From NWChem
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Posts 14
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| 7:32:34 PM PDT - Thu, Aug 9th 2012 |
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I get the following error message when i run a TDDFT calculation with CAM-B3LYP for a radical cation
"sym_movecs_adapt: no significant component? 0", I am not sure what it means.
echo
start molecule
MEMORY 7500 mb
title "3_10 Helix Radical Cation n=3"
charge 1
geometry units angstroms print xyz autosym
C -1.22260 5.98400 -1.84890
O -2.21620 6.69620 -1.98260
C -0.79600 5.08240 -2.93470
C 0.30150 4.24020 -2.96800
C -1.47140 4.92970 -4.20660
N 0.33860 3.57760 -4.16750
C -0.73460 3.97420 -4.95260
C -2.62270 5.50160 -4.77920
C -1.10580 3.57020 -6.24000
C -2.99640 5.10460 -6.05850
C -2.24810 4.15030 -6.78210
H 1.08420 4.07640 -2.23880
H 1.05480 2.92230 -4.44500
H -3.19130 6.24030 -4.22570
H -0.52800 2.83500 -6.79470
H -3.88190 5.53890 -6.51500
H -2.56900 3.86390 -7.78010
N -0.43950 6.06130 -0.60720
C -1.03880 7.03590 0.28190
C -1.43070 6.38200 1.59920
H -0.32750 7.83950 0.47260
H -1.93400 7.44000 -0.19070
N -1.68620 5.07210 1.56350
O -1.50130 7.04800 2.62950
C -2.06920 4.33400 2.75020
H -1.61040 4.58140 0.68390
C -1.11620 4.64090 3.89650
H -3.08390 4.60950 3.03760
H -2.02450 3.26720 2.53110
N 0.11690 5.02760 3.56150
O -1.48750 4.53040 5.06290
C 1.11660 5.34840 4.56020
H 0.35990 5.09870 2.58380
C 0.54270 6.30230 5.59810
H 1.44640 4.43280 5.05140
H 1.96280 5.82930 4.06960
N 0.36740 5.89190 6.85910
O 0.23310 7.47700 5.26980
C -0.12120 6.61040 7.97530
H 0.64420 4.93170 7.03120
C -0.54500 7.94520 7.90890
C -0.18220 5.93670 9.20680
C -1.02000 8.58020 9.05930
H -0.49870 8.47680 6.96790
C -0.65570 6.57200 10.35020
H 0.15130 4.90280 9.27440
C -1.07920 7.90290 10.27930
H -1.34500 9.61740 8.99500
H -0.69870 6.04940 11.30090
O -1.53880 8.48320 11.43710
H -1.79090 9.40370 11.26510
H 0.38000 5.52430 -0.40720
end
basis
* library 6-31+G*
end
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
mult 2
ITERATIONS 500
END
TDDFT
RPA
NROOTS 5
TARGET 1
END
TASK TDDFT ENERGY
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Huub Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Posts 18
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| 11:04:24 AM PDT - Fri, Aug 10th 2012 |
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| As far as I can see the basis set you are using contains linear dependencies. The code removes those and zeroes the linearly dependent vectors. It seems that the routine that purifies the symmetry of the orbitals gets confused about these zero vectors. I am having a closer look to see where exactly this happens and fix this.
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Threads 5
Posts 14
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| 12:12:36 PM PDT - Fri, Aug 10th 2012 |
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Quote:Huub Aug 10th 11:04 amAs far as I can see the basis set you are using contains linear dependencies. The code removes those and zeroes the linearly dependent vectors. It seems that the routine that purifies the symmetry of the orbitals gets confused about these zero vectors. I am having a closer look to see where exactly this happens and fix this.
Great, thanks very much
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Huub Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Posts 18
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| 6:10:08 PM PDT - Fri, Aug 10th 2012 |
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| A fix for this problem has just been checked in into the development version. Please drop me a line if you need a patch.
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Posts 14
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| 2:18:16 PM PDT - Tue, Aug 14th 2012 |
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Memory Issues: SHMMAX
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Quote:Huub Aug 10th 6:10 pmA fix for this problem has just been checked in into the development version. Please drop me a line if you need a patch.
Thanks for the patch. But right now I am getting the following memory related error
Memory Information
------------------
Available GA space size is 3220429150 doubles
Available MA space size is 805298131 doubles
Length of a trial vector is 56832 56430
Algorithm : Incore multiple tensor contraction
Estimated peak GA usage is 2333263668 doubles
Estimated peak MA usage is 18000 doubles
3: WARNING:armci_set_mem_offset: offset changed 691299565568 to 691299561472
1: WARNING:armci_set_mem_offset: offset changed 637311901696 to 637311897600
2: WARNING:armci_set_mem_offset: offset changed 315961344000 to 315961339904
id=-1 size=2273312768
******************* ARMCI INFO ************************
The application attempted to allocate a shared memory segment of 2273312768 bytes in size. This might be in addition to segments that were allocated succ
esfully previously. The current system configuration does not allow enough shared memory to be allocated to the application.
This is most often caused by:
1) system parameter SHMMAX (largest shared memory segment) being too small or
2) insufficient swap space.
Please ask your system administrator to verify if SHMMAX matches the amount of memory needed by your application and the system has sufficient amount of
swap space. Most UNIX systems can be easily reconfigured to allow larger shared memory segments,
see http://www.emsl.pnl.gov/docs/global/support.html
In some cases, the problem might be caused by insufficient swap space.
*******************************************************
0:allocate: failed to create shared region : -1
(rank:0 hostname:Doudou-PC pid:4121):ARMCI DASSERT fail. ../../ga-5-1/armci/src/memory/shmem.c:armci_allocate():1117 cond:0
Last System Error Message from Task 0:: No space left on device
I tried to increase the SHMMAX value using
sudo sysctl -w kernel.shmmax=4294967296
But I still got the same error.
System Specifications: Ubuntu 12.04 64-bit, NWChem 6.1 compiled with OpenMPI 1.6, i7-2600K (4 cores) 16 GB RAM and 16 GB Swap space.
export NWCHEM_TOP=/home/doudou/Programs/nwchem-6.1.1-src
export NWCHEM_TARGET=LINUX64
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/usr/local
export MPI_LIB=$MPI_LOC/lib
export LIBMPI="-lmpi_f90 -lmpi_f77 -lmpi -lpthread"
export MPI_INCLUDE=$MPI_LOC/include
export LARGE_FILES=TRUE
export NWCHEM_MODULES=all
cd $NWCHEM_TOP/src
make nwchem_config
make FC=gfortran >& make.log
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Edited On 7:13:10 PM PDT - Wed, Aug 15th 2012 by DouDou
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Posts 14
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| 7:15:10 PM PDT - Wed, Aug 15th 2012 |
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Okay I got it to work by export ARMCI_DEFAULT_SHMMAX=1024 I am not sure what the default value was in the first place. Can somebody please elaborate a little bit more on this. Thanks
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