[SIESTA-L] negative value for MESH
Dear SIESTA Users, We are facing an annoying problem for CG runs on a HPMPI intel machine. The siesta job runs fine for the first CG step and then crashes for the next step. On analysis we found an unreasonable value for MESH = -460324864(large & -ve ) . Could anybody help us out. OUT PUT FILE siesta: k-point coordinates (Bohr**-1) and weights: siesta:1 -0.073104 -0.15 -0.02 0.11 siesta:20.000.000.00 0.11 siesta:30.0731040.150.02 0.11 siesta:4 -0.0730860.084214 -0.05 0.22 siesta:50.180.084230 -0.03 0.22 siesta:60.0731220.084245 -0.01 0.22 siesta: k-grid: Number of k-points = 6 siesta: k-grid: Cutoff =15.075 Ang siesta: k-grid: Supercell and displacements siesta: k-grid:3 0 0 0.000 siesta: k-grid:0 3 0 0.000 siesta: k-grid:0 0 1 0.000 superc: Internal auxiliary supercell: 2 x 2 x 1 = 4 superc: Number of atoms, orbitals, and projectors:736 9232 11272 outcell: Unit cell vectors (Ang): 15.160609 -0.003215 -0.000482 -0.002785 13.1581040.000469 -0.0009600.001078 30.149929 outcell: Cell vector modules (Ang) : 15.160610 13.158104 30.149929 outcell: Cell angles (23,13,12) (deg): 89.9959 90.0036 90.0243 outcell: Cell volume (Ang**3): 6014.4545 InitMesh: MESH =864000 x829440 x984150 = -460324864 InitMesh: Mesh cutoff (required, used) = 400.000 414.060 Ry thanks swaroop -- M.Sairam Swaroop Theoretical Sciences Unit JNCASR,Jakkur Bangalore-64 INDIA
Re: [SIESTA-L] negative value for MESH
Dear M. Swaroop, Did you compile siesta with a 64 bit compiler? I think you used a 32 bit and you have overflown the number of grid points. (64000 x829440 x984150= 7.05E17) So you have to reduce the mesh cutoff and/or use a 64 bits compiler. The system is really big, where you able to diagonalize the hamiltoninan in a different CG step? If yes why it is rebuilding the mesh, are you using variable cell CG? For such a big system do you need so many kpoints? Best regards, Eduardo On 22/05/2008, at 11:20, M.Sairam Swaroop wrote: Dear SIESTA Users, We are facing an annoying problem for CG runs on a HPMPI intel machine. The siesta job runs fine for the first CG step and then crashes for the next step. On analysis we found an unreasonable value for MESH = -460324864(large & -ve ) . Could anybody help us out. OUT PUT FILE siesta: k-point coordinates (Bohr**-1) and weights: siesta:1 -0.073104 -0.15 -0.02 0.11 siesta:20.000.000.00 0.11 siesta:30.0731040.150.02 0.11 siesta:4 -0.0730860.084214 -0.05 0.22 siesta:50.180.084230 -0.03 0.22 siesta:60.0731220.084245 -0.01 0.22 siesta: k-grid: Number of k-points = 6 siesta: k-grid: Cutoff =15.075 Ang siesta: k-grid: Supercell and displacements siesta: k-grid:3 0 0 0.000 siesta: k-grid:0 3 0 0.000 siesta: k-grid:0 0 1 0.000 superc: Internal auxiliary supercell: 2 x 2 x 1 = 4 superc: Number of atoms, orbitals, and projectors:736 9232 11272 outcell: Unit cell vectors (Ang): 15.160609 -0.003215 -0.000482 -0.002785 13.1581040.000469 -0.0009600.001078 30.149929 outcell: Cell vector modules (Ang) : 15.160610 13.158104 30.149929 outcell: Cell angles (23,13,12) (deg): 89.9959 90.0036 90.0243 outcell: Cell volume (Ang**3): 6014.4545 InitMesh: MESH =864000 x829440 x984150 = -460324864 InitMesh: Mesh cutoff (required, used) = 400.000 414.060 Ry thanks swaroop -- M.Sairam Swaroop Theoretical Sciences Unit JNCASR,Jakkur Bangalore-64 INDIA
Re: [SIESTA-L] negative value for MESH
Dear Eduardo We have compiled siesta with a 64 bit compiler and we have allowed for a variable cell CG minimization. siesta was able to diagonalize the hamiltonian in the first CG step. We need these many k-points due to the periodicity in the system. Are there any issues with variable cell calculations and mesh rebuilding. please do help us out. regards swaroop > Dear M. Swaroop, > > Did you compile siesta with a 64 bit compiler? I think you used > a 32 bit and you have overflown the number of grid points. > (64000 x829440 x984150= 7.05E17) > > So you have to reduce the mesh cutoff and/or use a 64 bits compiler. > > The system is really big, where you able to diagonalize > the hamiltoninan in a different CG step? If yes why it is rebuilding > the mesh, are you using variable cell CG? > > For such a big system do you need so many kpoints? > > Best regards, > Eduardo > > On 22/05/2008, at 11:20, M.Sairam Swaroop wrote: > >> Dear SIESTA Users, >> >> We are facing an annoying problem for CG runs on a HPMPI intel >> machine. >> The siesta job runs fine for the first CG step and then crashes for >> the >> next step. On analysis we found an unreasonable value for MESH = >> -460324864(large & -ve ) . >> >> Could anybody help us out. >> >>OUT PUT FILE >> >>siesta: k-point coordinates (Bohr**-1) and weights: >>siesta:1 -0.073104 -0.15 -0.02 0.11 >>siesta:20.000.000.00 0.11 >>siesta:30.0731040.150.02 0.11 >>siesta:4 -0.0730860.084214 -0.05 0.22 >>siesta:50.180.084230 -0.03 0.22 >>siesta:60.0731220.084245 -0.01 0.22 >> >>siesta: k-grid: Number of k-points = 6 >>siesta: k-grid: Cutoff =15.075 Ang >>siesta: k-grid: Supercell and displacements >>siesta: k-grid:3 0 0 0.000 >>siesta: k-grid:0 3 0 0.000 >>siesta: k-grid:0 0 1 0.000 >> >>superc: Internal auxiliary supercell: 2 x 2 x 1 >> = 4 >>superc: Number of atoms, orbitals, and projectors:736 9232 >> 11272 >> >>outcell: Unit cell vectors (Ang): >> 15.160609 -0.003215 -0.000482 >> -0.002785 13.1581040.000469 >> -0.0009600.001078 30.149929 >> >>outcell: Cell vector modules (Ang) : 15.160610 13.158104 >> 30.149929 >>outcell: Cell angles (23,13,12) (deg): 89.9959 90.0036 >> 90.0243 >>outcell: Cell volume (Ang**3): 6014.4545 >> >>InitMesh: MESH =864000 x829440 x984150 = -460324864 >>InitMesh: Mesh cutoff (required, used) = 400.000 414.060 Ry >> >> thanks >> >> swaroop >> >> -- >> M.Sairam Swaroop >> Theoretical Sciences Unit >> JNCASR,Jakkur >> Bangalore-64 >> INDIA >> >> > -- M.Sairam Swaroop Theoretical Sciences Unit JNCASR,Jakkur Bangalore-64 INDIA
Re: [SIESTA-L] negative value for MESH
Dear Eduardo We have compiled siesta with a 64 bit compiler and we have allowed for a variable cell CG minimization. siesta was able to diagonalize the hamiltonian in the first CG step. We need these many k-points due to the periodicity in the system. Are there any issues with variable cell calculations and mesh rebuilding. please do help us out. If there are any other inputs that i should provide then please so let me know. regards swaroop
Re: [SIESTA-L] negative value for MESH
Dear Swaroop, Which are the values of the mesh in the previous CG steps? Are they very different? Maybe we can guess what is going on. Regards, Eduardo On 23/05/2008, at 14:24, M.Sairam Swaroop wrote: Dear Eduardo We have compiled siesta with a 64 bit compiler and we have allowed for a variable cell CG minimization. siesta was able to diagonalize the hamiltonian in the first CG step. We need these many k-points due to the periodicity in the system. Are there any issues with variable cell calculations and mesh rebuilding. please do help us out. If there are any other inputs that i should provide then please so let me know. regards swaroop
Re: [SIESTA-L] negative value for MESH
Dear Eduardo After you mentioned i noticed tha the mesh does not change ... i have grepped the "InitMesh: MESH =" from my output file and here is the output InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH =153600 x145800 x182250 = -1886683136 I really do not understand what is going on ... another anamoly that i see is that i have supplied the following lattice vectors as the input block LatticeVectors 14.9828910.0006800.015378 0.000589 12.947787 -0.003033 0.031384 -0.007147 30.441943 %endblock LatticeVectors but for CG =0 i get the following in the output file outcell: Unit cell vectors (Ang): 14.700.000.00 0.00 12.7305800.00 0.000.00 30.00 I notice that the job crashed when the cell vector became more then the input specified ie grep "outcell: Cell vector modules (Ang) :" *.out outcell: Cell vector modules (Ang) : 14.70 12.730580 30.00 outcell: Cell vector modules (Ang) : 14.917065 12.920354 30.024935 outcell: Cell vector modules (Ang) : 14.905544 12.910281 30.023611 outcell: Cell vector modules (Ang) : 14.919716 12.900398 30.139252 outcell: Cell vector modules (Ang) : 14.942395 12.884584 30.324281 outcell: Cell vector modules (Ang) : 14.928030 12.894601 30.207079 outcell: Cell vector modules (Ang) : 14.801968 13.042322 30.402947 outcell: Cell vector modules (Ang) : 14.896749 12.931255 30.255680 outcell: Cell vector modules (Ang) : 14.904436 12.918676 30.309642 outcell: Cell vector modules (Ang) : 14.916736 12.898548 30.395983 outcell: Cell vector modules (Ang) : 14.908514 12.912003 30.338265 outcell: Cell vector modules (Ang) : 14.982899 12.947787 30.441960 Could you help me out with what is going on here. regards swaroop
Re: [SIESTA-L] negative value for MESH
Clearly there is something wrong going on. Can you send me (privately) the hole output (including the output files with coordinates and cell) Best, Eduardo On 23/05/2008, at 18:26, M.Sairam Swaroop wrote: Dear Eduardo After you mentioned i noticed tha the mesh does not change ... i have grepped the "InitMesh: MESH =" from my output file and here is the output InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH = 180 x 160 x 384 =11059200 InitMesh: MESH =153600 x145800 x182250 = -1886683136 I really do not understand what is going on ... another anamoly that i see is that i have supplied the following lattice vectors as the input block LatticeVectors 14.9828910.0006800.015378 0.000589 12.947787 -0.003033 0.031384 -0.007147 30.441943 %endblock LatticeVectors but for CG =0 i get the following in the output file outcell: Unit cell vectors (Ang): 14.700.000.00 0.00 12.7305800.00 0.000.00 30.00 I notice that the job crashed when the cell vector became more then the input specified ie grep "outcell: Cell vector modules (Ang) :" *.out outcell: Cell vector modules (Ang) : 14.70 12.730580 30.00 outcell: Cell vector modules (Ang) : 14.917065 12.920354 30.024935 outcell: Cell vector modules (Ang) : 14.905544 12.910281 30.023611 outcell: Cell vector modules (Ang) : 14.919716 12.900398 30.139252 outcell: Cell vector modules (Ang) : 14.942395 12.884584 30.324281 outcell: Cell vector modules (Ang) : 14.928030 12.894601 30.207079 outcell: Cell vector modules (Ang) : 14.801968 13.042322 30.402947 outcell: Cell vector modules (Ang) : 14.896749 12.931255 30.255680 outcell: Cell vector modules (Ang) : 14.904436 12.918676 30.309642 outcell: Cell vector modules (Ang) : 14.916736 12.898548 30.395983 outcell: Cell vector modules (Ang) : 14.908514 12.912003 30.338265 outcell: Cell vector modules (Ang) : 14.982899 12.947787 30.441960 Could you help me out with what is going on here. regards swaroop
Re: [SIESTA-L] negative value for MESH
Dear Swaroop Please look for an .XV file (or maybe a .STRUCT one) to see if the cell sizes you are writing are there (.XV is in Bohr!) all the best lucas On Fri, 23 May 2008, M.Sairam Swaroop wrote: > Dear Eduardo > > After you mentioned i noticed tha the mesh does not change ... i have > grepped the "InitMesh: MESH =" from my output file and here is the output > > InitMesh: MESH = 180 x 160 x 384 =11059200 > InitMesh: MESH = 180 x 160 x 384 =11059200 > InitMesh: MESH = 180 x 160 x 384 =11059200 > InitMesh: MESH = 180 x 160 x 384 =11059200 > InitMesh: MESH = 180 x 160 x 384 =11059200 > InitMesh: MESH = 180 x 160 x 384 =11059200 > InitMesh: MESH = 180 x 160 x 384 =11059200 > InitMesh: MESH = 180 x 160 x 384 =11059200 > InitMesh: MESH = 180 x 160 x 384 =11059200 > InitMesh: MESH = 180 x 160 x 384 =11059200 > InitMesh: MESH = 180 x 160 x 384 =11059200 > InitMesh: MESH =153600 x145800 x182250 = -1886683136 > > I really do not understand what is going on ... another anamoly that i see > is that i have supplied the following lattice vectors as the input > > block LatticeVectors > 14.9828910.0006800.015378 > 0.000589 12.947787 -0.003033 > 0.031384 -0.007147 30.441943 > %endblock LatticeVectors > > but for CG =0 i get the following in the output file > outcell: Unit cell vectors (Ang): >14.700.000.00 > 0.00 12.7305800.00 > 0.000.00 30.00 > > I notice that the job crashed when the cell vector became more then the > input specified > ie > > grep "outcell: Cell vector modules (Ang) :" *.out > > outcell: Cell vector modules (Ang) : 14.70 12.730580 30.00 > outcell: Cell vector modules (Ang) : 14.917065 12.920354 30.024935 > outcell: Cell vector modules (Ang) : 14.905544 12.910281 30.023611 > outcell: Cell vector modules (Ang) : 14.919716 12.900398 30.139252 > outcell: Cell vector modules (Ang) : 14.942395 12.884584 30.324281 > outcell: Cell vector modules (Ang) : 14.928030 12.894601 30.207079 > outcell: Cell vector modules (Ang) : 14.801968 13.042322 30.402947 > outcell: Cell vector modules (Ang) : 14.896749 12.931255 30.255680 > outcell: Cell vector modules (Ang) : 14.904436 12.918676 30.309642 > outcell: Cell vector modules (Ang) : 14.916736 12.898548 30.395983 > outcell: Cell vector modules (Ang) : 14.908514 12.912003 30.338265 > outcell: Cell vector modules (Ang) : 14.982899 12.947787 30.441960 > > Could you help me out with what is going on here. > > regards > > swaroop > > ** CRM114 Whitelisted by: uam.es ** > # Ph.D. Student Lucas Fernández Seivane Tlf: (+34) 985 102946 # # Departamento de Fisica, Facultad de Ciencias Fax: (+34) 985 102952 # # Universidad de Oviedo Cell:(+34) 645 227396 # # 33007 Oviedo (Asturias) - Spain #
