AMBER Archive (2007)

Subject: Re: AMBER: Error in running replica exchange MD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Feb 20 2007 - 08:26:24 CST

thanks for your reply, I will send it to the committee.
good luck in your studies!
CS

On 2/20/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
>
> I don't know this problem, maybe you could send more information about
> what you are doing. I have used 32 replicas without trouble. can you do
> normal MD with that many nodes to test them? is there any error message in
> the sander outputs?
>
> On 2/20/07, Seongeun Yang <seongeun_at_korea.ac.kr> wrote:
> >
> > Hello all,
> >
> > I met a problem in running REMD.
> >
> > I'm using amber8 installed on Intel Xeon clusters (dual core).
> >
> > After I found that test REMD runs using 16 replicas on 4 nodes were
> > successful for at least 1000 exchanges,
> > I tried to run the same job using 32 replicas on 8 nodes.
> >
> > After just 4 exchanges, the job stopped giving the following error
> > messages.
> >
> > These are a few lines at the beginning of the error messages.
> >
> > .....
> > *** glibc detected *** double free or corruption (!prev):
> > 0x00000000016f2600 ***
> > p23_4663: p4_error: interrupt SIGx: 6
> > rm_l_23_4676: (405.574219) net_send: could not write to fd=5, errno = 32
> > p1_6052: p4_error: net_recv read: probable EOF on socket: 1
> > p2_6069: p4_error: net_recv read: probable EOF on socket: 1
> > rm_l_1_6065: (407.609375) net_send: could not write to fd=5, errno = 32
> > p3_6086: p4_error: net_recv read: probable EOF on socket: 1
> > rm_l_2_6082: ( 407.582031) net_send: could not write to fd=5, errno = 32
> > p28_3283: p4_error: net_recv read: probable EOF on socket: 1
> > rm_l_28_3297: (404.835938) net_send: could not write to fd=5, errno = 32
> > .....
> >
> > Please let me know what is the source of the error in this case.
> >
> > Thanks for your answers in advance.
> >
> > 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology   Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University        E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115
===================================================================

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