Can you email me an example that shows the iwrap behavior?
That's likely an easy fix...
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Sasha Buzko
Sent: Friday, May 28, 2010 09:40
To: AMBER Mailing List
Subject: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE
Hi all,
I've compiled pmemd.cuda on a 64-bit CentOS 5.3 for use with a GTX280.
The tests came out pretty good - one failure (proteosome, low memory),
and 5 more generated errors. I'm giving the deviceQuery output below.
I'm testing pmemd.cuda with a pre-equilibrated explicit solvent system
(about 60 000 atoms). The NPT version ran perfectly fine with no errors.
However, runs at NVT or NVE parameters lead to an immediate segmentation
fault whenever iwrap=1. There are no error messages, just instant
failure. At the same time, both sander and regular pmemd run normally
with the input files below. I had to remove the iwrap=1 line for
pmemd.cuda to run.
Ideally, I'd like to keep iwrap enabled for long runs, so I wonder if
it's a known issue and whether it can be fixed.
Here are the input files for each run of pmemd.cuda
The NPT input parameters (works ok):
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0, iwrap = 1,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
temp0 = 300.0,
ntt = 3, gamma_ln = 2.0,
nstlim = 20000, dt = 0.001,
ntpr = 1000, ntwx = 1000, ntwr = 1000
The NVT input parameters (segmentation fault):
imin = 0, irest = 1, ntx = 7,
ntb = 1,
iwrap = 1,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
temp0 = 300.0,
ntt = 3, gamma_ln = 2.0,
nstlim = 20000, dt = 0.001,
ntpr = 1000, ntwx = 1000, ntwr = 1000
The NVE input parameters (segmentation fault):
imin = 0, irest = 1, ntx = 7,
ntb = 1, ntp = 0,
iwrap = 1,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
temp0 = 300.0,
ntt = 0,
nstlim = 20000, dt = 0.001,
ntpr = 1000, ntwx = 1000, ntwe = 1000, ntwr = 1000
Any suggestions would be appreciated.
Thanks in advance
Sasha
[sasha.redwood release]$ ./deviceQuery
./deviceQuery Starting...
CUDA Device Query (Runtime API) version (CUDART static linking)
There is 1 device supporting CUDA
Device 0: "GeForce GTX 280"
CUDA Driver Version: 3.0
CUDA Runtime Version: 3.0
CUDA Capability Major revision number: 1
CUDA Capability Minor revision number: 3
Total amount of global memory: 1073020928 bytes
Number of multiprocessors: 30
Number of cores: 240
Total amount of constant memory: 65536 bytes
Total amount of shared memory per block: 16384 bytes
Total number of registers available per block: 16384
Warp size: 32
Maximum number of threads per block: 512
Maximum sizes of each dimension of a block: 512 x 512 x 64
Maximum sizes of each dimension of a grid: 65535 x 65535 x 1
Maximum memory pitch: 2147483647 bytes
Texture alignment: 256 bytes
Clock rate: 1.30 GHz
Concurrent copy and execution: Yes
Run time limit on kernels: Yes
Integrated: No
Support host page-locked memory mapping: Yes
Compute mode: Default (multiple host
threads can use this device simultaneously)
deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 4243455, CUDA
Runtime Version = 3.0, NumDevs = 1, Device = GeForce GTX 280
PASSED
Press <Enter> to Quit...
-----------------------------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
-----------------------------------------------------------------------------------
This email message is for the sole use of the intended recipient(s) and may contain
confidential information. Any unauthorized review, use, disclosure or distribution
is prohibited. If you are not the intended recipient, please contact the sender by
reply email and destroy all copies of the original message.
-----------------------------------------------------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 28 2010 - 13:30:03 PDT
