Category Archives: Rack Servers

Dealing with Performance degradation on ZFS (DRAID) Rebuilds when migrating from a single processor to a multiprocessor platform

This is the history it happen to me some time ago, and so the commands I used to troubleshot. The purpose is to share knowledge in a interactive way. There are some hidden gems that you’ll acquire if you have the patience to go over all the document and read it all…

I had qualified Intel Xeon single processor platform to run my DRAID (ZFS Declustered RAID) project for my employer.

The platforms I qualified were:

1) single processor for Cold Storage (SAS Spinning drives): 4U60, newest models 4602

2) for multiprocessor: the 4U90 (90 Spinning drives) and Flash: All-Flash-Arrays.

The amounts of RAM I was using for my tests range for 64GB to 384GB.

Somebody in the company, at executive level, assembled an experimental config that was totally new for us and wanted to try by their own. It was the 4602 with multiprocessor and 32GB of RAM.

When they were unable to make it work at the expected speed, they required me to troubleshot and to make it work.

The 4602 single processor had two IOC (Input Output Controller, LSI Logic / Symbios Logic SAS3008 PCI-Express Fusion-MPT SAS-3 (rev 02) ), while the 4602 double processor had four IOC, so given that each of those IOC can perform at peaks of 6GB/s, with a maximum total of 24 GB/s, the performance when reading/writing from all the drives should be better.

But this Server was returning double times for Rebuilding, respect the single processor version, which didn’t make any sense.

I had to check everything. There was the commands I ran:

Check the upgrade of the CPU:

htop
lscpu

Changing the Zoning.

Those Servers use SAS drives dual ported, which means that two different computers can be connected to the same drive and operate at the same time. Is up to you to make sure you don’t introduce corruption. Those systems are used mainly for HA (High Availability).

Those Systems allow to be configured in different zoning modes. That’s the way on how each of the two servers (Controllers) see the disk. In one zoning each Controller sees only 30 drives, in another each IOC sees all the drives (for redundancy but performance constrained to 1 IOC Speed).

The config I set is each IOC will see 15 drives, so each one of the 4 IOC will have 6GB/s for 15 drives. Given that these spinning drives perform in the outtermost part of the cylinder at 265MB/s, that means that at maximum speed one IOC will be using 3.97 GB/s, will say 4GB/s. Plenty of bandwidth.

Note: Spinning drives have different performance depending on how close you’re to the cylinder. In the innermost part it goes under 145 MB/s, and if you read all of those drive sequentially with dd it will return an average speed of 145 MB/s.

With this command you can sive live how it performs and the average read speed in real time. Use skip to jump to that position (relative to bs) in the drive, so you can test directly the speed at the innermost close to the cylinder part of t.

dd if=/dev/sda of=/dev/null bs=1M status=progress

I saw that the zoning was not right one, so I set it correctly:

[root@4602Carles ~]# sg_map -i | grep NEWISYS
/dev/sg30  NEWISYS   NDS-4602-CS       0112
/dev/sg61  NEWISYS   NDS-4602-CS       0112
/dev/sg63  NEWISYS   NDS-4602-CS       0112
/dev/sg64  NEWISYS   NDS-4602-CS       0112
[root@4602Carles10 ~]# sg_senddiag /dev/sg30  --pf --raw=04,00,00,01,53
[root@4602Carles10 ~]# sleep 50
[root@4602Carles10 ~]# sg_senddiag /dev/sg30 --pf -r 04,00,00,01,43
[root@4602Carles10 ~]# sleep 50
[root@4602Carles10 ~]# reboot

The sleeps after rebooting the expanders are recommended. Rebooting the Operating System too, to avoid problems with some Software as the expanders changed live.

If you have ZFS pools or workloads stop them and export the pool before messing with the expanders.

In order to check to which drives is connected each IOC:

[root@4602Carles10 ~]# sg_map -i -x
/dev/sg0  0 0 0 0  0  /dev/sda  TOSHIBA   MG07SCA14TA       0101
/dev/sg1  0 0 1 0  0  /dev/sdb  TOSHIBA   MG07SCA14TA       0101
/dev/sg2  0 0 2 0  0  /dev/sdc  TOSHIBA   MG07SCA14TA       0101
/dev/sg3  0 0 3 0  0  /dev/sdd  TOSHIBA   MG07SCA14TA       0101
/dev/sg4  0 0 4 0  0  /dev/sde  TOSHIBA   MG07SCA14TA       0101
/dev/sg5  0 0 5 0  0  /dev/sdf  TOSHIBA   MG07SCA14TA       0101
/dev/sg6  0 0 6 0  0  /dev/sdg  TOSHIBA   MG07SCA14TA       0101
/dev/sg7  0 0 7 0  0  /dev/sdh  TOSHIBA   MG07SCA14TA       0101
/dev/sg8  1 0 8 0  0  /dev/sdi  TOSHIBA   MG07SCA14TA       0101
/dev/sg9  1 0 9 0  0  /dev/sdj  TOSHIBA   MG07SCA14TA       0101
/dev/sg10  1 0 10 0  0  /dev/sdk  TOSHIBA   MG07SCA14TA       0101
/dev/sg11  1 0 11 0  0  /dev/sdl  TOSHIBA   MG07SCA14TA       0101
[...]
/dev/sg16  4 0 16 0  0  /dev/sdq  TOSHIBA   MG07SCA14TA       0101
/dev/sg17  4 0 17 0  0  /dev/sdr  TOSHIBA   MG07SCA14TA       0101
[...]
/dev/sg30  0 0 30 0  13  NEWISYS   NDS-4602-CS       0112
[...]

Still after setting the right zone the Rebuilds were slow, the scan rate half of the obtained with a single processor.

I tested that the system was able to provide the expected performance by reading from all the drives at the same time. This is done with:

dd if=/dev/sda of=/dev/null bs=1M status=progress &
dd if=/dev/sdb of=/dev/null bs=1M status=progress &
dd if=/dev/sdc of=/dev/null bs=1M status=progress &
dd if=/dev/sdd of=/dev/null bs=1M status=progress &
[...]

I do this for all the drives at the same time and with iostat:

iostat -y 1 1

I check the status of the memory with:

slabtop
free
htop

I checked the memory and htop during a Rebuild. Memory was more than enough. However CPU usage was higher than expected.

The red bars in the image correspond to kernel processes, in this case is the DRAID Rebuild. I see that the load is higher than the usual with a single processor.

I capture all the parameters from ZFS with:

zfs get all

All this information is logged into my forensics document, so later can be checked by my Team or I can share with other Architects or other members of the company. I started this methodology after I knew how Google do their SRE forensics / postmortem documents. Also for myself is useful for the future to have a log of the commands I executed and a verbose output of the results.

I install the smp_utils

yum install smp_utils

Check things:

ls -al  /dev/bsg/
total 0drwxr-xr-x.  2 root root     3020 May 22 10:16 .
drwxr-xr-x. 20 root root     8680 May 22 10:16 ..
crw-------.  1 root root 248,  76 May 22 10:00 1:0:0:0
crw-------.  1 root root 248, 126 May 22 10:00 10:0:0:0
crw-------.  1 root root 248, 127 May 22 10:00 10:0:1:0
crw-------.  1 root root 248, 136 May 22 10:00 10:0:10:0
crw-------.  1 root root 248, 137 May 22 10:00 10:0:11:0
crw-------.  1 root root 248, 138 May 22 10:00 10:0:12:0
crw-------.  1 root root 248, 139 May 22 10:00 10:0:13:0
[...]
[root@4602Carles10 ~]# smp_discover /dev/bsg/expander-1:0
[...]
[root@4602Carles10 ~]# smp_discover /dev/bsg/expander-1:1

I check for errors in the expander that could justify the problems of performance:

for i in `seq 0 64`; do smp_rep_phy_err_log -p $i /dev/bsg/expander-1\:0 ; done
Report phy error log response:
  Expander change count: 567
  phy identifier: 0
  invalid dword count: 0
  running disparity error count: 0
  loss of dword synchronization count: 0
  phy reset problem count: 0
[...]
Report phy error log response:
  Expander change count: 567
  phy identifier: 52
  invalid dword count: 168
  running disparity error count: 172
  loss of dword synchronization count: 5
  phy reset problem count: 0
Report phy error log response:
  Expander change count: 567
  phy identifier: 53
  invalid dword count: 6
  running disparity error count: 6
  loss of dword synchronization count: 0
  phy reset problem count: 0
Report phy error log response:
  Expander change count: 567
  phy identifier: 54
  invalid dword count: 267
  running disparity error count: 270
  loss of dword synchronization count: 4
  phy reset problem count: 0
Report phy error log response:
  Expander change count: 567
  phy identifier: 55
  invalid dword count: 127
  running disparity error count: 131
  loss of dword synchronization count: 5
  phy reset problem count: 0
Report phy error log result: Phy vacant
Report phy error log result: Phy vacant
Report phy error log result: Phy vacant
Report phy error log result: Phy vacant
Report phy error log result: Phy vacant
Report phy error log result: Phy vacant
Report phy error log result: Phy vacant
Report phy error log result: Phy vacant
Report phy error log result: Phy vacant

There are some errors, and I check with the Hardware Team, which pass a battery of tests on the machine and say that the machine passes. They tell me that if the errors counted were in order of millions then it would be a problem, but having few of them is usual.

My colleagues previously reported that the memory was performing well, and the CPU too. They told me that the speed was exactly double respect a platform with one single CPU of the same kind.

Even if they told me that, I ran cmips tests to make sure.

git clone https://github.com/cmips/cmips_bin

It scored 16,000. The performance was Ok in general terms but the problem is that I didn’t have a baseline for that processor in single processor, so I cannot make sure that the memory bandwidth was Ok. The performance was less that an Amazon c3.8xlarge. The system I was testing is a two processor system, but each CPU is cheap, around USD $400.

Still my gut feeling was telling me that this double processor server should score more.

lscpu
[root@DRAID-1135-14TB-2CPU ~]# lscpu
 Architecture:          x86_64
 CPU op-mode(s):        32-bit, 64-bit
 Byte Order:            Little Endian
 CPU(s):                32
 On-line CPU(s) list:   0-31
 Thread(s) per core:    2
 Core(s) per socket:    8
 Socket(s):             2
 NUMA node(s):          2
 Vendor ID:             GenuineIntel
 CPU family:            6
 Model:                 79
 Model name:            Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz
 Stepping:              1
 CPU MHz:               2299.951
 CPU max MHz:           3000.0000
 CPU min MHz:           1200.0000
 BogoMIPS:              4199.73
 Virtualization:        VT-x
 L1d cache:             32K
 L1i cache:             32K
 L2 cache:              256K
 L3 cache:              20480K
 NUMA node0 CPU(s):     0-7,16-23
 NUMA node1 CPU(s):     8-15,24-31
 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 nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb cat_l3 cdp_l3 intel_ppin intel_pt ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts spec_ctrl intel_stibp

I check the memory configuration with:

dmidecode -t memory

I examined the results, I see that the processor can only operate the DDR4 ECC 2400 Memory at 2133 and… I see something!. This Controller before was a single processor with 2 Memory Sticks of 16GB each, dual rank.

I see that now I have the same number of sticks in that machine, but I have two CPU!. So 2 Memory sticks in total, for 2 CPU.

That’s no good. The memory must be in pairs and in the right slots to get the maximum performance.

1 memory module for 1 CPU doesn’t allow to have Dual Channel and probably is affecting the performance. Many Servers will not even boot if you add an odd number of memory sticks per CPU.

And many Servers can operate at full speed only if all the banks are filled.

I request to the Engineers in Silicon Valley to add 4 modules in the right slots. They did, and I repeated the tests and the performance was doubled then.

After some days I had some time with the machine, I repeated the test and I got a CMIPS Score of around 20,000.

Multiprocessor world is far more complicated than single processor. Some times things can work not as expected, and not be evident, for example cache pipeline can act diferent for a program working in multiprocessor and single processor. Or the QPI could be saturated.

After this I shared my forensics document with as many Engineers as I could, so they could learn how I did to troubleshot the problem, and what was the origin of it, and I asked them to do the same so we can track their steps and progress if something needs to be troubleshoot.

After proper intensive testing the Server was qualified. Lesson here is that changes cannot be commited quickly, need their time.

Solving an infinite loop in CentOS after inducing a Kernel Panic in a Server

This trick may be useful for you.
Almost surely if you power cycle, completely powering down your Server you’ll fix booting too.
Unfortunately we do not always have access to the Data Center or Remote Hands service available, so this trick may be useful for you.

Just reset your BMC card with this:
ipmitool -H 172.30.30.7 -U admin -P thepassword bmc reset cold

After this use the remote control tool to request a reboot and it will do and power on normally.

This may not work in all the Servers, it depends on a lot of aspects (firmware, bmc manufacturer, etc…) but can do the trick for you maybe.

NAS and Gigabit

Note 2019-05-28: This article was written in 2013. It is still valid, but since then 10Gbps have dropped in price a lot. In my DRAID Solution I’ve qualified 10GbE based in copper, RJ45, and for fiber: 10, 25, 40 and 100 Gbps. Mellanox switches and NICs are a reference. 10GbE based in copper are cheap and easy to deploy, as you can reuse existing infrastructure and grow your segments. https://en.wikipedia.org/wiki/10_Gigabit_Ethernet

I’ve found this problem in several companies, and I’ve had to show their error and convince experienced SysAdmins, CTOs and CEO about the erroneous approach. Many of them made heavy investments in NAS, that they are really wasting, and offering very poor performance.

Normally the rack servers have their local disks, but for professional solutions, like virtual machines, blade servers, and hundreds of servers the local disk are not used.

NAS – Network Attached Storage- Servers are used instead.

This NAS Servers, when are powerful (and expensive) offer very interesting features like hot backups, hot backups that do not slow the system (the most advanced), hot disk replacement, hot increase of total available space, the Enterprise solutions can replicate and copy data from different NAS in different countries, etc…

Smaller NAS are also used in configurations like Webservers’ Webfarms, were all the nodes has to have the same information replicated, and when a used uploads a new profile image, has to be available to all the webservers for example.

In this configurations servers save and retrieve the needed data from the NAS Servers, through LAN (Local Area Network).

The main error I have seen is that no one ever considers the pipe where all the data is travelling, so most configurations are simply Gigabit, and so are bottleneck.

dell-blade-servers-enclosureImagine a Dell blade server, like this in the image on the left.

This enclosure hosts 16 servers, hot plugable, with up to two CPU’s each blade, we also call those blade servers “pizza” (like we call before to rack servers).

A common use is to use those servers to have Vmware, OpenStack, Xen or other virtualization software, so the servers run instances of customers. In this scenario the virtual disks (the hard disk of the virtual machines) are stored in the NAS Server.

So if a customer shutdown his virtual server, and start it later, the physical server where its virtual machine is running will be another, but the data (the disk of the virtual server) is stored in the NAS and all the data is saved and retrieved from the NAS.

The enclosure is connected to the NAS through a Gigabit connection, as 10 Gigabit connections are still too expensive and not yet supported in many servers.

Once we have explained that, imagine, those 16 servers, each with 4 or 5 virtual machines, accessing to their disks through a Gigabit connection.

If only one of these 80 virtual machines is accessing to disk, the will be no problem, but if more than one is accessing the Gigabit connection, that’s a maximum of 125 MB (Megabytes) per second, will be shared among all the virtual machines.

So imagine, 70 virtual machines are accessing NAS to serve web pages, with not much traffic, OK, but the other 10 virtual machines are doing heavy data transmission: for example one is serving data through FTP server, the other is broadcasting video, the other is copying heavy log files, and so… Imagine that scenario.

The 125 MB per second is divided between the 80 servers, so those 10 servers using extensively the disk will monopolize the bandwidth, but even those 10 servers will have around 12,5 MB each, that is 100 Mbit each and is very slow.

Imagine one of the virtual machines broadcast video. To broadcast video, first it has to get it from the NAS (the chunks of data), so this node serving video will be able to serve different videos to few customers, as the network will not provide more than 12,5 MB under the circumstances provided.

This is a simplified scenario, as many other things has to be taken in count, like the SATA, SCSI and SAS disks do not provide sustained speeds, speed depends on locating the info, fragmentation, etc… also has to be considered that NAS use protocol iSCSI, a sort of SCSI commands sent through the Ethernet. And Tcp/Ip uses verifications in their protocol, and protocol headers. That is also an overhead. I’ve considered only traffic in one direction, so the servers downloading from the NAS, as assuming Gigabit full duplex, so Gigabit for sending and Gigabit for receiving.

So instead of 125 MB per second we have available around 100 MB per second with a Gigabit or even less.

Also the virtualization servers try to handle a bit better the disk access, by keeping a cache in memory, and not writing immediately to disk.

So you can’t do dd tests in virtual machines like you would do in any Linux with local disks, and if you do go for big files, like 10 GB with random data (not just 0, they have optimizations for that).

Let’s recalculate it now:

70 virtual machines using as low as 0.10 MB/second each, that’s 7 MB/second. That’s really optimist as most webservers running PHP read many big files for attending a simple request and webservers server a lot of big images.

10 virtual machines using extensively the NAS, so sharing 100 MB – 7 MB = 93 MB. That is 9.3 MB each.

So under these circumstances for a virtual machine trying to read from disk a file of 1 GB (1000 MB), this operation will take 107 seconds, so 1:47 minutes.

So with this considerations in mind, you can imagine that the performance of the virtual machines under those configurations are leaved to the luck. The luck that nobody else of the other guests in the servers are abusing the disk I/O.

I’ve explained you in a theoretical plan. Sadly reality is worst. A lot worst. Those 70 web virtual machines with webservers will be so slow that they will leave your company very disappointed, and the other 10 will not even be happier.

One of the principal problems of Amazon EC2 has been always disk performance. Few months ago they released IOPS, high performance disks, that are more expensive, but faster.

It has to be recognized that in Amazon they are always improving.

They have also connection between your servers at 10 Gbit/second.

Returning to the Blades and NAS, an easy improvement is to aggregate two Gigabits, so creating a connection of 2 Gbit. This helps a bit. Is not the solution, but helps.

Probably different physical servers with few virtual machines and a dedicated 1 Gbit connection (or 2 Gbit by 1+1 aggregated if possible) to the NAS, and using local disks as much as possible would be much better (harder to maintain at big scale, but much much better performance).

But if you provide infrastructure as a Service (IaS) go with 2 x 10 Gbit Fibre aggregated, so 20 Gigabit, or better aggregate 2 x 20 Gbit Fibre. It’s expensive, but crucial.

Now compare the 9.3 MB per second, or even the 125 MB theoretical of Gigabit of the average real sequential read of 50 MB/second that a SATA disk can offer when connected on local, or nearly the double for modern SAS 15.000 rpm disks… (writing is always slower)

… and the 550 MB/s for reading and 550 MB/s for writing that some SSD disks offer when connected locally. (I own two OSZ SSD disks that performs 550 MB).

I’ve seen also better configuration for local disks, like a good disk controller with Raid 5 and disks SSD. With my dd tests I got more than 900 MB per second for writing!.

So if you are going to spend 30.000 € in your NAS with SATA disks (really bad solution as SATA is domestic technology not aimed to work 24×7 and not even fast) or SAS disks, and 30.000 € more in your blade servers, think very well what you need and what configuration you will use. Contact experts, but real experts, not supposedly real experts.

Otherwise you’ll waste your money and your customers will have very very poor performance on these times where applications on the Internet demand more and more performance.