[CP2K:5632] Re: Problem on the protonated water system.

Matt W MattWa... at gmail.com
Fri Aug 1 10:33:03 CEST 2014


Hi,

there are some statically compiled cp2k executable available on the 
sourceforge page

http://sourceforge.net/projects/cp2k/files/precompiled/

if you are running on a standard machine linux machine the should "just 
work" - not very quickly and only in serial/ssmp modes. But you could test 
smaller jobs to see whether problems are with your input or your executable.

Matt

On Thursday, July 31, 2014 8:09:30 PM UTC+1, Huan Wang wrote:
>
> Hi Matt,
>
> Thanks for your reply and suggestion. But I am not sure about what you 
> said "one of the precompiled ones to test". Should I try to install and 
> compile the new version 2.6? 
>
> Regards,
> Huan
>
>
>
>
>
>
>
> On Thu, Jul 31, 2014 at 7:24 PM, Matt W <Matt... at gmail.com <javascript:>
> > wrote:
>
>> Hi,
>>
>> your first input runs fine for me on my laptop (in a virtual box with 2GB 
>> of RAM). Your executable must be incorrectly built. Try one of the 
>> precompiled ones to test, maybe.
>>
>> Matt
>>
>>
>> On Thursday, July 31, 2014 3:33:18 PM UTC+1, hua... at mail.huji.ac.il 
>> wrote:
>>>
>>> Dear All,
>>> I tried to submit the H2O-128.inp which is the MD simulation of 128 
>>> water molecules in the cp2k/test/QS/benchmark directory. Unfortunately, I 
>>> got the same error.
>>>
>>> Another test is for the 64 water molecules with one proton as I asked 
>>> yesterday. This time, I used # to comment one of the coordinates of water 
>>> molecule in the &COORD section. After this modification, the program run 
>>> without any error!
>>>
>>> I was wondering if it because of the limitation of my computer that 
>>> could not deal with more than 64 atoms? But for DZVP basis sets the 64-H2O 
>>> with one excess proton system is 1477 orbital functions, only 5 more 
>>> functions compared with 64-H2O neutral system. Furthermore, in the 
>>> literature of *Computer Physics Communications 167 (2005) 103–128*,as 
>>> shown in the Fig. 13 below, that even 256 water molecules could be run in 
>>> 4, 8, 16 or 32 CPUs. The difference between them just the cost of time.
>>>
>>>
>>> <https://lh5.googleusercontent.com/-q_V5FcV5kAU/U9pSkxxjHII/AAAAAAAAAGQ/coqej90xWkE/s1600/Fig-13.png>
>>> I totally have no ideal about what happened in my test. Could someone 
>>> give me some suggestion? Thanks a lot.
>>>
>>> Regards,
>>> Huan
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Tuesday, July 29, 2014 3:23:10 PM UTC+3, hua... at mail.huji.ac.il 
>>> wrote:
>>>>
>>>> Dear All,
>>>>
>>>> I am running MD simulation test on 64 water molecules and 64 water with 
>>>> one proton systems with CP2K/Quickstep. For 64 water molecules, the program 
>>>> went well, however for 64 water molecules with on proton, it returned 
>>>> error. Please find the attached input file "p-H2O_64_BLYP_300K.inp". This 
>>>> file was based on the test file of H2O-64.inp at the 
>>>> ..cp2k/test/QS/benchmark directory of CP2K program. I changed the CHARGE to 
>>>> 1 to adapt the excess proton, the rest of settings were the same as the 
>>>> input file of neutral 64-H2O molecules. 
>>>>
>>>> The version of CP2K I used is 2.3. The CPU information is Intel(R) 
>>>> Xeon(R) CPU E5-2665 0 @ 2.40GHz, and the total memory is 32 GB available. I 
>>>> use 24 cores in one node for this test. The reported error are shown below,
>>>>
>>>>
>>>> [proton17:42359] *** Process received signal ***
>>>> [proton17:42359] Signal: Segmentation fault (11)
>>>> [proton17:42359] Signal code:  (128)
>>>> [proton17:42359] Failing at address: (nil)
>>>> [proton17:42357] *** Process received signal ***
>>>> [proton17:42357] Signal: Segmentation fault (11)
>>>> [proton17:42357] Signal code:  (128)
>>>> [proton17:42357] Failing at address: (nil)
>>>> [proton17:42364] *** Process received signal ***
>>>> [proton17:42364] Signal: Segmentation fault (11)
>>>> [proton17:42364] Signal code:  (128)
>>>> [proton17:42364] Failing at address: (nil)
>>>> [proton17:42366] *** Process received signal ***
>>>> [proton17:42366] Signal: Segmentation fault (11)
>>>> [proton17:42366] Signal code:  (128)
>>>> [proton17:42366] Failing at address: (nil)
>>>> [proton17:42371] *** Process received signal ***
>>>> [proton17:42371] Signal: Segmentation fault (11)
>>>> [proton17:42371] Signal code:  (128)
>>>> [proton17:42371] Failing at address: (nil)
>>>> [proton17:42376] *** Process received signal ***
>>>> [proton17:42376] Signal: Segmentation fault (11)
>>>> [proton17:42376] Signal code:  (128)
>>>> [proton17:42376] Failing at address: (nil)
>>>> [proton17:42377] *** Process received signal ***
>>>> [proton17:42377] Signal: Segmentation fault (11)
>>>> [proton17:42377] Signal code:  (128)
>>>> [proton17:42377] Failing at address: (nil)
>>>> [proton17:42355] *** Process received signal ***
>>>> [proton17:42355] Signal: Segmentation fault (11)
>>>> [proton17:42355] Signal code:  (128)
>>>> [proton17:42355] Failing at address: (nil)
>>>> [proton17:42356] *** Process received signal ***
>>>> [proton17:42356] Signal: Segmentation fault (11)
>>>> [proton17:42356] Signal code:  (128)
>>>> [proton17:42356] Failing at address: (nil)
>>>> [proton17:42358] *** Process received signal ***
>>>> [proton17:42358] Signal: Segmentation fault (11)
>>>> [proton17:42358] Signal code:  (128)
>>>> [proton17:42358] Failing at address: (nil)
>>>> [proton17:42362] *** Process received signal ***
>>>> [proton17:42362] Signal: Segmentation fault (11)
>>>> [proton17:42362] Signal code:  (128)
>>>> [proton17:42362] Failing at address: (nil)
>>>> [proton17:42365] *** Process received signal ***
>>>> [proton17:42365] Signal: Segmentation fault (11)
>>>> [proton17:42365] Signal code:  (128)
>>>> [proton17:42365] Failing at address: (nil)
>>>> [proton17:42367] *** Process received signal ***
>>>> [proton17:42367] Signal: Segmentation fault (11)
>>>> [proton17:42367] Signal code:  (128)
>>>> [proton17:42367] Failing at address: (nil)
>>>> [proton17:42369] *** Process received signal ***
>>>> [proton17:42369] Signal: Segmentation fault (11)
>>>> [proton17:42369] Signal code:  (128)
>>>> [proton17:42369] Failing at address: (nil)
>>>> [proton17:42370] *** Process received signal ***
>>>> [proton17:42370] Signal: Segmentation fault (11)
>>>> [proton17:42370] Signal code:  (128)
>>>> [proton17:42370] Failing at address: (nil)
>>>> [proton17:42372] *** Process received signal ***
>>>> [proton17:42372] Signal: Segmentation fault (11)
>>>> [proton17:42372] Signal code:  (128)
>>>> [proton17:42372] Failing at address: (nil)
>>>> [proton17:42373] *** Process received signal ***
>>>> [proton17:42373] Signal: Segmentation fault (11)
>>>> [proton17:42373] Signal code:  (128)
>>>> [proton17:42373] Failing at address: (nil)
>>>> [proton17:42363] *** Process received signal ***
>>>> [proton17:42363] Signal: Segmentation fault (11)
>>>> [proton17:42363] Signal code:  (128)
>>>> [proton17:42363] Failing at address: (nil)
>>>> [proton17:42361] *** Process received signal ***
>>>> [proton17:42361] Signal: Segmentation fault (11)
>>>> [proton17:42361] Signal code:  (128)
>>>> [proton17:42361] Failing at address: (nil)
>>>> [proton17:42368] *** Process received signal ***
>>>> [proton17:42368] Signal: Segmentation fault (11)
>>>> [proton17:42368] Signal code:  (128)
>>>> [proton17:42368] Failing at address: (nil)
>>>> [proton17:42374] *** Process received signal ***
>>>> [proton17:42374] Signal: Segmentation fault (11)
>>>> [proton17:42374] Signal code:  (128)
>>>> [proton17:42374] Failing at address: (nil)
>>>> [proton17:42375] *** Process received signal ***
>>>> [proton17:42375] Signal: Segmentation fault (11)
>>>> [proton17:42375] Signal code:  (128)
>>>> [proton17:42375] Failing at address: (nil)
>>>> [proton17:42354] *** Process received signal ***
>>>> [proton17:42360] *** Process received signal ***
>>>> [proton17:42360] Signal: Segmentation fault (11)
>>>> [proton17:42360] Signal code:  (128)
>>>> [proton17:42360] Failing at address: (nil)
>>>> [proton17:42354] Signal: Segmentation fault (11)
>>>> [proton17:42354] Signal code:  (128)
>>>> [proton17:42354] Failing at address: (nil)
>>>> [proton17:42377] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b46ae872d00]
>>>> [proton17:42377] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42377] *** End of error message ***
>>>> [proton17:42357] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b4fb84c9d00]
>>>> [proton17:42357] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42357] *** End of error message ***
>>>> [proton17:42376] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b35e5f2cd00]
>>>> [proton17:42376] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42376] *** End of error message ***
>>>> [proton17:42359] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b1c774d5d00]
>>>> [proton17:42359] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42359] *** End of error message ***
>>>> [proton17:42356] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2add3a4fed00]
>>>> [proton17:42356] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42356] *** End of error message ***
>>>> [proton17:42364] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b51161f1d00]
>>>> [proton17:42364] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42364] *** End of error message ***
>>>> [proton17:42367] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b1aef997d00]
>>>> [proton17:42367] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42367] *** End of error message ***
>>>> [proton17:42366] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b1724dffd00]
>>>> [proton17:42366] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42366] *** End of error message ***
>>>> [proton17:42371] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b4b366efd00]
>>>> [proton17:42371] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42371] *** End of error message ***
>>>> [proton17:42358] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2acbc8278d00]
>>>> [proton17:42358] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42358] *** End of error message ***
>>>> [proton17:42365] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2ba8a6352d00]
>>>> [proton17:42365] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42365] *** End of error message ***
>>>> [proton17:42373] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b7c8c157d00]
>>>> [proton17:42373] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42373] *** End of error message ***
>>>> [proton17:42369] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b951c33ed00]
>>>> [proton17:42369] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42369] *** End of error message ***
>>>> [proton17:42355] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b84d27d1d00]
>>>> [proton17:42355] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42355] *** End of error message ***
>>>> [proton17:42370] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b7e4a2fad00]
>>>> [proton17:42370] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42370] *** End of error message ***
>>>> [proton17:42363] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b1e83351d00]
>>>> [proton17:42363] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42363] *** End of error message ***
>>>> [proton17:42362] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b75186a5d00]
>>>> [proton17:42362] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42362] *** End of error message ***
>>>> [proton17:42372] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b162a405d00]
>>>> [proton17:42372] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42372] *** End of error message ***
>>>> [proton17:42374] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2abdbacb1d00]
>>>> [proton17:42374] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42374] *** End of error message ***
>>>> [proton17:42375] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b2c29737d00]
>>>> [proton17:42375] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42375] *** End of error message ***
>>>> [proton17:42361] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b50610a8d00]
>>>> [proton17:42361] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42361] *** End of error message ***
>>>> [proton17:42368] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b392e382d00]
>>>> [proton17:42368] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42368] *** End of error message ***
>>>> [proton17:42360] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2ba37b3d0d00]
>>>> [proton17:42360] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42360] *** End of error message ***
>>>> [proton17:42354] [ 0] /lib64/libpthread.so.0(+0xfd00) [0x2b86855ebd00]
>>>> [proton17:42354] [ 1] /opt/cp2k_new_libint/cp2k/
>>>> trunk/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt() [0x20ec04d]
>>>> [proton17:42354] *** End of error message ***
>>>> ------------------------------------------------------------
>>>> --------------
>>>> mpirun noticed that process rank 3 with PID 42357 on node proton17 
>>>> exited on signal 11 (Segmentation fault).
>>>> ------------------------------------------------------------
>>>> --------------
>>>>
>>>> [1]    Exit 139                      /usr/lib64/mpi/gcc/openmpi/bin/mpirun 
>>>> -np 24  ...
>>>>
>>>> The error seems related to the mpi. I am not sure is there any other 
>>>> mistake about my inputs. 
>>>> Any suggestion would be greatly appreciated. Thanks a lot.
>>>>
>>>> Regards,
>>>> Huan 
>>>>
>>>>
>>>>
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