From: Luis Rosales (ludwig_at_correo.biomedicas.unam.mx)
Date: Wed Apr 27 2005 - 21:29:51 CDT
Hi all!
John,
I just finished the tests that John suggested, namely, I ran a couple of IMD
simulations using a couple of linux servers. I used the same input files as in
the remote simulations on the alpha server.
I got the same behaviour on NAMD: For my system with 1 protein and 1 protein
fragment, the simulation is killed if I apply a force on the fragment if the
latter is bigger than 15 residues. Tests with smaller fragment sizes run fine,
unless I apply an excesive force on the fragment (but that is expected...).
This time I used as the local machine the same RedHat Linux server to run VMD
and I ran the simulations on a debian linux server with NAMD 2.5.
The error messages are attached at the end of the mail...
So, maybe the error is not related to a floating point exception...
Could be related to limitations on the memory buffer that NAMD uses to
communicate with VMD???
Again, thanks for your help,
Luis
***********************************************************
I ran this test on a system with 2 proteins and 0 waters, for a total
of 110 residues (1651 atoms). One protein is 85 residues long and the 2nd is
20 residues long.
***********************************************************
Info: Pausing IMD
Info: Resuming IMD
Info: Pausing IMD
Info: Resuming IMD
DEBUG: Detaching simulation from remote connection
------------- Processor 0 Exiting: Caught Signal ------------
Signal: segmentation violation
Suggestion: Try running with '++debug', or linking with '-memory paranoid'.
Stack Traceback:
[0] _ZN15GlobalMasterIMD9calculateEv+0x2ef [0x81c5b3f]
[1]
_ZN12GlobalMaster11processDataEPiS0_P6VectorS2_S2_S0_S0_S2_S0_S0_S2_+0x6f
[0x81c16df]
[2] _ZN18GlobalMasterServer11callClientsEv+0x428 [0x81c3384]
[3] _ZN18GlobalMasterServer8recvDataEP20ComputeGlobalDataMsg+0x44a [0x81c2b22]
[4] _ZN10ComputeMgr21recvComputeGlobalDataEP20ComputeGlobalDataMsg+0x1c
[0x811b034]
[5]
_ZN18CkIndex_ComputeMgr48_call_recvComputeGlobalData_ComputeGlobalDataMsgEPvP10ComputeMgr+0x11
[0x811b011]
[6] CkDeliverMessageFree+0x21 [0x827c1f9]
[7] _Z15_processHandlerPvP11CkCoreState+0x393 [0x827d5e3]
[8] CmiHandleMessage+0x1d [0x82b5e25]
[9] _ZN9ScriptTcl7suspendEv+0xc [0x8228c68]
[10] _ZN9ScriptTcl13runControllerEi+0x3f [0x8228c4f]
[11] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0xf4 [0x82292cc]
[12] TclInvokeStringCommand+0x6d [0x82c5145]
[13] /usr/local/NAMD_2.5_Linux-i686/namd2 [0x82f946a]
[14] Tcl_EvalEx+0x1cc [0x82f9b7c]
[15] Tcl_EvalFile+0x157 [0x82f1ce3]
[16] _ZN9ScriptTcl3runEPc+0x1a [0x8228b76]
[17] main+0x1d2 [0x80ed052]
[18] __libc_start_main+0xf4 [0xb7e87974]
[19] sinh+0x65 [0x80eaed1]
req_handle_abort called
Fatal error on PE 0> segmentation violation
---------- Original Message -----------
> Luis,
> It sounds to me like NAMD is encountering a floating point
> exception during your run. Alpha processors don't handle such
> exceptions gracefully unless you compile code specially (i.e. slower
> performance), it's possible that the version of NAMD you're running
> has some math that's problematic, or it's operating on FP values
> sent to it by VMD that give the Alpha CPUs problems. What happens
> if you run the NAMD side of things on a Linux box? It should be
> relatively easy to fix the problem if we can reproduce it on a
> machine we can run NAMD on. These FP exceptions are a familiar
> issue on the Alpha platform.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
From: John Stone <johns_at_ks.uiuc.edu>
To: Luis Rosales <ludwig_at_correo.biomedicas.unam.mx>
Cc: namd-l_at_ks.uiuc.edu, vmd-l_at_ks.uiuc.edu
Sent: Wed, 20 Apr 2005 16:12:20 -0500
Subject: namd-l: Re: vmd-l: Interactive Simulations, ligand size limits....
> Luis,
> How large is the molecule you're simulating? When you say that
> the simulation "crashed", does that mean that NAMD aborted because
> you pulled too hard (margin violation, exceeding the speed of light,
> etc...), or did NAMD actually have a seg fault or floating point exception
> of some kind? If you got a "margin violation" it means that you pulled
> on the structure so hard that you exceeded NAMD's internal limit on
> atom velocity imposed by the spatial decomposition it uses. If you
> pull to hard and impart a tremendous velocity per simulated timestep,
> this means that either you need to pull more gently, or you need to
> decrease the gap in timescale between your real-time pulling and the
> rate of simulated time in the simulation, either by using a smaller
> molecule or by using fixed atoms, or some combination of both.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
------- End of Original Message -------
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