Problem on the protonated water system.

[huan... at mail.huji.ac.il]

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 



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20140729/70af15b3/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: p-H2O_64_BLYP_300K.inp
Type: chemical/x-gamess-input
Size: 12804 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20140729/70af15b3/attachment.inp>