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zuocuiping木虫 (职业作家)
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[求助]
USPEX使用错误
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请问我使用uspex软件，出现下面的错误 {index exceeds array bounds. error in submitjob_local (line 27) jobnumber = b(1:end_marker(1)-1); error in submitjob (line 23) jobnumber = submitjob_local(); error in submitjobs_neb (line 26) pop_struc.population(do_now).jobid = submitjob(do_now); error in vcneb (line 14) submitjobs_neb(); error in neb_start (line 49) vcneb(); } 看了看说的submitjob_local。m文件%step 3: to get the jobid from the screen message end_marker = findstr(b,'.'); jobnumber = b(1:end_marker(1)-1); 这也没有什么错误 看了看submitjob 文件， function jobnumber = submitjob(ind_no) global pop_struc global org_struc step = pop_struc.population(ind_no).step; code = org_struc.abinitiocode(step); dimension = org_struc.dimension; jobnumber = 0; if org_struc.abinitiocode(step) == 0 % no optimization at all! (used in order optimization) jobnumber = 0.02; elseif org_struc.platform == 0 %nonparallel jobnumber=100; [a,b]=unix(org_struc.commandexecutable{step}); if org_struc.numparallelcalcs > 1 disp([ 'individual ' num2str(ind_no) ' @ step ' num2str(step) ' is submitted']); end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% elseif org_struc.platform == 1 %from user local submission jobnumber = submitjob_local(); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% elseif org_struc.platform == 2 %from user remote submission jobnumber = submitjob_remote(org_struc.remotefolder, pop_struc.population(ind_no).folder); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% elseif org_struc.platform == 3 %cfn fp = fopen('myrun_cfn', 'w'); fprintf(fp, '#!/bin/sh\n'); fprintf(fp, '#pbs -l nodes=1:ppn=8,walltime=1:30:00\n'); fprintf(fp, '#pbs -n uspex\n'); fprintf(fp, '#pbs -j oe\n'); fprintf(fp, '#pbs -v \n'); fprintf(fp, 'cd ${pbs_o_workdir}\n'); fprintf(fp, '/home1/qzhu/source/mpi/bin/mpirun -np 8 /home1/qzhu/source/vasp.5.2/vasp > vasp.out\n'); fclose(fp); [a,b]=unix(['qsub myrun_cfn']) end_marker = findstr(b,'.'); jobnumber = b(1:end_marker(1)-1); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% elseif org_struc.platform==4 %qsh if code == 12 numproc = 1; minproc = 1; else numproc = org_struc.numprocessors(step); if numproc > 8 minproc = 8; numproc = 8; else minproc = numproc; end end totalnowpath = [org_struc.homepath '/calcfold' num2str(pop_struc.population(ind_no).folder)]; [a,b]=unix(['cat /dev/null > myrun_qsh']); [a,b]=unix(['echo "#!/bin/sh" >> myrun_qsh']); [a,b]=unix(['echo "#bsub -sp 60" >> myrun_qsh']); [a,b]=unix(['echo "#bsub -q intel" >> myrun_qsh']); [a,b]=unix(['echo "#bsub -a intelmpi" >> myrun_qsh']); [a,b]=unix(['echo "#bsub -o output" >> myrun_qsh']); [a,b]=unix(['echo "#bsub -r \"span[ptile=' num2str(numproc) ']\"" >> myrun_qsh']); [a,b]=unix(['echo "#bsub -j uspex-',num2str(ind_no),'s',num2str(pop_struc.population(ind_no).step),'" >> myrun_qsh']); [a,b]=unix(['echo "#bsub -w 06:00" >> myrun_qsh']); [a,b]=unix(['echo "#bsub -n ' num2str(minproc) ' " >> myrun_qsh']); if code == 1 [a,b]=unix(['echo "yhrun.lsf vasp-vdw" >> myrun_qsh']); elseif code == 3 [a,b]=unix(['echo "gulp < input > output" >> myrun_qsh']); elseif code == 4 [a,b]=unix(['echo "mpirun.lsf lammps < lammps.in " >> myrun_qsh']); elseif code == 9 [a,b]=unix(['echo "mpirun.lsf aims.x > fhi_output" >> myrun_qsh']); elseif code == 11 [a,b]=unix(['echo "runcastep.sh -np 8 cstp >> log" >> myrun_qsh']); elseif code == 12 if dimension ~= -4 [a,b]=unix(['echo "bash ./tinker.sh" >> myrun_qsh']); else [a,b]=unix(['echo "python \$uspexpath/functionfolder/uspex/m400/random_protein/random_protein.py input 1 pseudo memory > output" >> myrun_qsh']); end elseif code == 13 [a,b]=unix(['echo "mopac2012.exe input.mop" >> myrun_qsh']); elseif code == 14 [a,b]=unix(['echo "mpirun.lsf boltztrap boltztrap.def > boltztrap.output" >> myrun_qsh']); end [a,b]=unix(['bsub < myrun_qsh > job.info']); [a,b] =unix([' cat job.info | grep job']); disp(b); start_marker=findstr(b,'<'); end_marker = findstr(b,'>'); jobnumber = b(start_marker(1)+1:end_marker(1)-1); disp([ 'individual : ' num2str(ind_no) ' -- jobid :', num2str(jobnumber) ]); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% elseif org_struc.platform==5 %qsh2 if code == 12 numproc = 1; minproc = 1; else numproc = org_struc.numprocessors(step); if numproc > 8 minproc = 8; numproc = 8; else minproc = numproc; end end totalnowpath = [org_struc.homepath '/calcfold' num2str(pop_struc.population(ind_no).folder)]; [nothing, nothing] = unix(['cat /dev/null > myrun_qsh']); [nothing, nothing] = unix(['echo "#!/bin/sh" >> myrun_qsh']); [nothing, nothing] = unix(['echo "#bsub -sp 60" >> myrun_qsh']); [nothing, nothing] = unix(['echo "#bsub -q amd" >> myrun_qsh']); [nothing, nothing] = unix(['echo "#bsub -a intelmpi" >> myrun_qsh']); [nothing, nothing] = unix(['echo "#bsub -o output" >> myrun_qsh']); [nothing, nothing] = unix(['echo "#bsub -r \"span[ptile=' num2str(numproc) ']\"" >> myrun_qsh']); [nothing, nothing] = unix(['echo "#bsub -j uspex-',num2str(ind_no),'s',num2str(pop_struc.population(ind_no).step),'" >> myrun_qsh']); [nothing, nothing] = unix(['echo "#bsub -w 06:00" >> myrun_qsh']); [nothing, nothing] = unix(['echo "#bsub -n ' num2str(minproc) ' " >> myrun_qsh']); if code == 1 [nothing, nothing] = unix(['echo "yhrun.lsf vasp-vdw" >> myrun_qsh']); elseif code == 3 [nothing, nothing] = unix(['echo "gulp < input > output" >> myrun_qsh']); elseif code == 4 [nothing, nothing] = unix(['echo "mpirun.lsf lammps < lammps.in > lammps.out " >> myrun_qsh']); elseif code == 9 [nothing, nothing] = unix(['echo "mpirun.lsf aims.x > fhi_output" >> myrun_qsh']); elseif code == 11 [a,b]=unix(['echo "runcastep.sh -np 8 cstp >> log" >> myrun_qsh']); elseif code == 12 if dimension ~= -4 [a,b]=unix(['echo "bash ./tinker.sh" >> myrun_qsh']); else [a,b]=unix(['echo "python \$uspexpath/functionfolder/uspex/m400/random_protein/random_protein.py input 1 pseudo memory > output" >> myrun_qsh']); end elseif code == 13 [a,b]=unix(['echo "mopac2012.exe input.mop" >> myrun_qsh']); elseif code == 14 [a,b]=unix(['echo "mpirun.lsf boltztrap boltztrap.def > boltztrap.output" >> myrun_qsh']); end [nothing, nothing] = unix(['bsub < myrun_qsh > job.info']); [a,b] =unix([' cat job.info | grep job']); disp(b); start_marker=findstr(b,'<'); end_marker = findstr(b,'>'); jobnumber = b(start_marker(1)+1:end_marker(1)-1); disp([ 'individual : ' num2str(ind_no) ' -- jobid :', num2str(jobnumber) ]); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% elseif org_struc.platform ==6 %xservde [nothing, nothing] = unix('cat /dev/null > job'); [nothing, nothing] = unix('echo "#\$ -s /bin/bash" > job'); [nothing, nothing] = unix('echo "#\$ -n r30" >> job'); [nothing, nothing] = unix('echo "#\$ -cwd" >> job'); [nothing, nothing] = unix('echo "#\$ -l arch=darwin-x86" >> job'); [nothing, nothing] = unix(['echo "#\$ -pe openmpi ' num2str(numprocessors) '" >> job']); [nothing, nothing] = unix('echo ". ~/.bashrc" >> job'); [nothing, nothing] = unix('echo "hostname" >> job'); [nothing, nothing] = unix(['echo "' org_struc.commandexecutable{step} '" >> job']); % qsub script | awk '{print $3}' [a,v] = unix('qsub job'); start_marker = 1; % format: your job 248264 ("looki"  has been submittedend_marker = findstr(v,')'); jobnumber = v(10:end_marker(1)-2) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% elseif org_struc.platform ==7 %mipt-cluster totalnowpath = [org_struc.homepath '/calcfold' num2str(pop_struc.population(ind_no).folder)]; [nothing, nothing] = unix(['cat /dev/null > myrun_mipt']); [nothing, nothing] = unix(['echo "#!/bin/sh" >> myrun_mipt']); [nothing, nothing] = unix(['echo "#sbatch -o out" >> myrun_mipt']); [nothing, nothing] = unix(['echo "#sbatch -p work " >> myrun_mipt']); [nothing, nothing] = unix(['echo "#sbatch -j uspex-' num2str(pop_struc.generation),'i',num2str(ind_no),'s',num2str(pop_struc.population(ind_no).step),'" >> myrun_mipt']); [nothing, nothing] = unix(['echo "#sbatch -t 06:00:00" >> myrun_mipt']); [nothing, nothing] = unix(['echo "#sbatch -n 1" >> myrun_mipt']); [nothing, nothing] = unix(['echo cd ' totalnowpath ' >> myrun_mipt']); [nothing, nothing] = unix(['echo mpdboot >>myrun_mipt']); [nothing, nothing] = unix(['echo "mpirun -np 16 vasp-vdw> log" >> myrun_mipt']); [nothing, nothing] = unix(['echo mpdallexit >>myrun_mipt']); ind_no [a,b] = unix(['sbatch myrun_mipt '] ); start_marker=findstr(b,'job '); jobnumber = b(start_marker(1)+4:end-1); disp([ 'individual : ' num2str(ind_no) ' -- jobid :', num2str(jobnumber) ]); elseif org_struc.platform ==8 %npu totalnowpath = [org_struc.homepath '/calcfold' num2str(pop_struc.population(ind_no).folder)]; cd (totalnowpath) %step 1: to prepare the job script which is required by your supercomputer fp = fopen('jobrun', 'w'); fprintf(fp, '#!/bin/sh \n'); fprintf(fp, '#pbs -n uspex \n'); fprintf(fp, '#pbs -l nodes=1:ppn=8 \n'); fprintf(fp, '#pbs -l walltime=6:00:00 \n'); fprintf(fp, '#pbs -q batch \n'); fprintf(fp, '#pbs -v \n'); fprintf(fp, '#pbs -s /bin/bash \n'); fprintf(fp, 'source /export/opensource/vasp.5.2/vaspenvset.sh \n'); fprintf(fp, 'exec=~/bin/vasp53 \n'); fprintf(fp, 'mpi_home=/export/compiler/intel/impi/4.1.0.024 \n'); fprintf(fp, 'np=`wc -l < $pbs_nodefile` \n'); fprintf(fp, ['cd ' totalnowpath ' \n']); fprintf(fp, '$mpi_home/bin/mpirun -machinefile $pbs_nodefile -np $np $exec > out \n'); fclose(fp); [a,b]=unix(['qsub jobrun']); end_marker = findstr(b,'.'); jobnumber = b(1:end_marker(1)-1); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% elseif org_struc.platform == 9 % cfn workshop 2014 fp = fopen('myrun_cfn', 'w'); fprintf(fp, '#!/bin/sh\n'); fprintf(fp, '#pbs -l nodes=1:ppn=8,walltime=1:30:00 -q cfn_workshop\n'); fprintf(fp, ['#pbs -n uspex' num2str(ind_no), 's' ,num2str(pop_struc.population(ind_no).step) '\n']); fprintf(fp, '#pbs -j oe\n'); fprintf(fp, '#pbs -v \n'); fprintf(fp, 'ulimit -s unlimited\n'); fprintf(fp, 'source /opt/intel/2013/bin/compilervars.sh intel64\n'); fprintf(fp, 'cd ${pbs_o_workdir}\n'); fprintf(fp, '/software/mpi/openmpi/1.8.1-intel/bin/mpirun -np 8 /software/workshop14/bin/vaspp > vasp.out\n'); fclose(fp); [a,b]=unix(['qsub myrun_cfn']) end_marker = findstr(b,'.'); jobnumber = b(1:end_marker(1)-1); elseif org_struc.platform == 10 % unn supercomputer (supz) totalnowpath = [org_struc.homepath '/calcfold' num2str(pop_struc.population(ind_no).folder)]; jobname = [num2str(pop_struc.generation),'i',num2str(ind_no),'s',num2str(pop_struc.population(ind_no).step)]; unix(['cat /dev/null > myrun_unn']); unix(['echo "#!/bin/sh" >> myrun_unn']); unix(['echo "#sbatch -o out" >> myrun_unn']); unix(['echo "#sbatch -p all " >> myrun_unn']); unix(['echo "#sbatch -j ' jobname '-uspex" >> myrun_unn']); unix(['echo "#sbatch -t 06:00:00" >> myrun_unn']); unix(['echo "#sbatch -n 1" >> myrun_unn']); unix(['echo "#sbatch -n 16" >> myrun_unn']); unix(['echo "" >> myrun_unn']); unix(['echo cd ' totalnowpath ' >> myrun_unn']); unix(['echo "srun vasp > log" >> myrun_unn']); [a,b] = unix(['sbatch myrun_unn '] ); start_marker=findstr(b,'job '); jobnumber = b(start_marker(1)+4:end-1); disp([ 'individual : ' num2str(ind_no) ' -- jobid :', num2str(jobnumber) ]); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% end if isempty(jobnumber) jobnumber = 0; end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% if org_struc.platform > 0 cd([org_struc.homepath,'/calcfoldtemp']); id=['.job-gen',num2str(pop_struc.generation),'ind',num2str(ind_no),'step',num2str(pop_struc.population(ind_no).step),'fold',num2str(pop_struc.population(ind_no).folder)]; [a,b]=unix(['touch ' num2str(jobnumber), id]); id=['generation ' num2str(pop_struc.generation), ' step ' num2str(num2str(pop_struc.population(ind_no).step)) ' of structure ' num2str(ind_no),' at calcfold' num2str(pop_struc.population(ind_no).folder) ' : jobid ' num2str(jobnumber) ]; [a,b]=unix(['echo -n "' id,' submitted " >> jobs.history ' ]); [a,b]=unix(['echo -e `date +"%b%d-%t"` >> jobs.history ' ]); end 太多了，没有看懂 submitjobs_neb 这个文件我计算中根本没有看到这个文件 不知道怎么处理，谢谢做过的人交流一下！ |
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您好，我在计算算例1时，因为我只有一个节点所以把批量计算改为了单节点计算（whichcluster=0，numparallelcalcs=1），计算结果两个文件都报错了，ERROR文件：Many structures failed after relaxation, Plz check the input files. Results maybe unreliable. Possible reasons: high bestFrac, bad optimization parameters or contraints.(把bestFrac改小还是一样的错误）。Warning：Read_VASP : VASP SCF is not converged! CalcFlod1中也没有进行计算。。。。。。。。。。。。。。。请问您有没有遇到这种情况？或者您知道这是为什么吗？ 发自小木虫Android客户端 |
7楼2022-07-22 11:07:45
5