[CP2K:6407] Re: CP2K Hangs

[Luiz Fernando Lopes Oliveira]

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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