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dalongmao木虫 (正式写手)
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[求助]
siesta提交任务出现错误
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在服务器上面提交任务，提交后出现错误，提交命令里面的内容是 #PBS -r n NPROCS=`wc -l < $PBS_NODEFILE` echo ------------------------------------------------------ echo 'This job is allocated on '${NPROCS}' cpu(s)' echo 'Job is running on node(s): ' cat $PBS_NODEFILE echo ------------------------------------------------------ echo PBS: qsub is running on $PBS_O_HOST echo PBS: originating queue is $PBS_O_QUEUE echo PBS: executing queue is $PBS_QUEUE echo PBS: working directory is $PBS_O_WORKDIR echo PBS: execution mode is $PBS_ENVIRONMENT echo PBS: this script pid is $$ echo PBS: job identifier is $PBS_JOBID echo PBS: job name is $PBS_JOBNAME echo PBS: node file is $PBS_NODEFILE echo PBS: current home directory is $PBS_O_HOME echo PBS: PATH = $PBS_O_PATH echo ------------------------------------------------------ cd $PBS_O_WORKDIR # Run the parallel MPI executable mpirun -v -machinefile $PBS_NODEFILE -np $NPROCS /Applications/siesta/siesta3b-ompi-em64t "siestajobintel.sh" 30L, 1044C ， 出现的错误是e文件里面是No species found!!! ERROR STOP from Node: 0 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun has exited due to process rank 0 with PID 14245 on node node157 exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). --------------------------------------------------------------------------， o文件里面是 Red Hat Enterprise Linux Server release 5.5 (Tikanga) MemTotal: 49449440 kB 12 Intel(R) Xeon(R) CPU X5650 @ 2.67GHz ------------------------------------------------------ This job is allocated on 12 cpu(s) Job is running on node(s): ibnode157 ibnode157 ibnode157 ibnode157 ibnode157 ibnode157 ibnode157 ibnode157 ibnode157 ibnode157 ibnode157 ibnode157 ------------------------------------------------------ PBS: qsub is running on node200 PBS: originating queue is intel PBS: executing queue is intel PBS: working directory is /public/Intel-IO/home/SongY/shi/INi4 PBS: execution mode is PBS_BATCH PBS: this script pid is 14240 PBS: job identifier is 49749.node200 PBS: job name is intel PBS: node file is /opt/gridview/pbs/dispatcher/aux//49749.node200 PBS: current home directory is /home/SongY PBS: PATH = /Applications/ompi142-intel/bin:/Applications/intel/Compiler/11.1/064/bin/intel64:/Applications/intel/Compiler/11.1/064/bin/intel64:/usr/lib64/qt-3.3/bin:/opt/gridview/pbs/dispatcher-sched/sbin:/opt/gridview/pbs/dispatcher/sbin:/opt/gridview/pbs/dispatcher-sched/bin:/opt/gridview/pbs/dispatcher/bin:/usr/local/bin:/bin:/usr/bin:/home/SongY/bin ------------------------------------------------------ Siesta Version: siesta-3.0-b Architecture : Ifort-MKL-OpenMPI Compiler flags: mpif90 -O3 -xW -w -unroll0 PARALLEL version (Dawning) Compiled for SSC Magic Cube by Z.J. 2010-04-08 * Running on 12 nodes in parallel >> Start of run: 14-JUL-2012 15:31:05 *********************** * WELCOME TO SIESTA * *********************** reinit: Reading from standard input ************************** Dump of input data file **************************** ************************** End of input data file ***************************** reinit: ----------------------------------------------------------------------- reinit: System Name: reinit: ----------------------------------------------------------------------- reinit: System Label: siesta reinit: ----------------------------------------------------------------------- initatom: Reading input for the pseudopotentials and atomic orbitals ---------- No species found!!! ERROR STOP from Node: 0 ，我用输入文件是in.fdf,改名为intel.fdf，siesta.fdf等等都不行，输入文件内容是 SystemName Water molecule SystemLabel h2o NumberOfAtoms 3 NumberOfSpecies 2 %block ChemicalSpeciesLabel 1 8 O # Species index, atomic number, species label 2 1 H %endblock ChemicalSpeciesLabel AtomicCoordinatesFormat Ang %block AtomicCoordinatesAndAtomicSpecies 0.000 0.000 0.000 1 0.757 0.586 0.000 2 -0.757 0.586 0.000 2 %endblock AtomicCoordinatesAndAtomicSpecies |
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dalongmao
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zhangfan2192
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dalongmao
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