[Beowulf] How to debug slow compute node?
gus at ldeo.columbia.edu
Thu Aug 10 10:45:11 PDT 2017
+ Leftover processes from previous jobs hogging resources.
That's relatively common.
That can trigger swapping, the ultimate performance killer.
"top" or "htop" on the node should show something.
(Will go away with a reboot, of course.)
Less likely, but possible:
+ Different BIOS configuration w.r.t. the other nodes.
+ Poorly sat memory, IB card, etc, or cable connections.
+ IPMI may need a hard reset.
Power down, remove the power cable, wait several minutes,
put the cable back, power on.
On 08/10/2017 11:17 AM, John Hearns via Beowulf wrote:
> Another thing to perhaps look at. Are you seeing messages abotu thermal
> throttling events in the system logs?
> Could that node have a piece of debris caught in its air intake?
> I dont think that will produce a 30% drop in perfoemance. But I have
> caught compute nodes with pieces of packaking sucked onto the front,
> following careless peeople unpacking kit in machine rooms.
> (Firm rule - no packaging in the machine room. This means you)
> On 10 August 2017 at 17:00, John Hearns <hearnsj at googlemail.com
> <mailto:hearnsj at googlemail.com>> wrote:
> ps. Look at watch cat /proc/interrupts also
> You might get a qualitative idea of a huge rate of interrupts.
> On 10 August 2017 at 16:59, John Hearns <hearnsj at googlemail.com
> <mailto:hearnsj at googlemail.com>> wrote:
> 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
> 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
> <mailto: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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