*** glibc detected *** namd2: invalid fastbin entry (free)

From: Wesley Lay (wesleyklay2_at_gmail.com)
Date: Thu May 22 2014 - 15:19:11 CDT

Hi All/NAMD support.

I've been trying to run a system with ~1 million atoms. For some reason,
this error is constantly produced when using NAMD with more than 12 cores
in a 48 core machine. Any help or insights will be greatly appreciated.

Thanks!
Wesley Lay

 *** glibc detected *** namd2: invalid fastbin entry (free):
0x00007f06df1db1c0 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3471e75746]
namd2(free_nomigrate+0x6)[0xbddc26]
namd2(CmiFree+0x1d)[0xcc03bd]
namd2(CkFreeMsg+0xf)[0xbfb5d1]
namd2(_ZN13ComputePmeMgr17recvSharedUntransEP19PmeSharedUntransMsg+0x66)[0x894052]
namd2(_ZN21CkIndex_ComputePmeMgr43_call_recvSharedUntrans_PmeSharedUntransMsgEPvP13ComputePmeMgr+0xf)[0x893fe9]
namd2(CkDeliverMessageFree+0x21)[0xbed3c1]
namd2(_Z15_processHandlerPvP11CkCoreState+0x67d)[0xbec295]
namd2(CsdScheduleForever+0xb6)[0xcbfc3e]
namd2(CsdScheduler+0x1c)[0xcbf81c]
namd2(_Z10slave_initiPPc+0x50)[0x5889d8]
namd2[0xcbe72c]
namd2[0xcb8cdf]
/lib64/libpthread.so.0[0x3472607761]
/lib64/libc.so.6(clone+0x6d)[0x3471ee150d]
======= Memory map: ========
00400000-00eb4000 r-xp 00000000 00:15 97386641
/home/wlay/NAMD_2.9_Linux-x86_64-multicore/namd2
00fb4000-01292000 rwxp 00ab4000 00:15 97386641
/home/wlay/NAMD_2.9_Linux-x86_64-multicore/namd2
01292000-0129d000 rwxp 00000000 00:00 0
02da8000-27c25000 rwxp 00000000 00:00 0
 [heap]
3471a00000-3471a1e000 r-xp 00000000 08:03 20578696
/lib64/ld-2.12.so
3471c1e000-3471c1f000 r-xp 0001e000 08:03 20578696
/lbc detected *** namd2: invalid fastbin entry (free)ib64/ld-2.12.so
3471c1f000-3471c20000 rwxp 0001f000 08:03 20578696
/lib64/ld-2.12.so
3471c20000-3471c21000 rwxp 00000000 00:00 0
3471e00000-3471f75000 r-xp 00000000 08:03 20578697
/lib64/libc-2.12.so
3471f75000-3472175000 ---p 00175000 08:03 20578697
/lib64/libc-2.12.so
3472175000-3472179000 r-xp 00175000 08:03 20578697
/lib64/libc-2.12.so
3472179000-347217a000 rwxp 00179000 08:03 20578697
/lib64/libc-2.12.so
347217a000-347217f000 rwxp 00000000 00:00 0
3472200000-3472202000 r-xp 00000000 08:03 20578699
/lib64/libdl-2.12.so
3472202000-3472402000 ---p 00002000 08:03 20578699
/lib64/libdl-2.12.so
3472402000-3472403000 r-xp 00002000 08:03 20578699
/lib64/libdl-2.12.so
3472403000-3472404000 rwxp 00003000 08:03 20578699
/lib64/libdl-2.12.so
3472600000-3472617000 r-xp 00000000 08:03 20578698
/lib64/libpthread-2.12.so
3472617000-3472816000 ---p 00017000 08:03 20578698
/lib64/libpthread-2.12.so
3472816000-3472817000 r-xp 00016000 08:03 20578698
/lib64/libpthread-2.12.so
3472817000-3472818000 rwxp 00017000 08:03 20578698
/lib64/libpthread-2.12.so
3472818000-347281c000 rwxp 00000000 00:00 0
3473200000-3473283000 r-xp 00000000 08:03 20578716
/lib64/libm-2.12.so
3472818000-347281c000 rwxp 00000000 00:00 0
3473200000-3473283000 r-xp 00000000 08:03 20578716
/lib64/libm-2.12.so
3473283000-3473482000 ---p 00083000 08:03 20578716
/lib64/libm-2.12.so
3473482000-3473483000 r-xp 00082000 08:03 20578716
/lib64/libm-2.12.so
3473483000-3473484000 rwxp 00083000 08:03 20578716
/lib64/libm-2.12.so
3474a00000-3474a16000 r-xp 00000000 08:03 20578717
/lib64/libgcc_s-4.4.4-20100503.so.1
3474a16000-3474c15000 ---p 00016000 08:03 20578717
/lib64/libgcc_s-4.4.4-20100503.so.1
3474c15000-3474c16000 rwxp 00015000 08:03 20578717
/lib64/libgcc_s-4.4.4-20100503.so.1
3475e00000-3475ee9000 r-xp 00000000 08:03 27668834
/usr/lib64/libstdc++.so.6.0.13
3475ee9000-34760e9000 ---p 000e9000 08:03 27668834
/usr/lib64/libstdc++.so.6.0.13
34760e9000-34760f0000 r-xp 000e9000 08:03 27668834
/usr/lib64/libstdc++.so.6.0.13
34760f0000-34760f2000 rwxp 000f0000 08:03 27668834
/usr/lib64/libstdc++.so.6.0.13
34760f2000-3476107000 rwxp 00000000 00:00 0
347ea00000-347ea16000 r-xp 00000000 08:03 20578734
/lib64/libnsl-2.12.so
347ea16000-347ec15000 ---p 00016000 08:03 20578734
/lib64/libnsl-2.12.so
347ec15000-347ec16000 r-xp 00015000 08:03 20578734
/lib64/libnsl-2.12.so
347ec16000-347ec17000 rwxp 00016000 08:03 20578734
/lib64/libnsl-2.12.so
347ec17000-347ec19000 rwxp 00000000 00:00 0
7f060c000000-7f060d35d000 rwxp 00000000 00:00 0
7f060d35d000-7f0610000000 ---p 00000000 00:00 0
7f0614000000-7f0614fb1000 rwxp 00000000 00:00 0
7f0614fb1000-7f0618000000 ---p 00000000 00:00 0
7f061c000000-7f061d17f000 rwxp 00000000 00:00 0
7f061d17f000-7f0620000000 ---p 00000000 00:00 0
7f0624000000-7f0625465000 rwxp 00000000 00:00 0
7f0625465000-7f0628000000 ---p 00000000 00:00 0
7f062c000000-7f062d2f0000 rwxp 00000000 00:00 0
7f062d2f0000-7f0630000000 ---p 00000000 00:00 0
7f0634000000-7f0635141000 rwxp 00000000 00:00 0
7f0635141000-7f0638000000 ---p 00000000 00:00 0
7f063c000000-7f063d0f2000 rwxp 00000000 00:00 0
7f063d0f2000-7f0640000000 ---p 00000000 00:00 0
7f0644000000-7f06452b5000 rwxp 00000000 00:00 0
7f06452b5000-7f0648000000 ---p 00000000 00:00 0
7f0648000000-7f06490ba000 rwxp 00000000 00:00 0
7f06490ba000-7f064c000000 ---p 00000000 00:00 0
7f0650000000-7f065286f000 rwxp 00000000 00:00 0
7f065286f000-7f0654000000 ---p 00000000 00:00 0
7f0658000000-7f0659158000 rwxp 00000000 00:00 0
7f0659158000-7f065c000000 ---p 00000000 00:00 0
7f065c000000-7f065d170000 rwxp 00000000 00:00 0
7f065d170000-7f0660000000 ---p 00000000 00:00 0
7f065c000000-7f065d170000 rwxp 00000000 00:00 0
7f065d170000-7f0660000000 ---p 00000000 00:00 0
7f0660000000-7f066138a000 rwxp 00000000 00:00 0
7f066138a000-7f0664000000 ---p 00000000 00:00 0
7f0668000000-7f0668f4a000 rwxp 00000000 00:00 0
7f0668f4a000-7f066c000000 ---p 00000000 00:00 0
7f0670000000-7f0671107000 rwxp 00000000 00:00 0
7f0671107000-7f0674000000 ---p 00000000 00:00 0
7f0678000000-7f06791f3000 rwxp 00000000 00:00 0
7f06791f3000-7f067c000000 ---p 00000000 00:00 0
7f0680000000-7f0681409000 rwxp 00000000 00:00 0
7f0681409000-7f0684000000 ---p 00000000 00:00 0
7f0684000000-7f068538a000 rwxp 00000000 00:00 0
7f068538a000-7f0688000000 ---p 00000000 00:00 0
7f0688000000-7f0688f3a000 rwxp 00000000 00:00 0
7f0688f3a000-7f068c000000 ---p 00000000 00:00 0
7f0690000000-7f069177c000 rwxp 00000000 00:00 0
7f069177c000-7f0694000000 ---p 00000000 00:00 0
7f0694000000-7f069523f000 rwxp 00000000 00:00 0
7f069523f000-7f0698000000 ---p 00000000 00:00 0
7f0698000000-7f0699445000 rwxp 00000000 00:00 0
7f0699445000-7f069c000000 ---p 00000000 00:00 0
7f06a0000000-7f06a14a5000 rwxp 00000000 00:00 0
7f06a14a5000-7f06a4000000 ---p 00000000 00:00 0
7f06a533a000-7f06a616f000 rwxp 00000000 00:00 0
7f06a616f000-7f06ac000000 r-xp 00000000 08:03 27660829
/usr/lib/locale/locale-archive
7f06ac000000-7f06affe6000 rwxp 00000000 00:00 0
7f06affe6000-7f06b0000000 ---p 00000000 00:00 0
7f06b03cd000-7f06b4000000 rwxp 00000000 00:00 0
7f06b4000000-7f06b7fb4000 rwxp 00000000 00:00 0
7f06b7fb4000-7f06b8000000 ---p 00000000 00:00 0
7f06b8000000-7f06bbf42000 rwxp 00000000 00:00 0
7f06bbf42000-7f06bc000000 ---p 00000000 00:00 0
7f06bc000000-7f06bffee000 rwxp 00000000 00:00 0
7f06bffee000-7f06c0000000 ---p 00000000 00:00 0
7f06c0000000-7f06c3fcd000 rwxp 00000000 00:00 0
7f06c3fcd000-7f06c4000000 ---p 00000000 00:00 0
7f06c4000000-7f06c7ffb000 rwxp 00000000 00:00 0
7f06c7ffb000-7f06c8000000 ---p 00000000 00:00 0
7f06c8000000-7f06cbea5000 rwxp 00000000 00:00 0
7f06cbea5000-7f06cc000000 ---p 00000000 00:00 0
7f06cc000000-7f06cfe7e000 rwxp 00000000 00:00 0
7f06cbea5000-7f06cc000000 ---p 00000000 00:00 0
7f06cc000000-7f06cfe7e000 rwxp 00000000 00:00 0
7f06cfe7e000-7f06d0000000 ---p 00000000 00:00 0
7f06d0000000-7f06d3f59000 rwxp 00000000 00:00 0
7f06d3f59000-7f06d4000000 ---p 00000000 00:00 0
7f06d4000000-7f06d7ffc000 rwxp 00000000 00:00 0
7f06d7ffc000-7f06d8000000 ---p 00000000 00:00 0
7f06d8000000-7f06dbefc000 rwxp 00000000 00:00 0
7f06dbefc000-7f06dc000000 ---p 00000000 00:00 0
7f06dc000000-7f06dffeb000 rwxp 00000000 00:00 0
7f06dffeb000-7f06e0000000 ---p 00000000 00:00 0
7f06e0ca1000-7f06e4000000 rwxp 00000000 00:00 0
7f06e4000000-7f06e7ffb000 rwxp 00000000 00:00 0
7f06e7ffb000-7f06e8000000 ---p 00000000 00:00 0
7f06e8000000-7f06ebf97000 rwxp 00000000 00:00 0
7f06ebf97000-7f06ec000000 ---p 00000000 00:00 0
7f06ec000000-7f06efe6c000 rwxp 00000000 00:00 0
7f06efe6c000-7f06f0000000 ---p 00000000 00:00 0
7f06f0160000-7f06f2bfe000 rwxp 00000000 00:00 0
7f06f2bfe000-7f06f2bff000 ---p 00000000 00:00 0
7f06f2bff000-7f06f35ff000 rwxp 00000000 00:00 0
7f06f35ff000-7f06f3600000 ---p 00000000 00:00 0
7f06f3600000-7f06f4000000 rwxp 00000000 00:00 0
7f06f4000000-7f06f7ff0000 rwxp 00000000 00:00 0
7f06f7ff0000-7f06f8000000 ---p 00000000 00:00 0
7f06f83fa000-7f06f83fb000 ---p 00000000 00:00 0
7f06f83fb000-7f06f8dfb000 rwxp 00000000 00:00 0
7f06f8dfb000-7f06f8dfc000 ---p 00000000 00:00 0
7f06f8dfc000-7f06f97fc000 rwxp 00000000 00:00 0
7f06f97fc000-7f06f97fd000 ---p 00000000 00:00 0
7f06f97fd000-7f06fa1fd000 rwxp 00000000 00:00 0
7f06fa1fd000-7f06fa1fe000 ---p 00000000 00:00 0
7f06fa1fe000-7f06fabfe000 rwxp 00000000 00:00 0
7f06fabfe000-7f06fabff000 ---p 00000000 00:00 0
7f06fabff000-7f06fb5ff000 rwxp 00000000 00:00 0
7f06fb5ff000-7f06fb600000 ---p 00000000 00:00 0
7f06fb600000-7f06fc000000 rwxp 00000000 00:00 0
7f06fc000000-7f06fffe2000 rwxp 00000000 00:00 0
7f06fffe2000-7f0700000000 ---p 00000000 00:00 0
7f0700000000-7f0703f30000 rwxp 00000000 00:00 0
7f0703f30000-7f0704000000 ---p 00000000 00:00 0
7f07043fa000-7f07043fb000 ---p 00000000 00:00 0

7f0703f30000-7f0704000000 ---p 00000000 00:00 0
7f07043fa000-7f07043fb000 ---p 00000000 00:00 0
7f07043fb000-7f0704dfb000 rwxp 00000000 00:00 0
7f0704dfb000-7f0704dfc000 ---p 00000000 00:00 0
7f0704dfc000-7f07057fc000 rwxp 00000000 00:00 0
7f07057fc000-7f07057fd000 ---p 00000000 00:00 0
7f07057fd000-7f07061fd000 rwxp 00000000 00:00 0
7f07061fd000-7f07061fe000 ---p 00000000 00:00 0
7f07061fe000-7f0706bfe000 rwxp 00000000 00:00 0
7f0706bfe000-7f0706bff000 ---p 00000000 00:00 0
7f0706bff000-7f07075ff000 rwxp 00000000 00:00 0
7f07075ff000-7f0707600000 ---p 00000000 00:00 0
7f0707600000-7f0708000000 rwxp 00000000 00:00 0
7f0708000000-7f070bdb8000 rwxp 00000000 00:00 0
7f070bdb8000-7f070c000000 ---p 00000000 00:00 0
7f070c000000-7f070ffef000 rwxp 00000000 00:00 0
7f070ffef000-7f0710000000 ---p 00000000 00:00 0
7f0710000000-7f0713f6c000 rwxp 00000000 00:00 0
7f0713f6c000-7f0714000000 ---p 00000000 00:00 0
7f0714000000-7f0717fe3000 rwxp 00000000 00:00 0
7f0717fe3000-7f0718000000 ---p 00000000 00:00 0
7f07183fa000-7f07183fb000 ---p 00000000 00:00 0
7f07183fb000-7f0718dfb000 rwxp 00000000 00:00 0
7f0718dfb000-7f0718dfc000 ---p 00000000 00:00 0
7f0718dfc000-7f07197fc000 rwxp 00000000 00:00 0
7f07197fc000-7f07197fd000 ---p 00000000 00:00 0
7f07197fd000-7f071a1fd000 rwxp 00000000 00:00 0
7f071a1fd000-7f071a1fe000 ---p 00000000 00:00 0
7f071a1fe000-7f071abfe000 rwxp 00000000 00:00 0
7f071abfe000-7f071abff000 ---p 00000000 00:00 0
7f071abff000-7f071b5ff000 rwxp 00000000 00:00 0
7f071b5ff000-7f071b600000 ---p 00000000 00:00 0
7f071b600000-7f071c000000 rwxp 00000000 00:00 0
7f071c000000-7f071fffb000 rwxp 00000000 00:00 0
7f071fffb000-7f0720000000 ---p 00000000 00:00 0
7f0720143000-7f072014d000 r-xp 00000000 08:03 20578338
/lib64/libnss_nis-
7f072014d000-7f072034c000 ---p 0000a000 08:03 20578338
/lib64/libnss_nis-
7f072034c000-7f072034d000 r-xp 00009000 08:03 20578338
/lib64/libnss_nis-
7f072034d000-7f072034e000 rwxp 0000a000 08:03 20578338
/lib64/libnss_nis-
7f072034e000-7f072035a000 r-xp 00000000 08:03 20578334
/lib64/libnss_file
7f072035a000-7f0720559000 ---p 0000c000 08:03 20578334
/lib64/libnss_file
7f0720559000-7f072055a000 r-xp 0000b000 08:03 20578334
/lib64/libnss_file
7f072035a000-7f0720559000 ---p 0000c000 08:03 20578334
/lib64/libnss_file
7f0720559000-7f072055a000 r-xp 0000b000 08:03 20578334
/lib64/libnss_file
7f072055a000-7f072055b000 rwxp 0000c000 08:03 20578334
/lib64/libnss_file
7f0720568000-7f0720589000 rwxp 00000000 00:00 0
7f0720589000-7f072058a000 ---p 00000000 00:00 0
7f072058a000-7f0720f8a000 rwxp 00000000 00:00 0
7f0720f8a000-7f0720f8b000 ---p 00000000 00:00 0
7f0720f8b000-7f072198b000 rwxp 00000000 00:00 0
7f072198b000-7f072198c000 ---p 00000000 00:00 0
7f072198c000-7f072238c000 rwxp 00000000 00:00 0
7f072238c000-7f072238d000 ---p 00000000 00:00 0
7f072238d000-7f0722d92000 rwxp 00000000 00:00 0
7f0722d9e000-7f0722da0000 rwxp 00000000 00:00 0
7fffd576d000-7fffd5782000 rwxp 00000000 00:00 0
 [stack]
7fffd57ff000-7fffd5800000 r-xp 00000000 00:00 0
 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
 [vsyscall]

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:48 CST