...
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|---|
module load vasp/5.4.4.vasp-mpi-intel
OR
module load vasp/5.4.4.vasp-serial-intelvasp541-gnu-openmpi
To use vasp on the cluster, one needs to be in the unix group named "vasp". Please contact the HPC admin to request this.
|
VASP-gnu
Not installed currently
...
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|---|
cd /sw/VASP/5.2.12
tar -zxvf /data1/vasp.5.lib.tar.gz
mv vasp.5.lib vasp.5.lib-intel
cd /sw/VASP/5.2.12/vasp.5.lib-intel
cp makefile.linux_ifc_P4 Makefile
module purge
module load intel-tools-11/11.1.072
module load fftw/3.2.2-intel
vi Makefile
Change the following ....
>>>>>>>>>>>>>
diff Makefile makefile.linux_ifc_P4
18,19c18,19
<
18,19c18,19
< CPP = icc -E -P -C $*.F >$*.f
< FC=ifort
---
> CPP = iccgcc -E -P -C $*.F >$*.f
<> FC=ifort
---
> CPP = gcc -E -P -C $*.F >$*.f
> FC=ifc
51c51
< icc $(CFLAGS) -c $*.c
---
> $(CC) $(CFLAGS) -c $*.c
>>>>>>>>>>>>>>
make 2>&1 |tee make_vasp_lib_intel.txt
|
vasp.5.2-intel
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|---|
module purge
module loadifc
51c51
< icc $(CFLAGS) -c $*.c
---
> $(CC) $(CFLAGS) -c $*.c
>>>>>>>>>>>>>>
make 2>&1 |tee make_vasp_lib_intel.txt
|
vasp.5.2-intel
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|---|
module purge
module load intel-cc-11/11.1.072
module load fftw/3.2.2-intel
module load intel-cmkl-11/11.1.072
module load intel-tools-11/11.1.072
module load fftw/3.3-alpha-intel
module unload intel-mpi/4.0.0.027
module list
Currently Loaded Modulefiles:
1) intel-cc-11/11.1.072 module load fftw/3.2.2-intel
module load 2) intel-fc-11/11.1.072 3) intel-cmkl-11/11.1.072 module load4) intel-tools-11/11.1.072 module load 5) fftw/3.3.3-alpha-intel
module unload intel-mpi/4.0.0.027
module list
Currently Loaded Modulefiles:
1) intel-cc-11/11.1.072 2) intel-fc-11/11.1.072 3) intel-cmkl-11/11.1.072 4) intel-tools-11/11.1.072 5) fftw/3.3-alpha-intel
cd /sw/VASP/5.2.12
tar -zxvf /data1/vasp.5.2.12.tar.gz
mv vasp.5.2 vasp.5.2-intel
cd /sw/VASP/5.2.12/vasp.5.2-intel
cp makefile.linux_ifc_P4 Makefile
>>>>>>>
diff Makefile makefile.linux_ifc_P4
53c53
< FC=ifort
---
> FC=ifc
126d125
< BLAS=-L/sw/sdev/intel/Compiler/11.1/072/mkl/lib/em64t -lmkl_lapack -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread
131c130
< #BLAS= /opt/libs/libgoto/libgoto.so
---
> BLAS= /opt/libs/libgoto/libgoto.so
134c133
< LAPACK=-alpha-intel
cd /sw/VASP/5.2.12
tar -zxvf /data1/vasp.5.2.12.tar.gz
mv vasp.5.2 vasp.5.2-intel
cd /sw/VASP/5.2.12/vasp.5.2-intel
cp makefile.linux_ifc_P4 Makefile
>>>>>>>
diff Makefile makefile.linux_ifc_P4
53c53
< FC=ifort
---
> FC=ifc
126d125
< BLAS=-L/sw/sdev/intel/Compiler/11.1/072/mkl/lib/em64t -lmkl_lapack -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread
131c130
< #BLAS= /opt/libs/libgoto/libgoto.so
---
> BLAS= /opt/libs/libgoto/libgoto.so
134c133
< LAPACK= ../vasp.5.lib-intel/lapack_double.o
---
> LAPACK= ../vasp.5.lib/lapack_double.o
141,142c140,141
< LIB = -L../vasp.5.lib-intel -ldmy \
< ../vasp.5.lib-intel/linpack_double.o $(LAPACK) \
---
> LIB = -L../vasp.5.lib -ldmy \
> ../vasp.5.lib-intel/lapacklinpack_double.o
---
> LAPACK= ../vasp.5.lib/lapack_double.o
141,142c140,141
< LIB = -L../vasp.5.lib-intel -ldmy \
< ../vasp.5.lib-intel/linpack_double.o $(LAPACK) \
---
> LIB = -L../vasp.5.lib -ldmy \
> ../vasp.5.lib/linpack_double.o $(LAPACK) \
>>>>>>>>>
make 2>&1 |tee make_vasp52_serial_intel.txt
|
VASP-5.4.1
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|---|
module purge
module load intel-mpi/4.0.0.027
module load intel-tools-11/11.1.072
module load fftw/3.2.2-intel $(LAPACK) \
>>>>>>>>>
make 2>&1 |tee make_vasp52_serial_intel.txt
|
VASP-5.4.1
| No Format |
|---|
module purge
module load intel-mpi/4.0.0.027
module load intel-tools-11/11.1.072
module load fftw/3.2.2-intel
cd /sw/VASP/5.4.1/intel-serial
cp arch/makefile.include.linux_intel_serial makefile.include
vi makefile.include
Add this: MKLROOT=/sw/sdev/intel/Compiler/11.1/072/mkl
make
This will build the standard, gamma-only, and non-collinear version
of VASP one after the other.
Patch
=====
module load vasp/5.4.1vasp-intel-serial
cd /sw/VASP/5.4.1/intel-serial
cp arch/makefile.include.linux_intel_serial makefile.include
vi makefile.include
Add this: MKLROOT=/sw/sdev/intel/Compiler/11.1/072/mkl
make
This will build the standard, gamma-only, and non-collinear version
of VASP one after the other.
Patch
=====
module load vasp/5.4.1vasp-intel-serial
cd /sw/VASP/5.4.1/intel-serial
gunzip the patch
e.g gunzip patch.5.4.1.03082016.gz
patch -p0 < patch.5.4.1.14032016
patch -p0 <patch.5.4.1.03082016
Special Patch (for Tim):
Replace the files in src by the updated ones from patch_vasp.5.4.1.05Feb16.tgz (including the newly created file tim_parameters.F) and replace/modify also the "hidden" file .objects so as to contain the item tim_parameters.o right after subdft3.o. |
VASP 5.4.4
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|---|
awoonga node only
module load mkl/2017.3
module load intel/2017.4
module load lapack/3.6.0
cp arch/makefile.include.linux_intel_serial makefile.include
vi makefile.include
Add this:
MKLROOT=/opt/intel/composer_xe_2017.4/mkl
make 2>&1 | tee makeLog.txt
|
Sample PBS script
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|---|
#!/bin/bash
#PBS -N vaspstd
#PBS -m abe
#PBS -M YourEmail@griffithuni.edu.au
#PBS -l select=1:ncpus=1:mem=18gb,walltime=96:00:00
module load vasp/vasp541-gnu-openmpi
alias
gunzip the patch
e.g gunzip patch.5.4.1.03082016.gz
patch -p0 < patch.5.4.1.14032016
patch -p0 <patch.5.4.1.03082016
Special Patch (for Tim):
Replace the files in src by the updated ones from patch_vasp.5.4.1.05Feb16.tgz (including the newly created file tim_parameters.F) and replace/modify also the "hidden" file .objects so as to contain the item tim_parameters.o right after subdft3.o. |
VASP 5.4.4
Note: Awoonga is a different HPC managed by QRIS. Awoonga has been replaced by a newer HPC called Tinaroo. Information as of 18/01/23; Tinaroo is soon to be replaced by a newer HPC called Bunya. Bunya will have VASP 6. VASP 5.4.4 will not be available on Bunya. View FAQ Qs38 for details on Awoonga: FAQ - Griffith HPC Cluster#GriffithHPCCluster-Qs38%3AHowdoIgetstartedontheawoongacluster
| No Format |
|---|
awoonga node only
module load mkl/2017.3
module load intel/2017.4
module load lapack/3.6.0
cp arch/makefile.include.linux_intel_serial makefile.include
vi makefile.include
Add this:
MKLROOT=/opt/intel/composer_xe_2017.4/mkl
make 2>&1 | tee makeLog.txt
|
Sample PBS script
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|---|
#!/bin/bash
#PBS -q workq
#PBS -m bea
#PBS -M email@griffithuni.edu.au
#PBS -N VaspTest
#PBS -l select=1:ncpus=4:mpiprocs=4:mem=35gb,walltime=4:00:00
## load vasp module to setup env variables to run vasp
cd $PBS_O_WORKDIR
module load vasp/vasp541-gnu-openmpi
## get the number of allocated cpu cores
export nprocs=`cat $PBS_NODEFILE | wc -l`
## run vasp in parallel over $nprocs processors
###alias vasp="vasp_std"
cdmpiexec $PBS_O_WORKDIR
vasp_std;vasp_std < /dev/null > vasp.debug;
echo "Done with job" |
Another Sample PBS Script
...