[AMBER] Random segfaults (invalid memory reference) in sander

From: Margarita I. Bernal-Uruchurtu <mabel.uaem.mx>
Date: Fri, 3 May 2019 11:11:59 +0200

Hi All!

Charo del Genio's message struck me this morning as something I've also
been experiencing.
It has been quite difficult to follow due to its randomness.
I'm using sander with SEBOMD and the error seems to come quite unexpectedly
and is not related to convergence in SEBOMD. It has happened with systems
of different sizes and in different thermodynamical conditions.
The strange thing is that I can build a restart file from the last stored
configuration and continue the trajectory without problems.
And also as posted by Charo, it happens in different nodes in the local


Program received signal SIGSEGV: Segmentation fault - invalid memory

Backtrace for this error:

#0 0x7f7e9fc6c2ef in ???

#1 0x7f7e9f2d5e9d in ???

#2 0x7f7e9f28559b in ???

#3 0x7f7ea0db0d54 in ???

#4 0x7f7ea0e0a309 in ???

#5 0x7f7ea0dc51b9 in ???

#6 0x7f7ea11cd5e2 in ???

#7 0x5b5360 in ???

#8 0x574684 in ???

#9 0x577394 in ???

#10 0x7e4097 in ???

#11 0x53b8e4 in ???

#12 0x4ea46f in ???

#13 0x4de8f2 in ???

#14 0x4de9e4 in ???

#15 0x7f7e9fc58444 in ???

#16 0x4592e6 in ???

#17 0xffffffffffffffff in ???


mpirun noticed that process rank 0 with PID 60283 on node nnode037 exited
on signal 11 (Segmentation fault).


Science is built with facts as a house is with stones, but a collection of
facts is no more a science than a heap of stones is a house. - Henri
Margarita I. Bernal-Uruchurtu
Centro de Investigaciones Química, UAEM
+52.777.329.7000 ext 6003
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Received on Fri May 03 2019 - 02:30:02 PDT
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