I'm using CentOS 5.4 x86_64 and Boost 1.42.0 on a cluster that uses Open-MPI 1.3.3. I'm writing a shared library that uses shared memory to store large amounts of data for multiple processes to use. There's also a loader application that will read in the data from the files and load them into the shared memory.
When I run the loader application, it determines the amount of memory that it needs to store the data exactly then adds 25% for overhead. For just about every file, it'll be over 2 gigs worth of data. When I make the memory request using Boost.Interprocess, it says it has successfully reserved the requested amount of memory. But when I use start to use it, I get a "Bus error". From what I can tell, the bus error is a result of accessing memory outside the range that is available for the memory segment.
So I started looking into how the shared memory is on Linux and what to check to make sure my system is correctly configured to allow that large amount of shared memory.
/proc/sys/kernel/shm*:
shmall - 4294967296 (4 Gb)shmmax - 68719476736 (68 Gb)shmmni - 4096ipcs -lm command:
------ Shared Memory Limits --------
max number of segments = 4096
max seg size (kbytes) = 67108864
max total shared memory (kbytes) = 17179869184
min seg size (bytes) = 1
From what I can tell, those settings indicate that I should be able to allocate enough shared memory for my purposes. So I created a stripped down program that created large amounts of data in shared memory:
#include <iostream>
#include <boost/interprocess/managed_shared_memory.hpp>
#include <boost/interprocess/allocators/allocator.hpp>
#include <boost/interprocess/containers/vector.hpp>
namespace bip = boost::interprocess;
typedef bip::managed_shared_memory::segment_manager segment_manager_t;
typedef bip::allocator<long, segment_manager_t> long_allocator;
typedef bip::vector<long, long_allocator> long_vector;
int main(int argc, char ** argv) {
struct shm_remove {
shm_remove() { bip::shared_memory_object::remove("ShmTest"); }
~shm_remove() { bip::shared_memory_object::remove("ShmTest"); }
} remover;
size_t szLength = 280000000;
size_t szRequired = szLength * sizeof(long);
size_t szRequested = (size_t) (szRequired * 1.05);
bip::managed_shared_memory segment(bip::create_only, "ShmTest", szRequested);
std::cout <<
"Length: " << szLength << "\n" <<
"sizeof(long): " << sizeof(long) << "\n" <<
"Required: " << szRequired << "\n" <<
"Requested: " << szRequested << "\n" <<
"Allocated: " << segment.get_size() << "\n" <<
"Overhead: " << segment.get_size() - segment.get_free_memory() << "\n" <<
"Free: " << segment.get_free_memory() << "\n\n";
long_allocator alloc(segment.get_segment_manager());
long_vector vector(alloc);
if (argc > 1) {
std::cout << "Reserving Length of " << szLength << "\n";
vector.reserve(szLength);
std::cout << "Vector Capacity: " << vector.capacity() << "\tFree: " << segment.get_free_memory() << "\n\n";
}
for (size_t i = 0; i < szLength; i++) {
if ((i % (szLength / 100)) == 0) {
std::cout << i << ": " << "\tVector Capacity: " << vector.capacity() << "\tFree: " << segment.get_free_memory() << "\n";
}
vector.push_back(i);
}
std::cout << "end: " << "\tVector Capacity: " << vector.capacity() << "\tFree: " << segment.get_free_memory() << "\n";
return 0;
}
Hi,
I'm using CentOS 5.4 x86_64 and Boost 1.42.0 on a cluster that uses Open-MPI 1.3.3. I'm writing a shared library that uses shared memory to store large amounts of data for multiple processes to use. There's also a loader application that will read in the data from the files and load them into the shared memory.
When I run the loader application, it determines the amount of memory that it needs to store the data exactly then adds 25% for overhead. For just about every file, it'll be over 2 gigs worth of data. When I make the memory request using Boost's Interprocess library, it says it has successfully reserved the requested amount of memory. But when I use start to use it, I get a "Bus error". From what I can tell, the bus error is a result of accessing memory outside the range that is available for the memory segment.
So I started looking into how the shared memory is on Linux and what to check to make sure my system is correctly configured to allow that large amount of shared memory.
/proc/sys/kernel/shm*:
shmall - 4294967296 (4 Gb)shmmax - 68719476736 (68 Gb)shmmni - 4096ipcs -lm command:
------ Shared Memory Limits --------
max number of segments = 4096
max seg size (kbytes) = 67108864
max total shared memory (kbytes) = 17179869184
min seg size (bytes) = 1
From what I can tell, those settings indicate that I should be able to allocate enough shared memory for my purposes. So I created a stripped down program that created large amounts of data in shared memory:
#include <iostream>
#include <boost/interprocess/managed_shared_memory.hpp>
#include <boost/interprocess/allocators/allocator.hpp>
#include <boost/interprocess/containers/vector.hpp>
namespace bip = boost::interprocess;
typedef bip::managed_shared_memory::segment_manager segment_manager_t;
typedef bip::allocator<long, segment_manager_t> long_allocator;
typedef bip::vector<long, long_allocator> long_vector;
int main(int argc, char ** argv) {
struct shm_remove {
shm_remove() { bip::shared_memory_object::remove("ShmTest"); }
~shm_remove() { bip::shared_memory_object::remove("ShmTest"); }
} remover;
size_t szLength = 280000000;
size_t szRequired = szLength * sizeof(long);
size_t szRequested = (size_t) (szRequired * 1.05);
bip::managed_shared_memory segment(bip::create_only, "ShmTest", szRequested);
std::cout <<
"Length: " << szLength << "\n" <<
"sizeof(long): " << sizeof(long) << "\n" <<
"Required: " << szRequired << "\n" <<
"Requested: " << szRequested << "\n" <<
"Allocated: " << segment.get_size() << "\n" <<
"Overhead: " << segment.get_size() - segment.get_free_memory() << "\n" <<
"Free: " << segment.get_free_memory() << "\n\n";
long_allocator alloc(segment.get_segment_manager());
long_vector vector(alloc);
if (argc > 1) {
std::cout << "Reserving Length of " << szLength << "\n";
vector.reserve(szLength);
std::cout << "Vector Capacity: " << vector.capacity() << "\tFree: " << segment.get_free_memory() << "\n\n";
}
for (size_t i = 0; i < szLength; i++) {
if ((i % (szLength / 100)) == 0) {
std::cout << i << ": " << "\tVector Capacity: " << vector.capacity() << "\tFree: " << segment.get_free_memory() << "\n";
}
vector.push_back(i);
}
std::cout << "end: " << "\tVector Capacity: " << vector.capacity() << "\tFree: " << segment.get_free_memory() << "\n";
return 0;
}
Compiled it with the line:
g++ ShmTest.cpp -lboost_system -lrt
Then ran it with the following output (edited to make it smaller):
Length: 280000000
sizeof(long): 8
Required: 2240000000
Requested: 2352000000
Allocated: 2352000000
Overhead: 224
Free: 2351999776
0: Vector Capacity: 0 Free: 2351999776
2800000: Vector Capacity: 3343205 Free: 2325254128
5600000: Vector Capacity: 8558607 Free: 2283530912
8400000: Vector Capacity: 8558607 Free: 2283530912
11200000: Vector Capacity: 13693771 Free: 2242449600
14000000: Vector Capacity: 21910035 Free: 2176719488
...
19600000: Vector Capacity: 21910035 Free: 2176719488
22400000: Vector Capacity: 35056057 Free: 2071551312
...
33600000: Vector Capacity: 35056057 Free: 2071551312
36400000: Vector Capacity: 56089691 Free: 1903282240
...
56000000: Vector Capacity: 56089691 Free: 1903282240
58800000: Vector Capacity: 89743507 Free: 1634051712
...
89600000: Vector Capacity: 89743507 Free: 1634051712
92400000: Vector Capacity: 143589611 Free: 1203282880
...
142800000: Vector Capacity: 143589611 Free: 1203282880
145600000: Vector Capacity: 215384417 Free: 628924432
...
212800000: Vector Capacity: 215384417 Free: 628924432
215600000: Vector Capacity: 293999969 Free: 16
...
260400000: Vector Capacity: 293999969 Free: 16
Bus error
If you run the program with the a parameter (any will work, just need
to increase the argc), it preallocate the vector but will
still result in a bus error at the same array index.
I checked the size of the "files" at /dev/shm using the ls
-ash /dev/shm command:
total 2.0G
0 . 0 .. 2.0G ShmTest
And just like with my original application it the size of the allocated shared memory is capped at 2 gigs. Given that it "successfully" allocated 2352000000 bytes of memory, in gigabytes (using 1024*1024*1024) it should be 2.19 Gb.
When I run my actual program to load data using MPI, I get this error output:
Requested: 2808771120
Recieved: 2808771120
[c1-master:13894] *** Process received signal ***
[c1-master:13894] Signal: Bus error (7)
[c1-master:13894] Signal code: (2)
[c1-master:13894] Failing at address: 0x2b3190157000
[c1-master:13894] [ 0] /lib64/libpthread.so.0 [0x3a64e0e7c0]
[c1-master:13894] [ 1] ../LookupPopulationLib/Release/libLookupPopulation.so(_ZN5boost12interprocess26uninitialized_copy_or_moveINS0_10offset_ptrIlEEPlEET0_T_S6_S5_PNS_10disable_ifINS0_11move_detail16is_move_iteratorIS6_EEvE4typeE+0x218) [0x2b310dcf3fb8]
[c1-master:13894] [ 2] ../LookupPopulationLib/Release/libLookupPopulation.so(_ZN5boost9container6vectorIlNS_12interprocess9allocatorIlNS2_15segment_managerIcNS2_15rbtree_best_fitINS2_12mutex_familyENS2_10offset_ptrIvEELm0EEENS2_10iset_indexEEEEEE15priv_assign_auxINS7_IlEEEEvT_SG_St20forward_iterator_tag+0xa75) [0x2b310dd0a335]
[c1-master:13894] [ 3] ../LookupPopulationLib/Release/libLookupPopulation.so(_ZN5boost9container17containers_detail25advanced_insert_aux_proxyINS0_6vectorIlNS_12interprocess9allocatorIlNS4_15segment_managerIcNS4_15rbtree_best_fitINS4_12mutex_familyENS4_10offset_ptrIvEELm0EEENS4_10iset_indexEEEEEEENS0_17constant_iteratorISF_lEEPSF_E25uninitialized_copy_all_toESI_+0x1d7) [0x2b310dd0b817]
[c1-master:13894] [ 4] ../LookupPopulationLib/Release/libLookupPopulation.so(_ZN5boost9container6vectorINS1_IlNS_12interprocess9allocatorIlNS2_15segment_managerIcNS2_15rbtree_best_fitINS2_12mutex_familyENS2_10offset_ptrIvEELm0EEENS2_10iset_indexEEEEEEENS3_ISD_SB_EEE17priv_range_insertENS7_ISD_EEmRNS0_17containers_detail23advanced_insert_aux_intISD_PSD_EE+0x771) [0x2b310dd0d521]
[c1-master:13894] [ 5] ../LookupPopulationLib/Release/libLookupPopulation.so(_ZN5boost12interprocess6detail8Ctor3ArgINS_9container6vectorINS4_IlNS0_9allocatorIlNS0_15segment_managerIcNS0_15rbtree_best_fitINS0_12mutex_familyENS0_10offset_ptrIvEELm0EEENS0_10iset_indexEEEEEEENS5_ISF_SD_EEEELb0EiSF_NS5_IvSD_EEE11construct_nEPvmRm+0x157) [0x2b310dd0d9a7]
[c1-master:13894] [ 6] ../LookupPopulationLib/Release/libLookupPopulation.so(_ZN5boost12interprocess15segment_managerIcNS0_15rbtree_best_fitINS0_12mutex_familyENS0_10offset_ptrIvEELm0EEENS0_10iset_indexEE28priv_generic_named_constructIcEEPvmPKT_mbbRNS0_6detail18in_place_interfaceERNS7_INSE_12index_configISB_S6_EEEENSE_5bool_ILb1EEE+0x6fd) [0x2b310dd0c85d]
[c1-master:13894] [ 7] ../LookupPopulationLib/Release/libLookupPopulation.so(_ZN5boost12interprocess15segment_managerIcNS0_15rbtree_best_fitINS0_12mutex_familyENS0_10offset_ptrIvEELm0EEENS0_10iset_indexEE22priv_generic_constructEPKcmbbRNS0_6detail18in_place_interfaceE+0xf8) [0x2b310dd0dd58]
[c1-master:13894] [ 8] ../LookupPopulationLib/Release/libLookupPopulation.so(_ZN7POP_LTL16ExportPopulation22InitializeSharedMemoryEPKc+0x1609) [0x2b310dceea99]
[c1-master:13894] [ 9] ../LookupPopulationLib/Release/libLookupPopulation.so(_ZN7POP_LTL10InitializeEPKc+0x349) [0x2b310dd0ebb9]
[c1-master:13894] [10] MPI_Release/LookupPopulation.MpiLoader(main+0x372) [0x4205d2]
[c1-master:13894] [11] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3a6461d994]
[c1-master:13894] [12] MPI_Release/LookupPopulation.MpiLoader(__gxx_personality_v0+0x239) [0x420009]
[c1-master:13894] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 13894 on node c1-master exited on signal 7 (Bus error).
--------------------------------------------------------------------------
I'm really not sure where to go with this. Does anyone have any suggestions of what to try?
Thank you!