[CP2K:6405] Re: CP2K Hangs

[Manav Kumar]

Hi James,

I'm assuming when you say the software environment, you mean the 
dependencies for CP2K. Here are the dependencies that are added to my 
environment when I use the CP2K module:

'gcc/4.9.1'

'openmpi/gcc_4.9.1/1.8.3'

'mpiblacs/gcc_4.9.1/openmpi_1.8.3/2.0.2'

'lapack/gcc_4.9.1/3.5.0'

'scalapack/gcc_4.9.1/openmpi_1.8.3/2.0.2'

'fftw3/gcc_4.9.1/3.3.4'


Let me know if there is any other information that might help!


Best,

MK

On Friday, April 24, 2015 at 5:56:32 PM UTC-4, JamesChen wrote:
>
> Hi,
> Could you provide us your software environment? Are you using mvapich2 as 
> MPI? I will suggest you follow the CP2K manual and choose Gfortran/Gnu 
> compiler, Netlib Math library and Openmpi as the reference software stack.
> http://www.cp2k.org/howto:compile 
>
> Cheers,
> James
>
> On Sat, Apr 25, 2015 at 5:08 AM, Manav Kumar <mk3... at nyu.edu <javascript:>
> > wrote:
>
>> Hi Matt,
>>
>> Thank you for your response!
>>
>> I'm sorry I mis-spoke earlier, I meant to say that NVT not NVE that's my 
>> mistake. When I ran NVT with CP2K module it worked fine.
>>
>> I ran a cell optimization using the CP2K module, and it went through fine.
>>
>> I have talked to some of the other members in my group, and they 
>> mentioned that it is possible that when I am running the simulation on 
>> multiple nodes that one of them is faulty and therefore causing the 
>> calculations to hang. However, it seems like the probability of me hitting 
>> the same faulty node every time I submit a job seems highly unlikely. Also, 
>> if this was the case then wouldn't the jobs that I submit using my own 
>> compiled version of CP2K also hang?
>>
>> When you said that the it was a problem with the cell size, what did you 
>> mean exactly?
>>
>> Best,
>> Manav Kumar
>>
>>
>> On Friday, April 24, 2015 at 11:51:29 AM UTC-4, Matt W wrote:
>>>
>>> Hi,
>>>
>>> nothing is obviously wrong with your input that I can see. Maybe (i) 
>>> problem with the executable (ii) problem with cell size.
>>>
>>>
>>> To start debugging -
>>> You say you can run NVE - can you run NVT as you've got it set up?
>>> Can you run a cell optimization, maybe just a few steps, to check that 
>>> the stress tensor/cell volume change is working OK.
>>>
>>> Matt
>>>
>>> On Friday, April 24, 2015 at 12:52:48 PM UTC+1, Manav Kumar wrote:
>>>>
>>>> Hi users and developers,
>>>>
>>>> This is my first project using CP2K, so I'm sorry in advance if some of 
>>>> the things I say might be wrong.
>>>>
>>>> I am currently trying to generate a trajectory for a simulation of 
>>>> diacetone diperoxide (DADP) using a NPT ensemble. I am attaching the input 
>>>> file, and the submit script below.
>>>>
>>>> The HPC that I am using has a CP2K module. I performed a wave-function 
>>>> optimization, geometry optimization, cell optimization, and a NVE ensemble 
>>>> calculation all using the module. However, now that I am running the NPT 
>>>> calculation using the module it seems to hang. It reads in all the 
>>>> parameters from a previous restart file, it starts to initiate the process 
>>>> but gets stuck in the SCF optimization routine. It doesn't print an error 
>>>> message, it just stays at that position until the wall time comes along and 
>>>> kills the process. Sometimes it completes a lot of SCF optimization steps, 
>>>> sometimes it gets through none.
>>>>
>>>> What I've done so far to try to remedy the problem is that I've tried 
>>>> compiling CP2K myself and running the calculation using that executable 
>>>> instead of the module. I've had a bit more success with my own compiled 
>>>> executable, but even with that it sometimes hangs. The system 
>>>> administrators responsible for the HPC checked the binaries and said that 
>>>> everything was fine.
>>>>
>>>> Has anyone else had an issue similar to this?
>>>>
>>>> Best,
>>>> Manav Kumar
>>>>
>>>> I will attach my input file, output file, and submit script below so 
>>>> that you can see what I have been doing.
>>>>
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