Hi Chinh,
Can you send me (offlist) all of your input files please along with details
of your computer system. OS, NVIDIA compiler and driver version, hardware
spec (especially the GPU version). I need to be able to replicate this in
order to investigate what is going wrong.
Please also include the output from the run that gave what looked like a
disk error.
Thank you.
All the best
Ross
> -----Original Message-----
> From: Chinh Su Tran To [mailto:chinh.sutranto.gmail.com]
> Sent: Monday, December 12, 2011 8:04 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] AMBER11, pmemd.cuda: the system crashed.
>
> Dear Dr. Walker,
>
> As you suggested, we ran the check for the hard disk, but both were
> clean!
> I tried to run the same code using pmemd only, and it was fine, i.e. no
> crash, no error.
>
> But then I returned using pmemd.cuda, it happened again (crashed).
>
> There were also 2 problems that I noticed when I was using pmemd.cuda:
>
> 1. When I used *iwrap=0* (in the input file as below), it showed
> "segmentation
> fault" immediately. I knew that it was an old error I encountered (but
> I
> wanted to try it to detect the pmemd.cuda only).
> 2. Then I switched it* iwrap=1* with some modification in the
> *gpu.cpp*(the solution that I found in the AMBER forum), it crashed. (
> *However, it also crashed before these modifications)*
>
> Please help. We did not know what was wrong.
>
> The input is:
>
> &cntrl
> imin=0,
> * iwrap=1 => I also tried iwrap=0*
> irest=0,
> ntx=1,
> ntb=1,
> cut=10.0,
> ntr=0,
> ntc=2,
> ntf=2,
> tempi=500.0,
> temp0=500.0,
> ntt=3,
> gamma_ln=1.0,
> nstlim=3000000, dt=0.002,
> ntpr=1500, ntwx=1500,ntwr=1000
> /
>
>
> Thank you.
> Chinsu
>
>
>
>
> On Tue, Dec 6, 2011 at 1:01 PM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
>
> > Hi Chinsu,
> >
> > This looks like a hard drive failure to me (or pending hard drive
> failure).
> > Please try things with the CPU version of the code and see what
> happens. I
> > can't see how this could be generated by the GPU code. You might want
> to
> > try
> > booting the machine in single user (or recovery mode) and running an
> fsck
> > on
> > the file system. You could also try running a smartctl check on the
> hard
> > drive to see what it's diagnostics are reporting.
> >
> > All the best
> > Ross
> >
> > > -----Original Message-----
> > > From: Chinh Su Tran To [mailto:chinh.sutranto.gmail.com]
> > > Sent: Monday, December 05, 2011 7:33 PM
> > > To: AMBER Mailing List
> > > Subject: [AMBER] AMBER11, pmemd.cuda: the system crashed.
> > >
> > > Dear AMBER users,
> > >
> > > I was running pmemd.cuda using Amber11 on a GPU which is installed
> in a
> > > workstation.
> > > The process was of 2 steps of short minimizations and a 6ns of
> heating
> > > the
> > > protein (270 residues) at 500K.
> > >
> > > The minimizations were fine, but when i ran the heating, my system
> > > "crashed". The errors are as below:
> > >
> > > *[2932683.628873] EXT4-fs (sda1): previous I/O error to superblock
> > > detected*
> > > *
> > > [2932683.646789] EXT4-fs (device sda1): ext4_find_entry:933:
> > > inode#9699494:
> > > comm init: reading directory lblock 0**
> > > *
> > > *
> > > *
> > > I re-booted the system, and tried to run it again. The same errors
> > > came.
> > > My input file is:
> > >
> > > &cntrl
> > > imin=0,
> > > * iwrap=1 => I also tried iwrap=0*
> > > irest=0,
> > > ntx=1,
> > > ntb=1,
> > > cut=10.0,
> > > ntr=0,
> > > ntc=2,
> > > ntf=2,
> > > tempi=500.0,
> > > temp0=500.0,
> > > ntt=3,
> > > gamma_ln=1.0,
> > > nstlim=3000000, dt=0.002,
> > > ntpr=1500, ntwx=1500,ntwr=1000
> > > /
> > > *
> > > *
> > > *
> > > *
> > > We tried to find out what was going on, but we did not know where
> the
> > > crash
> > > came from?
> > > Please help.
> > >
> > > Thank you.
> > >
> > > Regards,
> > > Chinsu
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Dec 12 2011 - 20:30:04 PST
