On 10/29/2015 03:01 PM, Ralph Castain wrote:
You need to also install libnuma-devel, I’m afraid - just has to do with how
they chose to split the library
sudo apt-get install libnuma-devel
...
E: Unable to locate package libnuma-devel
sudo apt-get install libnuma-dev
...
libnuma-dev is already the newest version.
Somhow my system seems to be mixed up.
What exactly is needed? I have a lot numa.h on the system:
/usr/include/numa.h
/usr/local/include/hwloc/linux-libnuma.h
/usr/local/include/likwid/numa.h
/usr/src/linux-headers-3.19.0-31/arch/ia64/include/asm/numa.h
/usr/src/linux-headers-3.19.0-31/arch/x86/include/asm/numa.h
/usr/src/linux-headers-3.19.0-31/include/acpi/acpi_numa.h
/usr/src/linux-headers-3.19.0-31/include/linux/numa.h
/usr/src/linux-headers-3.19.0-31-generic/include/config/numa.h
/usr/src/linux-headers-3.19.0-31-generic/include/config/acpi/numa.h
/usr/src/linux-headers-3.19.0-31-generic/include/config/amd/numa.h
/usr/src/linux-headers-3.19.0-31-generic/include/config/x86/64/acpi/numa.h
/home/fwein/tmp/numactl-2.0.9/numa.h
/home/fwein/tmp/openmpi-1.10.0/opal/mca/hwloc/hwloc191/hwloc/include/hwloc/linux-libnuma.h
At least /usr/include/numa.h is identical to
/home/fwein/tmp/numactl-2.0.9/numa.h
Is there any hint in the configure output?
Thanks!
Fabian
On Oct 29, 2015, at 2:01 AM, Fabian Wein <fabian.w...@fau.de> wrote:
Hello,
I'm new to the list, maybe the issue was somewhere else already solved. I found
a similar question in the mailing list archive but no solution.
By comparing to a similar system I found that for my 4 sockets Opteron system
it is necessary to run mpi with -bind-to numa option.
On my ubunut 14.04 system I get
----------------------
A request was made to bind a process, but at least one node does NOT
support binding processes to cpus.
Node: leo
This usually is due to not having libnumactl and libnumactl-devel
installed on the node.
-----------------------
locate libnuma | grep so
results in
/usr/lib/x86_64-linux-gnu/libnuma.so
/usr/lib/x86_64-linux-gnu/libnuma.so.1
/usr/lib64/libnuma.so
/usr/lib64/libnuma.so.1
When I configure hwloc 1.11.1 it detects numa (it tells me at the end of
configure)
and "grep numa config.status" results in
S["HWLOC_LIBS"]="-lm -lnuma -lxml2 "
S["HWLOC_LINUX_LIBNUMA_LIBS"]="-lnuma"
When I configure openmpi-1.10.0 it also finds libnuma
grep numa config.status
S["OMPI_WRAPPER_EXTRA_LIBS"]="-lm -lnuma -ldl -lutil "
S["ORTE_WRAPPER_EXTRA_LIBS"]="-lm -lnuma -ldl -lutil "
S["OPAL_WRAPPER_EXTRA_LIBS"]="-lm -lnuma -ldl -lutil "
S["HWLOC_EMBEDDED_LIBS"]="-lm -lnuma"
S["HWLOC_LINUX_LIBNUMA_LIBS"]="-lnuma"
D["WRAPPER_EXTRA_LIBS"]=" \"-lm -lnuma -ldl -lutil \""
However I have no idea how I could install libnumactl and libnumactl-devel. I
cannot google it.
I built numactl-2.0.9 manually but
~/tmp/numactl-2.0.9$ ll lib*
only gives libnuma.a and libnuma.so
Even the source for open-mpi gives no hint
/tmp/openmpi-1.10.0$ grep -r numactl
opal/mca/hwloc/hwloc191/hwloc/README: * libnuma for memory binding and
migration support on Linux (numactl-devel or
orte/mca/rmaps/base/help-orte-rmaps-base.txt:This usually is due to not having
libnumactl and libnumactl-devel
orte/mca/rmaps/base/help-orte-rmaps-base.txt:contained in the libnumactl and
libnumactl-devel packages.
orte/mca/rmaps/base/help-orte-rmaps-base.txt:contained in the libnumactl and
libnumactl-devel packages.
Please help, I have no idea what to try next. The only options I currently see
are to try with mpich or by intel-mpi.
Thanks,
Fabian
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--
Dr. Fabian Wein, University of Erlangen-Nuremberg
Department of Mathematics/ Excellence Cluster for Engineering of
Advanced Materials
phone: +49 9131 85 20849
