Parallel execution of calypso for surface reconstruction

[Sravan Kumar]

Hello everyone,

Firstly, I want to appreciate the great work done by the developers of the code. Calypso is pretty useful and pretty good at predicting stable configurations. 

I have been trying to run the individual vasp calculations of the configurations in each generation simultaneously on different nodes. The general approach of giving a execution statement for vasp in submit.sh file won't help my cause. So, what I did is I asked submit.sh to execute a script in another file for me. The submit.sh file contains

#!/bin/sh

sbatch /uhpc/grabow/skanchar/Au_TiO2_nanorod_water/hydroxylated/calypso/1_layer/trial_2/multiple.csh

In the multiple.csh, I have the following script

#!/bin/csh

#  UHPC

#SBATCH -p batch

#SBATCH -o alpha.o%j

#SBATCH -e alpha.e%j

#SBATCH -N 1 -n 20       # Each node has 20 processors

#SBATCH -t 336:00:00

#SBATCH --mail-type=END

/share/apps/vasp/5.4.1/bin/vasp > ./vasp.out # Run the MPI executable named "vasp.out"

This makes me successful in initializing the vasp execution parallelly in the individual configurations in the generation folder. But, the problem is, it does not copy the POTCAR file into the individual directories, despite having the required POTCAR files in the main directory. The vasp execution gets terminated with the following error. 

forrtl: No such file or directory

forrtl: severe (29): file not found, unit 10, file /uhpc/grabow/skanchar/Au_TiO2_nanorod_water/hydroxylated/calypso/1_layer/trial_4/results/Generation_1/Indv_1/POTCAR

Image              PC                Routine            Line        Source

vasp               00000000016A8383  Unknown               Unknown  Unknown

vasp               00000000016BDD2B  Unknown               Unknown  Unknown

vasp               000000000051F6B6  Unknown               Unknown  Unknown

vasp               00000000014E118B  Unknown               Unknown  Unknown

vasp               0000000000412E2E  Unknown               Unknown  Unknown

libc.so.6          0000003260C1ED5D  Unknown               Unknown  Unknown

vasp               0000000000412D39  Unknown               Unknown  Unknown

I am wondering what might be going wrong with the copying of POTCAR files into the individual directories. When I run the calypso code in a single node (as suggested by the manual), everything works, POTCAR gets copied into the individual directories. But, it is not computationally efficient for me run the jobs in series mode. 

So, now I try to copy the POTCAR into individual directories by adding a line in the submit.sh script, but for some reason, it does not get executed. My new submit.sh script is

#!/bin/sh

cwd=$PWD

echo $cwd

cp /uhpc/grabow/skanchar/Au_TiO2_nanorod_water/hydroxylated/calypso/1_layer/trial_4/POTCAR-all $cwd/POTCAR

sbatch /uhpc/grabow/skanchar/Au_TiO2_nanorod_water/hydroxylated/calypso/1_layer/trial_2/multiple.csh

The I add the extra lines in submit.sh, it only executes the sbatch command, but it does not execute the copy command.

I am wondering what the problem could be with the execution of copy command.

Thanks for going through the post. Any help is greatly appreciated. 

best regards,

Sravan Kumar.

[Shaohua Lu]

Dear Sravan Kumar;

According to your description, this error is caused by missing concatenated POTCAR in the calculation directory.

There is no need to copy this POTCAR to each individual directory, either manually or using a script. 

All you need is prepare POTCARs for each elements, and rename it using this format: POTCAR-[Name of elements],

for example, if you are predicting  carbon monolayer on copper, then you need two POTCARs:  POTCAR-C and POTCAR-Cu

there is no need to concatenate the POTCARs before run structure predictions, CALYPSO will do the job automatically.

If it still does not work, you may tar your calculation directory, and send it to me  ( l...@calypso.cn).

good luck.

Shaohua Lu

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