From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 21 2005 - 16:28:08 CDT
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
On Wed, Apr 20, 2005 at 10:22:10PM -0500, Luis Rosales wrote:
>
> Hi all!
> John,
>
> Here is more concrete info on my problem,
>
> I am using:
>
> VMD for LINUX, version 1.8.3 (February 15, 2005) and NAMD 2.5 for
> Tru64-Alpha-Elan (both precompiled binaries).
>
> I run vmd on a local machine with 2 processors on RedHat Linux kernel
> 2.4.20-8smp and 4 Gb RAM
> NAMD, on the other hand, is running on a remote alpha server SC45, true unix
> 5.1b, using 2 nodes (total 4 processors) with 2 Gb of RAM.
>
> I ran this test on a system with 2 protein fragments and 0 waters, for a total
> of 110 residues (1651 atoms). One protein is 85 residues long and the 2nd is
> 25 residues long.
> In this case the simulation runs smoothly until I apply a force on the small
> fragment:
>
> ------------------------------------
> ENERGY: 115 142.9833 560.0360 549.5308 22.2029
> -2084.3060 -333.2643 0.0000 0.0000 257.1398
> -885.6774 52.2506 -886.1811 -885.7428 52.2506
>
> ENERGY: 116 150.6783 545.7365 553.3336 22.7285
> -2088.9056 -333.2312 0.0000 0.0000 271.5344
> -878.1255 55.1756 -878.5663 -878.3913 55.1756
>
> ENERGY: 117 152.8667 531.2275 557.0184 23.1223
> -2093.8173 -333.8267 0.0000 0.0000 290.1404
> -873.2688 58.9563 -873.2699 -874.7542 58.9563
>
> ENERGY: 118 148.2011 516.6806 560.5185 23.1648
> -2099.0759 -335.1546 0.0000 0.0000 316.7026
> -868.9628 64.3537 -869.0747 -870.0510 64.3537
>
> ENERGY: 119 141.9092 502.4293 563.7315 22.9768
> -2104.5040 -337.0257 0.0000 0.0000 348.3684
> -862.1145 70.7882 -862.8035 -861.5549 70.7882
>
> ETITLE: TS BOND ANGLE DIHED IMPRP
> ELECT VDW BOUNDARY MISC KINETIC
> TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
>
> ENERGY: 120 140.7723 488.7814 566.6368 22.7672
> -2110.2922 -339.3565 0.0000 0.0000 371.7358
> -858.9554 75.5364 -859.0029 -860.2378 75.5364
>
> DEBUG: Detaching simulation from remote connection
> ENERGY: 121 145.9771 475.7318 569.2369 22.4984
> -2116.4710 -341.5928 0.0000 0.0000 388.6565
> -855.9630 78.9747 -855.7663 -857.8394 78.9747
>
> prun: ../namd/NAMD_2.5_Tru64-Alpha-Elan/namd2 (host bakliz8 process 1 pid
> 4857226) killed by signal 8 (FPE)
> prun: no core file for job 30792 in /local/core/rms/30792
> ----------------------------------------
>
> If I look over vmd I only can see:
>
> Info) Connected to same-endian machine
> Info) Using multithreaded IMD implementation.
> Info) picked atom:
> Info) ------------
> Info) molecule id: 0
> Info) name: HD1
> Info) type: HD1
> Info) index: 1499
> Info) resname: TRP
> Info) resid: 72
> Info) chain: X
> Info) segname: C
> Info) x: 7.481662
> Info) y: 2.785722
> Info) z: 1.172789
> Info) IMD connection ended unexpectedly; connection terminated.
>
> **************************************************
>
> On some cases, specially for the peptides approaching to the 15 residue limit,
> the message from NAMD is a little different, as if NAMD tried to pause the
> simulation before quit: (this is the output for a system with a 85 residues
> protein and a 16 residues peptide)
>
> --------------------------------------
> ENERGY: 146 174.5181 464.8836 526.1484 23.4186
> -2026.8350 -269.8708 0.0000 0.0000 381.4379
> -726.2993 84.9705 -725.8214 -727.5702 84.9705
>
> ENERGY: 147 167.6455 468.3555 525.3417 23.7755
> -2026.7811 -270.8533 0.0000 0.0000 390.5575
> -721.9588 87.0020 -721.9038 -721.9578 87.0020
>
> NAMD ABORTING DUE TO HARD NAMD_quit().
> Info: Pausing IMD
> prun: ../namd/NAMD_2.5_Tru64-Alpha-Elan/namd2 (host bakliz8 process 0 pid
> 4857107) killed by signal 11 (SEGV)
> prun: no core file for job 30793 in /local/core/rms/30793
> ----------------------------------------
>
> As far as I can tell, the problem is not related to the duration of the
> minimization, even with longer minimization runs, the process is killed when
> the system enters the MD if I try to apply a force on a fragment longer than
> 15 residues, and usually the simulation is killed as soon as I click on the
> fragment with my mouse....
> [So, I dont have chance to exceed the speed of light... :( ]
>
> So, in theory, there is a limit to the size of the fragment that I could
> move/affect by aplying a reasonable force ?
>
> Again, thanks for your time and help.
>
> Kind regards,
>
> Luis
>
>
> --
> Open WebMail Project (http://openwebmail.org)
>
>
> ---------- Original Message -----------
> 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 -------
-- 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
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