My guess would be that your coordinates are messed up in some way. Either
your system is incredibly small - less than a few angstroms in size or you
have a very large system, likely from feeding in some kind of unimagined
coordinate set.
On 6/19/13 10:15 AM, "Scott Le Grand" <varelse2005.gmail.com> wrote:
>| ERROR: nfft1 must be in the range of 6 to 512!
>| ERROR: nfft2 must be in the range of 6 to 512!
>| ERROR: nfft3 must be in the range of 6 to 512!
>| ERROR: a must be in the range of 0.10000E+01 to 0.10000E+04!
>| ERROR: b must be in the range of 0.10000E+01 to 0.10000E+04!
>| ERROR: c must be in the range of 0.10000E+01 to 0.10000E+04!
>
>That's not the CUDA code or the GPU. That's something *very* bad with
>your
>machine having somehow convinced itself of something even worse. No idea
>what though
>
>
>
>
>On Mon, Jun 17, 2013 at 10:24 PM, ET <sketchfoot.gmail.com> wrote:
>
>> ps. The machine is running in headless mode on centos 6
>>
>>
>> #### bandwitdh test for currently installed TITAN-b:
>>
>> [CUDA Bandwidth Test] - Starting...
>> Running on...
>>
>> Device 0: GeForce GTX TITAN
>> Quick Mode
>>
>> Host to Device Bandwidth, 1 Device(s)
>> PINNED Memory Transfers
>> Transfer Size (Bytes) Bandwidth(MB/s)
>> 33554432 6002.5
>>
>> Device to Host Bandwidth, 1 Device(s)
>> PINNED Memory Transfers
>> Transfer Size (Bytes) Bandwidth(MB/s)
>> 33554432 6165.5
>>
>> Device to Device Bandwidth, 1 Device(s)
>> PINNED Memory Transfers
>> Transfer Size (Bytes) Bandwidth(MB/s)
>> 33554432 220723.8
>>
>>
>>
>> ### deviceQuery
>>
>> deviceQuery Starting...
>>
>> CUDA Device Query (Runtime API) version (CUDART static linking)
>>
>> Detected 1 CUDA Capable device(s)
>>
>> Device 0: "GeForce GTX TITAN"
>> CUDA Driver Version / Runtime Version 5.5 / 5.0
>> CUDA Capability Major/Minor version number: 3.5
>> Total amount of global memory: 6143 MBytes (6441730048
>> bytes)
>> (14) Multiprocessors x (192) CUDA Cores/MP: 2688 CUDA Cores
>> GPU Clock rate: 928 MHz (0.93 GHz)
>> Memory Clock rate: 3004 Mhz
>> Memory Bus Width: 384-bit
>> L2 Cache Size: 1572864 bytes
>> Max Texture Dimension Size (x,y,z) 1D=(65536),
>> 2D=(65536,65536), 3D=(4096,4096,4096)
>> Max Layered Texture Size (dim) x layers 1D=(16384) x 2048,
>> 2D=(16384,16384) x 2048
>> Total amount of constant memory: 65536 bytes
>> Total amount of shared memory per block: 49152 bytes
>> Total number of registers available per block: 65536
>> Warp size: 32
>> Maximum number of threads per multiprocessor: 2048
>> Maximum number of threads per block: 1024
>> Maximum sizes of each dimension of a block: 1024 x 1024 x 64
>> Maximum sizes of each dimension of a grid: 2147483647 x 65535 x
>>65535
>> Maximum memory pitch: 2147483647 bytes
>> Texture alignment: 512 bytes
>> Concurrent copy and kernel execution: Yes with 1 copy
>>engine(s)
>> Run time limit on kernels: No
>> Integrated GPU sharing Host Memory: No
>> Support host page-locked memory mapping: Yes
>> Alignment requirement for Surfaces: Yes
>> Device has ECC support: Disabled
>> Device supports Unified Addressing (UVA): Yes
>> Device PCI Bus ID / PCI location ID: 3 / 0
>> Compute Mode:
>> < Exclusive Process (many threads in one process is able to use
>> ::cudaSetDevice() with this device) >
>>
>> deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 5.5, CUDA
>>Runtime
>> Version = 5.0, NumDevs = 1, Device0 = GeForce GTX TITAN
>>
>>
>>
>> On 18 June 2013 06:21, ET <sketchfoot.gmail.com> wrote:
>>
>> > Hi,
>> >
>> > I am trying to run NPT simulations using pmemd.cuda using TITAN
>>graphics
>> > cards. The equilibration & steps were completed with the CPU version
>>of
>> > sander.
>> >
>> > I have 2x EVGA superclocked TITAN cards.There have been problems with
>>the
>> > TITAN graphics cards and I RMA'd one. I have benchmarked both the
>>cards
>> > after the RMA and determined that they have no obvious problems that
>> would
>> > warrant them being RMA'd again. Though there is an issue with the
>>AMBER
>> > cuda code and TITANs in general as discussed in the following thread:
>> >
>> > < sorry, can't find it, but it's a ~200 posts long and titled:
>> experiences
>> > with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in
>>Linux ?
>> >
>> >
>> > As I'm not sure whether this is the same issue, I'm posting this in a
>>new
>> > thread.
>> >
>> > I began running 12 100ns production run using TITAN-a. There were no
>> > problems. After waiting for and testing the replacement card
>>(TITAN-b), I
>> > put that into the machine as well. So both cards were working on
>> finishing
>> > the total of 300 segments.
>> >
>> > Very shortly, all the segments had failed, though the cards still
>>showed
>> a
>> > 100% utilisation and I did not realise until I checked the outfiles
>>which
>> > showed "ERROR: nfft1 must be in the range of blah, blah, blah"
>>(error
>> > posted below). This was pretty weird as I am used to the jobs visibly
>> > failing and not carrying on eating resources, whilst doing nothing.
>> >
>> > So I pulled the TITAN-a out and restarted the calculations with
>>TITAN-b
>> > from the last good rst. Usually 2 back. There have been no problems at
>> all
>> > and all the simulations have completed.
>> >
>> > My hardware specs are:
>> > Gigabyte GA-X58-UD7 mobo
>> > i7-930 processor
>> > 6GB RAM
>> > 1200 Watt Bequiet power supply
>> >
>> >
>> >
>> > Does anyone have any idea as to what's going on?
>> >
>> >
>> > br,
>> > g
>> >
>> > ############################################################
>> > ############################################################
>> > -------------------------------------------------------
>> > Amber 12 SANDER 2012
>> > -------------------------------------------------------
>> >
>> > | PMEMD implementation of SANDER, Release 12
>> >
>> > | Run on 06/09/2013 at 16:26:10
>> >
>> > [-O]verwriting output
>> >
>> > File Assignments:
>> > | MDIN: prod.in
>> >
>> > | MDOUT: md_4.out
>> >
>> > | INPCRD: md_3.rst
>> >
>> > | PARM: ../leap/TMC_I54V-V82S_Complex_25.parm
>> >
>> > | RESTRT: md_4.rst
>> >
>> > | REFC: refc
>> >
>> > | MDVEL: mdvel
>> >
>> > | MDEN: mden
>> >
>> > | MDCRD: md_4.ncdf
>> >
>> > | MDINFO: mdinfo
>> >
>> >
>> >
>> > Here is the input file:
>> >
>> > Constant pressure constant temperature production run
>> >
>> > &cntrl
>> >
>> > nstlim=2000000, dt=0.002, ntx=5, irest=1, ntpr=250, ntwr=1000,
>> ntwx=500,
>> >
>> > temp0=300.0, ntt=1, tautp=2.0, ioutfm=1, ig=-1, ntxo=2,
>> >
>> >
>> >
>> > ntb=2, ntp=1,
>> >
>> >
>> >
>> > ntc=2, ntf=2,
>> >
>> >
>> >
>> > nrespa=1,
>> >
>> > &end
>> >
>> >
>> >
>> > Note: ig = -1. Setting random seed based on wallclock time in
>> microseconds.
>> >
>> > |--------------------- INFORMATION ----------------------
>> > | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
>> > | Version 12.3
>> > |
>> > | 04/24/2013
>> > |
>> > | Implementation by:
>> > | Ross C. Walker (SDSC)
>> > | Scott Le Grand (nVIDIA)
>> > | Duncan Poole (nVIDIA)
>> > |
>> > | CAUTION: The CUDA code is currently experimental.
>> > | You use it at your own risk. Be sure to
>> > | check ALL results carefully.
>> > |
>> > | Precision model in use:
>> > | [SPFP] - Mixed Single/Double/Fixed Point Precision.
>> > | (Default)
>> > |
>> > |--------------------------------------------------------
>> >
>> > |----------------- CITATION INFORMATION -----------------
>> > |
>> > | When publishing work that utilized the CUDA version
>> > | of AMBER, please cite the following in addition to
>> > | the regular AMBER citations:
>> > |
>> > | - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
>> > | Poole; Scott Le Grand; Ross C. Walker "Routine
>> > | microsecond molecular dynamics simulations with
>> > | AMBER - Part II: Particle Mesh Ewald", J. Chem.
>> > | Theory Comput., 2012, (In review).
>> > |
>> > | - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
>> > | Duncan Poole; Scott Le Grand; Ross C. Walker
>> > | "Routine microsecond molecular dynamics simulations
>> > | with AMBER - Part I: Generalized Born", J. Chem.
>> > | Theory Comput., 2012, 8 (5), pp1542-1555.
>> > |
>> > | - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
>> > | "SPFP: Speed without compromise - a mixed precision
>> > | model for GPU accelerated molecular dynamics
>> > | simulations.", Comp. Phys. Comm., 2013, 184
>> > | pp374-380, DOI: 10.1016/j.cpc.2012.09.022
>> > |
>> > |--------------------------------------------------------
>> >
>> > |------------------- GPU DEVICE INFO --------------------
>> > |
>> > | CUDA Capable Devices Detected: 2
>> > | CUDA Device ID in use: 0
>> > | CUDA Device Name: GeForce GTX TITAN
>> > | CUDA Device Global Mem Size: 6143 MB
>> > | CUDA Device Num Multiprocessors: 14
>> > | CUDA Device Core Freq: 0.93 GHz
>> > |
>> > |--------------------------------------------------------
>> >
>> > | ERROR: nfft1 must be in the range of 6 to 512!
>> > | ERROR: nfft2 must be in the range of 6 to 512!
>> > | ERROR: nfft3 must be in the range of 6 to 512!
>> > | ERROR: a must be in the range of 0.10000E+01 to 0.10000E+04!
>> > | ERROR: b must be in the range of 0.10000E+01 to 0.10000E+04!
>> > | ERROR: c must be in the range of 0.10000E+01 to 0.10000E+04!
>> >
>> > Input errors occurred. Terminating execution.
>> > ############################################################
>> > ############################################################
>> >
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Thu Jun 20 2013 - 08:30:02 PDT
