[CP2K:6407] Re: CP2K Hangs

[Luiz Fernando Lopes Oliveira]

Hi Manav.

We are having similar problems and were wondering if you had a solution for 
that.

Do you think the problem was finally with the intel compilers?

Thanks!

On Saturday, April 25, 2015 at 2:26:16 AM UTC-7, Manav Kumar wrote:
>
> Hi James,
>
> No, I haven't tried that yet. I will pass on the information to the system 
> administrators at our HPC and see what they say. Did that fix the issue 
> with you?
>
> Best,
> Manav Kumar
>
>
> On Saturday, April 25, 2015 at 5:05:16 AM UTC-4, JamesChen wrote:
>>
>> Hi Manav,
>> I have a similar issue with mvapich2 and some buggy version of Intel 
>> compilers. It seems that you are using rather standard software stack. Have 
>> you ever downgraded your openmpi to 1.6.5 (prior stable version)? 
>> James
>>
>> On Sat, Apr 25, 2015 at 6:08 AM, Manav Kumar <mk3... at nyu.edu> wrote:
>>
>>> 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> 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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