On 04/30/2018 02:44 PM, Bart Oldeman wrote:
Hello Ole,
the issue is here:
ld: cannot find -lpciaccess
ld: cannot find -lxml2
to solve this you can either install OS packages (.rpm, .deb, etc.) for
libpciaccess and libxml2, and perhaps add them as OS dependencies.
Yes, I thought about this, but these packages are already present on the
system:
# rpm -q libxml2 libpciaccess
libxml2-2.9.1-6.el7_2.3.x86_64
libpciaccess-0.13.4-3.1.el7_4.x86_64
Alternatively you can put in dependencies for ('libxml2', '2.9.8') and
('libpciaccess', '0.13.4'), where you would need to install libpciaccess
using GCCcore instead of an intel or foss toolchain.
So you mean that I may need to install these libraries as modules using EB?
Thanks,
Ole
On Mon, 30 Apr 2018 at 05:31, Ole Holm Nielsen
<[email protected] <mailto:[email protected]>> wrote:
When we build on nodes with Intel Omni-Path software installed, the
build of "iomkl" fails:
$ eb iomkl-2018.02.eb -r
== temporary log file in case of crash
/tmp/eb-MDUNmr/easybuild-UxI3tr.log
== resolving dependencies ...
== processing EasyBuild easyconfig
/home/modules/software/EasyBuild/3.6.0/lib/python2.7/site-packages/easybuild_easyconfigs-3.6.0-py2.7.egg/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb
== building and installing
OpenMPI/2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== FAILED: Installation ended unsuccessfully (build directory:
/home/modules/build/OpenMPI/2.1.3/iccifort-2018.2.199-GCC-6.4.0-2.28):
build failed (first 300 chars): cmd " make -j 48 " exited with exit
code
2 and output:
Making all in config
make[1]: Entering directory
`/home/modules/build/OpenMPI/2.1.3/iccifort-2018.2.199-GCC-6.4.0-2.28/openmpi-2.1.3/config'
Intel Omni-Path systems
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/modules/build/OpenMPI/2.1.3/icc
== Results of the build can be found in the log file(s)
/tmp/eb-MDUNmr/easybuild-OpenMPI-2.1.3-20180430.105741.vWNYR.log
ERROR: Build of
/home/modules/software/EasyBuild/3.6.0/lib/python2.7/site-packages/easybuild_easyconfigs-3.6.0-py2.7.egg/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb
failed (err: 'build failed (first 300 chars): cmd " make -j 48 " exited
with exit code 2 and output:\nMaking all in config\nmake[1]: Entering
directory
`/home/modules/build/OpenMPI/2.1.3/iccifort-2018.2.199-GCC-6.4.0-2.28/openmpi-2.1.3/config\'\nmake[1]:
Nothing to be done for `all\'.\nmake[1]: Leaving directory
`/home/modules/build/OpenMPI/2.1.3/icc')
The OpenMPI error log file contains near the end:
CCLD libopen-pal.la <http://libopen-pal.la>
ld: cannot find -lpciaccess
ld: cannot find -lxml2
make[2]: *** [libopen-pal.la <http://libopen-pal.la>] Error 1
make[2]: Leaving directory
`/home/modules/build/OpenMPI/2.1.3/iccifort-2018.2.199-GCC-6.4.0-2.28/openmpi-2.1.3/opal'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/home/modules/build/OpenMPI/2.1.3/iccifort-2018.2.199-GCC-6.4.0-2.28/openmpi-2.1.3/opal'
make: *** [all-recursive] Error 1
(at easybuild/tools/run.py:501 in parse_cmd_output)
== 2018-04-30 11:03:17,152 easyblock.py:2702 WARNING build failed
(first
300 chars): cmd " make -j 48 " exited with exit code 2 and output:
Making all in config
make[1]: Entering directory
`/home/modules/build/OpenMPI/2.1.3/iccifort-
Intel Omni-Path systems2018.2.199-GCC-6.4.0-2.28/openmpi-2.1.3/config'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/modules/build/OpenMPI/2.1.3/icc
== 2018-04-30 11:03:17,152 easyblock.py:280 INFO Closing log for
application name OpenMPI version 2.1.3
Question: Can anyone point to the cause of this error? Did OpenMPI
2.1.3 introduce this error?
Extra information: The issue
https://github.com/easybuilders/easybuild-easyconfigs/issues/5805 is
fixed with EB 3.6.0 and OpenMPI 2.1.3. On our systems with Mellanox
Infiniband software installed, the line in
OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb *does* fix the
issue
5805 on this platform:
configopts += '--without-ucx ' # hard disable UCX, to dance around bug
(https://github.com/open-mpi/ompi/issues/4345)
On the Intel Omni-Path system I tried to comment out this line, but the
build still fails with the same error.
/Ole
On 03/05/2018 03:44 PM, Åke Sandgren wrote:
> To clarify, it's a bug in the OpenMPI configure script when
dealing with
> UCX which they haven't fixed.
>
> On 03/05/2018 03:36 PM, Balázs Hajgató wrote:
>> Dear Ole,
>>
>> use
>> configopts += '--without-ucx '
>>
>> in the OpenMPI easyconfig
>>
>> Sincerely,
>>
>> Balazs
>>
>>>>>
>>> Thanks for any suggestions!
>>>
>>
>
--
Ole Holm Nielsen
PhD, Senior HPC Officer
Department of Physics, Technical University of Denmark,
Building 307, DK-2800 Kongens Lyngby, Denmark
E-mail: [email protected] <mailto:[email protected]>
Homepage: http://dcwww.fysik.dtu.dk/~ohnielse/
Tel: (+45) 4525 3187 / Mobile (+45) 5180 1620
>> On 05/03/2018 15:27, Ole Holm Nielsen wrote:
>>> Using EB 3.5.2 I'm trying to build the latest iomkl:
>>>
>>> eb iomkl-2018a.eb -r
>>>
>>> This works like a charm on 2 of our 3 binary architectures, but
on our
>>> Sandy Bridge nodes with Mellanox Infiniband the build aborts:
>>>
>>> # eb iomkl-2018a.eb -r
>>> == temporary log file in case of crash
>>> /tmp/eb-Dnjmix/easybuild-6WeIK9.log
>>> == resolving dependencies ...
>>> == processing EasyBuild easyconfig
>>>
/home/modules/software/EasyBuild/3.5.2/lib/python2.7/site-packages/easybuild_easyconfigs-3.5.2-py2.7.egg/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb
>>>
>>> == building and installing
>>> OpenMPI/2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28...
>>> == fetching files...
>>> == creating build dir, resetting environment...
>>> == unpacking...
>>> == patching...
>>> == preparing...
>>> == configuring...
>>> == building...
>>> == FAILED: Installation ended unsuccessfully (build directory:
>>>
/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28):
>>> build failed (first 300 chars): cmd " make -j 16 " exited with exit
>>> code 2 and output:
>>> Making all in config
>>> make[1]: Entering directory
>>>
`/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28/openmpi-2.1.2/config'
>>>
>>> make[1]: Nothing to be done for `all'.
>>> make[1]: Leaving directory `/home/modules/build/OpenMPI/2.1.2/icc
>>> ...
>>>
>>> The end of the log file
>>> /tmp/eb-Dnjmix/easybuild-OpenMPI-2.1.2-20180305.144907.SAFtP.log
>>> contains:
>>>
>>> libtool: error: require no space between '-L' and '-lrt'
>>> make[2]: *** [libmca_pml_ucx.la <http://libmca_pml_ucx.la>] Error 1
>>> make[2]: Leaving directory
>>>
`/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28/openmpi-2.1.2/ompi/mca/pml/ucx'
>>>
>>> make[1]: *** [all-recursive] Error 1
>>>
>>> I can't make out what's causing this. Perhaps the build server
has a
>>> library installed triggering an error?
