Interrupted system call

From: claudia (claudia.Bertonati_at_uniroma1.it)
Date: Thu Oct 18 2007 - 08:25:22 CDT

• Next message: Wang, Boyang: "how to apply different damping coefficients simultaneously to different atoms in the same system."
• Previous message: George Madalin Giambasu: "pmf segname for amber ff. MAIN?"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi all

I'm running NAMD on a production cluster composed of two machine
architectures : ia64 (2 Itanium CPUs) and x86_64 ( 2 Xeon CPUs and 2
Dualcore2 Duo CPUs). My system is around 60,000 atoms, it happens
several times that my job has been killed abruptly with the following
error: ( or something similar instead of the restart file could be the
*.dcd one)

FATAL ERROR: Error on write to binary file comp_dyn_IV.restart.vel:
Interrupted system call
Stack Traceback:
 [0] CmiAbort+0x20000000005de970 [0x4000000000992b90]
 [1] _Z8NAMD_errPKc+0x1fffffffffd0c0d0 [0x40000000000c0300]
 [2] _ZN6Output17write_binary_fileEPciP6Vector+0x2000000000159970
[0x400000000050dbb0]
 [3]
_ZN6Output25output_restart_velocitiesEiiP6Vector+0x2000000000158ff0
[0x400000000050d240]
 [4] _ZN6Output8velocityEiiP6Vector+0x200000000015b150
[0x400000000050f3b0]
 [5]
_ZN16CollectionMaster17disposeVelocitiesEPNS_21CollectVectorInstanceE+0x1fffffffffd361a0
[0x40000000000ea410]
 [6]
_ZN16CollectionMaster17receiveVelocitiesEP16CollectVectorMsg+0x1fffffffffd32f60
[0x40000000000e71e0]
 [7]
_ZN24CkIndex_CollectionMaster40_call_receiveVelocities_CollectVectorMsgEPvP16CollectionMaster+0x1fffffffffd2df00
[0x40000000000def30]
 [8] CkDeliverMessageFree+0x20000000003c2cf0 [0x4000000000776f80]
 [9] _Z15_processHandlerPvP11CkCoreState+0x20000000003c9090
[0x400000000077aad0]
 [10] CmiHandleMessage+0x20000000005ec100 [0x40000000009a03a0]
 [11] CsdScheduleForever+0x20000000005ec710 [0x40000000009a09c0]
 [12] CsdScheduler+0x20000000005ec620 [0x40000000009a08e0]
 [13] _ZN7BackEnd7suspendEv+0x1fffffffffd1b360 [0x40000000000cf630]
 [14] _ZN9ScriptTcl7suspendEv+0x200000000022a000 [0x40000000005de2e0]
 [15] _ZN9ScriptTcl13runControllerEi+0x200000000022a370
[0x40000000005de660]
 [16] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x200000000022e700
[0x40000000005e1a90]
 [17] /mnt/local/bin/namd2 [0x4000000000a0ea40]
 [18] /mnt/local/bin/namd2 [0x4000000000a9e520]
 [19] /mnt/local/bin/namd2 [0x4000000000a9f940]
 [20] /mnt/local/bin/namd2 [0x4000000000a89070]
 [21] _ZN9ScriptTcl3runEPc+0x2000000000229cb0 [0x40000000005ddfb0]
 [22] main+0x1fffffffffd13e30 [0x40000000000c6bf0]
 [23] __libc_start_main-0x272ee0 [0x2000000000141430]
 [24] _start+0x1fffffffffd0a3e0 [0x40000000000be700]

does anyone know what it is the meaning? it is a problem of connection
between the nodes ( i'm running either on 32 or 16 nodes)? or something
related to my system, i'm able to restart my system without problems

Thanks to all!

Claudia

• Next message: Wang, Boyang: "how to apply different damping coefficients simultaneously to different atoms in the same system."
• Previous message: George Madalin Giambasu: "pmf segname for amber ff. MAIN?"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:23 CST