Script para DICE:
|
#!/bin/bash
#PBS -S /bin/bash
#PBS -l nodes=1:ppn=12
#PBS -l walltime=300:00:00
#PBS -l mem=16GB
#PBS -N nkx_q6_in2
#PBS -q biomol
## Configure se quiser receber emails
#PBS -m ae
##PBS -M mail@mail.com
#Definindo local de execucao
SCRATCH=/scratch/local/
WORKDIR=$SCRATCH/$PBS_JOBID
mkdir -p $WORKDIR
## Informacoes do job impressos no arquivo de saida.
echo -e "## Job iniciado em $(date +'%d-%m-%Y as %T') #####################\n"
echo -e "## Node de execucao do job: $(hostname -s) \n"
echo -e "## Pasta de execucao do job: $WORKDIR \n"
echo -e "## Diretorio de submissao do job: $PBS_O_WORKDIR \n"
#########################################
##------- Inicio do trabalho ----- #
#########################################
## Configura o ambiente de execucao do software.
module load softwares/diceandorder/diceandorder
module load gnu8/8.3.0
export LD_LIBRARY_PATH=/opt/ohpc/pub/compiler/gcc/8.3.0/lib64/:$LD_LIBRARY_PATH
export OMP_STACKSIZE=32M
#Copiando arquivos para a pasta remota
echo -e "Copiando seus arquivos"
cd $PBS_O_WORKDIR
cp -v nkx_q6.txt $WORKDIR/.
cp -v nkx_q6.in $WORKDIR/.
cp -v nkx_q6.dat $WORKDIR/.
cd $WORKDIR
EXE=dice3
INP2=nkx_q6.in
OUT2=nkx_q6.in2.out
# Execucao do job
$EXE < $INP1 > $OUT1
$EXE < $INP2 > $OUT2
#Copiando os resultados
cp -vr * $PBS_O_WORKDIR/.
echo -e "\n## Job finalizado em $(date +'%d-%m-%Y as %T') ###################"
rm -vrf $WORKDIR
|
Script para o Gaussian 09:
|
#!/bin/bash -l
#PBS -S /bin/bash
#PBS -l nodes=1:ppn=4
#PBS -l walltime=300:00:00
#PBS -l vmem=16GB
#PBS -l mem=16GB
#PBS -m ae
#PBS -M mail@mail.com
#PBS -N job
#PBS -q biomol
echo -e "\n## Job iniciado em $(date +'%d-%m-%Y as %T') #####################\n"
## Informacoes do job impressos no arquivo de saida.
echo -e "\n## Jobs ativos de $USER: \n"
qstat -an -u $USER
echo -e "\n## Node de execucao do job: $(hostname -s) \n"
echo -e "\n## Numero de tarefas para este job: $PBS_TASKNUM \n"
#########################################
##------- Inicio do trabalho ----- #
#########################################
#Definindo local de execucao
WorkDir=/scratch/local/$PBS_JOBID
mkdir -p $WorkDir
## Modulo que carrega o software Gaussian09
# Gaussian
g09root=/opt/versatushpc/softwares/gaussian/09d01-pgi-14.3
GAUSS_SCRDIR=$WorkDir
export g09root GAUSS_SCRDIR
source $g09root/g09/bsd/g09.profile
cd $PBS_O_WORKDIR
## Informacoes sobre o ambiente de execucao impressos no arquivo de saida.
echo -e "\n## Diretorio de submissao do job: $PBS_O_WORKDIR \n"
echo -e "\n## Diretorio de scratch do job: $GAUSS_SCRDIR \n"
## Execucao do software.
## Manual do Gaussian09 <http://www.gaussian.com/g_tech/g_ur/g09help.htm>.
g09 input.gjf
echo -e "\n## Job finalizado em $(date +'%d-%m-%Y as %T') ###################"
rm -vrf $WORKDIR
|
Script para o g16
|
#!/bin/bash -l
#PBS -S /bin/bash
#PBS -l nodes=1:ppn=4
#PBS -l walltime=300:00:00
#PBS -l vmem=16GB
#PBS -l mem=16GB
#PBS -m ae
#PBS -M ricardo2.lima@usp.br
#PBS -N RO_MP2_neutra
#PBS -q biomol
echo -e "\n## Job iniciado em $(date +'%d-%m-%Y as %T') #####################\n"
## Informacoes do job impressos no arquivo de saida.
echo -e "\n## Jobs ativos de $USER: \n"
qstat -an -u $USER
echo -e "\n## Node de execucao do job: $(hostname -s) \n"
echo -e "\n## Numero de tarefas para este job: $PBS_TASKNUM \n"
#########################################
##------- Inicio do trabalho ----- #
#########################################
#Definindo local de execucao
WorkDir=/scratch/local/$PBS_JOBID
mkdir -p $WorkDir
## Modulo que carrega o software Gaussian16
# Gaussian
g16root=/opt/versatushpc/softwares/gaussian/g16
GAUSS_SCRDIR=$WorkDir
export g16root GAUSS_SCRDIR
source $g16root/g16/bsd/g16.profile
cd $PBS_O_WORKDIR
## Informacoes sobre o ambiente de execucao impressos no arquivo de saida.
echo -e "\n## Diretorio de submissao do job: $PBS_O_WORKDIR \n"
echo -e "\n## Diretorio de scratch do job: $GAUSS_SCRDIR \n"
## Execucao do software.
## Manual do Gaussian16 <https://gaussian.com/man/>.
g16 3a-NKX-B3LYP_rotacionada.gjf
echo -e "\n## Job finalizado em $(date +'%d-%m-%Y as %T') ###################"
rm -vrf $WORKDIR
|
Script para GROMACS GPU:
|
#!/bin/bash
#PBS -S /bin/bash
#PBS -l nodes=gpu-0-1:ppn=20
#PBS -l walltime=300:00:00
#PBS -N MD
#PBS -q biomolgpu
#PBS -o saida
#PBS -e erro
SCRATCH=/scratch/local/
WRKDIR=$SCRATCH/$PBS_JOBID
qstat -an -u $USER
cat $PBS_NODEFILE
module load gnu8/8.3.0
GROMACS=/home/sw/softwares/gromacs/515/installgpu
export PATH=$GROMACS/bin:$PATH
export LD_LIBRARY_PATH=$GROMACS/lib:/opt/ohpc/pub/compiler/gcc/8.3.0/lib64:$LD_LIBRARY_PATH
mkdir -p $WRKDIR
cd $PBS_O_WORKDIR
cp -r * $WRKDIR/
cd $WRKDIR
export GMX_MAXCONSTRWARN=-1
which gmx
gmx mdrun -ntomp 20 -gpu_id 0 -s topol.tpr -deffnm run -v > run.out
cp -r $WRKDIR/ $PBS_O_WORKDIR/
if [ "$APAGA_SCRATCH" = "Y" ]; then
rm -rf $WRKDIR
else
echo -e "\nO diretorio \e[00;31m$WRKDIR\e[00m deve ser removido manualmente"
echo -e "para evitar problemas para outros jobs e/ou usuarios. \n"
fi
|
