Core dumped , glibc detected

Hi,
I successfully generated a Cassandra executable with gfortran compiler on Ubuntu , but when i run an NPT simulation SPC water or Diethylether in the example directory i get SEGMETATION FAULT ERROR. Some time it give "glibc detected error".

Below is the error:

openmp_flag = F
*** glibc detected *** /opt/Cassandra_V1.0/Src/cassandra_gfortran.exe: double free or corruption (out): 0x00007f7544dfc010 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7f7548433b96]
/opt/Cassandra_V1.0/Src/cassandra_gfortran.exe[0x4c8644]
/opt/Cassandra_V1.0/Src/cassandra_gfortran.exe[0x490ff3]
/opt/Cassandra_V1.0/Src/cassandra_gfortran.exe[0x4074f1]
/opt/Cassandra_V1.0/Src/cassandra_gfortran.exe[0x408381]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f75483d676d]
/opt/Cassandra_V1.0/Src/cassandra_gfortran.exe[0x4015d9]
======= Memory map: ========
00400000-00506000 r-xp 00000000 08:06 10619237 /opt/Cassandra_V1.0/Src/cassandra_gfortran.exe
00706000-00707000 r--p 00106000 08:06 10619237 /opt/Cassandra_V1.0/Src/cassandra_gfortran.exe
00707000-00708000 rw-p 00107000 08:06 10619237 /opt/Cassandra_V1.0/Src/cassandra_gfortran.exe
00708000-01034000 rw-p 00000000 00:00 0
02039000-0239e000 rw-p 00000000 00:00 0 [heap]
7f7538e51000-7f753ee41000 rw-p 00000000 00:00 0
7f7541e4d000-7f754817f000 rw-p 00000000 00:00 0
7f754817f000-7f75481b4000 r-xp 00000000 08:06 2891145 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f75481b4000-7f75483b3000 ---p 00035000 08:06 2891145 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f75483b3000-7f75483b4000 r--p 00034000 08:06 2891145 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f75483b4000-7f75483b5000 rw-p 00035000 08:06 2891145 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f75483b5000-7f754856a000 r-xp 00000000 08:06 26607729 /lib/x86_64-linux-gnu/libc-2.15.so
7f754856a000-7f754876a000 ---p 001b5000 08:06 26607729 /lib/x86_64-linux-gnu/libc-2.15.so
7f754876a000-7f754876e000 r--p 001b5000 08:06 26607729 /lib/x86_64-linux-gnu/libc-2.15.so
7f754876e000-7f7548770000 rw-p 001b9000 08:06 26607729 /lib/x86_64-linux-gnu/libc-2.15.so
7f7548770000-7f7548775000 rw-p 00000000 00:00 0
7f7548775000-7f754878a000 r-xp 00000000 08:06 26611372 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f754878a000-7f7548989000 ---p 00015000 08:06 26611372 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f7548989000-7f754898a000 r--p 00014000 08:06 26611372 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f754898a000-7f754898b000 rw-p 00015000 08:06 26611372 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f754898b000-7f7548a86000 r-xp 00000000 08:06 26607740 /lib/x86_64-linux-gnu/libm-2.15.so
7f7548a86000-7f7548c85000 ---p 000fb000 08:06 26607740 /lib/x86_64-linux-gnu/libm-2.15.so
7f7548c85000-7f7548c86000 r--p 000fa000 08:06 26607740 /lib/x86_64-linux-gnu/libm-2.15.so
7f7548c86000-7f7548c87000 rw-p 000fb000 08:06 26607740 /lib/x86_64-linux-gnu/libm-2.15.so
7f7548c87000-7f7548d9b000 r-xp 00000000 08:06 2891678 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f7548d9b000-7f7548f9b000 ---p 00114000 08:06 2891678 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f7548f9b000-7f7548f9c000 r--p 00114000 08:06 2891678 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f7548f9c000-7f7548f9e000 rw-p 00115000 08:06 2891678 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f7548f9e000-7f7548fc0000 r-xp 00000000 08:06 26607741 /lib/x86_64-linux-gnu/ld-2.15.so
7f754903c000-7f75491a0000 rw-p 00000000 00:00 0
7f75491bd000-7f75491c0000 rw-p 00000000 00:00 0
7f75491c0000-7f75491c1000 r--p 00022000 08:06 26607741 /lib/x86_64-linux-gnu/ld-2.15.so
7f75491c1000-7f75491c3000 rw-p 00023000 08:06 26607741 /lib/x86_64-linux-gnu/ld-2.15.so
7fffa25ab000-7fffa25cc000 rw-p 00000000 00:00 0 [stack]
7fffa25fe000-7fffa2600000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)


Second, i have a question regarding parallel Cassandra,
What the developers mean by the parallel capability?
Does you mean running multiple independent jobs on a collection of processors as the Towhee does?
or Cassandra is able to speed up a single simulation using multiple cores as most MD packages?

Leila

Lelia,

Is the error reproducible? What are the last few lines of the output in the log file?

Cassandra uses openMP to parallelize energy calculations. Thus, your simulation can be sped up by running on multiple cores on the same node. For small systems, we recommend using up to 4 cores.

Please have a look at the Makefiles that are named as *.openMP

Jindal