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35. Out Of Core

# 35.1 Introduction

When using StarPU, one may need to store more data than what the main memory (RAM) can store. This part describes the method to add a new memory node on a disk and to use it.

Similarly to what happens with GPUs (it's actually exactly the same code), when available main memory becomes scarce, StarPU will evict unused data to the disk, thus leaving room for new allocations. Whenever some evicted data is needed again for a task, StarPU will automatically fetch it back from the disk.

The principle is that one first registers a disk memory node with a set of functions to manipulate data by calling starpu_disk_register(), and then registers a disk location, seen by StarPU as a `void*`, which can be for instance a Unix path for the `stdio`, `unistd` or `unistd_o_direct` backends, or a leveldb database for the `leveldb` backend, an HDF5 file path for the `HDF5` backend, etc. The `disk` backend opens this place with the plug() method.

StarPU can then start using it to allocate room and store data there with the disk write method, without user intervention.

Users can also use starpu_disk_open() to explicitly open an object within the disk, e.g. a file name in the `stdio` or `unistd` cases, or a database key in the `leveldb` case, and then use `starpu_*_register` functions to turn it into a StarPU data handle. StarPU will then use this file as an external source of data, and automatically read and write data as appropriate. In the end use starpu_disk_close() to close an existing object.

In any case, users also need to set STARPU_LIMIT_CPU_MEM to the amount of data that StarPU will be allowed to afford. By default, StarPU will use the machine memory size, but part of it is taken by the kernel, the system, daemons, and the application's own allocated data, whose size can not be predicted. That is why users need to specify what StarPU can afford.

Some Out-of-core tests are worth giving a read, see `tests/disk/*.c`

# 35.2 Use a new disk memory

To use a disk memory node, you have to register it with this function:

int new_dd = starpu_disk_register(&starpu_disk_unistd_ops, (void *) "/tmp/", 1024*1024*200);
starpu_disk_unistd_ops
struct starpu_disk_ops starpu_disk_unistd_ops
starpu_disk_register
int starpu_disk_register(struct starpu_disk_ops *func, void *parameter, starpu_ssize_t size)

Here, we use the `unistd` library to realize the read/write operations, i.e. `fread/`fwrite`.` This structure must have a path where to store files, as well as the maximum size the software can afford to store on the disk.

Don't forget to check if the result is correct!

This can also be achieved by just setting environment variables STARPU_DISK_SWAP, STARPU_DISK_SWAP_BACKEND and STARPU_DISK_SWAP_SIZE :

    export STARPU_DISK_SWAP=/tmp
    export STARPU_DISK_SWAP_BACKEND=unistd
    export STARPU_DISK_SWAP_SIZE=200

The backend can be set to `stdio` (some caching is done by `libc` and the kernel), `unistd` (only caching in the kernel), `unistd_o_direct` (no caching), `leveldb`, or `hdf5`.

It is important to understand that when the backend is not set to `unistd_o_direct`, some caching will occur at the kernel level (the page cache), which will also consume memory... STARPU_LIMIT_CPU_MEM might need to be set to less than half of the machine memory just to leave room for the kernel's page cache, otherwise the kernel will struggle to get memory. Using `unistd_o_direct` avoids this caching, thus allowing to set STARPU_LIMIT_CPU_MEM to the machine memory size (minus some memory for normal kernel operations, system daemons, and application data).

When the register call is made, StarPU will benchmark the disk. This can take some time.

Warning: the size thus has to be at least STARPU_DISK_SIZE_MIN bytes !

StarPU will then automatically try to evict unused data to this new disk. One can also use the standard StarPU memory node API to prefetch data etc., see the Standard Memory Library and the Data Interfaces.

The disk is unregistered during the execution of starpu_shutdown().

# 35.3 Data Registration

StarPU will only be able to achieve Out-Of-Core eviction if it controls memory allocation. For instance, if the application does the following:

p = malloc(1024*1024*sizeof(float));
fill_with_data(p);
starpu_matrix_data_register(&h, STARPU_MAIN_RAM, (uintptr_t) p, 1024, 1024, 1024, sizeof(float));
STARPU_MAIN_RAM
#define STARPU_MAIN_RAM
Definition starpu_task.h:144
starpu_matrix_data_register
void starpu_matrix_data_register(starpu_data_handle_t *handle, int home_node, uintptr_t ptr, uint32_t ld, uint32_t nx, uint32_t ny, size_t elemsize)

StarPU will not be able to release the corresponding memory since it's the application which allocated it, and StarPU can not know how, and thus how to release it. One thus have to use the following instead:

starpu_matrix_data_register(&h, -1, NULL, 1024, 1024, 1024, sizeof(float));
starpu_task_insert(cl_fill_with_data, STARPU_W, h, 0);
STARPU_W
@ STARPU_W
Definition starpu_data.h:59
starpu_task_insert
int starpu_task_insert(struct starpu_codelet *cl,...)

Which makes StarPU automatically do the allocation when the task running cl_fill_with_data gets executed. And then if it needs to, it will be able to release it after having pushed the data to the disk. Since no initial buffer is provided to starpu_matrix_data_register(), the handle does not have any initial value right after this call, and thus the very first task using the handle needs to use the STARPU_W mode like above, STARPU_R or STARPU_RW would not make sense.

By default, StarPU will try to push any data handle to the disk. To specify whether a given handle should be pushed to the disk, starpu_data_set_ooc_flag() should be used. To get to know whether a given handle should be pushed to the disk, starpu_data_get_ooc_flag() should be used.

# 35.4 Using Wont Use

By default, StarPU uses a Least-Recently-Used (LRU) algorithm to determine which data should be evicted to the disk. This algorithm can be hinted by telling which data will not be used in the coming future thanks to starpu_data_wont_use(), for instance:

starpu_task_insert(&cl_work, STARPU_RW, h, 0);
starpu_data_wont_use(h);
starpu_data_wont_use
void starpu_data_wont_use(starpu_data_handle_t handle)
STARPU_RW
@ STARPU_RW
Definition starpu_data.h:60

StarPU will mark the data as "inactive" and tend to evict to the disk that data rather than others.

# 35.5 Examples: disk_copy

/* Try to write into disk memory
* Use mechanism to push data from main ram to disk ram
*/
#include <starpu.h>
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
/* size of one vector */
#define NX (30*1000000/sizeof(double))
#define FPRINTF(ofile, fmt, ...) do { if (!getenv("STARPU_SSILENT")) {fprintf(ofile, fmt, ## __VA_ARGS__); }} while(0)
int main(int argc, char **argv)
{
double *A, *F;
/* limit main ram to force to push in disk */
setenv("STARPU_LIMIT_CPU_MEM", "160", 1);
/* Initialize StarPU with default configuration */
int ret = starpu_init(NULL);
if (ret == -ENODEV) goto enodev;
/* register a disk */
int new_dd = starpu_disk_register(&starpu_disk_unistd_ops, (void *) "/tmp/", 1024*1024*200);
/* can't write on /tmp/ */
if (new_dd == -ENOENT) goto enoent;
/* allocate two memory spaces */
starpu_malloc_flags((void **)&A, NX*sizeof(double), STARPU_MALLOC_COUNT);
starpu_malloc_flags((void **)&F, NX*sizeof(double), STARPU_MALLOC_COUNT);
FPRINTF(stderr, "TEST DISK MEMORY \n");
unsigned int j;
/* initialization with bad values */
for(j = 0; j < NX; ++j)
{
A[j] = j;
F[j] = -j;
}
starpu_data_handle_t vector_handleA, vector_handleB, vector_handleC, vector_handleD, vector_handleE, vector_handleF;
/* register vector in starpu */
starpu_vector_data_register(&vector_handleA, STARPU_MAIN_RAM, (uintptr_t)A, NX, sizeof(double));
starpu_vector_data_register(&vector_handleB, -1, (uintptr_t) NULL, NX, sizeof(double));
starpu_vector_data_register(&vector_handleC, -1, (uintptr_t) NULL, NX, sizeof(double));
starpu_vector_data_register(&vector_handleD, -1, (uintptr_t) NULL, NX, sizeof(double));
starpu_vector_data_register(&vector_handleE, -1, (uintptr_t) NULL, NX, sizeof(double));
starpu_vector_data_register(&vector_handleF, STARPU_MAIN_RAM, (uintptr_t)F, NX, sizeof(double));
/* copy vector A->B, B->C... */
starpu_data_cpy(vector_handleB, vector_handleA, 0, NULL, NULL);
starpu_data_cpy(vector_handleC, vector_handleB, 0, NULL, NULL);
starpu_data_cpy(vector_handleD, vector_handleC, 0, NULL, NULL);
starpu_data_cpy(vector_handleE, vector_handleD, 0, NULL, NULL);
starpu_data_cpy(vector_handleF, vector_handleE, 0, NULL, NULL);
/* StarPU does not need to manipulate the array anymore so we can stop
* monitoring it */
/* free them */
starpu_data_unregister(vector_handleA);
starpu_data_unregister(vector_handleB);
starpu_data_unregister(vector_handleC);
starpu_data_unregister(vector_handleD);
starpu_data_unregister(vector_handleE);
starpu_data_unregister(vector_handleF);
/* check if computation is correct */
int try = 1;
for (j = 0; j < NX; ++j)
if (A[j] != F[j])
{
printf("Fail A %f != F %f \n", A[j], F[j]);
try = 0;
}
/* free last vectors */
starpu_free_flags(A, NX*sizeof(double), STARPU_MALLOC_COUNT);
starpu_free_flags(F, NX*sizeof(double), STARPU_MALLOC_COUNT);
/* terminate StarPU, no task can be submitted after */
starpu_shutdown();
if(try)
FPRINTF(stderr, "TEST SUCCESS\n");
else
FPRINTF(stderr, "TEST FAIL\n");
return (try ? EXIT_SUCCESS : EXIT_FAILURE);
enodev:
return 77;
enoent:
return 77;
}
starpu_vector_data_register
void starpu_vector_data_register(starpu_data_handle_t *handle, int home_node, uintptr_t ptr, uint32_t nx, size_t elemsize)
starpu_data_unregister
void starpu_data_unregister(starpu_data_handle_t handle)
starpu_data_handle_t
struct _starpu_data_state * starpu_data_handle_t
Definition starpu_data.h:45
starpu_shutdown
void starpu_shutdown(void)
starpu_init
int starpu_init(struct starpu_conf *conf)
starpu_data_cpy
int starpu_data_cpy(starpu_data_handle_t dst_handle, starpu_data_handle_t src_handle, int asynchronous, void(*callback_func)(void *), void *callback_arg)
STARPU_MALLOC_COUNT
#define STARPU_MALLOC_COUNT
Definition starpu_stdlib.h:48
starpu_free_flags
int starpu_free_flags(void *A, size_t dim, int flags)
starpu_malloc_flags
int starpu_malloc_flags(void **A, size_t dim, int flags)
starpu.h

The full code is provided in the file `tests/disk/disk_copy.c`

# 35.6 Examples: disk_compute

/* Try to write into disk memory
* Use mechanism to push data from main ram to disk ram
*/
#include <starpu.h>
#include <stdlib.h>
#include <stdio.h>
#include <sys/types.h>
#include <unistd.h>
#include <math.h>
#define NX (1024)
int main(int argc, char **argv)
{
/* Initialize StarPU with default configuration */
int ret = starpu_init(NULL);
if (ret == -ENODEV) goto enodev;
/* Initialize path and name */
char pid_str[16];
int pid = getpid();
snprintf(pid_str, sizeof(pid_str), "%d", pid);
const char *name_file_start = "STARPU_DISK_COMPUTE_DATA_";
const char *name_file_end = "STARPU_DISK_COMPUTE_DATA_RESULT_";
char * path_file_start = malloc(strlen(base) + 1 + strlen(name_file_start) + 1);
strcpy(path_file_start, base);
strcat(path_file_start, "/");
strcat(path_file_start, name_file_start);
char * path_file_end = malloc(strlen(base) + 1 + strlen(name_file_end) + 1);
strcpy(path_file_end, base);
strcat(path_file_end, "/");
strcat(path_file_end, name_file_end);
/* register a disk */
int new_dd = starpu_disk_register(&starpu_disk_unistd_ops, (void *) base, 1024*1024*1);
/* can't write on /tmp/ */
if (new_dd == -ENOENT) goto enoent;
unsigned dd = (unsigned) new_dd;
printf("TEST DISK MEMORY \n");
/* Imagine, you want to compute data */
int *A;
int *C;
starpu_malloc_flags((void **)&A, NX*sizeof(int), STARPU_MALLOC_COUNT);
starpu_malloc_flags((void **)&C, NX*sizeof(int), STARPU_MALLOC_COUNT);
unsigned int j;
/* you register them in a vector */
for(j = 0; j < NX; ++j)
{
A[j] = j;
C[j] = 0;
}
/* you create a file to store the vector ON the disk */
FILE * f = fopen(path_file_start, "wb+");
if (f == NULL)
goto enoent2;
/* store it in the file */
fwrite(A, sizeof(int), NX, f);
/* close the file */
fclose(f);
/* create a file to store result */
f = fopen(path_file_end, "wb+");
if (f == NULL)
goto enoent2;
/* replace all data by 0 */
fwrite(C, sizeof(int), NX, f);
/* close the file */
fclose(f);
/* And now, you want to use your data in StarPU */
/* Open the file ON the disk */
void * data = starpu_disk_open(dd, (void *) name_file_start, NX*sizeof(int));
void * data_result = starpu_disk_open(dd, (void *) name_file_end, NX*sizeof(int));
starpu_data_handle_t vector_handleA, vector_handleC;
/* register vector in starpu */
starpu_vector_data_register(&vector_handleA, dd, (uintptr_t) data, NX, sizeof(int));
/* and do what you want with it, here we copy it into an other vector */
starpu_vector_data_register(&vector_handleC, dd, (uintptr_t) data_result, NX, sizeof(int));
starpu_data_cpy(vector_handleC, vector_handleA, 0, NULL, NULL);
/* free them */
starpu_data_unregister(vector_handleA);
starpu_data_unregister(vector_handleC);
/* close them in StarPU */
starpu_disk_close(dd, data, NX*sizeof(int));
starpu_disk_close(dd, data_result, NX*sizeof(int));
/* check results */
f = fopen(path_file_end, "rb+");
if (f == NULL)
goto enoent;
/* take data */
fread(C, sizeof(int), NX, f);
/* close the file */
fclose(f);
int try = 1;
for (j = 0; j < NX; ++j)
if (A[j] != C[j])
{
printf("Fail A %d != C %d \n", A[j], C[j]);
try = 0;
}
starpu_free_flags(A, NX*sizeof(int), STARPU_MALLOC_COUNT);
starpu_free_flags(C, NX*sizeof(int), STARPU_MALLOC_COUNT);
unlink(path_file_start);
unlink(path_file_end);
free(path_file_start);
free(path_file_end);
/* terminate StarPU, no task can be submitted after */
starpu_shutdown();
if(try)
printf("TEST SUCCESS\n");
else
printf("TEST FAIL\n");
return (try ? EXIT_SUCCESS : EXIT_FAILURE);
enodev:
return 77;
enoent2:
starpu_free_flags(A, NX*sizeof(int), STARPU_MALLOC_COUNT);
starpu_free_flags(C, NX*sizeof(int), STARPU_MALLOC_COUNT);
enoent:
unlink(path_file_start);
unlink(path_file_end);
free(path_file_start);
free(path_file_end);
starpu_shutdown();
return 77;
}
starpu_disk_close
void starpu_disk_close(unsigned node, void *obj, size_t size)
starpu_disk_open
void * starpu_disk_open(unsigned node, void *pos, size_t size)

The full code is provided in the file `tests/disk/disk_compute.c`

# 35.7 Performances

Scheduling heuristics for Out-of-core are still relatively experimental. The tricky part is that you usually have to find a compromise between privileging locality (which avoids back and forth with the disk) and privileging the critical path, i.e. taking into account priorities to avoid lack of parallelism at the end of the task graph.

It is notably better to avoid defining different priorities to tasks with low priority, since that will make the scheduler want to schedule them by levels of priority, at the expense of locality.

The scheduling algorithms worth trying are thus `dmdar` and `lws`, which privilege data locality over priorities. There will be work on this area in the coming future.

# 35.8 Feedback Figures

Beyond pure performance feedback, some figures are interesting to have a look at.

Using `export STARPU_BUS_STATS=1` (STARPU_BUS_STATS and STARPU_BUS_STATS_FILE to define a filename in which to display statistics, by default the standard error stream is used) gives an overview of the data transfers which were needed. The values can also be obtained at runtime by using starpu_bus_get_profiling_info(). An example can be read in `src/profiling/profiling_helpers.c`.

    #---------------------
    Data transfer speed for /tmp/sthibault-disk-DJzhAj (node 1):
    0 -> 1: 99 MB/s
    1 -> 0: 99 MB/s
    0 -> 1: 23858 µs
    1 -> 0: 23858 µs

    #---------------------
    TEST DISK MEMORY

    #---------------------
    Data transfer stats:
            Disk 0 -> NUMA 0        0.0000 GB       0.0000 MB/s     (transfers : 0 - avg -nan MB)
            NUMA 0 -> Disk 0        0.0625 GB       63.6816 MB/s    (transfers : 2 - avg 32.0000 MB)
    Total transfers: 0.0625 GB
    #---------------------

Using `export STARPU_ENABLE_STATS=1` gives information for each memory node on data miss/hit and allocation miss/hit.

    #---------------------
    MSI cache stats :
    memory node NUMA 0
            hit : 32 (66.67 %)
            miss : 16 (33.33 %)
    memory node Disk 0
            hit : 0 (0.00 %)
            miss : 0 (0.00 %)
    #---------------------

    #---------------------
    Allocation cache stats:
    memory node NUMA 0
            total alloc : 16
            cached alloc: 0 (0.00 %)
    memory node Disk 0
            total alloc : 8
            cached alloc: 0 (0.00 %)
    #---------------------

# 35.9 Disk functions

There are various ways to operate a disk memory node, described by the structure starpu_disk_ops. For instance, the variable starpu_disk_unistd_ops uses read/write functions.

All structures are in Out Of Core.

Examples are provided in `src/core/disk_ops/disk_*.c`