Cosmomc(vesrion July 2014) run time error: *** glibc detected *** ./cosmomc: free(): corrupted unsorted chunks

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Brajesh Gupt
Posts: 6
Joined: January 04 2015
Affiliation: Pennsylvania State University

Cosmomc(vesrion July 2014) run time error: *** glibc detecte

Post by Brajesh Gupt » January 15 2015

Hi,

I am trying to run the latest version of cosmomc. It compiles fine but gives the following runtime error. I will be grateful if someone can shed some light on this.

On running:

Code: Select all

 mpirun -np 4 ./cosmomc params_generic.ini
I get the following, which remains the same for different ini files.

Code: Select all

 Number of MPI processes:           4
 file_root:test
 Random seeds: 25827,  6785 rand_inst:   1
*** glibc detected *** ./cosmomc: free(): corrupted unsorted chunks: 0x00000000022d1670 ***
 Random seeds: 25938,  6786 rand_inst:   2
 Random seeds: 26139,  6786 rand_inst:   4
======= Backtrace: =========
 Random seeds: 26040,  6786 rand_inst:   3
/lib64/libc.so.6[0x35da676166]
/lib64/libc.so.6[0x35da678ca3]
./cosmomc(for__free_vm+0x2a)[0x6dbb6a]
./cosmomc(for__close_proc+0x497)[0x69bca7]
./cosmomc(for_close+0x2b1)[0x69b371]
./cosmomc[0x412607]
./cosmomc[0x443664]
./cosmomc[0x48690b]
./cosmomc[0x48637a]
./cosmomc[0x557b8b]
./cosmomc[0x40bace]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x35da61ed1d]
./cosmomc[0x40b969]
======= Memory map: ========
00400000-0087a000 r-xp 00000000 00:18 31761242                           /gpfs/home/bkg12/cosmomc/cosmomc
00a79000-01046000 rw-p 00479000 00:18 31761242                           /gpfs/home/bkg12/cosmomc/cosmomc
01046000-014cd000 rw-p 00000000 00:00 0 
022c4000-022e5000 rw-p 00000000 00:00 0                                  [heap]
35da200000-35da220000 r-xp 00000000 08:03 22937992                       /lib64/ld-2.12.so
35da41f000-35da420000 r--p 0001f000 08:03 22937992                       /lib64/ld-2.12.so
35da420000-35da421000 rw-p 00020000 08:03 22937992                       /lib64/ld-2.12.so
35da421000-35da422000 rw-p 00000000 00:00 0 
35da600000-35da78b000 r-xp 00000000 08:03 22937993                       /lib64/libc-2.12.so
35da78b000-35da98a000 ---p 0018b000 08:03 22937993                       /lib64/libc-2.12.so
35da98a000-35da98e000 r--p 0018a000 08:03 22937993                       /lib64/libc-2.12.so
35da98e000-35da98f000 rw-p 0018e000 08:03 22937993                       /lib64/libc-2.12.so
35da98f000-35da994000 rw-p 00000000 00:00 0 
35daa00000-35daa02000 r-xp 00000000 08:03 22937737                       /lib64/libdl-2.12.so
35daa02000-35dac02000 ---p 00002000 08:03 22937737                       /lib64/libdl-2.12.so
35dac02000-35dac03000 r--p 00002000 08:03 22937737                       /lib64/libdl-2.12.so
35dac03000-35dac04000 rw-p 00003000 08:03 22937737                       /lib64/libdl-2.12.so
35dae00000-35dae17000 r-xp 00000000 08:03 22937998                       /lib64/libpthread-2.12.so
35dae17000-35db017000 ---p 00017000 08:03 22937998                       /lib64/libpthread-2.12.so
35db017000-35db018000 r--p 00017000 08:03 22937998                       /lib64/libpthread-2.12.so
35db018000-35db019000 rw-p 00018000 08:03 22937998                       /lib64/libpthread-2.12.so
35db019000-35db01d000 rw-p 00000000 00:00 0 
35db200000-35db283000 r-xp 00000000 08:03 22937994                       /lib64/libm-2.12.so
35db283000-35db482000 ---p 00083000 08:03 22937994                       /lib64/libm-2.12.so
35db482000-35db483000 r--p 00082000 08:03 22937994                       /lib64/libm-2.12.so
35db483000-35db484000 rw-p 00083000 08:03 22937994                       /lib64/libm-2.12.so
35dba00000-35dba07000 r-xp 00000000 08:03 22938055                       /lib64/librt-2.12.so
35dba07000-35dbc06000 ---p 00007000 08:03 22938055                       /lib64/librt-2.12.so
35dbc06000-35dbc07000 r--p 00006000 08:03 22938055                       /lib64/librt-2.12.so
35dbc07000-35dbc08000 rw-p 00007000 08:03 22938055                       /lib64/librt-2.12.so
2b342a178000-2b342a17a000 rw-p 00000000 00:00 0 
2b342a17a000-2b342a181000 r-xp 00000000 00:18 32009782                   /gpfs/home/bkg12/plancklikelihood/plc-1.0/lib/libclik_f90.so
2b342a181000-2b342a380000 ---p 00007000 00:18 32009782                   /gpfs/home/bkg12/plancklikelihood/plc-1.0/lib/libclik_f90.so
2b342a380000-2b342a381000 rw-p 00006000 00:18 32009782                   /gpfs/home/bkg12/plancklikelihood/plc-1.0/lib/libclik_f90.so
2b342a381000-2b342a8bc000 r-xp 00000000 00:1b 14747806                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2013.0.079/composer_xe_2013.0.079/mkl/lib/intel64/libmkl_intel_lp64.so
2b342a8bc000-2b342aabb000 ---p 0053b000 00:1b 14747806                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2013.0.079/composer_xe_2013.0.079/mkl/lib/intel64/libmkl_intel_lp64.so
2b342aabb000-2b342aac8000 rw-p 0053a000 00:1b 14747806                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2013.0.079/composer_xe_2013.0.079/mkl/lib/intel64/libmkl_intel_lp64.so
2b342aac8000-2b342aacd000 rw-p 00000000 00:00 0 
2b342aacd000-2b342b70d000 r-xp 00000000 00:1b 14747810                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2013.0.079/composer_xe_2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so
2b342b70d000-2b342b90c000 ---p 00c40000 00:1b 14747810                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2013.0.079/composer_xe_2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so
2b342b90c000-2b342ba3e000 rw-p 00c3f000 00:1b 14747810                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2013.0.079/composer_xe_2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so
2b342ba3e000-2b342ba42000 rw-p 00000000 00:00 0 
2b342ba42000-2b342c9e0000 r-xp 00000000 00:1b 14747795                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2013.0.079/composer_xe_2013.0.079/mkl/lib/intel64/libmkl_core.so
2b342c9e0000-2b342cbdf000 ---p 00f9e000 00:1b 14747795                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2013.0.079/composer_xe_2013.0.079/mkl/lib/intel64/libmkl_core.so
2b342cbdf000-2b342cc23000 rw-p 00f9d000 00:1b 14747795                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2013.0.079/composer_xe_2013.0.079/mkl/lib/intel64/libmkl_core.so
2b342cc23000-2b342cc3d000 rw-p 00000000 00:00 0 
2b342cc3d000-2b342cd31000 r-xp 00000000 00:1b 17281924                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libiomp5.so
2b342cd31000-2b342cf31000 ---p 000f4000 00:1b 17281924                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libiomp5.so
2b342cf31000-2b342cf3c000 rw-p 000f4000 00:1b 17281924                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libiomp5.so
2b342cf3c000-2b342cf68000 rw-p 00000000 00:00 0 
2b342cf90000-2b342cf92000 rw-p 00000000 00:00 0 
2b342cf92000-2b342cfa7000 r-xp 00000000 00:1b 13398017                   /gpfs/apps/x86_64-rhel6/gcc/4.8.2/lib64/libgcc_s.so.1
2b342cfa7000-2b342d1a7000 ---p 00015000 00:1b 13398017                   /gpfs/apps/x86_64-rhel6/gcc/4.8.2/lib64/libgcc_s.so.1
2b342d1a7000-2b342d1a8000 rw-p 00015000 00:1b 13398017                   /gpfs/apps/x86_64-rhel6/gcc/4.8.2/lib64/libgcc_s.so.1
2b342d1a8000-2b342d36c000 r-xp 00000000 00:18 32009835                   /gpfs/home/bkg12/plancklikelihood/plc-1.0/lib/libclik.so
2b342d36c000-2b342d56b000 ---p 001c4000 00:18 32009835                   /gpfs/home/bkg12/plancklikelihood/plc-1.0/lib/libclik.so
2b342d56b000-2b342d57a000 rw-p 001c3000 00:18 32009835                   /gpfs/home/bkg12/plancklikelihood/plc-1.0/lib/libclik.so
2b342d57a000-2b342eec1000 rw-p 00000000 00:00 0 
2b342eec1000-2b342ef18000 r-xp 00000000 00:1b 17281915                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libintlc.so.5
2b342ef18000-2b342f118000 ---p 00057000 00:1b 17281915                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libintlc.so.5
2b342f118000-2b342f11a000 rw-p 00057000 00:1b 17281915                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libintlc.so.5
2b342f11a000-2b342f11b000 rw-p 00000000 00:00 0 
2b342f11b000-2b342f140000 r-xp 00000000 00:1b 17748170                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libifport.so.5
2b342f140000-2b342f340000 ---p 00025000 00:1b 17748170                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libifport.so.5
2b342f340000-2b342f342000 rw-p 00025000 00:1b 17748170                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libifport.so.5
2b342f342000-2b342f348000 rw-p 00000000 00:00 0 
2b342f348000-2b342f5c1000 r-xp 00000000 00:1b 17281927                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libimf.so
2b342f5c1000-2b342f7c0000 ---p 00279000 00:1b 17281927                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libimf.so
2b342f7c0000-2b342f802000 rw-p 00278000 00:1b 17281927                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libimf.so
2b342f802000-2b342f803000 rw-p 00000000 00:00 0 
2b342f803000-2b343021b000 r-xp 00000000 00:1b 17281919                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libsvml.so
2b343021b000-2b343041b000 ---p 00a18000 00:1b 17281919                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libsvml.so
2b343041b000-2b3430452000 rw-p 00a18000 00:1b 17281919                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libsvml.so
2b3430452000-2b343057e000 r-xp 00000000 00:1b 17748180                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libifcoremt.so.5
2b343057e000-2b343077d000 ---p 0012c000 00:1b 17748180                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libifcoremt.so.5
2b343077d000-2b3430785000 rw-p 0012b000 00:1b 17748180                   /gpfs/apps/x86_64-rhel6/intel/composer_xe/2015.0.090/composer_xe_2015.0.090/compiler/lib/intel64/libifcoremt.so.5
2b3430785000-2b34307b7000 rw-p 00000000 00:00 0 
2b34307b7000-2b34310f6000 r-xp 00000000 00:18 32009759                   /gpfs/home/bkg12/plancklikelihood/plc-1.0/lib/libclik_mkl.so
2b34310f6000-2b34312f5000 ---p 0093f000 00:18 32009759                   /gpfs/home/bkg12/plancklikelihood/plc-1.0/lib/libclik_mkl.so
2b34312f5000-2b3431310000 rw-p 0093e000 00:18 32009759                   /gpfs/home/bkg12/plancklikelihood/plc-1.0/lib/libclik_mkl.so
2b3431310000-2b343135b000 rw-p 00000000 00:00 0 
2b343135b000-2b343241c000 rw-s 00000000 00:10 658612364                  /dev/shm/mpich_shar_tmpH30P12 (deleted)
2b343241c000-2b343245f000 r--s 00000000 08:03 10785479                   /var/db/nscd/hosts
2b343245f000-2b3432460000 rw-p 00000000 00:00 0 
7fffaad88000-7fffaad9e000 rw-p 00000000 00:00 0                          [stack]
7fffaadff000-7fffaae00000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

=====================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 134
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=====================================================================================
APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)
I tried compiling the code again and again with various settings but the same error every time.

Antony Lewis
Posts: 1941
Joined: September 23 2004
Affiliation: University of Sussex
Contact:

Re: Cosmomc(vesrion July 2014) run time error: *** glibc det

Post by Antony Lewis » January 16 2015

not sure. You can "make cosmomc_debug" and run "cosmomc_debug" to maybe get a more helpful error.

Brajesh Gupt
Posts: 6
Joined: January 04 2015
Affiliation: Pennsylvania State University

Cosmomc(vesrion July 2014) run time error: *** glibc detecte

Post by Brajesh Gupt » January 18 2015

Thanks for you response Antony.

cosmoc_debug gave the same error. I tried a fresh installation of cosmomc and it worked. I still don't know what the issue was.

B

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