[petsc-users] memory corruption

[Xuefei (Rebecca) Yuan]

Hello all,

I tried to use superlu as a direct solver running on Hopper, but found that there are some memory corruption errors:

x/xyuan> cd $PBS_O_WORKDIR
Directory: /global/homes/x/xyuan/Workspace_Nersc/cartmhdpdslin/trunk/test_superlu_as_direct_solver/m256_p1024
test_superlu_as_direct_solver/m256_p1024> aprun -n 1024 ./twcartffxmhd.exe -options_file option_twcartffxmhd_256 
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25137 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25146 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25144 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25133 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25136 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25142 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25145 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25148 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25149 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25147 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25135 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25134 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25138 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25141 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25140 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25139 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25132 : Permission denied
[0] ERROR - MPIU_nem_gni_get_hugepages(): Can't create file /var/lib/hugetlbfs/global/pagesize-2097152/hugepagefile.MPICH.1.25143 : Permission denied
*********************************************
cartesian coordinate code(np = 1024)
start time = 0.0000
time accuracy order = 2
viscosity = 0.0500
resistivity = 0.0050
skin depth = 1.0000
hyper resistivity = 0.00000630
hyper viscosity = 0.00503929
problem size: 256 by 256
dt = 0.1000
*********************************************
******* start solving for time = 0.10000 at time step = 1******
  0 SNES Function norm 6.220836330249e-03 
Linear solve converged due to CONVERGED_ITS iterations 1
  1 SNES Function norm 3.041982522542e-07 
*** glibc detected *** *** glibc detected *** *** glibc detected *** *** glibc detected *** ./twcartffxmhd.exe: *** glibc detected *** *** glibc detected *** *** glibc detected *** *** glibc detected *** *** glibc detected *** ./twcartffxmhd.exe: *** glibc detected *** *** glibc detected *** *** glibc detected *** *** glibc detected *** *** glibc detected *** ./twcartffxmhd.exe*** glibc detected *** *** glibc detected *** *** glibc detected *** ./twcartffxmhd.exe: malloc(): memory corruption: 0x0000000001e31280 ***

Any idea what is wrong here?

Thanks very much!

Xuefei (Rebecca) Yuan
Postdoctoral Fellow
Lawrence Berkeley National Laboratory
Tel: 1-510-486-7031