All,
I have been experimenting with large window allocations recently and
have made some interesting observations that I would like to share.
The system under test:
- Linux cluster equipped with IB,
- Open MPI 2.1.1,
- 128GB main memory per node
- 6GB /tmp filesystem per node
My observations:
1) Running with 1 process on a single node, I can allocate and write to
memory up to ~110 GB through MPI_Allocate, MPI_Win_allocate, and
MPI_Win_allocate_shared.
2) If running with 1 process per node on 2 nodes single large
allocations succeed but with the repeating allocate/free cycle in the
attached code I see the application being reproducibly being killed by
the OOM at 25GB allocation with MPI_Win_allocate_shared. When I try to
run it under Valgrind I get an error from MPI_Win_allocate at ~50GB that
I cannot make sense of:
```
MPI_Alloc_mem: 53687091200 B
[n131302:11989] *** An error occurred in MPI_Alloc_mem
[n131302:11989] *** reported by process [1567293441,1]
[n131302:11989] *** on communicator MPI_COMM_WORLD
[n131302:11989] *** MPI_ERR_NO_MEM: out of memory
[n131302:11989] *** MPI_ERRORS_ARE_FATAL (processes in this communicator
will now abort,
[n131302:11989] *** and potentially your MPI job)
```
3) If running with 2 processes on a node, I get the following error from
both MPI_Win_allocate and MPI_Win_allocate_shared:
```
--------------------------------------------------------------------------
It appears as if there is not enough space for
/tmp/openmpi-sessions-31390@n131702_0/23041/1/0/shared_window_4.n131702
(the shared-memory backing
file). It is likely that your MPI job will now either abort or experience
performance degradation.
Local host: n131702
Space Requested: 6710890760 B
Space Available: 6433673216 B
```
This seems to be related to the size limit of /tmp. MPI_Allocate works
as expected, i.e., I can allocate ~50GB per process. I understand that I
can set $TMP to a bigger filesystem (such as lustre) but then I am
greeted with a warning on each allocation and performance seems to drop.
Is there a way to fall back to the allocation strategy used in case 2)?
4) It is also worth noting the time it takes to allocate the memory:
while the allocations are in the sub-millisecond range for both
MPI_Allocate and MPI_Win_allocate_shared, it takes >24s to allocate
100GB using MPI_Win_allocate and the time increasing linearly with the
allocation size.
Are these issues known? Maybe there is documentation describing
work-arounds? (esp. for 3) and 4))
I am attaching a small benchmark. Please make sure to adjust the
MEM_PER_NODE macro to suit your system before you run it :) I'm happy to
provide additional details if needed.
Best
Joseph
--
Dipl.-Inf. Joseph Schuchart
High Performance Computing Center Stuttgart (HLRS)
Nobelstr. 19
D-70569 Stuttgart
Tel.: +49(0)711-68565890
Fax: +49(0)711-6856832
E-Mail: schuch...@hlrs.de
#include <assert.h>
#include <stdio.h>
#include <mpi.h>
#include <string.h>
#define MEM_PER_NODE (100*1024*1024*1024UL)
#define NUM_STEPS 10
//#define USE_MEM(__mem, __size) memset(__mem, 0, __size)
//#define USE_MEM(__mem, __size) parallel_memset(__mem, 0, __size)
#define USE_MEM(__mem, __size)
static int comm_rank;
static void parallel_memset(char *baseptr, int val, size_t size)
{
#pragma omp parallel for
for (size_t i = 0; i < size; ++i) {
baseptr[i] = val;
}
}
static void test_alloc_mem(size_t size)
{
char *baseptr;
if (comm_rank == 0) {
printf("MPI_Alloc_mem: %12zu B ", size);
}
double start = MPI_Wtime();
MPI_Alloc_mem(size, MPI_INFO_NULL, &baseptr);
double end = MPI_Wtime();
if (comm_rank == 0) {
printf("(%fs)\n", end - start);
}
USE_MEM(baseptr, size);
MPI_Free_mem(baseptr);
}
static void test_win_allocate(size_t size)
{
char *baseptr;
MPI_Win win;
if (comm_rank == 0) {
printf("MPI_Win_allocate: %12zu B ", size);
}
double start = MPI_Wtime();
MPI_Win_allocate(size, 1, MPI_INFO_NULL, MPI_COMM_WORLD, &baseptr, &win);
double end = MPI_Wtime();
if (comm_rank == 0) {
printf("(%fs)\n", end - start);
}
USE_MEM(baseptr, size);
MPI_Win_free(&win);
}
static void test_win_allocate_shared(size_t size, MPI_Comm sharedmem_comm)
{
char *baseptr;
MPI_Win win;
if (comm_rank == 0) {
printf("MPI_Win_allocate_shared %12zu B ", size);
}
double start = MPI_Wtime();
MPI_Win_allocate_shared(size, 1, MPI_INFO_NULL, sharedmem_comm, &baseptr, &win);
double end = MPI_Wtime();
if (comm_rank == 0) {
printf("(%fs)\n", end - start);
}
USE_MEM(baseptr, size);
MPI_Win_free(&win);
}
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
int procs_per_node;
MPI_Comm sharedmem_comm;
MPI_Comm_split_type(
MPI_COMM_WORLD,
MPI_COMM_TYPE_SHARED,
1,
MPI_INFO_NULL,
&sharedmem_comm);
MPI_Comm_size(sharedmem_comm, &procs_per_node);
size_t max_alloc = (MEM_PER_NODE) / procs_per_node;
size_t min_alloc = (max_alloc / (1<<(NUM_STEPS-1)));
MPI_Comm_rank(MPI_COMM_WORLD, &comm_rank);
if (comm_rank == 0) {
printf("Processes per node: %d\n", procs_per_node);
printf("Minimum allocation per process: %zu\n", min_alloc);
printf("Maximum allocation per process: %zu\n", max_alloc);
}
for (size_t size = min_alloc; size <= max_alloc; size *= 2) {
test_alloc_mem(size);
}
for (size_t size = min_alloc; size <= max_alloc; size *= 2) {
test_win_allocate(size);
}
for (size_t size = min_alloc; size <= max_alloc; size *= 2) {
test_win_allocate_shared(size, sharedmem_comm);
}
MPI_Finalize();
return 0;
}
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