[CP2K:6407] Re: CP2K Hangs

[Manav Kumar]

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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