Hi Reuti.
On 28.05.2017 19:56, Reuti wrote:
Hi,
Am 26.05.2017 um 17:16 schrieb Roberto Nunnari:
Hello.
I need to upgrade our cluster HPC and would like to hear from the experts the
caveats and thinks to keep in mind.
For instance, I heard that at a certain point openmpi (after 1.5.4)
Unless you are the only user on a node, it's usually advisable to turn off the automatic core
binding in Open MPI: "--bind-to-none" or "--bind-to none" (please check the man
page for your version). The latter one applies for 2.1.1.
The rationale is, that otherwise each Open MPI job doesn't know anything about
any other one, and they may bind to the same cores (both counting from core
zero on). Some cores would be oversubscribed, others are idling.
The Tight Integration of Open MPI into SGE was not automatically detected with
2.0.x and 2.1.0, but 2.1.1 is fine again. Workarounds exist to get the broken
ones functional again.
Good. I'll deinstall the CentOS distribution version and install 2.1.1
trying to build from source.
introduced some changes that cause incompatibilities with my present version of
OGE...
At present:
queuing system: Oracle Grid Engine 6.2u7
OS: CentOS 6.4
openmpi: 1.5.4
Parallel Envs: smp(only on one node) and orte(can span multiple nodes)
After upgrade:
queuing system: Son of Grid Engine 8.1.9
OS: CentOS 7.3
openmpi: 1.10.3
Why 1.10.3? Nowadays I would jump to 2.1.1. It's even straight forward to
compile it and put it in a place of your choice, like /usr/local or /opt/local
to avoid to mix up with any library from the distribution.
Because it's what comes with CentOS 7.3
Parallel Envs: smp(only on one node) and orte(can span multiple nodes)
I never worked with Son of Grid Engine before.. I'll need to build it all..
then import the configuration from OGE.. and make sure integration with openmpi
is working right..
There is a tool to save and load the configuration. But as you are new to SGE,
I think the best could be to save the text files, but implement all the
settings by hand. Then you know exactly what was changed where (i.e.: not to
simply load the configuration, but check the differences compared to the
default, and then make the necessary adjustments). But the differences between
OGE and SGE are not huge.
$SGE_ROOT/util/upgrade_modules/{load_sge_config.sh,save_sge_config.sh}
Yes.. I already used that tools in december.. but I could not import
back everything into GE2011.11p1 (tomorrow I'll try with SoGE 8.1.9)..
As a wild guess I think it was because I had it compiled without
berkeleydb while the OGE was with berkeleydb..
Anyways.. I built Soge 8.1.9 with
cd source
sh scripts/bootstrap.sh && ./aimk
and now? how will I install that? it scattered the files in several
places under source.. Is there a make install?
Thank you and best regards.
Roberto
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