AMBER Archive (2005)

Subject: AMBER: Error in "restrt" output file

From: Alexander Rubinstein (arubin_at_unmc.edu)
Date: Wed Sep 14 2005 - 16:30:49 CDT

Dear AMBER users,

I would like to carry out a long time high temperature MD simulation for
30- residue peptide in explicit water by ABMER 7. I am performing all
calculations on the Beowulf cluster containing 32x nodes Atipa Dual-Xeon
(32x Xeon 3.06 GHz and 32x Xeon 2.4 GHz) running RedHat Linux 7.3. I have
done it for time simulations over 10 ns by multiple runs 200-400 ps, but
after some runs errors become in the output coordinate
 “restrt” file - the final set of coordinates from the MD run.

I would very appreciate if some one helps me to find out this problem.
Please find enclosed below the relevant files:

sander_53_PP_p3.o1738:
Date: Wed Aug 10 11:28:47 CDT 2005
The master node of this job is node027
The working directory is /home/......../MD_PPII_T500
The node file is /usr/spool/PBS/aux/1738.head
This job runs on the following nodes:
node027 node027 node026 node026 node025 node025 node024 node024
This job has allocated 8 cpus
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

PGFIO-F-231/formatted read/unit=9/error on data conversion.
 File name = md_52_Ab40_WN.xyz formatted, sequential access record = 3254
 In source file _ew_setup_.f, at line number 3260
p7_13395: p4_error: net_recv read: probable EOF on socket: 1
p6_13386: p4_error: net_recv read: probable EOF on socket: 1
p5_13395: p4_error: net_recv read: probable EOF on socket: 1
p3_13395: p4_error: net_recv read: probable EOF on socket: 1
p4_13386: p4_error: net_recv read: probable EOF on socket: 1
p2_13386: p4_error: net_recv read: probable EOF on socket: 1
bm_list_14395: (0.195413) wakeup_slave: unable to interrupt slave 0 pid
14394
p1_14398: p4_error: net_recv read: probable EOF on socket: 1
bm_list_14395: (0.195510) wakeup_slave: unable to interrupt slave 0 pid
14394
bm_list_14395: (0.195574) wakeup_slave: unable to interrupt slave 0 pid
14394
bm_list_14395: (0.195610) wakeup_slave: unable to interrupt slave 0 pid
14394
bm_list_14395: (0.195648) wakeup_slave: unable to interrupt slave 0 pid
14394
bm_list_14395: (0.195690) wakeup_slave: unable to interrupt slave 0 pid
14394
bm_list_14395: (0.195756) wakeup_slave: unable to interrupt slave 0 pid
14394


md_52_Ab40_WN.xyz (“restrt” file):
 
line 1 > 17267 0.1160200E+05
           -46.8339026 188.5295923 38.0942556 -45.8985398 188.1987971
37.9051236
           .................................................
           .................................................
line 3254> 310.0074935 299.7106465 -96.1944303 116.7414444 -30.3483541
************
           116.4267112 -31.2457463************ 116.9960680 -30.0752141
************
           -97.6000294-125.1316991 265.1031660 -97.6053942-124.2881423
264.6508223
           .................................................
           .................................................
           -0.3018643 -0.0648276 0.3413060 -0.6228245 0.8959412
0.4736578

Alexander Rubinshtein, Ph.D.
UNMC Eppley Cancer Center
Molecular Modeling Core Facility
_________________________________
University of Nebraska Medical Center
986805 Nebraska Medical Center
Omaha, Nebraska 68198-6805
USA
Office: (402) 559-7809
Fax: (402) 559-4651
E-mail: arubin_at_unmc.edu
WWW: http://www.unmc.edu/Eppley
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