cannot run example 4 in USPEX 10.5

[Keshav Singh]

Dear developers, 

I am new to the USPEX and I am trying to run example 4 of the USPEX. When I try that, I get following error

Structure29 step1 at CalcFold1

/home/keshav/Desktop/lamps/CalcFold1

lmp: /home/keshav/software/v91/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by lmp)

lmp: /home/keshav/software/v91/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by lmp)

Structure30 step1 at CalcFold1

/home/keshav/Desktop/lamps/CalcFold1

status = Local optimization finished

 

===== USPEX ERROR @ 16:26:24 24-Aug-2021 ===== 

Many structures failed after relaxation,

Plz check the input files. Results maybe unreliable.

Possible reasons: high bestFrac, bad optimization parameters or contraints.

I have uninstall and reinstall USPEX and lammps individually,  USPEX is working fine with quantum espresso but not with lammps. it is producing initiall structures but when cone to optimization, it through error. lammps is also working fine if used individually.

I am using Ubuntu 20.4 in virtual box (latest) with 8 processor and 8gb ram

thank you 

[Zahed]

Dear Keshavs...

The problem raises from the inconsistency between MCR and Ubuntu libs. In your machine, Lammps requires newer libs which is provided by Ubuntu and not by MCR 2016b. Therefor, it is enough to use the library of your system using the following line in your terminal:

export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu

IMPORTANT

Do NOT put the line mentioned above in your .bashrc, as it might make problems for calling other libs from other software, including MCR.

 -----------------------------------------------------------------------------

Recommended Solution (for PC):

1- Go to the USPEX calculation directory: 

2- Copy and paste the following lines into your terminal, and enter.

echo '#!/bin/sh 

export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu

lmp_stable < lammps.in > lammps.out'   >   Specific/runLammps

3- Replace the commandExecutable part of the INPUT.txt with the following:

% commandExecutable

bash runLammps

% EndExecutable

-----

Best regards,

Zahed

[Keshav Singh]

thank you Zahed sir for your reply. I now understand the problem. I will follow the steps you suggest and i face any problem, I will ask again.

[Ziqi Cui]

Hi Zahed,

I'm running USPEX with VASP on the cluster with one node, and I got the following error:

Individual 1 @ step 1 is submitted
srun /project/def-jsong/share/vasp.6.1.1/bin/vasp_std > output: Terminated
/project/def-jsong/share/vasp.6.1.1/bin/vasp_std: /home/ziqicui/USPEX_v10.5//v91/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /project/def-jsong/share/vasp.6.1.1/bin/vasp_std)
/project/def-jsong/share/vasp.6.1.1/bin/vasp_std: /home/ziqicui/USPEX_v10.5//v91/sys/os/glnxa64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /project/def-jsong/share/vasp.6.1.1/bin/vasp_std)

This is my input.txt:

PARAMETERS EVOLUTIONARY ALGORITHM
******************************************
*      TYPE OF RUN AND SYSTEM            *
******************************************
USPEX : calculationMethod (USPEX, VCNEB, META)
301   : calculationType
1     : AutoFrac
 
% optType
enthalpy
% EndOptType

% atomType
Ti C N
% EndAtomType

% numSpecies
1  0  0
0  1  0
0  0  1
% EndNumSpecies

% symmetries
2-230
% EndSymmetries

******************************************
*               POPULATION               *
******************************************
20    : populationSize (how many individuals per generation)
30    : initialPopSize (how many individuals in the first generation)
20    : numGenerations (how many generations shall be calculated)
5     : stopCrit       (after how many generations with identical minima to stop)
0     : reoptOld       (reoptimize KeptBest structures 0/1)
0.6   : bestFrac       (fraction of best structures to keep)

*********************************
*    VARCOMP VARIABLE    *
*********************************
10    : firstGeneMax (how many different composition in the first generation)
3     : minAt
20     : maxAt
******************************************
*          VARIATION OPERATORS           *
******************************************
0.50  : fracGene (fraction of generation produced by heredity)
0.10  : fracRand (fraction of generation produced randomly from space groups)
0.10  : fracAtomsMut (fraction of the generation produced by softmutation)
0.10  : fracTrans (variation operator specific of variable composition runs)
0.10  : fracLatMut (fraction of the generation produced by softmutation)
0.10  : fracPerm   (fractions of the generation produced by permutation)

*****************************************
*   DETAILS OF AB INITIO CALCULATIONS   *
*****************************************
% abinitioCode
1 1 1 1 1  
% ENDabinit

% KresolStart
0.14 0.12 0.10 0.08 0.03
% Kresolend


% commandExecutable
srun /project/def-jsong/share/vasp.6.1.1/bin/vasp_std
% EndExecutable

0     : whichCluster (0: no-job-script, 1: local submission, 2: remote submission)
20     : numParallelCalcs
0   : ExternalPressure 

Can you help me fix this error? I don't really understand where the problem is.

Thank you so much!