segmentation fault when running with mpirun

From: Puneet Singh (singh.punit1990_at_gmail.com)
Date: Fri Jul 24 2015 - 08:05:23 CDT

Dear Sir/Madam,
I had compiled *NAMD 2.10 *using intel 2015 compiler suite.
Now presently i am benchmarking the application on my system (CentOS 6.5
Xeon 2670 v3), though i will incrementally add optimization flags as per my
architecture.

I am using *apoa1.tar.gz* example for benchmarking NAMD.

Now when i use:

   - *mpirun -np 1 ./namd2 +ppn 23 +idlepoll ./apoa1/apoa1.namd*

i get:
[0] Stack Traceback:
  [0:0] CmiAbortHelper+0x71 [0xf02481]
  [0:1] ConverseInit+0x30a [0xf03a6a]
  [0:2] _ZN7BackEnd4initEiPPc+0x89 [0x612c09]
  [0:3] main+0x43 [0x60b5e3]
  [0:4] __libc_start_main+0xfd [0x339c61ed5d]
  [0:5] [0x568839]

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 48184 RUNNING AT shavak249
= EXIT CODE: 139
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)

   - *mpirun -np 1 ./namd2 ./apoa1/apoa1.namd*
   WallClock: 517.594604 CPUTime: 517.594604 Memory: 469.996094 MB
   [Partition 0][Node 0] End of program
   - *mpirun -np 8 ./namd2 ./apoa1/apoa1.namd*
   WallClock: 77.789726 CPUTime: 77.789726 Memory: 335.437500 MB
   [Partition 0][Node 0] End of program
   - *mpirun -np 23 ./namd2 ./apoa1/apoa1.namd*
   WallClock: 40.764713 CPUTime: 40.764709 Memory: 464.347656 MB
   [Partition 0][Node 0] End of progra

Though i guess i am getting my task done with *np* flag of mpirun, but i
want to know why the segfault occurs when *ppn* flag is used with mpirun.
The bench mark here <http://www.hpc.cineca.it/content/namd-benchmark> uses
ppn flag hence , so i doubt now that weather i have built the binary
correctly or not ( Attached : NAMD installation script)!

Eagerly awaiting your reply,

Thanks & Regards,

Puneet Singh


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