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.
- I looked at the “files” at
/proc/sys/kernel/shm*:shmall– 4294967296 (4 Gb)shmmax– 68719476736 (68 Gb)shmmni– 4096
- I called the
ipcs -lmcommand:------ 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?
Posted to the Boost bug trac at: https://svn.boost.org/trac/boost/ticket/4374
Well, if you keep looking for the answer long enough…
On Linux the shared memory mechanisms it uses (
tmpfs) by default limits it to half the system RAM. So on the my cluster it’s 2 Gb because we have 4 Gb system RAM. So when it tried to allocate the shared memory segment, it allocated up to the max size left on the/dev/shm.But issue came when the Boost library didn’t indicate an error or even the report correct amount of free memory when it couldn’t allocate the requested amount of memory. It was just happy to apparently chug along until it reached the end of the segment and then errored.
The long term solution is to update the
/etc/fstabfile to make the change permanently, but a command line call can be run to increase the size of the available shared memory on each node until reboot.mount -o remount,size=XXX /dev/shmWhere the
XXXis the amount of memory to make available (for examplesize=4G).This was figured out/taken from http://www.cyberciti.biz/tips/what-is-devshm-and-its-practical-usage.html