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
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:59 CST