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
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Received on Mon Dec 05 2011 - 21:30:03 PST
