binary file fread/fwrite and calloc/free memory leak? - c

I'm trying to process some rather big binary files (up to 20gb per file). To do so, I want to read them in chunks, process and write to the new file.
To read the file, I use:
fp = fopen(filename,"rb"); //open binary file to read
fseek(fp, start_of_chunk, SEEK_SET); //set cursor to current chunk
fread(data,size_of_chunk,1,fp); //read one chunk of data
fclose(fp);
I then allocate some arrays using calloc and process the data.
To write it back, I use:
fout = fopen(file_out,"ab"); //open output binary file in append mode
fwrite(processed_data,size_of_processed_data,1,fout);
fclose(fout);
At the end, I use free() on each of the allocated variables (biggest one is the read data chunk (~400 MB), smallest one is about 1kB) and start all over with reading the next chunk.
The output works fine but the process keeps up eating memory like there's no tomorrow. An 800 MB test file eats up to 6 GB of RAM, rising steadily. Reading the whole file at once uses pretty much the same amount of memory as reading the chunks. Using free() between the loops releases not even 5% of the used memory even though those variables contain 99% of the data.
As I am pretty new to C programming, is there anything I might be missing? I read in another thread that the OS (Windows 10 x64 in my case, same problem on Windows 7 x64) might be too slow to release memory. Reading bigger chunks did not help in my case. All the file handles are closed after reading/writing and all allocated arrays are freed at the end.
Edit: I am allocating multiple times within the loop. I'm using
free(data);
data = (uint16_t*)calloc(number_of_elements,sizeof(uint16_t));
before each call to read data. To process a certain part of the chunk, I'm using
data_part = (uint16_t*)calloc(number_of_elements,sizeof(uint16_t));
memmove(data_part,pointer_to_part_of_chunk, size_of_data_part);
Edit 2: I changed some stuff, thanks to the comments. Still, memory load keeps rising steadily (tho slower than before). Here's the code once again:
//initiate variables
//allocate arrays
data = (uint16_t*)calloc(number_of_elements,sizeof(uint16_t));
array1 = (uint16_t*)calloc(number_of_elements1,sizeof(uint16_t));
array2 = (uint16_t*)calloc(number_of_elements2,sizeof(uint16_t)); //and so on
//some precalculations
//start of the loop
while (not_end_of_the_file){
fp = fopen(filename,"rb"); //open binary file to read
fseek(fp, start_of_chunk, SEEK_SET); //set cursor to current chunk
fread(data,size_of_chunk,1,fp); //read one chunk of data
fclose(fp);
//calculate stuff
start_of_chunk = start_of_chunk + increment;
for (i=0;i<I;i++){
memmove(array1,pointer_to_part_of_data, size_of_array1);
if (statement){
subfunction1(array1);
}
else{
subfunction2(array1);
}; //nothing more than some for loops, if statements and arithmetic operations
//NO further allocations here, all buffers will be reused
};
//write result
fout = fopen(file_out,"ab"); //open output binary file in append mode
fwrite(processed_data,size_of_processed_data,1,fout);
fclose(fout);
};
There's some allocating happening in the subfunctions but that memory should be freed after the subfunction is done, shouldn't it?

free(data);
data = (uint16_t*)calloc(number_of_elements,sizeof(uint16_t));
Are you sure the value of data in the free line is the value returned from the previous call to calloc? If it's NULL when you call free, that is a no-op.

Related

C: open file before loop and close after or open/close within loop?

I have a loop that writes out processed data to a file. The data is contained in a linked list and is written out in a while loop which iterates the list.
My question is, should I open/close the write-out files before/after the while loop as shown below, or should I move the open/close within the loop so each iteration opens and then closes the file rather than keeping the file open for the entire duration of the loop?
The linked list has hundreds of MB of data, potentially several GB. Each iteration writes out a line which isn't much more than 80 characters. This is run on a modern linux system.
EDIT: this is not an embedded/critical system. In the unlikely event the process is interrupted before closing the file, it will be restarted.
void msgs_output_to_file(Node *head) {
Node *l = head;
MsgType msg_type;
char line[MAX_LINE_SIZE];
FILE *file1 = NULL;
FILE *file2 = NULL;
file1 = fopen("file1.csv", "w");
file2 = fopen("file2.csv", "w");
while (l && l->data) {
memset(line, 0, (size_t) MAX_LINE_SIZE);
sprintf_msg(line, l->data);
line[strlen(line)] = '\n'; // add new line
msg_type = get_msg_type(l->data);
switch (msg_type) {
case TYPE_1:
fputs(line, file1);
break;
case TYPE_2:
fputs(line, file2);
break;
default:
break;
}
l = l->next;
}
fclose(file1);
fclose(file2);
}
The general rule is that you should open the file only once (so out of the loop) and keep it opened for the duration of the whole loop. The rationale is that opening a file is a rather expensive operation.
But (as for any general rule) there are exceptions... What matters is what happens is your program experiences a crash in the middle of the loop. If the consequences are only that you will have to restart the job and if the probability is low, just move on. If you are processing mission critical data that will be lost if the resulting file ends to be broken and if (whatever the cause) crashes are to be expected, then things will be different. You will have to handle a balance between performance (only one open/close) and robustness. At least you should flush the file every n rows (n being the max rows you can accept to lose) to minimize the possible data loss.
What I understand about opening a file (in Python) is that you do not load the entire file in memory, but rather receive a file handle. Using this file handle, your script has access to "high level" operations like reading and writing a line. When writing a line to the file, the file contents is not directly written to the hard disk. Instead the contents is placed in a buffer and the contents is actually written to the file by the operating system when the operating system feels like doing so, or when you close the file using fclose().
The advantage of this buffer system is that when you are writing to a file in a loop, the amount of write operations to the hard disk is limited, since the content is not directly written to the disk but rather to the buffer. The buffer contents is then written to the disk when enough contents is in the buffer or when you close the file. If you would open and close the file each iteration you would increase the number of write operations to the disk and increase overhead.
So the short answer is, I would open the files before the loop and close the files after the loop.

Strange results with reading binary files in C

I'm working on 64-bit Xubuntu 14.04.
I have a fairly large C program and to test new features, I usually implement them in a separate program to iron out any bugs and whatnot before incorporating them into the main program.
I have a function that takes a const char* as argument, to indicate the path of a file (/dev/rx.bin in this case). It opens the file, reads a specific number of bytes into an array and then does some things before exporting the new data to a different file.
First off I allocate the array:
int16_t samples = (int16_t *)calloc(rx_length, 2 * sizeof(samples[0]));
Note that rx_length is for example 100 samples (closer to 100 000 in the actual program), and it's calculated from the same constants.
Next I open the file and read from it:
uint32_t num_samples_read;
FILE *in_file = fopen(file, "rb");
if (in_file == NULL){
ferror(in_file);
return 1;
}
num_samples_read = fread(samples, 2 * sizeof(samples[0]), rx_length, in_file);
Here's the kicker; the return value from fread is not the same between the test program and the main program, while the code is identical. For example, when I should be reading 100 000 samples from a 400 kB file (100 000 samples, one int16_t for the real part and one int16_t for the imaginary part, adds up to four bytes per sample), the value returned is 99328 in the main program. For the life of me I cannot figure out why.
I've tested the output of every single variable used in any calculation, and up until fread() everything is identical.
I should also note that the function is in a separate header in my main program, but I figured that since printing every constant / definition gives the expected result, that it's not there where I'm making a mistake.
If there's anything that I might have missed, any input would be greatly appreciated.
Regards.
Thank you chux for reminding me to close and answer.
Closing the file was the problem in my main program, it never occurred within the test environment because the input file was not being modified there.
Once the RX thread has completed its task, make a call to fclose():
rx_task_out:
fclose(p->out_file);
// close device
// free sample buffer
return NULL;
Previously, only an error status with creating the RX thread caused it to close the file.

Why is my Memory dumping soo slow?

The idea behind this program is to simply access the ram and download the data from it to a txt file.
Later Ill convert the txt file to jpeg and hopefully it will be readable .
However when I try and read from the RAM using NEW[] it takes waaaaaay to long to actually copy all the values into the file?
Isnt it suppose to be really fast? I mean I save pictures everyday and it doesn't even take a second?
Is there some other method I can use to dump memory to a file?
#include <stdio.h>
#include <stdlib.h>
#include <hw/pci.h>
#include <hw/inout.h>
#include <sys/mman.h>
main()
{
FILE *fp;
fp = fopen ("test.txt","w+d");
int NumberOfPciCards = 3;
struct pci_dev_info info[NumberOfPciCards];
void *PciDeviceHandler1,*PciDeviceHandler2,*PciDeviceHandler3;
uint32_t *Buffer;
int *BusNumb; //int Buffer;
uint32_t counter =0;
int i;
int r;
int y;
volatile uint32_t *NEW,*NEW2;
uintptr_t iobase;
volatile uint32_t *regbase;
NEW = (uint32_t *)malloc(sizeof(uint32_t));
NEW2 = (uint32_t *)malloc(sizeof(uint32_t));
Buffer = (uint32_t *)malloc(sizeof(uint32_t));
BusNumb = (int*)malloc(sizeof(int));
printf ("\n 1");
for (r=0;r<NumberOfPciCards;r++)
{
memset(&info[r], 0, sizeof(info[r]));
}
printf ("\n 2");
//Here the attach takes place.
for (r=0;r<NumberOfPciCards;r++)
{
(pci_attach(r) < 0) ? FuncPrint(1,r) : FuncPrint(0,r);
}
printf ("\n 3");
info[0].VendorId = 0x8086; //Wont be using this one
info[0].DeviceId = 0x3582; //Or this one
info[1].VendorId = 0x10B5; //WIll only be using this one PLX 9054 chip
info[1].DeviceId = 0x9054; //Also PLX 9054
info[2].VendorId = 0x8086; //Not used
info[2].DeviceId = 0x24cb; //Not used
printf ("\n 4");
//I attached the device and give it a handler and set some setting.
if ((PciDeviceHandler1 = pci_attach_device(0,PCI_SHARE|PCI_INIT_ALL, 0, &info[1])) == 0)
{
perror("pci_attach_device fail");
exit(EXIT_FAILURE);
}
for (i = 0; i < 6; i++)
//This just prints out some details of the card.
{
if (info[1].BaseAddressSize[i] > 0)
printf("Aperture %d: "
"Base 0x%llx Length %d bytes Type %s\n", i,
PCI_IS_MEM(info[1].CpuBaseAddress[i]) ? PCI_MEM_ADDR(info[1].CpuBaseAddress[i]) : PCI_IO_ADDR(info[1].CpuBaseAddress[i]),
info[1].BaseAddressSize[i],PCI_IS_MEM(info[1].CpuBaseAddress[i]) ? "MEM" : "IO");
}
printf("\nEnd of Device random info dump---\n");
printf("\nNEWs Address : %d\n",*(int*)NEW);
//Not sure if this is a legitimate way of memory allocation but I cant see to read the ram any other way.
NEW = mmap_device_memory(NULL, info[1].BaseAddressSize[3],PROT_READ|PROT_WRITE|PROT_NOCACHE, 0,info[1].CpuBaseAddress[3]);
//Here is where things are starting to get messy and REALLY long to just run through all the ram and dump it.
//Is there some other way I can dump the data in the ram into a file?
while (counter!=info[1].BaseAddressSize[3])
{
fprintf(fp, "%x",NEW[counter]);
counter++;
}
fclose(fp);
printf("0x%x",*Buffer);
}
A few issues that I can see:
You are writing blocks of 4 bytes - that's quite inefficient. The stream buffering in the C library may help with that to a degree, but using larger blocks would still be more efficient.
Even worse, you are writing out the memory dump in hexadecimal notation, rather than the bytes themselves. That conversion is very CPU-intensive, not to mention that the size of the output is essentially doubled. You would be better off writing raw binary data using e.g. fwrite().
Depending on the specifics of your system (is this on QNX?), reading from I/O-mapped memory may be slower than reading directly from physical memory, especially if your PCI device has to act as a relay. What exactly is it that you are doing?
In any case I would suggest using a profiler to actually find out where your program is spending most of its time. Even a rudimentary system monitor would allow you to determine if your program is CPU-bound or I/O-bound.
As it is, "waaaaaay to long" is hardly a valid measurement. How much data is being copied? How long does it take? Where is the output file located?
P.S.: I also have some concerns w.r.t. what you are trying to do, but that is slightly off-topic for this question...
For fastest speed: write the data in binary form and use the open() / write() / close() API-s. Since your data is already available in a contiguous block of (virtual) memory it is a waste to copy it to a temporary buffer (used by the fwrite(), fprintf(), etc. API-s).
The code using write() will be similar to:
int fd = open("filename.bin", O_RDWR|O_CREAT, S_IRWXU);
write(fd, (void*)NEW, 4*info[1].BaseAddressSize[3]);
close(fd);
You will need to add error handling and make sure that the buffer size is specified correctly.
To reiterate, you get the speed-up from:
avoiding the conversion from binary to ASCII (as pointed out by others above)
avoiding many calls to libc
reducing the number of system-calls (from inside libc)
eliminating the overhead of copying data to a temporary buffer inside the fwrite()/fprintf() and related functions (buffering would be useful if your data arrived in small chunks, including the case of converting to ASCII in 4 byte units)
I intentionally ignore commenting on other parts of your code as it is apparently not intended to be production quality yet and your question is focused on how to speed up writing data to a file.

Fast Creation of a very large File in Debian Linux

I am currently working on a project that involves transferring a very large file (about 6GB) from one Linux Server to another. The servers run on Debian Squeeze.
In order to achieve my main goal, I initially send the file's name and size to the destination machine, and I create an empty file for storing the data blocks that I progressively receive from the source machine.
My problem is that the creation of a 6GB file takes too long in my server. To make it more clear I use the following C routine in order to create the new file:
void create_file(char* f_name, long long f_size) {
char* bs, *of, *s_f_size, *count;
if((pid = fork()) < 0) {
perror("fork() failed.");
return;
}
if(pid == 0) {
//Call execl
of = (char*) malloc(sizeof(char)*(strlen("of=") + strlen(f_name) + 1));
s_f_size = (char*) malloc(sizeof(char)*32);
sprintf(s_f_size, "%lld", file_size);
count = (char*) malloc(sizeof(char)*(strlen("count=") + strlen(s_f_size) + 1));
strcpy(of, "of=");
strcat(of, f_name);
strcpy(count, "count=");
strcat(count, s_f_size);
ret = execl("/bin/dd", "dd", "if=/dev/zero", of, "bs=1", count, (char*) 0);
if(ret < 0) {
perror("execl() failed");
free(s_f_size);
free(of);
free(count);
return;
}else {
free(s_f_size);
free(of);
free(count);
return;
}
}else {
status = 0;
wpid = wait(&status);
}
}
I used the Linux dd command because I thought that it would be the quickest way to create an empty 6GB file. However, it takes about 15 minutes to complete. Is there a way to create the empty file faster? What am I doing wrong?
Thank you for your time.
Sincerely,
Nick
In addition to what Joachim Pileborg suggested, you can also use posix_fallocate() to pre-allocate space for your file.
First creat the file, then lseek to the wanted end, and write a dummy byte. Very quick way to create an arbitrary large but sparse file.
If you don't want the file to be sparse, then find out the block size of the drive (can be found out using stat on most POSIX platforms). Create a buffer of that size, and write it to the file until the wanted size.
If the stat structure doesn't have the st_blksize member, then most filesystems have a blocksize of 4 or 8 kB. You can probably make this buffer larger, but not too large. Experiment and benchmark!
If you're using kernel v2.6.31+ and if filesystem supports it, consider using fallocate:
fallocate -l 6GB hugefile
It preallocates blocks to a file.
Creating large files takes long because there's a lot on the file system the OS has to do. Only in case of sparse files this can be skipped (see Joachim Pileborg's answer for that). A sparse file is a file containing "holes" (large chunks of zero bytes). Such a file does not use as much space as it is large. Creating such a file beforehand will produce the file with the correct size very fast.
In case you want to reserve the disk space to avoid running out of it before the transmission is complete, a sparse file won't do. You will have to write at least one byte into each block then to avoid the holes of a sparse file. I'm not sure this will be faster than simply dump zeros into the file until it has the desired size, as you already do.
i remember, i've used open system call to create a empty file. Then dump data to file.
In case of partial data write, keep seek the position and dump from there. If file exists use the file to overwrite the data into it.
With respect to performance this approach was quite good.

Seg fault with open command when trying to open very large file

I'm taking a networking class at school and am using C/GDB for the first time. Our assignment is to make a webserver that communicates with a client browser. I am well underway and can open files and send them to the client. Everything goes great till I open a very large file and then I seg fault. I'm not a pro at C/GDB so I'm sorry if that is causing me to ask silly questions and not be able to see the solution myself but when I looked at the dumped core I see my seg fault comes here:
if (-1 == (openfd = open(path, O_RDONLY)))
Specifically we are tasked with opening the file and the sending it to the client browser. My Algorithm goes:
Open/Error catch
Read the file into a buffer/Error catch
Send the file
We were also tasked with making sure that the server doesn't crash when SENDING very large files. But my problem seems to be with opening them. I can send all my smaller files just fine. The file in question is 29.5MB.
The whole algorithm is:
ssize_t send_file(int conn, char *path, int len, int blksize, char *mime) {
int openfd; // File descriptor for file we open at path
int temp; // Counter for the size of the file that we send
char buffer[len]; // Buffer to read the file we are opening that is len big
// Open the file
if (-1 == (openfd = open(path, O_RDONLY))) {
send_head(conn, "", 400, strlen(ERROR_400));
(void) send(conn, ERROR_400, strlen(ERROR_400), 0);
logwrite(stdout, CANT_OPEN);
return -1;
}
// Read from file
if (-1 == read(openfd, buffer, len)) {
send_head(conn, "", 400, strlen(ERROR_400));
(void) send(conn, ERROR_400, strlen(ERROR_400), 0);
logwrite(stdout, CANT_OPEN);
return -1;
}
(void) close(openfd);
// Send the buffer now
logwrite(stdout, SUC_REQ);
send_head(conn, mime, 200, len);
send(conn, &buffer[0], len, 0);
return len;
}
I dunno if it is just a fact that a I am Unix/C novice. Sorry if it is. =( But you're help is much appreciated.
It's possible I'm just misunderstanding what you meant in your question, but I feel I should point out that in general, it's a bad idea to try to read the entire file at once, in case you deal with something that's just too big for your memory to handle.
It's smarter to allocate a buffer of a specific size, say 8192 bytes (well, that's what I tend to do a lot, anyway), and just always read and send that much, as much as necessary, until your read() operation returns 0 (and no errno set) for end of stream.
I suspect you have a stackoverflow (I should get bonus points for using that term on this site).
The problem is you are allocating the buffer for the entire file on the stack all at once. For larger files, this buffer is larger than the stack, and the next time you try to call a function (and thus put some parameters for it on the stack) the program crashes.
The crash appears at the open line because allocating the buffer on the stack doesn't actually write any memory, it just changes the stack pointer. When your call to open tries tow rite the parameters to the stack, the top of the stack is now overflown and this causes a crash.
The solution is as Platinum Azure or dreamlax suggest, read in the file little bits at a time or allocate your buffer on the heap will malloc or new.
Rather than using a variable length array, perhaps try allocated the memory using malloc.
char *buffer = malloc (len);
...
free (buffer);
I just did some simple tests on my system, and when I use variable length arrays of a big size (like the size you're having trouble with), I also get a SEGFAULT.
You're allocating the buffer on the stack, and it's way too big.
When you allocate storage on the stack, all the compiler does is decrease the stack pointer enough to make that much room (this keeps stack variable allocation to constant time). It does not try to touch any of this stacked memory. Then, when you call open(), it tries to put the parameters on the stack and discovers it has overflowed the stack and dies.
You need to either operate on the file in chunks, memory-map it (mmap()), or malloc() storage.
Also, path should be declared const char*.

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