Tutorial-l Mailing List

From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Tue Dec 15 2015 - 22:43:52 CST

Hi,

I am running the tutorial "One-dimensionalumbrellareplica-exchange sampling". I have followed the steps mentioned in the tutorial:

cd umbrella-sampling
mkdir output; cd output
mkdir {0..15}; cd ..

cbme_at_cbme:~$ mpirun --version
mpirun (Open MPI) 1.6.5

The job0.conf file is as follows:

source stretch_alanin.conf

# prevent VMD from reading umbrella.namd by trying command only NAMD has
if { ! [catch numPes] } { source ../usr/local/lib/replica/umbrella/umbrella.namd }

After running the following command:

mpirun -np 16 namd2 +replicas 16 job0.conf +stdout output/%d/job0.%d.log

ERROR appears:

cbme_at_cbme:~/Desktop/replica/umbrella_1d/umbrella_1d$ mpirun -np 16 namd2 +replicas 16 job0.conf _stdout output/%d/job0.%d.log
Charm++: standalone mode (not using charmrun)
Charm++: standalone mode (not using charmrun)
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads
Charm++: standalone mode (not using charmrun)
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads
Charm++: standalone mode (not using charmrun)
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads
Charm++> Running in Multicore mode: 1 threads
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads
Charm++> Running in Multicore mode: 1 threads
Charm++: standalone mode (not using charmrun)
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads
Charm++> Running in Multicore mode: 1 threads
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads
Charm++> Running in Multicore mode: 1 threads
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads
Charm++> Running in Multicore mode: 1 threads
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads
--------------------------------------------------------------------------
mpirun noticed that process rank 15 with PID 2979 on node cbme exited on signal 11 (Segmentation fault).

Computer specification:

Memory: 32gb

Processor: intel@ Core i7-3770 CPU @ 3.40Hz x 8

Graphics: Gallium 0.4 llvmpipe (LLVM 3.5, 256 bits)

OS type: 64-bit

Disk: 3 TB

After this step their is nothing appears, could anyone please help me where is the problem. I am running MPI on single computer. I think I am not able to connect the mpi with the tutorial path.

Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

**
** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
**