[AMBER] Error in running energy minimization

From: DEBOSTUTI GHOSHDASTIDAR <debostutighosh.gmail.com>
Date: Mon, 6 Feb 2012 16:42:11 +0530

*Sir,
     I am running energy minimization for my system which has about 50000
atoms.
     When I am running only the steepest descent the minimization is
complete but
     when I am running both steepest descent and conjugate gradient I am
getting the
     following error:*

-- 
*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: 0x2b6ad2b1eec8
[0,1,9][btl_tcp_frag.c:202:mca_btl_tcp_frag_recv]
[nobel6][0,1,16][btl_tcp_frag.c:202:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed with errno=104
[0,1,24][btl_tcp_frag.c:202:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv:
readv failed with errno=104
[ 0] /lib64/libpthread.so.0 [0x3186e0de80]
[ 1] sander.MPI(nb_adjust_+0x649) [0x5080b9]
[ 2] sander.MPI(ewald_force_+0x135b) [0x50aa8b]
[ 3] sander.MPI(force_+0x2e8d) [0x67a9dd]
[ 4] sander.MPI(sander_+0x40a6) [0x4ac2e6]
[ 5] sander.MPI(MAIN__+0xe27) [0x4a81c3]
[ 6] sander.MPI(main+0xe) [0x88da1e]
[ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x318621d8b4]
[ 8] sander.MPI [0x43a799]
*** End of error message ***
*Also in the output file in both the cases with conjugate gradient and
without it I am getting the following note.*
| Note: 1-4 EEL scale factors were NOT found in the topology file.
|       Using default value of 1.2.
| Note: 1-4 VDW scale factors were NOT found in the topology file.
|       Using default value of 2.0.
*Even when I reduced the number of atoms to 36000. I am getting the same
error.
Please help me out. *
Thanks
Vipul Garg
Final year student
Dept. of Biotechnology
IIT Madras, Chennai-600036
INDIA
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Received on Mon Feb 06 2012 - 03:30:02 PST