luajit qsort callback example memory leak - callback

I have the following qsort example to try out callbacks in luajit. However it has a memory leak (luajit: not enough memory when executing) which is not obvious to me.
Can somebody give me some hints on how to create a proper callback example?
local ffi = require("ffi")
-- ===============================================================================
ffi.cdef[[
void qsort(void *base, size_t nel, size_t width, int (*compar)(const void *, const void *));
]]
function compare(a, b)
return a[0] - b[0]
end
-- ===============================================================================
-- Explicitly convert to a callback via cast
local callback = ffi.cast("int (*)(const char *, const char *)", compare)
local data = "efghabcd"
local size = 8
local loopSize = 1000 * 1000 * 100.
local bytes = ffi.new("char[15]")
-- ===============================================================================
for i=1,loopSize do
ffi.copy(bytes, data, size)
ffi.C.qsort(bytes, size, 1, callback)
end
Platform: OSX 10.8
luajit: 2.0.1

The problem appears to be that lua never gets a chance to perform a full garbage collection cycle inside the tight loop. As hinted by the comment, you can correct this by calling collectgarbage() yourself inside the loop.
Note that calling collectgarbage() on every iteration will impact the running time of whatever you're benching. To minimize this, you should set a threshold to limit how often collectgarbage() gets called:
local memthreshold = 2 ^ 20 / 1024
local start = os.clock()
for i = 1, loopSize do
ffi.copy(bytes, data, size)
ffi.C.qsort(bytes, size, 1, callback)
if collectgarbage'count' > memthreshold then
collectgarbage()
end
end
local elapse = os.clock() - start
print("elapsed:", elapse..'s')

Related

getting illegal instructions when vectorized code writes to PCI

I am writing a program that writes to a device's range of HW registers. I am using mmap to map the HW addresses to virtual address (user space). I tested the result from the mmap and it is OK. I implemented a copy of a buffer into the device:
void bufferCopy(void *dest, void *src, const size_t size) {
uint8_t *pdest = static_cast<uint8_t *>(dest);
uint8_t *psrc = static_cast<uint8_t *>(src);
size_t iters = 0, tailBytes = 0;
/* iterate 64bit */
iters = (size / sizeof(uint64_t));
for (size_t index = 0; index < iters; ++index) {
*(reinterpret_cast<uint64_t *>(pdest)) =
*(reinterpret_cast<uint64_t *>(psrc));
pdest += sizeof(uint64_t);
psrc += sizeof(uint64_t);
}
.
.
.
but when running it on QEMU I get illegal instruction exception. When I debugged got it crashes on the next instruction (below is the asm of the main loop):
movdqu (%rsi,%rax,1),%xmm0
movups %xmm0,(%rdi,%rax,1) <----- this instruction crashes ...
add $0x10,%rax
cmp %rax,%r9
jne 0x7ffff7eca1e0 <_ZN12_GLOBAL__N_110bufferCopyEPvS0_m+64>
any ideas why ? my guess that you can write to PCI only 32/64 bit.
The compile doesn’t know my limitations, so it optimize my code and create vectorized loop (each iteration loads 128 bit and saves 128 bit). Is is making sense ?? can I write to PCI with vectorized instructions ?
Also, whether it is a missing feature in QEMU or a bug or just a recommendation, how can I prevent from the compiler to generate those vector instructions ?

How to change quantum in xv6? [duplicate]

Right now it seems that on every click tick, the running process is preempted and forced to yield the processor, I have thoroughly investigated the code-base and the only relevant part of the code to process preemption is below (in trap.c):
// Force process to give up CPU on clock tick.
// If interrupts were on while locks held, would need to check nlock.
if(myproc() && myproc() -> state == RUNNING && tf -> trapno == T_IRQ0 + IRQ_TIMER)
yield();
I guess that timing is specified in T_IRQ0 + IRQ_TIMER, but I can't figure out how these two can be modified, these two are specified in trap.h:
#define T_IRQ0 32 // IRQ 0 corresponds to int T_IRQ
#define IRQ_TIMER 0
I wonder how I can change the default RR scheduling time-slice (which is right now 1 clock tick, fir example make it 10 clock-tick)?
If you want a process to be executed more time than the others, you can allow it more timeslices, *without` changing the timeslice duration.
To do so, you can add some extra_slice and current_slice in struct proc and modify the TIMER trap handler this way:
if(myproc() && myproc()->state == RUNNING &&
tf->trapno == T_IRQ0+IRQ_TIMER)
{
int current = myproc()->current_slice;
if ( current )
myproc()->current_slice = current - 1;
else
yield();
}
Then you just have to create a syscall to set extra_slice and modify the scheduler function to reset current_slice to extra_slice at process wakeup:
// Switch to chosen process. It is the process's job
// to release ptable.lock and then reacquire it
// before jumping back to us.
c->proc = p;
switchuvm(p);
p->state = RUNNING;
p->current_slice = p->extra_slice
You can read lapic.c file:
lapicinit(void)
{
....
// The timer repeatedly counts down at bus frequency
// from lapic[TICR] and then issues an interrupt.
// If xv6 cared more about precise timekeeping,
// TICR would be calibrated using an external time source.
lapicw(TDCR, X1);
lapicw(TIMER, PERIODIC | (T_IRQ0 + IRQ_TIMER));
lapicw(TICR, 10000000);
So, if you want the timer interrupt to be more spaced, change the TICR value:
lapicw(TICR, 10000000); //10 000 000
can become
lapicw(TICR, 100000000); //100 000 000
Warning, TICR references a 32bits unsigned counter, do not go over 4 294 967 295 (0xFFFFFFFF)

How to modify process preemption policies (like RR time-slices) in XV6?

Right now it seems that on every click tick, the running process is preempted and forced to yield the processor, I have thoroughly investigated the code-base and the only relevant part of the code to process preemption is below (in trap.c):
// Force process to give up CPU on clock tick.
// If interrupts were on while locks held, would need to check nlock.
if(myproc() && myproc() -> state == RUNNING && tf -> trapno == T_IRQ0 + IRQ_TIMER)
yield();
I guess that timing is specified in T_IRQ0 + IRQ_TIMER, but I can't figure out how these two can be modified, these two are specified in trap.h:
#define T_IRQ0 32 // IRQ 0 corresponds to int T_IRQ
#define IRQ_TIMER 0
I wonder how I can change the default RR scheduling time-slice (which is right now 1 clock tick, fir example make it 10 clock-tick)?
If you want a process to be executed more time than the others, you can allow it more timeslices, *without` changing the timeslice duration.
To do so, you can add some extra_slice and current_slice in struct proc and modify the TIMER trap handler this way:
if(myproc() && myproc()->state == RUNNING &&
tf->trapno == T_IRQ0+IRQ_TIMER)
{
int current = myproc()->current_slice;
if ( current )
myproc()->current_slice = current - 1;
else
yield();
}
Then you just have to create a syscall to set extra_slice and modify the scheduler function to reset current_slice to extra_slice at process wakeup:
// Switch to chosen process. It is the process's job
// to release ptable.lock and then reacquire it
// before jumping back to us.
c->proc = p;
switchuvm(p);
p->state = RUNNING;
p->current_slice = p->extra_slice
You can read lapic.c file:
lapicinit(void)
{
....
// The timer repeatedly counts down at bus frequency
// from lapic[TICR] and then issues an interrupt.
// If xv6 cared more about precise timekeeping,
// TICR would be calibrated using an external time source.
lapicw(TDCR, X1);
lapicw(TIMER, PERIODIC | (T_IRQ0 + IRQ_TIMER));
lapicw(TICR, 10000000);
So, if you want the timer interrupt to be more spaced, change the TICR value:
lapicw(TICR, 10000000); //10 000 000
can become
lapicw(TICR, 100000000); //100 000 000
Warning, TICR references a 32bits unsigned counter, do not go over 4 294 967 295 (0xFFFFFFFF)

Is it possible to disable JVM JIT loop optimisation

I have pretty trivial scala code:
def main(): Int = {
var i: Int = 0
var limit = 0
while (limit < 1000000000) {
i = inc(i)
limit = limit + 1
}
i
}
def inc(i: Int): Int = i + 1
I am playing with JVM JIT method inlining on inc method. When inlining is enabled I get surprisingly good examples 2s vs 4ns - what I would like to make sure or at least validate is that no loop optimisation took palace in the mean time. I took look at machine code which seems ok
0x000000010b22a4d6: mov 0x8(%rbp),%r10d ; implicit exception: dispatches to 0x000000010b22a529
0x000000010b22a4da: cmp $0xf8033d43,%r10d ; {metadata('IncWhile$')}
0x000000010b22a4e1: jne L0001 ;*iload_3
; - IncWhile$::main#4 (line 7)
0x000000010b22a4e3: cmp $0x3b9aca00,%ebx
0x000000010b22a4e9: jge L0000 ;*if_icmpge
; - IncWhile$::main#7 (line 7)
0x000000010b22a4eb: sub %ebx,%r14d
0x000000010b22a4ee: add $0x3b9aca00,%r14d ;*iadd
; - IncWhile$::inc#2 (line 16)
; - IncWhile$::main#12 (line 9)
0x000000010b22a4f5: mov $0x3b9aca00,%ebx ;*if_icmpge
; - IncWhile$::main#7 (line 7)
L0000: mov $0xffffff65,%esi
I also checked flight recorder and didn't find anything suspicious but as I am not regular user I would like to double check with someone more experienced.
Code can be found on github
Of course, the loop has been optimized. No regular CPU can execute
1 billion operations in just a few nanoseconds.
There are many loop optimizations in HotSpot - do you want to disable all of them? E.g.
-XX:LoopUnrollLimit=0
-XX:+UseCountedLoopSafepoints
-XX:-UseLoopPredicate
-XX:-PartialPeelLoop
-XX:-LoopUnswitching
-XX:-LoopLimitCheck
etc. To disable most of loop optimizations, use
-XX:LoopOptsCount=0

Meaning of the benchmark variables in snakemake

I included a benchmark directive to some of the rules in my snakemake workflow, and the resulting files have the following header:
s h:m:s max_rss max_vms max_uss max_pss io_in io_out mean_load
The only documentation I've found mentions a "benchmark txt file (which will contain a tab-separated table of run times and memory usage in MiB)".
I can guess that columns 1 and 2 are two different ways of displaying the time taken to execute the rule (in seconds, and converted to hours, minutes and seconds).
io_in and io_out likely related to disk read and write activity, but in what units are they measured?
What are the others? Is this documented somewhere?
Edit: Looking at the source code
I've found the following piece of code in /snakemake/benchmark.py, that might well be where the benchmark data come from:
def _update_record(self):
"""Perform the actual measurement"""
# Memory measurements
rss, vms, uss, pss = 0, 0, 0, 0
# I/O measurements
io_in, io_out = 0, 0
# CPU seconds
cpu_seconds = 0
# Iterate over process and all children
try:
main = psutil.Process(self.pid)
this_time = time.time()
for proc in chain((main,), main.children(recursive=True)):
meminfo = proc.memory_full_info()
rss += meminfo.rss
vms += meminfo.vms
uss += meminfo.uss
pss += meminfo.pss
ioinfo = proc.io_counters()
io_in += ioinfo.read_bytes
io_out += ioinfo.write_bytes
if self.bench_record.prev_time:
cpu_seconds += proc.cpu_percent() / 100 * (
this_time - self.bench_record.prev_time)
self.bench_record.prev_time = this_time
if not self.bench_record.first_time:
self.bench_record.prev_time = this_time
rss /= 1024 * 1024
vms /= 1024 * 1024
uss /= 1024 * 1024
pss /= 1024 * 1024
io_in /= 1024 * 1024
io_out /= 1024 * 1024
except psutil.Error as e:
return
# Update benchmark record's RSS and VMS
self.bench_record.max_rss = max(self.bench_record.max_rss or 0, rss)
self.bench_record.max_vms = max(self.bench_record.max_vms or 0, vms)
self.bench_record.max_uss = max(self.bench_record.max_uss or 0, uss)
self.bench_record.max_pss = max(self.bench_record.max_pss or 0, pss)
self.bench_record.io_in = io_in
self.bench_record.io_out = io_out
self.bench_record.cpu_seconds += cpu_seconds
So this seems to come from functionalities provided by psutil.
I will just leave this here for future reference.
Reading through
snakemake >= 6.0.0 benchmark module
psutil's memory_info(), memory_full_info(), io_counters(), cpu_times()
as previously suggested:
colname
type (unit)
description
s
float (seconds)
Running time in seconds
h:m:s
string (-)
Running time in hour, minutes, seconds format
max_rss
float (MB)
Maximum "Resident Set Size”, this is the non-swapped physical memory a process has used.
max_vms
float (MB)
Maximum “Virtual Memory Size”, this is the total amount of virtual memory used by the process
max_uss
float (MB)
“Unique Set Size”, this is the memory which is unique to a process and which would be freed if the process was terminated right now.
max_pss
float (MB)
“Proportional Set Size”, is the amount of memory shared with other processes, accounted in a way that the amount is divided evenly between the processes that share it (Linux only)
io_in
float (MB)
the number of MB read (cumulative).
io_out
float (MB)
the number of MB written (cumulative).
mean_load
float (-)
CPU usage over time, divided by the total running time (first row)
cpu_time
float(-)
CPU time summed for user and system
Benchmarking in snakemake could certainly be better documented, but psutil is documanted here:
get_memory_info()
Return a tuple representing RSS (Resident Set Size) and VMS (Virtual Memory Size) in bytes.
On UNIX RSS and VMS are the same values shown by ps.
On Windows RSS and VMS refer to "Mem Usage" and "VM Size" columns of taskmgr.exe.
psutil.disk_io_counters(perdisk=False)
Return system disk I/O statistics as a namedtuple including the following attributes:
read_count: number of reads
write_count: number of writes
read_bytes: number of bytes read
write_bytes: number of bytes written
read_time: time spent reading from disk (in milliseconds)
write_time: time spent writing to disk (in milliseconds)
The code you found confirms that all the memory usage and IO counts are reported in MB (= bytes * 1024 * 1024).