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.
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 17 2010 - 21:00:04 PST
