Thank you Bruno for the reply.
First, I did not modify step-17. I just try to run the original code with
no modification. The memory I requested is huge. It is really wired.
Second, for "#PBS -l nodes=1:ppn=x", no matter what the value x is, the
error always exists.
Third, I don't know what is batch mode (forgive me). In my own laptop, I
directly use cmake ., make, mpirun -np 4 ./step-17 to run a job. How can
you see it is batch mode and could you please tell me how should I modify
it?
Fourth, I used to use "mpirun -np 4 ./step-17", but someone told me to use
"mpirun step-17" directly because the number of nodes can be know from the
resources I requested (such #PBS -l nodes=1:ppn=4). Anyway, there is no
difference in my practice, and probably it is not the main issue that
results in the memory error.
Thank you very much for you time!!
Best,
Chenchen
在 2016年10月4日星期二 UTC-4下午5:44:41，Bruno Turcksin写道：
>
> Chenchen,
>
> On Tuesday, October 4, 2016 at 5:16:12 PM UTC-4, Chenchen Liu wrote:
>>
>>
>> ***Memory allocation failed for SetupCtrl: maxvwgt. Requested size:
>> 18446744073709551608 bytes
>>
> This line says that you are asking for 18446744073 GB of memory...
>
>
>> It is said that there is a bottleneck for METIS, and it is better to use
>> p4est. However, p4est does not support 1D problem, which is what I am
>> working on. Therefore, I have to work out with METIS. I am wondering where
>> is my problem when running step-17 or 18 on cluster. The softwares are
>> supposed to be installed correctly. Here I attach my pbs file, and I hope
>> anyone could help me check it. Or anyone can share the pbs file to run
>> step-17 with multiple nodes?
>>
>> Did you modify step-17?
>
>
>> ==========================
>>
>> #!/bin/sh
>>
>> #PBS -q MyName
>>
>> #PBS -l nodes=1:ppn=4
>>
> This asks for only 4 processors on 1 node.
>
>
>> #PBS -l pmem=15000MB
>>
>> #PBS -l walltime=20:00:00:00
>>
>>
>> module load cmake-2.8
>>
> module load dealii-8.3.0
>>
>>
>> cd $PBS_O_WORKDIR
>>
>>
>> NO_OF_NODES=`cat $PBS_NODEFILE | egrep -v '^#'\|'^$' | wc -l | awk
>> '{print $1}'`
>>
>> NODE_LIST=`cat $PBS_NODEFILE`
>>
>>
>> time cmake . < CMakeLists.txt >LOG
>>
>> time make
>>
> Why are you compiling in batch mode? Do it interactively and make sure
> that everything is correct and then run the executable in batch.
>
>
>> time mpirun step-17
>>
> Don't you need to do something like mpirun -np 4 ./step-17
>
> Best,
>
> Bruno
>
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