Thanks for your reply.
I sent my reply about what I'm working on, but the post seems to be evaporated, believe it or not.
The system of interest is an (Ala)21 peptide in TIP3P water.
Amber8 definitely did not work with 32 replicas and the size of mdcrd files on the same node was different.
Is this normal?
With amber9, the REMD job with 32 replicas seems to run without problem up to now.
But some trivial points in preparing 'groupfile' should be clearly mentioned in the manual, I think.
Such as 'no blank line in the groupfile is allowed' and '-rem 1 -remlog rem.log options should be'.
But it's my fault no to look up files in testcases, of course.
Thanks anyway.
Seongeun
----- Original Message -----
From: Carlos Simmerling
To: amber.scripps.edu
Sent: Saturday, February 24, 2007 12:16 AM
Subject: Re: AMBER: Error in running Replica Exchange MD with amber9
Did the REMD test case pass?
you really need to give more information, it's impossible to help without knowing more about what you are doing. let us know if the test case worked or not and we can try to fix it from there.
On 2/23/07, Seongeun Yang <seongeun.korea.ac.kr> wrote:
Hello all,
After I failed to run REMD using 32 replicas with amber8 as posted a few days ago,
I tried the same REMD job with amber9.
The parallel version of amber9 was installed without error on Intel Xeon cluster,
and the MPI version of sander with no replica exchange did the job without problem.
But a number of attempts to run the REMD job gave the error messages such as below.
.....
0 - MPI_COMM_RANK : Null communicator
[0] Aborting program !
[0] Aborting program!
1 - MPI_COMM_RANK : Null communicator
[1] Aborting program !
[1] Aborting program!
p1_16499: p4_error: : 197
p3_16533: p4_error: : 197
3 - MPI_COMM_RANK : Null communicator
[3] Aborting program !
[3] Aborting program!
p21_1181: p4_error: : 197
19 - MPI_COMM_RANK : Null communicator
[19] Aborting program !
[19] Aborting program!
p19_3303: p4_error: : 197
p0_16494: p4_error: : 197
rm_l_1_16512: (1.417969) net_send: could not write to fd=5, errno = 32
rm_l_3_16547: (1.359375) net_send: could not write to fd=5, errno = 32
.....
.....
Please let me know how to fix this problem.
Thanks a lot.
Seongeun
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Received on Sun Feb 25 2007 - 06:07:57 PST
