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cluster & band calculations Date: 2017/06/10 03:26 Name: tata Hi, I would like to report some problem related to the calculations using "cluster" eigenvalue solver. First of all system specification: HP Proliant DL580 G7, centos 6.9, GNU compilers, MKL 2017 CC=mpicc -O3 -fopenmp -I/home/dft/opt/fftw-3.3.6/include -I/$MKLROOT/include FC=mpif90 -O3 -fopenmp -I/$MKLROOT/include LIB= -L/home/dft/opt/openmpi-2.1.1/lib -lmpi_mpifh -L/home/dft/opt/fftw-3.3.6/lib -lfftw3 -L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -ldl -lgfortran mpiexec -np 32 ... -nt 2 I tried standard example: C16_BFGS.dat with some modifications: ------------------------------------------ System.CurrrentDirectory ./ # default=./ System.Name C16_BFGS level.of.stdout 1 # default=1 (1-3) level.of.fileout 0 # default=1 (0-2) Species.Number 1 <Definition.of.Atomic.Species C C5.0-s2p2d1 C_PBE13 Definition.of.Atomic.Species> Atoms.Number 16 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU <Atoms.SpeciesAndCoordinates 1 C -0.4491250 -0.4491250 6.7177785 2.00000 2.00000 2 C -1.3473750 0.4491250 5.8978544 2.00000 2.00000 3 C 1.3473750 -0.4491250 4.9613564 2.00000 2.00000 4 C 0.4491250 0.4491250 4.0676584 2.00000 2.00000 5 C -0.4491250 -0.4491250 3.1621674 2.00000 2.00000 6 C -1.3473750 0.4491250 2.2581139 2.00000 2.00000 7 C 1.3473750 -0.4491250 1.3550285 2.00000 2.00000 8 C 0.4491250 0.4491250 0.4526505 2.00000 2.00000 9 C -0.4491250 -0.4491250 -0.4526938 2.00000 2.00000 10 C -1.3473750 0.4491250 -1.3550841 2.00000 2.00000 11 C 1.3473750 -0.4491250 -2.2581877 2.00000 2.00000 12 C 0.4491250 0.4491250 -3.1622633 2.00000 2.00000 13 C -0.4491250 -0.4491250 -4.0677786 2.00000 2.00000 14 C -1.3473750 0.4491250 -4.9614883 2.00000 2.00000 15 C 1.3473750 -0.4491250 -5.8980559 2.00000 2.00000 16 C 0.4491250 0.4491250 -6.7179699 2.00000 2.00000 Atoms.SpeciesAndCoordinates> Atoms.UnitVectors.Unit Ang # Ang|AU <Atoms.UnitVectors 1.796500 1.796500 0.000000 1.796500 -1.796500 0.000000 0.000000 0.000000 23.473750 Atoms.UnitVectors> scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE scf.SpinPolarization off # On|Off|NC scf.ElectronicTemperature 800.0 # default=300 (K) scf.energycutoff 100.0 # default=150 (Ry) scf.maxIter 100 # default=40 scf.EigenvalueSolver band # DC|GDC|Cluster|Band scf.Kgrid 5 5 1 # means n1 x n2 x n3 scf.Mixing.Type Rmm-Diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk scf.Init.Mixing.Weight 0.10 # default=0.30 scf.Min.Mixing.Weight 0.01 # default=0.001 scf.Max.Mixing.Weight 0.200 # default=0.40 scf.Mixing.History 14 # default=5 scf.Mixing.StartPulay 7 # default=6 scf.criterion 1.0e-6 # default=1.0e-6 (Hartree) MD.Type OptC5 # Nomd|Opt|NVE|NVT_VS|NVT_NH MD.Opt.DIIS.History 3 # default=3 MD.Opt.StartDIIS 7 # default=5 MD.maxIter 200 # default=1 MD.Opt.criterion 1.0e-3 # default=1.0e-4 (Hartree/bohr) <MD.Fixed.Cell.Vectors 0 0 1 0 0 1 1 1 0 MD.Fixed.Cell.Vectors> ------------------------------------- Using "scf.EigenvalueSolver band" always leads to the end without errors. However, the cluster eigenvalue solver results randomly in errors when forces or stresses are evaluated: .... ******************* MD=47 SCF=21 ******************* <Poisson> Poisson's equation using FFT... <Set_Hamiltonian> Hamiltonian matrix for VNA+dVH+Vxc... <Cluster> Solving the eigenvalue problem... 1 C MulP 2.0727 2.0727 sum 4.1453 2 C MulP 1.9644 1.9644 sum 3.9288 3 C MulP 1.9699 1.9699 sum 3.9399 4 C MulP 1.9933 1.9933 sum 3.9866 5 C MulP 2.0001 2.0001 sum 4.0002 6 C MulP 2.0007 2.0007 sum 4.0014 7 C MulP 1.9988 1.9988 sum 3.9976 8 C MulP 2.0002 2.0002 sum 4.0004 9 C MulP 2.0002 2.0002 sum 4.0004 10 C MulP 1.9988 1.9988 sum 3.9976 11 C MulP 2.0007 2.0007 sum 4.0014 12 C MulP 2.0001 2.0001 sum 4.0002 13 C MulP 1.9933 1.9933 sum 3.9866 14 C MulP 1.9699 1.9699 sum 3.9399 15 C MulP 1.9644 1.9644 sum 3.9288 16 C MulP 2.0725 2.0725 sum 4.1450 Sum of MulP: up = 32.00000 down = 32.00000 total= 64.00000 ideal(neutral)= 64.00000 <DFT> Total Spin Moment (muB) = 0.000000000000 <DFT> Mixing_weight= 0.020000000000 <DFT> Uele = -43.156499924661 dUele = 0.000000304256 <DFT> NormRD = 0.000324828290 Criterion = 0.000001000000 <MD=47> Force calculation Force calculation #1 [localhost.localdomain:26291] Read -1, expected 18446744073709548224, errno = 22 [localhost.localdomain:26291] Read -1, expected 18446744073709546432, errno = 22 [localhost.localdomain:26291] Read -1, expected 18446744073709546432, errno = 22 [localhost.localdomain:26291] Read -1, expected 18446744073709546432, errno = 22 [localhost.localdomain:26291] Read -1, expected 18446744073709547200, errno = 22 [localhost.localdomain:26291] Read -1, expected 18446744073709547200, errno = 22 [localhost.localdomain:26291] Read -1, expected 18446744073709547200, errno = 22 [localhost.localdomain:26291] Read -1, expected 18446744073709546432, errno = 22 [localhost.localdomain:26291] Read -1, expected 18446744073709546432, errno = 22 [localhost.localdomain:26291] Read -1, expected 18446744073709546432, errno = 22 [localhost.localdomain:26291] Read -1, expected 18446744073709546432, errno = 22 [localhost.localdomain:26291] Read -1, expected 18446744073709547200, errno = 22 [localhost.localdomain:26291] Read -1, expected 18446744073709547200, errno = 22 [localhost.localdomain:26291] Read -1, expected 18446744073709547200, errno = 22 [localhost.localdomain:26291] Read -1, expected 18446744073709547200, errno = 22 Best regards

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Re: cluster & band calculations ( No.1 ) Date: 2017/06/11 09:30 Name: Kylin Dear tata before you start your calculation, have you ever tested the validation of compiled openmx by "-runtest" and "-forcetest" argument in the work directory? For my perspective, I didn't prefer to do a mixture compilation between gcc and Intel MKL. Maybe you can try icc+MKL, gcc+openblas or gcc+ACML, the later was shown to be more stable for openmx. I just quickly review the code of DFT.c and Force.c, and find there would be no different for the force and stress calculation between Band and Cluster solver. the only special treatment was the linear solver for DC and Krylov in Force.c. Thus I think you should check the validation of your executable first, then the structure of your system after minimization. Sometimes, the impractical configuration may induce the instability of openmx. Cheers Kylin Re: cluster & band calculations ( No.2 ) Date: 2017/06/12 17:59 Name: tata Dear Kylin, Thank you for quick response. After some additional test performed under GNU+MKL environment I come to conclusion that evaluation of forces and stresses works well for band and cluster solvers when only the one openMP thread is run. Best regards, tata Re: cluster & band calculations ( No.3 ) Date: 2017/06/18 18:41 Name: tata Hi, The errors appear when #1 contribution to forces and stresses is calculated: <MD= 5> Force calculation Force calculation #1 [s3:03456] *** Process received signal *** [s3:03456] Signal: Segmentation fault (11) [s3:03456] Signal code: Address not mapped (1) [s3:03456] Failing at address: 0x19ceecd8 [s3:03450] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xf890)[0x7fa0bd567890] [s3:03450] [ 1] /home/dft/opt/openmpi-2.1.1/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_recv_request_progress_frag+0x3e)[0x7fa0af5e5bee] [s3:03450] [ 2] /home/dft/opt/openmpi-2.1.1/lib/openmpi/mca_btl_vader.so(mca_btl_vader_poll_handle_frag+0x71)[0x7fa0afbf7b51] [s3:03450] [ 3] /home/dft/opt/openmpi-2.1.1/lib/openmpi/mca_btl_vader.so(+0x3f78)[0x7fa0afbf7f78] [s3:03450] [ 4] /home/dft/opt/openmpi-2.1.1/lib/libopen-pal.so.20(opal_progress+0x3c[s3:03456] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xf890)[0x7f585bda7890] [s3:03456] [ 1] /home/dft/opt/openmpi-2.1.1/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_recv_request_progress_frag+0x3e)[0x7f584dd94bee] [s3:03456] [ 2] /home/dft/opt/openmpi-2.1.1/lib/openmpi/mca_btl_vader.so(mca_btl_vader_poll_handle_frag+0x71)[0x7f584e3a6b51] [s3:03456] [ 3] /home/dft/opt/openmpi-2.1.1/lib/openmpi/mca_btl_vader.so(+0x3f78)[0x7f584e3a6f78] [s3:03456] [ 4] /home/dft/opt/openmpi-2.1.1/lib/libopen-pal.so.20(opal_progress+0x3c)[0x7f585b4a3e2c] Finally I come to conclusion that it is somehow related to the use of openmpi-2.1.1, and not connected to to compiling environment and/or math libraries. When I switched to mpich-3.2 the above errors "miraculously" disappeared and I am very contend that OpenMX (hybrid parallelization) works perfectly when cell optimization is enabled. Best regards, tata

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