Dear amber users. When I run pmemd.cuda, sometimes computer will be rebooted automatically, without error message. Normally the mdout file shows the gpu information. But in this case mdout files do not show the gpu information. And hang then after automatically rebooted. It happens randomly in each 105 nodes. What is the problem? Is it unknown bug, or hardware problem?
My system isE5-2650v2, GTX titan.CentOS 6.4, Intel compiler 14.0.0.080, cuda5.5 (Nvidia driver 334.21)amberTools13 bugfix.22, amber12 bugfix.21
Thanks and regards. Mooseok Kang
normal mdout : ------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 12 | Run on 04/04/2014 at 20:37:03 [-O]verwriting output File Assignments:| MDIN: ../md_shake.in| MDOUT: md571.out| INPCRD: mth_md570.rst| PARM: ../mth_WAT.top| RESTRT: mth_md571.rst| REFC: refc| MDVEL: mdvel| MDEN: mden| MDCRD: mdcrd| MDINFO: mth_md571.info Here is the input file: MD, NPT, 300 K &cntrl imin = 0, irest = 1, ntx = 5, nstlim = 50000, dt = 0.002, ntt = 3, ntb = 2, ntp = 1, gamma_ln=1.0, temp0 = 300.0, pres0 = 1.0, taup = 2.0, ntc = 2, ntf = 2, cut = 9.0, ioutfm = 1, iwrap = 1, ntwx = 5000, ntwr = 5000, ntpr = 5000 / |--------------------- INFORMATION ----------------------| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.| Version 12.3.1||
08/07/2013|| 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., 2013, DOI: 10.1021/ct400314y. adnormal mdout -------------------------------------
------------------ Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 12 | Run on 04/04/2014 at 20:40:36 [-O]verwriting output File Assignments:| MDIN: ../md_shake.in| MDOUT: md572.out| INPCRD: mth_md571.rst| PARM: ../mth_WAT.top| RESTRT: mth_md572.rst| REFC: refc| MDVEL: mdvel| MDEN: mden| MDCRD: mdcrd| MDINFO: mth_md572.info Here is the input file: MD, NPT, 300 K &cntrl imin = 0, irest = 1, ntx = 5, nstlim = 50000, dt = 0.002, ntt = 3, ntb = 2, ntp = 1, gamma_ln=1.0, temp0 = 300.0, pres0 = 1.0, taup = 2.0, ntc = 2, ntf = 2, cut = 9.0, ioutfm = 1, iwrap = 1, ntwx = 5000, ntwr = 5000, ntpr = 5000 /
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Received on Mon Apr 07 2014 - 23:00:02 PDT
