kr malloc failed
Gets Around
10:55:39 AM PDT - Thu, Oct 17th 2013
Hi, I am calculating TDDFT and not sure why it is aborting at this point. I am specifying memory 18000 mb on a 24 Gb RAM node

thanks

JOnas



Entering Davidson iterations
 Restricted singlet excited states



 Iter   NTrls   NConv    DeltaV     DeltaE      Time   

 ----  ------  ------  ---------  ---------  ---------
0:CreateSharedRegion:kr_malloc failed KB=: 190440
(rank:0 hostname:compute-14-410.local pid:23426):ARMCI DASSERT fail. ../../ga-5-2/armci/src/memory/shmem.c:Create_Shared_Re

Forum Vet
11:09:41 AM PDT - Thu, Oct 17th 2013
Jonas
This can be probably solved by setting an appropriate value of the ARMCI_DEFAULT_SHMMAX env. variable.
If you could post your input file and more details about your failed run (e.g. total number of processes used, characteristics of the HW used, etc ... ), we would be in a better position to help you.
Cheers, Edo

Gets Around
11:11:52 AM PDT - Thu, Oct 17th 2013
with pleasure. I used 12 cores on a dedicated INtel processor. input is below. what else would you need?

title "JF34_3_4_3 Gaussian M062X geometry UVVIS and CD"
echo

memory 18000 mb

permanent_dir /Users/jbaltrus/Gloer/JF34_3_4_3/nwchem
scratch_dir /Users/jbaltrus/Gloer/JF34_3_4_3/nwchem

geometry
H 0.199127000 2.382080000 2.801032000
C -0.505942000 1.581743000 3.008654000
C -2.368787000 -0.444282000 3.584499000
C -0.772223000 0.611725000 2.049311000
C -1.154195000 1.557727000 4.247886000
C -2.081459000 0.556131000 4.543004000
C -1.702976000 -0.372135000 2.364284000
H -0.955084000 2.317060000 4.995275000
C -3.285827000 -1.553102000 3.815324000
C -3.282612000 -2.634555000 2.752759000
H -4.212562000 -3.203960000 2.826588000
H -2.458409000 -3.312393000 3.017186000
C -3.086830000 -2.152976000 1.299798000
N -1.931119000 -1.227791000 1.292040000
O -3.958283000 -1.652425000 4.839819000
C -2.799334000 -3.371446000 0.422551000
H -2.746068000 -3.094493000 -0.629983000
H -3.601975000 -4.102199000 0.558797000
H -1.852598000 -3.835743000 0.715672000
C -4.321904000 -1.394882000 0.803901000
H -4.540128000 -0.534701000 1.445902000
H -5.192955000 -2.056554000 0.802883000
H -4.152411000 -1.037502000 -0.215574000
C -0.290763000 0.366892000 0.641823000
C -1.274467000 -0.732390000 0.177089000
O -1.459967000 -1.098007000 -0.968409000
O -2.691980000 0.556437000 5.739250000
H -3.316139000 -0.202932000 5.755201000
C 1.192608000 -0.179206000 0.525768000
C -0.345441000 1.568991000 -0.336129000
H -1.317148000 1.624067000 -0.834641000
H -0.212906000 2.503109000 0.218593000
C 0.796301000 1.369574000 -1.344844000
C 1.428915000 0.004884000 -0.984908000
H 0.803656000 -0.742393000 -1.483400000
C 1.323407000 -1.643720000 0.947038000
H 2.370987000 -1.956961000 0.881361000
H 0.733939000 -2.306339000 0.304053000
H 0.997517000 -1.782831000 1.984706000
C 2.127025000 0.666556000 1.397922000
H 3.170237000 0.403160000 1.198971000
H 1.935013000 0.469150000 2.456826000
H 2.015451000 1.739443000 1.219585000
N 1.813812000 2.422020000 -1.215076000
H 1.561804000 3.334576000 -0.849958000
C 0.430260000 1.314477000 -2.832712000
H 0.123547000 2.316782000 -3.173078000
H -0.402645000 0.619175000 -2.990559000
N 1.632454000 0.843704000 -3.532463000
C 2.884399000 0.963135000 -2.732954000
C 1.922947000 1.467570000 -4.816953000
H 1.943646000 2.570849000 -4.740978000
H 1.162862000 1.196166000 -5.556049000
C 2.835108000 -0.082584000 -1.601061000
H 3.632109000 0.122545000 -0.878060000
H 3.012279000 -1.076314000 -2.022749000
C 2.881764000 2.342379000 -2.053590000
O 3.689401000 3.244992000 -2.232868000
C 3.311985000 0.918114000 -5.143409000
H 3.853410000 1.548157000 -5.852192000
H 3.213932000 -0.078835000 -5.580974000
C 4.010055000 0.831344000 -3.765167000
H 4.723885000 1.645102000 -3.622271000
H 4.542294000 -0.115169000 -3.642340000
end

  1. B3LYP/aug-cc-PVDZ used in ChemPhysChem, 2011, 12, 3224

basis
  *  library aug-cc-pVDZ
end

cosmo
dielec 32.63

rsolv  1.30
end


  1. TDDFT B3LYP
DFT
XC B3LYP
direct
convergence energy 1e-8
iterations 100
grid fine
END

TDDFT
RPA
NROOTS 20
SINGLET
NOTRIPLET
CDSPECTRUM
END

task tddft energy


  1. TDDFT cam-B3LYP
DFT
xc xcamb88 1.00 lyp 0.81 vwn_5 0.19 hfexch 1.00
cam 0.33 cam_alpha 0.19 cam_beta 0.46
direct
convergence energy 1e-8
iterations 100
grid fine
END


TDDFT
RPA
NROOTS 20
SINGLET
NOTRIPLET
CDSPECTRUM
END

task tddft energy

  1. TDDFT asymptotically corrected B3LYP
DFT
XC B3LYP

CS00

direct
convergence energy 1e-8
iterations 100
grid fine
END

TDDFT
RPA
NROOTS 20
SINGLET
NOTRIPLET
CDSPECTRUM
END

TASK TDDFT ENERGY

Forum Vet
3:56:38 PM PDT - Mon, Oct 21st 2013
ARMCI_DEFAULT_SHMMAX=2048
Jonas,
Have you tried running your job with an ARMCI_DEFAULT_SHMMAX of 2048?
I have done a few tests with your input and ARMCI_DEFAULT_SHMMAX=2048 makes the code start the Davidson iterative process.

Gets Around
1:33:30 AM PDT - Tue, Oct 22nd 2013
I have done and it worked, thanks


Forum >> NWChem's corner >> Running NWChem