Written by Shuah Khan, Linux Fellow at the Linux Foundation and member of the ELISA Project TSC
Key Points
- Understanding system resources necessary to build and run a workload is important.
- Linux tracing and strace can be used to discover the system resources in use by a workload.
- Tracing OpenAPS commands with strace generated detailed view of system activity during the common run and helped with generating flowcharts for normal and error paths when commands detected device busy conditions.
- Once we discover and understand the workload needs, we can focus on them to avoid regressions and evaluate safety.
OpenAPS is an open source Artificial Pancreas System designed to automatically adjust an insulin pump’s insulin delivery to keep Blood Glucose in a safe range at all times. It is an open and transparent effort to make safe and effective basic Automatic Pancreas System technology widely available to anyone with compatible medical devices who is willing to build their own system.
Broadly speaking, the OpenAPS system can be thought of performing 3 main functions. Monitoring the environment and operational status of devices with as much data relevant to therapy as possible collected, predicting what should happen to glucose levels next, and enacting changes through issuing commands, emails and even phone calls.
The ELISA Medical Devices Working Group has set out to discover the Linux kernel subsystems used by OpenAPS. Understanding the kernel footprint necessary to run a workload helps us focus on the subsystem and modules that make up the footprint for safety. We set out to answer the following questions:
- What happens when an OpenAPS workload runs on Linux and discovers the subsystems and modules that are in active use when OpenAPS is running?
- What are the interactions between OpenAPS and the kernel when a user checks how much insulin is left in the insulin pump?
Fine grained view of system activity
As mentioned earlier, the approach we gathered higher level of information about the OpenAPS usage. This higher information doesn’t tell us the system usage by individual OpenAPS commands. For example, watching the brain activity during the entire dinner vs. isolating the activity as we take the first bite of a delicious dessert and enjoy it.
Following up on our previous work, we gathered the fine grained information about individual OpenAPS commands and important use-cases. We used the strace command to trace the OpenAPS commands based on the process we identified to trace a generic workload which is now in the Linux kernel user’s and administrator’s guide. We traced several OpenAPS commands on an OpenAPS instance running on RasPi managing a Medtronic Insulin Pump. “mdt” in the following text refers to the command provided by https://github.com/ecc1/medtronic:
- Get Insulin Pump model (mdt model)
- Get Insulin Pump time (mdt clock)
- Get Insulin Pump battery (mdt battery)
- Get Insulin Pump basal rate schedule (mdt basal)
- Suspend Insulin Pump (mdt suspend)
- Resume Insulin Pump (mdt resume)
- Get the remaining insulin in the Insulin Pump reservoir (mdt reservoir)
- Get Insulin Pump temporary basal rate (mdt tempbasal)
- Get Insulin Pump history (pumphistory)
- Reference: https://github.com/ecc1/medtronic/tree/main/cmd/pumphistory
- Send button press to the Insulin Pump (mdt button)
- Command the Insulin Pump to deliver a given amount of insulin as bolus (mdt bolus)
- Reference: https://github.com/ecc1/medtronic/blob/main/button.go
- Set Insulin Pump temporary basal rate (mdt settempbasal)
- Reference: Advanced OpenAPS features: https://openaps.readthedocs.io/en/latest/docs/Customize-Iterate/oref1.html
We ran these commands in normal mode and under strace to get summary (strace -c ) and complete trace (strace) information. The following shows a few selected commands, their output, trace information, and our analysis of the trace.
Running the command to get the remaining insulin in the reservoir
mdt reservoir &> reservoir.out # Get the remaining insulin in the reservoir
strace -c mdt reservoir &> reservoir.summary # trace summary
strace mdt reservoir &> reservoir.full # full trace
Output from the get the remaining insulin in the reservoir command
Run the get the reservoir status command
connected to CC111x radio on /dev/spidev0.0
setting frequency to 916.600
waking pump
model 722 pump
108.5
disconnecting CC111x radio on /dev/spidev0.0
Process startup (process mgmt)
Open files (fs -> driver sysfs)
Open pump device “/dev/spidev0.0”
Open “/sys/class/gpio/gpio4/active_low”
Open “/sys/class/gpio/gpio4/direction”
Open “/sys/class/gpio/gpio4/value”
Open “/sys/class/gpio/gpio4/value”
Send SPI_IOC_MESSAGE(s) to talk to the pump (driver ioctl)
Close files (fs -> driver sysfs)
Exit program (process mgmt)
This output shows that the Pump wakeup path was invoked.
mdt reservoir command flowchart
Complete strace -c output
2022/10/12 11:50:59 connected to CC111x radio on /dev/spidev0.0
2022/10/12 11:50:59 setting frequency to 916.600
2022/10/12 11:51:00 model 722 pump
108.5
2022/10/12 11:51:00 disconnecting CC111x radio on /dev/spidev0.0
% time seconds usecs/call calls errors syscall
—— ———– ———– ——— ——— —————-
38.55 0.012979 270 48 ioctl
31.50 0.010605 87 121 1 futex
9.90 0.003333 27 120 rt_sigaction
3.86 0.001300 54 24 clock_gettime
3.04 0.001022 170 6 write
1.95 0.000658 658 1 readlinkat
1.73 0.000584 26 22 mmap2
1.66 0.000558 111 5 read
1.63 0.000548 49 11 openat
1.61 0.000543 181 3 clone
1.55 0.000521 47 11 fcntl
1.08 0.000362 40 9 rt_sigprocmask
0.77 0.000259 25 10 close
0.72 0.000243 24 10 mprotect
0.26 0.000088 22 4 brk
0.14 0.000046 23 2 sigaltstack
0.06 0.000020 20 1 gettid
0.00 0.000000 0 1 execve
0.00 0.000000 0 1 getpid
0.00 0.000000 0 1 access
0.00 0.000000 0 1 readlink
0.00 0.000000 0 2 munmap
0.00 0.000000 0 1 uname
0.00 0.000000 0 1 flock
0.00 0.000000 0 1 ugetrlimit
0.00 0.000000 0 5 fstat64
0.00 0.000000 0 1 sched_getaffinity
0.00 0.000000 0 8 epoll_ctl
0.00 0.000000 0 1 set_tid_address
0.00 0.000000 0 2 fstatat64
0.00 0.000000 0 1 set_robust_list
0.00 0.000000 0 1 epoll_create1
0.00 0.000000 0 1 set_tls
—— ———– ———– ——— ——— —————-
100.00 0.033669 437 1 total
Get temp basal rate
mdt tempbasal &> tempbasal.out # Get temp basal rate
strace -c mdt tempbasal &> tempbasal.summary # trace summary
strace mdt tempbasal &> tempbasal.full # full trace
Output from the get temp basal rate command
Run get basal temperature command
connected to CC111x radio on /dev/spidev0.0
setting frequency to 916.600
model 722 pump
{
“duration”: 28,
“temp”: “absolute”,
“rate”: 0.9
}
disconnecting CC111x radio on /dev/spidev0.0
Process startup (process mgmt)
Open files (fs -> driver sysfs)
Open pump device “/dev/spidev0.0”
Open “/sys/class/gpio/gpio4/active_low”
Open “/sys/class/gpio/gpio4/direction”
Open “/sys/class/gpio/gpio4/value”
Open “/sys/class/gpio/gpio4/value”
Sends SPI_IOC_MESSAGE(s) to talk to the pump (driver ioctl SPI_IOC_MESSAGE)
Close files (fs -> driver sysfs)
Exit program (process mgmt)
mdt tempbasal command flowchart
Complete strace -c output
2022/10/12 11:51:06 connected to CC111x radio on /dev/spidev0.0
2022/10/12 11:51:06 setting frequency to 916.600
2022/10/12 11:51:06 model 722 pump
{
“duration”: 28,
“temp”: “absolute”,
“rate”: 0.9
}
2022/10/12 11:51:06 disconnecting CC111x radio on /dev/spidev0.0
% time seconds usecs/call calls errors syscall
—— ———– ———– ——— ——— —————-
44.07 0.015195 316 48 ioctl
31.19 0.010755 93 115 1 futex
8.35 0.002879 23 120 rt_sigaction
2.43 0.000837 34 24 clock_gettime
2.10 0.000723 65 11 openat
2.10 0.000723 723 1 readlinkat
1.90 0.000655 109 6 write
1.46 0.000503 167 3 clone
1.05 0.000362 72 5 read
0.95 0.000326 32 10 close
0.92 0.000317 28 11 fcntl
0.80 0.000277 34 8 epoll_ctl
0.67 0.000232 10 22 mmap2
0.62 0.000215 23 9 rt_sigprocmask
0.52 0.000181 18 10 mprotect
0.41 0.000140 70 2 fstatat64
0.27 0.000094 23 4 brk
0.11 0.000039 39 1 flock
0.08 0.000029 29 1 epoll_create1
0.00 0.000000 0 1 execve
0.00 0.000000 0 1 getpid
0.00 0.000000 0 1 access
0.00 0.000000 0 1 readlink
0.00 0.000000 0 2 munmap
0.00 0.000000 0 1 uname
0.00 0.000000 0 2 sigaltstack
0.00 0.000000 0 1 ugetrlimit
0.00 0.000000 0 5 fstat64
0.00 0.000000 0 1 gettid
0.00 0.000000 0 1 sched_getaffinity
0.00 0.000000 0 1 set_tid_address
0.00 0.000000 0 1 set_robust_list
0.00 0.000000 0 1 set_tls
—— ———– ———– ——— ——— —————-
100.00 0.034482 431 1 total
Get insulin pump history
pumphistory -n 1 &> pumphistory.out # Get insulin pump history
strace -c pumphistory -n 1 &> pumphistory.summary # trace summary
strace pumphistory -n 1 &> pumphistory.full # full trace
Output from the get pumphistory command
Run pumphistory command
retrieving pump history since 2022-10-12 10:54:03
cannot connect to CC111x radio on /dev/spidev0.0
null
/dev/spidev0.0: device is in use
Process startup (process mgmt)
Open files (fs -> driver sysfs)
Open pump device “/dev/spidev0.0”
Open “/sys/class/gpio/gpio4/active_low”
Open “/sys/class/gpio/gpio4/direction”
Close files (fs -> driver sysfs)
Exit program (process mgmt)
This output shows that the pump busy path is invoked
Pump history command flowchart
Complete strace -c output
2022/10/12 11:54:03 retrieving pump history since 2022-10-12 10:54:03
2022/10/12 11:54:03 cannot connect to CC111x radio on /dev/spidev0.0
null
2022/10/12 11:54:03 /dev/spidev0.0: device is in use
% time seconds usecs/call calls errors syscall
—— ———– ———– ——— ——— —————-
40.92 0.003106 25 120 rt_sigaction
15.91 0.001208 109 11 futex
8.09 0.000614 204 3 clone
7.84 0.000595 59 10 mprotect
7.52 0.000571 190 3 fcntl
5.23 0.000397 44 9 rt_sigprocmask
5.20 0.000395 17 22 mmap2
4.23 0.000321 321 1 readlinkat
3.77 0.000286 13 21 clock_gettime
1.29 0.000098 24 4 brk
0.00 0.000000 0 5 read
0.00 0.000000 0 4 write
0.00 0.000000 0 7 close
0.00 0.000000 0 1 execve
0.00 0.000000 0 1 getpid
0.00 0.000000 0 1 access
0.00 0.000000 0 1 readlink
0.00 0.000000 0 2 munmap
0.00 0.000000 0 1 uname
0.00 0.000000 0 1 1 flock
0.00 0.000000 0 2 sigaltstack
0.00 0.000000 0 1 ugetrlimit
0.00 0.000000 0 5 fstat64
0.00 0.000000 0 1 gettid
0.00 0.000000 0 1 sched_getaffinity
0.00 0.000000 0 1 set_tid_address
0.00 0.000000 0 7 openat
0.00 0.000000 0 1 set_robust_list
0.00 0.000000 0 1 set_tls
—— ———– ———– ——— ——— —————-
100.00 0.007591 248 1 total
The following diagram shows the run-time context for these commands and their mapping to the Linux subsystems used by them.
System view
The following system view was updated after high level tracing analysis. This system view remains unchanged after the fine grained tracing analysis as expected.
References
https://github.com/ecc1/medtronic/blob/main/button.go
Conclusion
Using strace to trace OpenAPS commands helped us understand the detailed view of system files opened and closed while the commands run. We were able to generate flowcharts for normal and error paths when commands detected device busy conditions. As mentioned earlier, this tracing method gave us insight into the parts of the kernel used by the individual OpenAPS commands.
Credits
The ELISA Medical Working Group would like to sincerely acknowledge Chance Harrison for running the OpenAPS commands and providing information critical for making this effort a successful one.
SPDX-License-Identifier: CC-BY-4.0
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