mvapich2-psm/intel/2.1, ...). After
reading about EXTERNAL_MODULE, I adapted the gompi-2016.06.eb
toolchain easyconfig:
3c3
< name = 'gompi'
---
> name = 'pic-gompi'
17c17
< ('OpenMPI', '1.10.3', '', ('GCC', gccver)),
---
> ('openmpi/gnu/1.10.2', EXTERNAL_MODULE),
And wrote external module metadata:
[openmpi/gnu/1.10.2]
name = OpenMPI
version = 1.10.2
prefix = MPI_HOME
And defined a new toolchain:
from easybuild.toolchains.gompi import Gompi
class PicGompi(Gompi):
"""PIC compiler toolchain with GNU compilers and OpenMPI"""
NAME = 'pic-gompi'
This allows me to build a toolchain. But when I run this:
eb FFTW-3.3.4-gompi-2016.06.eb --try-toolchain=pic-gompi,2016.06
I get this error:
ERROR: Build of
/tmp/eb-HkZNza/tweaked_easyconfigs/FFTW-3.3.4-pic-gompi-2016.06.eb
failed (err: "build failed (first 300 chars): List of
toolchain dependency modules and toolchain definition do not
match (found ['GCC/5.4.0-2.26', 'openmpi/gnu/1.10.2'] vs
expected set(['GCC', 'OpenMPI']))")
I get similar errors when repeating this process for the other
vendor-provided libraries. Can somebody please point me in
the right direction?
You're hitting this because EasyBuild verifies the module for the
toolchain with the definition of the toolchain.
This is done using module names, see for example
https://github.com/hpcugent/easybuild-framework/blob/master/easybuild/toolchains/mpi/openmpi.py#L44
<https://github.com/hpcugent/easybuild-framework/blob/master/easybuild/toolchains/mpi/openmpi.py#L44>
.
You should be able to fix your problem by including this in your
pic-gompi toolchain definition (i.e. reset it to the default):
MPI_MODULE_NAME = []
This should only affect the toolchain definition verification
mechanism, nothing else.
regards,
Kenneth
--
Tim Slauson
GI/RCS
University of Alaska Fairbanks
