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USPEX使用与错误解决方案

已有 10422 次阅读 2012-12-27 23:33 |个人分类:USPEX|系统分类:科研笔记| MATLAB, VASP, uspex

Q1:

最近学习USPEX, 对T0进行测试，运行 nohup matlab < USPEX.m > log & ，大概几秒钟后，就显示如下的错误。整个过程完全没有调用vasp进行优化计算，你能帮我分析一下吗，或者要做什么修改？谢谢。

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February 9, 2012

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ans =

status = Local optimisation finished

status =

Too many structures have errors or failed the constraints after optimization. Please check the input files. The calculation has to stop.

status1 =

Possible reasons: badly tuned optimization parameters or unreasonable contraints.
1, 上面的提示，完全不是INPUT.txt的设置问题，真是KD，害我不断调试了好多参数。
2. matlab普通用户的执行参考http://wenku.baidu.com/view/01f08cd126fff705cc170ad7.html
3 我的root帐户没有vasp.5.2的执行权限，而多次测试是在root帐户下进行的（CalcFold1 ）

4. 重新提交任务时，必须删除上次的Current_EXE.mat Current_ORG.mat Current_POP.mat三个文件，不然仍然会显示上面的错误提示。

Q2:moab作用的作用提交系统与uspex结合时，submitJob_local.m需要做红色的修改，不然

function jobNumber = submitJob_local()

%-------------------------------------------------------------

%This routine is to check if the submitted job is done or not

%One needs to do a little edit based on your own case.

%1 : whichCluster (default 0, 1: local submission, 2: remote submission)

%-------------------------------------------------------------

%Step 1: to prepare the job script which is required by your supercomputer

fp = fopen('myrun', 'w');

fprintf(fp, '#!/bin/shn');

fprintf(fp, '#MSUB -l nodes=1:ppn=16,walltime=01:00:00n');

fprintf(fp, '#MSUB -N USPEXn');

fprintf(fp, '#MSUB -q jscn');

fprintf(fp, '#MSUB -j oen');

fprintf(fp, '#MSUB -V tpt=1n');

fprintf(fp, 'cd $PBS_O_WORKDIR n');

fprintf(fp, 'mpiexec -np 16 /lustre/jhome15/hhb17/hhb172/bin/vasp.st.5.3 > vasp.outn');

fclose(fp);

%Step 2: to submit the job with the command like qsub, bsub, llsubmit, .etc.

%It will output some message on the screen like '2350873.nano.cfn.bnl.local'

[a,b]=unix(['msub myrun'])

%Step 3: to get the jobID from the screen message

end_marker = findstr(b,'.');

jobNumber = b(2:end-1);

disp([' JobID ' jobNumber ' has been submitted ...'])

%jobNumber = b(1:end_marker(1)-1);

(moab提交作业时，msub myrun会空一行再显示进程号，所以这里要改为2，不然显示提交uspex后，显示这样的提示

??? Attempted to access end_marker(1); index out of bounds because
numel(end_marker)=0.
Error in ==> submitJob_local at 27
jobNumber = b(1:end_marker(1)-1);
Error in ==> submitJob at 26
jobNumber = submitJob_local();
Error in ==> SubmitJobs_M200 at 26
POP_STRUC.POPULATION(DO_NOW).JobID = submitJob(DO_NOW);

Error in ==> EA_M200 at 12
SubmitJobs_M200();
Error in ==> Start at 73
eval(['EA_' calcTypeStr '()']);)

Q3:USPEX调用matlab提交vasp的优化计算，能够成功提交任务，但会显示如下的错误：

而我单独在alcfold*目录里面msub myrun却能成功运行vasp．后通过ldd /lustre/jhome15/hhb17/hhb172/bin/vasp.2d.5.3与在matlab里面!ldd /lustre/jhome15/hhb17/hhb172/bin/vasp.2d.5.3发现vasp依赖的库不一样，需在环境变量里面把依赖的库加到export LD_LIBRARY_PATH里