ABINIT-MP is a software for fast fragment molecular orbital (FMO) calculations. Second-order perturbation calculations using four-body fragment expansions (FMO4) are also possible.
Please see this page for a detal of this software.
We have general-purpose CPU nodes version and vector nodes version, but there is a limitation on the modules that can be used. In addition, only processing by batch request is allowed. Examples of job scripts and job execution methods are described below.
| Node type | With F function | Without F function | ||
|---|---|---|---|---|
| SMP support | SMP non-support | SMP support | SMP non-support | |
| General-purpose CPU node group | abinitmp_smp-fint | abinitmp-fint | abinitmp_smp | abinitmp | Vector node group | (not available) | (not available) | (not available) | (not available) | abinitmp-vec |
Creating a Job Script: General Purpose CPU Nodes
The following example is a job script for executing ABINIT-MP with 19 MPI processes x 4 threads (using 1 node). There is no particular specification for the file name, but it is assumed to be abinit.sh in this section.
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#!/bin/bash #PBS -q SQUID #PBS -l cpunum_job=76 #PBS --group=[your group name] #PBS -l elapstim_req=01:00:00 #PBS -b 1 #PBS -T intmpi #PBS -v NUM_PROCS=19 #PBS -v NUM_THREADS=4 #PBS -v OMP_NUM_THREADS=${NUM_THREADS} #PBS -v OMP_STACKSIZE=5G #PBS -v BINARY_NAME=abinitmp_smp #PBS -v FILE_NAME=gly5 #PBS -v NUM_CORE=_16n-144p-4t-smp-2020.1-intel #PBS -v OUT_NAME=${FILE_NAME}${NUM_CORE} ulimit –s unlimited module load BaseApp/2021 module load abinit-mp/1.22 cd ${PBS_O_WORKDIR} mpirun ${NQSV_MPIOPTS} -np ${NUM_PROCS} ${BINARY_NAME} < ${FILE_NAME}.ajf > ${OUT_NAME} |
Creating a Job Script: Vector Node Group
The following example is a job script for running ABINIT-MP on a 40 MPI process (using 4 vector engines per node). There is no particular specification for the file name, but it is abinit-vec.sh in this section.
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#!/bin/bash #PBS -q SQUID #PBS --group=[group name] #PBS -T necmpi #PBS -l elapstim_req=01:00:00 #PBS --venode=4 #PBS -v NUM_PROCS=40 #PBS -v FILE_NAME=gly5 #PBS -v AJF_NAME=${FILE_NAME}.ajf #PBS -v VE_FORT5=${AJF_NAME} module load BaseApp/2021 module load abinit-mp/1.22.VEC cd ${PBS_O_WORKDIR} BINARY_NAME=`which abinitmp-vec` mpirun -np ${NUM_PROCS} ${BINARY_NAME} |
For other lines of the job script, see here.
execution method
Submit the job script you created.
% qsub abinit.sh
To check the status of the submitted job, here. When the execution is finished, the calculation result is output to the result file. For a sample input file and manual, please refer to the following.
/system/apps/rhel8/cpu/ABINIT-MP/intel2020u4/1.22/no-fint/
/system/apps/rhel8/cpu/ABINIT-MP/intel2020u4/1.22/fint/
/system/apps/rhel8/vec/ABINIT-MP/nec2.3.1/1.22/no-fint/
