[Beowulf] How to debug slow compute node?

John Hearns hearnsj at googlemail.com
Thu Aug 10 07:59:27 PDT 2017

   I think you might have to buy me a virtual coffee. Or a beer!
Please look at the hardware health of that machine. Specifically the
DIMMS.  I have seen this before!
If you have some DIMMS which are faulty and are generating ECC errors, then
if the mcelog service is enabled
an interrupt is generated for every ECC event. SO the system is spending
time servicing these interrupts.

So:   look in your /var/log/mcelog for hardware errors
Look in your /var/log/messages for hardware errors also
Look in the IPMI event logs for ECC errors:    ipmitool sel elist

I would also bring that node down and boot it with memtester.
If there is a DIMM which is that badly faulty then memtester will discover
it within minutes.

Or it could be something else - in which case I get no coffee.

Also Intel cluster checker is intended to exacly deal with these situations.
What is your cluster manager, and is Intel CLuster Checker available to you?
I would seriously look at getting this installed.

On 10 August 2017 at 16:39, Faraz Hussain <info at feacluster.com> wrote:

> One of our compute nodes runs ~30% slower than others. It has the exact
> same image so I am baffled why it is running slow . I have tested OMP and
> MPI benchmarks. Everything runs slower. The cpu usage goes to 2000%, so all
> looks normal there.
> I thought it may have to do with cpu scaling, i.e when the kernel changes
> the cpu speed depending on the workload. But we do not have that enabled on
> these machines.
> Here is a snippet from "cat /proc/cpuinfo". Everything is identical to our
> other nodes. Any suggestions on what else to check? I have tried rebooting
> it.
> processor       : 19
> vendor_id       : GenuineIntel
> cpu family      : 6
> model           : 62
> model name      : Intel(R) Xeon(R) CPU E5-2670 v2 @ 2.50GHz
> stepping        : 4
> cpu MHz         : 2500.098
> cache size      : 25600 KB
> physical id     : 1
> siblings        : 10
> core id         : 12
> cpu cores       : 10
> apicid          : 56
> initial apicid  : 56
> fpu             : yes
> fpu_exception   : yes
> cpuid level     : 13
> wp              : yes
> flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
> cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx
> pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology
> nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2
> ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt
> tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm ida arat xsaveopt pln
> pts dts tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms
> bogomips        : 5004.97
> clflush size    : 64
> cache_alignment : 64
> address sizes   : 46 bits physical, 48 bits virtual
> power management:
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