RE: AMBER: Sander (Amber 9) crash on cortex

From: Ross Walker <>
Date: Thu, 10 May 2007 13:09:19 -0700

Hi Evan,
This means that an allocation failed. In this case likely the allocation of
ipairs. Note you have an extremely large number of pairs (178,595,354) which
suggests that you are using an extremely big cut off. You are running with
periodic boundaries and PME turned on yes? In which case you only need to
set cut to somewhere between 8 and 10.
If you are running with a solvent cap and really want a large cut off then
you will likely need to recompile sander with 64 bit support. On AIX (I
assume you are running AIX) it is by default only built for 32 bit support.
On AIX this limits the addressable memory space to 256MB (why 256Mb I have
know idea - typical IBM...). The -bmaxdata:0x80000000 on the FC and LOAD
lines in the config.h file increase this to 2GB but you are likely still
exceeding this or some system wide limit. Note often by default the max
datasize in AIX is limited to 1048575 kB by enviroment variables. Your 178
million long pair list takes 681 MB on it's own so you are probably pretty
close to this limit as it is. Try running 'limit' to see...
Anyway, compiling for 64 bit should address this although it may harm
cd $AMBERHOME/src/
make clean
./configure -mpi xlf90_aix
edit config.h and delete all occurances of -bmaxdata=0x80000000
add -q64 to the beginning of the FFLAGS and FOPTFLAGS lines and after
mpxlf90_r on the LOAD line.
make parallel
This should hopefully work although I have not actually tried it.
All the best

|\oss Walker

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From: [] On Behalf Of
Evan Kelly
Sent: Thursday, May 10, 2007 11:57
Subject: AMBER: Sander (Amber 9) crash on cortex

Hi everyone,

I was recently met with the following error in the output file after a
sander crash. The simulation I called for was an energy minimization at the
force-field level of a small (148 residue) protein in a larger box of water
(16000 water molecules). The crash occurred running in parallel on 4 cpus on
an IBM 595 cluster. The error is found below:

| Memory Use Allocated
| Real 3301101
| Hollerith 318114
| Integer 1271200
| Max Pairs 178595354
ASSERTion 'ier == 0' failed in sander.f at line 223.

Please note that the same simulation ran successfully on my iMac G5 with
only one cpu. Does anybody have any suggestions as to what might cause this
sort of crash? Please note that I have successfully run different sander
simulations on this same cluster (QM/MM of a smaller system).


Evan Kelly

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Received on Sun May 13 2007 - 06:07:30 PDT
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