[CP2K:6407] Re: CP2K Hangs

[Luiz Fernando Lopes Oliveira]

Sure. But, are there some particular tests for these types of problems.
I asked because there so many and there are really specific. 

On Tuesday, February 21, 2017 at 11:46:36 AM UTC-8, Manav Kumar wrote:
>
> Hey Luiz,
>
> There should be some test files that come with the source code.
>
> Best,
> Manav
>
> On Tuesday, February 21, 2017 at 2:34:55 PM UTC-5, Luiz Fernando Lopes 
> Oliveira wrote:
>>
>> Thanks a lot, Manav. I'm compiling it myself.  Could you please point me 
>> to tests files that you mentioned revealed the problem?
>>
>> Thanks
>>
>> On Monday, February 20, 2017 at 12:36:14 PM UTC-8, Manav Kumar wrote:
>>>
>>> Hi Luiz,
>>>
>>> James's recommendation of using a downgraded version of openmpi worked. 
>>> If there is a CP2K module that you are using, you might want to ask your 
>>> HPC system administrators to re-compile it for you. There are some tests 
>>> that come with CP2K that weren't run and they revealed the problem with our 
>>> version of CP2K.
>>>
>>> Best,
>>> Manav
>>>
>>>
>>> On Monday, February 20, 2017 at 1:26:14 PM UTC-5, Luiz Fernando Lopes 
>>> Oliveira wrote:
>>>>
>>>> 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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>>>>>>>>>
>>>>>>>>
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>>>>>>
>>>>>>
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