[Beowulf] How to debug slow compute node?
andrew.holway at gmail.com
Thu Aug 10 11:04:15 PDT 2017
I put €10 on the nose for a faulty power supply.
On 10 August 2017 at 19:45, Gus Correa <gus at ldeo.columbia.edu> wrote:
> + 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.
> Gus Correa
> 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
>> 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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