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sharc-md / sharc

The SHARC molecular dynamics (MD) program suite is an ab initio MD software package developed to study the excited-state dynamics of molecules.
https://www.sharc-md.org
GNU General Public License v3.0
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wfoverlap.x': munmap_chunk(): invalid pointer: #19

Closed tobigithub closed 1 year ago

tobigithub commented 3 years ago

Hi, when using the precompiled binaries, are there any prerequisites for the test files? water and the CH triplet works, but the CH2_dyson fails with munmap_chunk(): invalid pointer.

cd sharc-master/wfoverlap/source
make test
tkind@shark-ubuntu16:~/shark/sharc-master/wfoverlap/source$ make test
cd ../; ./scripts/ovl_test.bash /home/tkind/shark/sharc-master/wfoverlap/source/.. | tee test.out
Starting ovl_test.bash ...
TDIR=/home/tkind/shark/sharc-master/wfoverlap/source/../test_jobs
================================================
Starting test water ...
Checking output files:
  -> ciovl.out.1thr
  -> ciovl.out.2thr
  -> ciovl.out.direct
  -> ciovl.out.lumorb
 *** Test water finished (error code: 0).
================================================
Starting test CH2_triplet ...
Checking output files:
  -> ciovl.out.ms0
  -> ciovl.out.ms1
  -> ciovl.out.ms-1
 *** Test CH2_triplet finished (error code: 0).
================================================
Starting test CH2_dyson ...
*** Error in `/home/tkind/shark/sharc-master/wfoverlap/source/../../bin/wfoverlap.x': munmap_chunk(): invalid pointer: 0x0000000002653700 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777f5)[0x7f70505f37f5]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7f70506006e8]
/home/tkind/shark/sharc-master/wfoverlap/source/../../bin/wfoverlap.x[0x422eed]
/home/tkind/shark/sharc-master/wfoverlap/source/../../bin/wfoverlap.x[0x408354]
/home/tkind/shark/sharc-master/wfoverlap/source/../../bin/wfoverlap.x[0x4596ba]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f705059c840]
/home/tkind/shark/sharc-master/wfoverlap/source/../../bin/wfoverlap.x[0x4019f9]
======= Memory map: ========
00400000-00461000 r-xp 00000000 08:01 263845                             /home/tkind/shark/sharc-master/bin/wfoverlap_ascii.x
00660000-00661000 rw-p 00060000 08:01 263845                             /home/tkind/shark/sharc-master/bin/wfoverlap_ascii.x
00661000-00662000 rw-p 00000000 00:00 0 
0260f000-0267d000 rw-p 00000000 00:00 0                                  [heap]
7f7048000000-7f7048030000 rw-p 00000000 00:00 0 
7f7048030000-7f704c000000 ---p 00000000 00:00 0 
7f704f39a000-7f704f39b000 ---p 00000000 00:00 0 
7f704f39b000-7f704fb9b000 rw-p 00000000 00:00 0 
7f704fb9b000-7f704fb9e000 r-xp 00000000 08:01 2096                       /lib/x86_64-linux-gnu/libdl-2.23.so
7f704fb9e000-7f704fd9d000 ---p 00003000 08:01 2096                       /lib/x86_64-linux-gnu/libdl-2.23.so
7f704fd9d000-7f704fd9e000 r--p 00002000 08:01 2096                       /lib/x86_64-linux-gnu/libdl-2.23.so
7f704fd9e000-7f704fd9f000 rw-p 00003000 08:01 2096                       /lib/x86_64-linux-gnu/libdl-2.23.so
7f704fd9f000-7f704fddd000 r-xp 00000000 08:01 64620                      /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f704fddd000-7f704ffdc000 ---p 0003e000 08:01 64620                      /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f704ffdc000-7f704ffdd000 r--p 0003d000 08:01 64620                      /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f704ffdd000-7f704ffde000 rw-p 0003e000 08:01 64620                      /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f704ffde000-7f7050375000 r-xp 00000000 08:01 263562                     /usr/lib/atlas-base/libatlas.so.3.0
7f7050375000-7f7050575000 ---p 00397000 08:01 263562                     /usr/lib/atlas-base/libatlas.so.3.0
7f7050575000-7f705057c000 rw-p 00397000 08:01 263562                     /usr/lib/atlas-base/libatlas.so.3.0
7f705057c000-7f705073c000 r-xp 00000000 08:01 2098                       /lib/x86_64-linux-gnu/libc-2.23.so
7f705073c000-7f705093c000 ---p 001c0000 08:01 2098                       /lib/x86_64-linux-gnu/libc-2.23.so
7f705093c000-7f7050940000 r--p 001c0000 08:01 2098                       /lib/x86_64-linux-gnu/libc-2.23.so
7f7050940000-7f7050942000 rw-p 001c4000 08:01 2098                       /lib/x86_64-linux-gnu/libc-2.23.so
7f7050942000-7f7050946000 rw-p 00000000 00:00 0 
7f7050946000-7f705095e000 r-xp 00000000 08:01 2099                       /lib/x86_64-linux-gnu/libpthread-2.23.so
7f705095e000-7f7050b5d000 ---p 00018000 08:01 2099                       /lib/x86_64-linux-gnu/libpthread-2.23.so
7f7050b5d000-7f7050b5e000 r--p 00017000 08:01 2099                       /lib/x86_64-linux-gnu/libpthread-2.23.so
7f7050b5e000-7f7050b5f000 rw-p 00018000 08:01 2099                       /lib/x86_64-linux-gnu/libpthread-2.23.so
7f7050b5d000-7f7050b5e000 r--p 00017000 08:01 2099                       /lib/x86_64-linux-gnu/libpthread-2.23.so
7f7050b5e000-7f7050b5f000 rw-p 00018000 08:01 2099                       /lib/x86_64-linux-gnu/libpthread-2.23.so
7f7050b5f000-7f7050b63000 rw-p 00000000 00:00 0 
7f7050b63000-7f7050b79000 r-xp 00000000 08:01 1955                       /lib/x86_64-linux-gnu/libgcc_s.so.1
7f7050b79000-7f7050d78000 ---p 00016000 08:01 1955                       /lib/x86_64-linux-gnu/libgcc_s.so.1
7f7050d78000-7f7050d79000 rw-p 00015000 08:01 1955                       /lib/x86_64-linux-gnu/libgcc_s.so.1
7f7050d79000-7f7050d9a000 r-xp 00000000 08:01 64555                      /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f7050d9a000-7f7050f99000 ---p 00021000 08:01 64555                      /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f7050f99000-7f7050f9a000 r--p 00020000 08:01 64555                      /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f7050f9a000-7f7050f9b000 rw-p 00021000 08:01 64555                      /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f7050f9b000-7f70510a3000 r-xp 00000000 08:01 2102                       /lib/x86_64-linux-gnu/libm-2.23.so
7f70510a3000-7f70512a2000 ---p 00108000 08:01 2102                       /lib/x86_64-linux-gnu/libm-2.23.so
7f70512a2000-7f70512a3000 r--p 00107000 08:01 2102                       /lib/x86_64-linux-gnu/libm-2.23.so
7f70512a3000-7f70512a4000 rw-p 00108000 08:01 2102                       /lib/x86_64-linux-gnu/libm-2.23.so
7f70512a4000-7f70513cd000 r-xp 00000000 08:01 64744                      /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f70513cd000-7f70515cc000 ---p 00129000 08:01 64744                      /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f70515cc000-7f70515cd000 r--p 00128000 08:01 64744                      /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f70515cd000-7f70515cf000 rw-p 00129000 08:01 64744                      /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f70515cf000-7f7051bae000 r-xp 00000000 08:01 263560                     /usr/lib/atlas-base/atlas/liblapack.so.3.0
7f7051bae000-7f7051dae000 ---p 005df000 08:01 263560                     /usr/lib/atlas-base/atlas/liblapack.so.3.0
7f7051dae000-7f7051db3000 rw-p 005df000 08:01 263560                     /usr/lib/atlas-base/atlas/liblapack.so.3.0
7f7051db3000-7f7051df0000 r-xp 00000000 08:01 263561                     /usr/lib/atlas-base/atlas/libblas.so.3.0
7f7051df0000-7f7051ff0000 ---p 0003d000 08:01 263561                     /usr/lib/atlas-base/atlas/libblas.so.3.0
7f7051ff0000-7f7051ff1000 rw-p 0003d000 08:01 263561                     /usr/lib/atlas-base/atlas/libblas.so.3.0
7f7051ff1000-7f7052017000 r-xp 00000000 08:01 2109                       /lib/x86_64-linux-gnu/ld-2.23.so
7f7052207000-7f705220f000 rw-p 00000000 00:00 0 
7f7052215000-7f7052216000 rw-p 00000000 00:00 0 
7f7052216000-7f7052217000 r--p 00025000 08:01 2109                       /lib/x86_64-linux-gnu/ld-2.23.so
7f7052217000-7f7052218000 rw-p 00026000 08:01 2109                       /lib/x86_64-linux-gnu/ld-2.23.so
7f7052218000-7f7052219000 rw-p 00000000 00:00 0 
7ffce1dc8000-7ffce1de9000 rw-p 00000000 00:00 0                          [stack]
7ffce1df4000-7ffce1df7000 r--p 00000000 00:00 0                          [vvar]
7ffce1df7000-7ffce1df9000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
  ... failed!
 *** Test CH2_dyson finished (error code: 134).
================================================
felixplasser commented 3 years ago

I have seen the same error but then it disappeared once I linked against different BLAS/LAPACK libraries. Don't know ...