[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,
More information about the flash-users
mailing list