From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Mar 17 2012 - 14:52:17 CDT
On Sat, Mar 17, 2012 at 3:33 PM, Albert <mailmd2011_at_gmail.com> wrote:
> Dear:
[...]
> I am submitting NAMD jobs in IBM blue gene cluster by command:
> # read system values written by CHARMM (need to convert uppercases to
> lowercases)
> exec tr "\[:upper:\]" "\[:lower:\]" < ../step5_assembly.str | sed -e "s/ =
> //g" > step5_assembly.namd.str
you cannot do that on a blue gene compute node.
those compute nodes have a minimalist operating
system that doesn't support multiple processes.
http://en.wikipedia.org/wiki/CNK_operating_system
this has to be done before launching the job.
[...]
> exec mkdir -p toppar
> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" ../toppar/par_all22_prot.prm >
> toppar/par_all22_prot.prm
> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" ../toppar/par_all27_na.prm >
> toppar/par_all27_na.prm
> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" ../toppar/par_all36_carb.prm >
> toppar/par_all36_carb.prm
> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" ../toppar/par_all36_lipid.prm >
> toppar/par_all36_lipid.prm
> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" ../toppar/par_all36_cgenff.prm
>> toppar/par_all36_cgenff.prm
> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" -e "1,/read para/d" \
> -e "278,296d" -e "s/^BOM/!&/g" -e "s/^WRN/!&/g"
> ../toppar/toppar_water_ions.str > toppar/toppar_water_ions.str
> exec sed -e "s/^ATOM/!&/g" -e "s/^MASS/!&/g" -e "1,/read para/d" \
> -e "278,296d" -e "s/^BOM/!&/g" -e "s/^WRN/!&/g"
> ../toppar/toppar_all36_lipid_cholesterol.str >
> toppar/toppar_all36_lipid_cholesterol.str
same thing here.
[...]
> # PME (for full-system periodic electrostatics)
> exec python ../checkfft.py $a $b $c > checkfft.str
.. and here and so on.
> after I submitted the job, I've got the following error messages:
>
> albert_at_notos:~/charmm-gui/namd> more namd.err
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> {snd:3262,rcv:0} Reason: FATAL ERROR: couldn't create pipe: function not
> implemented
> while executing
> "exec tr "\[:upper:\]" "\[:lower:\]" <
> /home/users/albert/charmm-gui/step5_assembly.str
> | sed -e "s/ = //g" > step5_assembly.namd.str"
> (file "step6.1_equilibration.inp" line 8)
>
> namd2: machine.c:1022: CmiAbort: Assertion `0' failed.
> <Mar 17 20:23:46.877519> BE_MPI (ERROR): The error message in the job record
> is as follo
> ws:
> <Mar 17 20:23:46.877575> BE_MPI (ERROR): "killed with signal 6"
>
as you should. please read through the documentation on how
to use a blue gene and what you can and cannot do on a compute
node or talk to some user support person to get that kind of information.
axel.
> thank you very much
> best wishes
> ALBERT
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA.
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