From: Madhulika Gupta (gmadhulika1909_at_gmail.com)
Date: Fri Nov 20 2015 - 01:20:05 CST
Hi
I am attaching the config and log file below. The same input file works
perfectly fine with NAMD2.10 and other lower versions (both cuda and
non-cuda versions) with no errors at all. But as stated earlier NAMD2.11
results in the error listed below in the log file.
*.conf file*:
structure ../../common/ionized.psf
coordinates ./min.coor
set temperature 290
set outputname equi290-ew
firsttimestep 0
seed 3000
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
temperature $temperature
waterModel tip4
parameters ../../common/par_all27_prot_lipid.inp
parameters ../../common/tip4p-ew.par
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 20
switching on
switchdist 18
pairlistdist 21.5
langevin on
langevinTemp 290
langevinDamping 1
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
rigidTolerance 0.00001
rigidIterations 100
#constant pressure control
useGroupPressure yes
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1
langevinPistonperiod 100
langevinPistonDecay 50
langevinPistonTemp 290
# Periodic Boundary Conditions
extendedSystem ../heat/heat290-ew.xsc
wrapAll on
wrapWater on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 40
PMEGridSizeY 40
PMEGridSizeZ 40
# Output
outputName $outputname
restartfreq 1000 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100
outputTiming 500
binaryoutput no
binaryrestart yes
run 500000
reinitvels $temperature
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
*Log file: *
Info: Startup phase 8 took 6.10352e-05 s, 97.8086 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 9 took 8.39233e-05 s, 97.8398 MB of memory in use
Info: CREATING 28 COMPUTE OBJECTS
CUDA device 0 stream priority range 0 -1
Info: Found 154 unique exclusion lists needing 400 bytes
Pe 0 hosts 0 local and 1 remote patches for pe 0
Info: Startup phase 10 took 0.00324798 s, 97.9961 MB of memory in use
Info: Startup phase 11 took 8.2016e-05 s, 97.9961 MB of memory in use
Info: Startup phase 12 took 6.69956e-05 s, 98 MB of memory in use
Info: Finished startup at 4.729 s, 98 MB of memory in use
TCL: Running for 500000 steps
Pe 0 has 0 local and 1 remote patches and 0 local and 14 remote computes.
PRESSURE: 0 -nan -nan -nan -nan -nan -nan -nan -nan -nan
GPRESSURE: 0 -nan -nan -nan -nan -nan -nan -nan -nan -nan
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG
PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 19.8296 73.0513 69.3552
1.5311 -40403.8961 2068829.2175 0.0000
0.0000 -nan -nan -nan
2028589.0887 nan -nan -nan
-nan 81378.6329 -nan -nan
OPENING EXTENDED SYSTEM TRAJECTORY FILE
Exclusions: detected 16049 expected 16709
FATAL ERROR: Incorrect number of exclusions detected
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
[0] Stack Traceback:
[0:0] CmiAbort+0x41 [0xf067a8]
[0:1] _Z8NAMD_bugPKc+0x9e [0x64ce2e]
[0:2] _ZN20ComputeNonbondedCUDA16finishReductionsEv+0x31a [0x81d3fa]
[0:3] _Z19cuda_check_progressPvd+0xf1 [0x81ced1]
[0:4] CcdCallBacks+0x22b [0xf1bffb]
[0:5] CsdScheduler+0x636 [0xf0fbc6]
[0:6] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x2b5 [0xc482c5]
[0:7] TclInvokeStringCommand+0x88 [0xfb37c8]
[0:8] [0xfb62e0]
[0:9] [0xfb76c6]
[0:10] Tcl_EvalEx+0x16 [0xfb7ea6]
[0:11] Tcl_FSEvalFileEx+0x151 [0x1019cb1]
[0:12] Tcl_EvalFile+0x2e [0x1019e6e]
[0:13] _ZN9ScriptTcl4loadEPc+0xf [0xc44e7f]
[0:14] main+0x3d2 [0x6525a2]
[0:15] __libc_start_main+0xfd [0x378621ed5d]
[0:16] _ZNSt8ios_base4InitD1Ev+0x4a [0x5aa00a]
[0] Stack Traceback:
[0:0] LrtsAbort+0x70 [0xf06e88]
[0:1] CmiAbortHelper+0x102 [0xf06761]
[0:2] CmiAbort+0x41 [0xf067a8]
[0:3] _Z8NAMD_bugPKc+0x9e [0x64ce2e]
[0:4] _ZN20ComputeNonbondedCUDA16finishReductionsEv+0x31a [0x81d3fa]
[0:5] _Z19cuda_check_progressPvd+0xf1 [0x81ced1]
[0:6] CcdCallBacks+0x22b [0xf1bffb]
[0:7] CsdScheduler+0x636 [0xf0fbc6]
[0:8] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x2b5 [0xc482c5]
[0:9] TclInvokeStringCommand+0x88 [0xfb37c8]
[0:10] [0xfb62e0]
[0:11] [0xfb76c6]
[0:12] Tcl_EvalEx+0x16 [0xfb7ea6]
[0:13] Tcl_FSEvalFileEx+0x151 [0x1019cb1]
[0:14] Tcl_EvalFile+0x2e [0x1019e6e]
[0:15] _ZN9ScriptTcl4loadEPc+0xf [0xc44e7f]
[0:16] main+0x3d2 [0x6525a2]
[0:17] __libc_start_main+0xfd [0x378621ed5d]
[0:18] _ZNSt8ios_base4InitD1Ev+0x4a [0x5aa00a]
Regards,
Madhulika Gupta
On Thu, Nov 19, 2015 at 2:25 AM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>
> Can you point me at a complete copy of the input files for your simulation
> so I can do further testing? Please also send a complete log file showing
> the error. Thanks.
>
>
> Jim
>
> On Wed, 18 Nov 2015, Madhulika Gupta wrote:
>
> The simulation yielding the exclusion error works perfectly fine with all
>> the other versions except NAMD2.11. It doesn't run even for the zeroth
>> step. If I try to minimize the system and then run further, it terminates
>> with the same exclusion error as soon as minimization completes.
>>
>> Regards,
>> Madhulika
>> On Nov 18, 2015 8:51 PM, "Jim Phillips" <jim_at_ks.uiuc.edu> wrote:
>>
>>
>>> The build error means exactly what it says. If you really want to you
>>> can
>>> remove the "exit -1" command from the error message in the config script.
>>>
>>> Did your simulation that is yielding the exclusion error work for a
>>> non-CUDA build or NAMD 2.10? Is there anything unusual about it? Do you
>>> get the error on the first timestep or later in the run?
>>>
>>> Jim
>>>
>>> On Wed, 18 Nov 2015, Madhulika Gupta wrote:
>>>
>>> Dear All,
>>>
>>>> I am trying to compile NAMD2.11 Source code on the central computing
>>>> facility at our institute and I get the error as listed below. I have
>>>> tried
>>>> compiling both MPI version and Infiniband version but both result in the
>>>> same error. The earlier versions worked just fine on the same machine.
>>>>
>>>> ./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64 --with-cuda
>>>> --cuda-prefix /home/soft/cuda-7.0/
>>>>
>>>> Selected arch file arch/Linux-x86_64-g++.arch contains:
>>>>
>>>> NAMD_ARCH = Linux-x86_64
>>>> CHARMARCH = multicore-linux64
>>>>
>>>> CXX = g++ -m64 -std=c++0x -O3
>>>> CXXOPTS = -fexpensive-optimizations -ffast-math
>>>> CC = gcc -m64 -O3
>>>> COPTS = -fexpensive-optimizations -ffast-math
>>>>
>>>>
>>>> ERROR: CUDA builds require non-MPI SMP or multicore Charm++ arch for
>>>> reasonable performance.
>>>>
>>>> Consider ibverbs-smp or verbs-smp (InfiniBand), gni-smp (Cray), or
>>>> multicore (single node).
>>>>
>>>> -------------------------------------------------------------------------
>>>>
>>>> I have also tried using namd binaries under the following
>>>>
>>>>
>>>> - Linux-x86_64-multicore-CUDA
>>>> <
>>>>
>>>> http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1357
>>>>
>>>>>
>>>>> (NVIDIA CUDA acceleration)
>>>> - Linux-x86_64-ibverbs-smp-CUDA
>>>> <
>>>>
>>>> http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1356
>>>>
>>>>>
>>>>> (NVIDIA CUDA with InfiniBand)
>>>>
>>>> but they result in the following error:
>>>> Exclusions: detected 16049 expected 16709
>>>> FATAL ERROR: Incorrect number of exclusions detected
>>>>
>>>> Please pay heed to the issue and please help me to resolve the same.
>>>>
>>>> Regards
>>>> Madhulika
>>>> Research Scholar
>>>> Department of Chemistry
>>>> Indian Institute of Technology, Delhi
>>>> New Delhi-110016
>>>>
>>>>
>>>>
>>
-- Madhulika Gupta Research Scholar Department of Chemistry Indian Institute of Technology, Delhi New Delhi-110016
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