[FLASH-USERS] invalid pointer: 0x00000000114f0f30 in Sod problem

g.granda at irya.unam.mx g.granda at irya.unam.mx
Wed Mar 21 18:22:28 EDT 2018


Hello Flash users,

I'm tetsing FLASH 4.5 using the provided Sod Problem. I was able to 
compile the problem without problem (using ./setup Sod -site=irya.guido 
-2d). The executable have all the libraries linked (as far as I know) :

$ ldd flash4
linux-vdso.so.1 =>  (0x00002b7154fec000)
	libhdf5.so.10 => /home/guido/libraries/hdf5-1.8.20/lib/libhdf5.so.10 
(0x00002b7154ff1000)
	libz.so.1 => /lib64/libz.so.1 (0x0000003530c00000)
	libmpifort.so.12 => 
/home/guido/libraries/mpich-3.2.1/lib/libmpifort.so.12 
(0x00002b71554e2000)
	libmpi.so.12 => /home/guido/libraries/mpich-3.2.1/lib/libmpi.so.12 
(0x00002b7155719000)
	libgfortran.so.1 => /usr/lib64/libgfortran.so.1 (0x00002b7155baf000)
	libm.so.6 => /lib64/libm.so.6 (0x0000003530800000)
	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000039a4800000)
	libc.so.6 => /lib64/libc.so.6 (0x0000003530400000)
	libdl.so.2 => /lib64/libdl.so.2 (0x0000003531000000)
	libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003531400000)
	librt.so.1 => /lib64/librt.so.1 (0x0000003531800000)
	/lib64/ld-linux-x86-64.so.2 (0x0000003530000000)

But after running it with ./flash4 flash.par, I got the following error:

------------------------------------------------------------------------------

  Grid_init: resolution based on runtime params:
   lrefine          dx              dy
       1             0.125           0.125
       2             0.063           0.063
       3             0.031           0.031
       4             0.016           0.016
       5             0.008           0.008
       6             0.004           0.004
  MaterialProperties initialized
  Cosmology initialized
  Source terms initialized
   iteration, no. not moved =            0           0
  refined: total leaf blocks =            1
  refined: total blocks =            1
  [amr_morton_process]: Initializing surr_blks using standard orrery 
implementation
  INFO: Grid_fillGuardCells is ignoring masking.
   iteration, no. not moved =            0           0
  refined: total leaf blocks =            4
  refined: total blocks =            5
   iteration, no. not moved =            0           0
  refined: total leaf blocks =           16
  refined: total blocks =           21
   iteration, no. not moved =            0           3
   iteration, no. not moved =            1           0
  refined: total leaf blocks =           46
  refined: total blocks =           61
   iteration, no. not moved =            0          20
   iteration, no. not moved =            1           0
  refined: total leaf blocks =          124
  refined: total blocks =          165
   iteration, no. not moved =            0          53
   iteration, no. not moved =            1           0
  refined: total leaf blocks =          298
  refined: total blocks =          397
   Finished with Grid_initDomain, no restart
  Ready to call Hydro_init
  Hydro initialized
  Gravity initialized
  Initial dt verified
  *** Wrote checkpoint file to sod_hdf5_chk_0000 ****
  *** Wrote plotfile to sod_hdf5_plt_cnt_0000 ****
  Initial plotfile written
  Driver init all done
*** glibc detected *** ./flash4: munmap_chunk(): invalid pointer: 
0x0000000006aa0f30 ***
======= Backtrace: =========
/lib64/libc.so.6(cfree+0x166)[0x35304712f6]
/usr/lib64/libgfortran.so.1(_gfortran_deallocate+0x26)[0x2b890770c2a6]
./flash4[0x54c51e]
./flash4[0x45dd54]
./flash4[0x42c5d3]
./flash4[0x437067]
./flash4[0x84a1de]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x353041d994]
./flash4(memcmp+0x3b1)[0x424369]
======= Memory map: ========
00400000-008c6000 r-xp 00000000 09:05 84909473                           
/home/guido/FLASH4.5/object/flash4
00ac5000-00acd000 rw-p 004c5000 09:05 84909473                           
/home/guido/FLASH4.5/object/flash4
00acd000-0106a000 rw-p 00acd000 00:00 0
0684b000-06bea000 rw-p 0684b000 00:00 0                                  
[heap]
3530000000-353001c000 r-xp 00000000 09:01 325758                         
/lib64/ld-2.5.so
353021c000-353021d000 r--p 0001c000 09:01 325758                         
/lib64/ld-2.5.so
353021d000-353021e000 rw-p 0001d000 09:01 325758                         
/lib64/ld-2.5.so
3530400000-353054d000 r-xp 00000000 09:01 325759                         
/lib64/libc-2.5.so
353054d000-353074d000 ---p 0014d000 09:01 325759                         
/lib64/libc-2.5.so
353074d000-3530751000 r--p 0014d000 09:01 325759                         
/lib64/libc-2.5.so
3530751000-3530752000 rw-p 00151000 09:01 325759                         
/lib64/libc-2.5.so
3530752000-3530757000 rw-p 3530752000 00:00 0
3530800000-3530882000 r-xp 00000000 09:01 325767                         
/lib64/libm-2.5.so
3530882000-3530a81000 ---p 00082000 09:01 325767                         
/lib64/libm-2.5.so
3530a81000-3530a82000 r--p 00081000 09:01 325767                         
/lib64/libm-2.5.so
3530a82000-3530a83000 rw-p 00082000 09:01 325767                         
/lib64/libm-2.5.so
3530c00000-3530c14000 r-xp 00000000 09:01 325768                         
/lib64/libz.so.1.2.3
3530c14000-3530e13000 ---p 00014000 09:01 325768                         
/lib64/libz.so.1.2.3
3530e13000-3530e14000 rw-p 00013000 09:01 325768                         
/lib64/libz.so.1.2.3
3531000000-3531002000 r-xp 00000000 09:01 325761                         
/lib64/libdl-2.5.so
3531002000-3531202000 ---p 00002000 09:01 325761                         
/lib64/libdl-2.5.so
3531202000-3531203000 r--p 00002000 09:01 325761                         
/lib64/libdl-2.5.so
3531203000-3531204000 rw-p 00003000 09:01 325761                         
/lib64/libdl-2.5.so
3531400000-3531416000 r-xp 00000000 09:01 325762                         
/lib64/libpthread-2.5.so
3531416000-3531615000 ---p 00016000 09:01 325762                         
/lib64/libpthread-2.5.so
3531615000-3531616000 r--p 00015000 09:01 325762                         
/lib64/libpthread-2.5.so
3531616000-3531617000 rw-p 00016000 09:01 325762                         
/lib64/libpthread-2.5.so
3531617000-353161b000 rw-p 3531617000 00:00 0
3531800000-3531807000 r-xp 00000000 09:01 325763                         
/lib64/librt-2.5.so
3531807000-3531a07000 ---p 00007000 09:01 325763                         
/lib64/librt-2.5.so
3531a07000-3531a08000 r--p 00007000 09:01 325763                         
/lib64/librt-2.5.so
3531a08000-3531a09000 rw-p 00008000 09:01 325763                         
/lib64/librt-2.5.so
39a4800000-39a480d000 r-xp 00000000 09:01 325443                         
/lib64/libgcc_s-4.1.2-20080825.so.1
39a480d000-39a4a0d000 ---p 0000d000 09:01 325443                         
/lib64/libgcc_s-4.1.2-20080825.so.1
39a4a0d000-39a4a0e000 rw-p 0000d000 09:01 325443                         
/lib64/libgcc_s-4.1.2-20080825.so.1
2b8906b3b000-2b8906b3d000 rw-p 2b8906b3b000 00:00 0
2b8906b3d000-2b8906e08000 r-xp 00000000 09:05 85001708                   
/home/guido/libraries/hdf5-1.8.20/lib/libhdf5.so.10.3.1
2b8906e08000-2b8907008000 ---p 002cb000 09:05 85001708                   
/home/guido/libraries/hdf5-1.8.20/lib/libhdf5.so.10.3.1
2b8907008000-2b8907013000 rw-p 002cb000 09:05 85001708                   
/home/guido/libraries/hdf5-1.8.20/lib/libhdf5.so.10.3.1
2b8907013000-2b8907015000 rw-p 2b8907013000 00:00 0
2b890702d000-2b890702e000 rw-p 2b890702d000 00:00 0
2b890702e000-2b8907064000 r-xp 00000000 09:05 85000426                   
/home/guido/libraries/mpich-3.2.1/lib/libmpifort.so.12.1.1
2b8907064000-2b8907264000 ---p 00036000 09:05 85000426                   
/home/guido/libraries/mpich-3.2.1/lib/libmpifort.so.12.1.1
2b8907264000-2b8907265000 rw-p 00036000 09:05 85000426                   
/home/guido/libraries/mpich-3.2.1/lib/libmpifort.so.12.1.1
2b8907265000-2b89074af000 r-xp 00000000 09:05 85000421                   
/home/guido/libraries/mpich-3.2.1/lib/libmpi.so.12.1.1
2b89074af000-2b89076af000 ---p 0024a000 09:05 85000421                   
/home/guido/libraries/mpich-3.2.1/lib/libmpi.so.12.1.1
2b89076af000-2b89076c1000 rw-p 0024a000 09:05 85000421                   
/home/guido/libraries/mpich-3.2.1/lib/libmpi.so.12.1.1
2b89076c1000-2b89076fb000 rw-p 2b89076c1000 00:00 0
2b89076fb000-2b8907791000 r-xp 00000000 09:01 2705597                    
/usr/lib64/libgfortran.so.1.0.0
2b8907791000-2b8907990000 ---p 00096000 09:01 2705597                    
/usr/lib64/libgfortran.so.1.0.0
2b8907990000-2b8907992000 rw-p 00095000 09:01 2705597                    
/usr/lib64/libgfortran.so.1.0.0
2b8907992000-2b8907d97000 rw-p 2b8907992000 00:00 0
2b8907daf000-2b8907db9000 r-xp 00000000 09:01 325467                     
/lib64/libnss_files-2.5.so
2b8907db9000-2b8907fb8000 ---p 0000a000 09:01 325Aborted
[guido at calzonzin object]$
[guido at calzonzin object]$
[guido at calzonzin object]$ ldd flash4
	linux-vdso.so.1 =>  (0x00002b7154fec000)
	libhdf5.so.10 => /home/guido/libraries/hdf5-1.8.20/lib/libhdf5.so.10 
(0x00002b7154ff1000)
	libz.so.1 => /lib64/libz.so.1 (0x0000003530c00000)
	libmpifort.so.12 => 
/home/guido/libraries/mpich-3.2.1/lib/libmpifort.so.12 
(0x00002b71554e2000)
	libmpi.so.12 => /home/guido/libraries/mpich-3.2.1/lib/libmpi.so.12 
(0x00002b7155719000)
	libgfortran.so.1 => /usr/lib64/libgfortran.so.1 (0x00002b7155baf000)
	libm.so.6 => /lib64/libm.so.6 (0x0000003530800000)
	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000039a4800000)
	libc.so.6 => /lib64/libc.so.6 (0x0000003530400000)
	libdl.so.2 => /lib64/libdl.so.2 (0x0000003531000000)
	libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003531400000)
	librt.so.1 => /lib64/librt.so.1 (0x0000003531800000)
	/lib64/ld-linux-x86-64.so.2 (0x0000003530000000)
--------------------------------------------------------------------------------

I also ran using the debugging flags (./setup Sod -site=irya.guido -2d 
-debug), and I've just got warning messages of unused variables and a 
success at the end. After running I got:


  Grid_init: resolution based on runtime params:
   lrefine          dx              dy
       1             0.125           0.125
       2             0.063           0.063
       3             0.031           0.031
       4             0.016           0.016
       5             0.008           0.008
       6             0.004           0.004
  MaterialProperties initialized
  Cosmology initialized
  Source terms initialized
   iteration, no. not moved =            0           0
  refined: total leaf blocks =            1
  refined: total blocks =            1
  [amr_morton_process]: Initializing surr_blks using standard orrery 
implementation
  INFO: Grid_fillGuardCells is ignoring masking.
   iteration, no. not moved =            0           0
  refined: total leaf blocks =            4
  refined: total blocks =            5
   iteration, no. not moved =            0           0
  refined: total leaf blocks =           16
  refined: total blocks =           21
   iteration, no. not moved =            0           3
   iteration, no. not moved =            1           0
  refined: total leaf blocks =           46
  refined: total blocks =           61
   iteration, no. not moved =            0          20
   iteration, no. not moved =            1           0
  refined: total leaf blocks =          124
  refined: total blocks =          165
   iteration, no. not moved =            0          53
   iteration, no. not moved =            1           0
  refined: total leaf blocks =          298
  refined: total blocks =          397
   Finished with Grid_initDomain, no restart
  Ready to call Hydro_init
  Hydro initialized
  Gravity initialized
  Initial dt verified
  *** Wrote checkpoint file to sod_hdf5_chk_0000 ****
  *** Wrote plotfile to sod_hdf5_plt_cnt_0000 ****
  Initial plotfile written
  Driver init all done
Fortran runtime error: Array reference out of bounds for array 
'scrch_ptr', upper bound of dimension 2 exceeded (in file 
'hy_uhd_getFaceFlux.F90', at line 584)


I have not idea what is wrong. Could you please help me? I'm using

- gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-55)
- GNU Fortran (GCC) 4.1.2
- hdf5-1.8.20. Which was compiled using: ./configure 
--prefix=/home/guido/libraries/hdf5-1.8.20 --enable-parallel 
--enable-static --enable-shared --enable-fortran 
CC=/home/guido/libraries/mpich-3.2.1/bin/mpicc

- and mpich-3.2.1 . which was compiled using ./configure 
--prefix=/home/guido/libraries/mpich-3.2.1 --enable-fortran=all 
FC=gfortran CC=gcc CXX=g++


Cheers,



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