Hello,
On Wed, Nov 17, 2010 at 10:34 PM, Catein Catherine
<askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
>
> I have AMBER10 installed on our supercomputer facilites. We have
> experience of doing molecular dynamics calculation for a system with ~800
> amino acid residues. We are trying very hard now to do the analysis for a
> system with ~1500 amino acid residues. However, the following error message
> was found. I double check the jobs. It is an error message occurs when I
> do minization for the whole system. I found no error message in out file,
> but it just hang at ~1800 steps. when I tried to check the rst file
> generated, nothing could be found in the xxx.rst file. It seems to me that
> the jobs is trying to store temperary files (somewhere in the supercomputer)
> before it can write to the xxx.rst. However, since the file is too large
> for the temperary file. All the jobs dead before ending properly.
>
Sander and pmemd do not use "temporary" files. It will write directly to
the file specified on the command line, nothing else. If you do not specify
a path, it will simply write it in the present working directory, which on a
cluster may be unknown unless you specifically change directories (i.e. cd
$PBS_O_WORKDIR for many PBS systems).
Also, sander/pmemd are easily capable handling systems of such size. My
suggestion would be to try a shorter minimization, printing out each step to
see if you can reproduce the problem.
Lastly, did you apply all bug fixes?
Good luck!
Jason
>
> I am writing to ask if (a) my explanation seems reasonable for the
> observation that I got so far? (b) did any one tried to use amber to
> calculate a system with ~1500 residues (including water)? (c) are there any
> easy way to solve this problem? (d) Can I define where to store the
> temperaray files? If yes, how to do so, without compiling the amber10 all
> over again?
>
> p2_28577: p4_error: net_recv read: probable EOF on socket: 1
> p3_28618: p4_error: net_recv read: probable EOF on socket: 1
> p7_28782: p4_error: net_recv read: probable EOF on socket: 1
> p6_28741: p4_error: net_recv read: probable EOF on socket: 1
> p5_28700: p4_error: net_recv read: probable EOF on socket: 1
> rm_l_6_28780: (1536.687500) net_send: could not write to fd=5, errno = 32
> rm_l_3_28657: (1536.921875) net_send: could not write to fd=5, errno = 32
> rm_l_2_28616: (1537.000000) net_send: could not write to fd=5, errno = 32
> rm_l_1_28575: (1537.074219) net_send: could not write to fd=6, errno = 9
> rm_l_1_28575: p4_error: net_send write: -1
> to fd=5, errno = 32
>
>
> Many thanks in advance.
>
> Best regards,
>
> Catherine
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Nov 18 2010 - 07:30:25 PST
