Re: [easybuild] installing lm-sensors
Hi,
I tried to install using the following eb file :
easyblock = 'ConfigureMake'
name = "lm-sensors"
version = "3.4.0"
homepage = "https://github.com/groeck/lm-sensors;
description = """The lm-sensors package, provides user-space support for
the
hardware monitoring drivers in Linux. """
buildopts = 'all'
toolchain = {'name': 'dummy', 'version': ''}
source_urls = ['https://github.com/groeck/lm-sensors.git']
sources = [SOURCE_TAR_GZ]
checksums =
['e79c58404f8d792c153207a957b1ed59ed5df109b25482a39526106a4a4acbd3']
dependencies = [('GCC', '4.9.2'), ('Bison', '3.0.4'), ('flex', '2.6.0')]
skipsteps = ['configure']
installopts = 'PREFIX=%(installdir)s'
moduleclass = "lang"
But i keep getting this error:
mkdir -p /etc /etc/sensors.d
mkdir: cannot create directory '/etc/sensors.d': Read-only file system
make: *** [install-etc] Error 1
(at
easybuild/centos/7.3.1611/Broadwell/software/EasyBuild/3.5.0/lib/python2.7/site-packages/easybuild_framework-3.5.0-py2.7.egg/easybuild/tools/run.py:481
in parse_cmd_output)
== 2018-05-02 01:21:36,082 easyblock.py:2685 WARNING build failed (first
300 chars): cmd " make install
PREFIX=/sNow/easybuild/centos/7.3.1611/Broadwell/software/lm-sensors/3.4.0"
exited with exit code 2 and output:
mkdir -p
/sNow/easybuild/centos/7.3.1611/Broadwell/software/lm-sensors/3.4.0/lib
/sNow/easybuild/centos/7.3.1611/Broadwell/software/lm-sensors/3.4.0/include/sensors
/sNo
== 2018-05-02 01:21:36,082 easyblock.py:279 INFO Closing log for
application name lm-sensors version 3.4.0
Is there anyway to set these permissions through easybuild or should I
change the permission separately?
Yours sincerely,
*Joseph John*
*Assistant Professor*
*Department of Computer Science & Engineering*
*Rajagiri School of Engineering & Technology*
*https://josephjohnjj.github.io/
Re: [easybuild] EB 3.6.0: Build of iomkl-2018.02.eb fails on Intel Omni-Path systems
Thanks Kenneth and Bart,
On 04/30/2018 03:24 PM, Kenneth Hoste wrote:
On 30/04/2018 15:12, Ole Holm Nielsen wrote:
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
You may need to -devel versions of these...
I confirm that the OpenMPI build problem is solved if I install these
CentOS 7 devel libraries prior to building:
yum install libxml2-devel libpciaccess-devel
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?
Yes, that's what Bart is suggesting.
I wonder why this hasn't popped up before though...
Do you mind opening an issue on this at
https://github.com/easybuilders/easybuild-easyconfigs/issues?
I've opened a new issue
https://github.com/easybuilders/easybuild-easyconfigs/issues/6257.
Maybe an extra "osdependencies" would be the preferred solution?
Thanks a lot,
Ole
On Mon, 30 Apr 2018 at 05:31, Ole Holm Nielsen
> 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
ld: cannot find -lpciaccess
ld: cannot find -lxml2
make[2]: *** [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
