Bin, Check the list archives for emails of the last week. Someone had a problem similar to yours for a small system, it couls be something related.
Marcos On Thu, Jul 8, 2010 at 3:51 PM, Bin Shao <[email protected]> wrote: > Dear siesta users, > > When I tried to do the Ex1 of Barcelona 07 - CH4, there came something wrong > with setting the PAO.BasisSize to be DZP and running the siesta in parallel. > And I compiled the siesta with impi. Here is the wrong message: > > stepf: Fermi-Dirac step function > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line Source > siesta 00000000004AA7ED Unknown Unknown Unknown > siesta 0000000000498890 Unknown Unknown Unknown > siesta 00000000005E0FA2 Unknown Unknown Unknown > siesta 000000000046316C Unknown Unknown Unknown > libc.so.6 0000003F9681D994 Unknown Unknown Unknown > siesta 0000000000463079 Unknown Unknown Unknown > rank 7 in job 1 node18c.emlab_58968 caused collective abort of all ranks > exit status of rank 7: return code 174 > > and the input file: > > #General system specifications > SystemName CH4 molecule > SystemLabel ch4 > NumberOfAtoms 5 > NumberOfSpecies 2 > > %block ChemicalSpeciesLabel > 1 6 C # Species index, atomic number, species label > 2 1 H # Species index, atomic number, species label > %endblock ChemicalSpeciesLabel > > > #Atomic coordinates > AtomicCoordinatesFormat Ang > > %block AtomicCoordinatesAndAtomicSpecies > 0.000 0.000 0.000 1 > 1.219 -0.284 -0.377 2 > -0.284 1.219 -0.377 2 > -0.140 -0.140 1.219 2 > -0.833 -0.833 -0.503 2 > %endblock AtomicCoordinatesAndAtomicSpecies > > > # Basis set definition > PAO.EnergyShift 250 meV > PAO.SplitNorm 0.15 > PAO.BasisSize DZP > > #Real space grid > MeshCutoff 10.0 Ry > > # Convergence of SCF > MaxSCFIterations 50 > DM.MixingWeight 0.9 > DM.NumberPulay 2 > > # Type of solution (diagon is the default for less than 100 atoms) > SolutionMethod diagon > > If I set the PAO.BasisSize to be DZ or SZ or do not run the siesta in > parallel, the calculation will finish successfully. In addition, there is 8 > nodes of my cluster and I run the program with the command mpirun -r ssh -np > X siesta < ch4.fdf, (X is the number of the nodes I needed). If X < 8, the > calculation will finish successfully even setting the PAO.BasisSize to be > DZP. > > What's the problem? How can I run the program with 8 nodes, meanwhile > setting the PAO.BasisSize to be DZP? > > Any suggestion will be appriciated. Thank you in advance! > > Best regards, > > > -- > Bin Shao > College of Information Technical Science, Nankai University > 94 Weijin Rd. Nankai Dist. Tianjin 300071, China > Email: [email protected] >
