Merge pull request #18 from Exabyte-io/chore/SOF-7595

chore: pbs job script for lammps calculation using gpu + cleanup

Author: pranabdas

espresso/gpu/README.md

@@ -15,3 +15,6 @@ Time taken by CPU job (8 MPI on 8 CPUs):
 ```
     PWSCF        :  18m 0.56s CPU  18m25.33s WALL
 ```
+
+- A step-by-step guide is available in our [documentation](
+https://docs.mat3ra.com/tutorials/jobs-cli/qe-gpu/).

espresso/gpu/job.cpu.pbs

@@ -1,5 +1,4 @@
 #!/bin/bash
-
 # ---------------------------------------------------------------- #
 #                                                                  #
 #  Example job submission script for Mat3ra.com platform           #
@@ -20,7 +19,6 @@
 
 #PBS -N QE-GPU
 #PBS -j oe
-##PBS -q comp-002-zone-a-production-20160630-cluster-007.exabyte.io
 #PBS -l nodes=1
 #PBS -l ppn=8
 #PBS -l walltime=00:01:00:00

espresso/gpu/job.gpu.pbs

@@ -1,8 +1,7 @@
 #!/bin/bash
-
 # ---------------------------------------------------------------- #
 #                                                                  #
-#  Example job submission script for Mat3ra.com platform          #
+#  Example job submission script for Mat3ra.com platform           #
 #                                                                  #
 #  Shows resource manager directives for:                          #
 #                                                                  #
@@ -20,7 +19,6 @@
 
 #PBS -N QE-GPU
 #PBS -j oe
-##PBS -q comp-002-zone-a-production-20160630-cluster-007.exabyte.io
 #PBS -l nodes=1
 #PBS -l ppn=8
 #PBS -l walltime=00:01:00:00

lammps/Cu_u3.eam

@@ -9,7 +9,13 @@ Most of the funding for LAMMPS has come from the US Department of Energy (DOE).
 LAMMPS is open-source software distributed under the terms of the GNU Public
 License Version 2 (GPLv2).
 
-# LAMMPS+M3GNet
+## Examples
+
+### Energy minimization
+An example calculation of energy minimization of two dimensional Lennard-Jones
+melt is available under [emin](./emin) directory.
+
+### LAMMPS+M3GNet
 The example under the [m3gnet](./m3gnet) directory uses M3GNet pair potential.
 
 

lammps/README.md

@@ -0,0 +1,48 @@
+#!/bin/bash
+# ---------------------------------------------------------------- #
+#                                                                  #
+#  Example job submission script for Mat3ra.com platform           #
+#                                                                  #
+#  Shows resource manager directives for:                          #
+#                                                                  #
+#    1. the name of the job                (-N)                    #
+#    2. the number of nodes to be used     (-l nodes=)             #
+#    3. the number of processors per node  (-l ppn=)               #
+#    4. the walltime in dd:hh:mm:ss format (-l walltime=)          #
+#    5. queue                              (-q) D, OR, OF, SR, SF  #
+#    6. merging standard output and error  (-j oe)                 #
+#    7. email about job abort, begin, end  (-m abe)                #
+#    8. email address to use               (-M)                    #
+#                                                                  #
+#  For more info visit https://docs.mat3ra.com/jobs-cli/overview/  #
+# ---------------------------------------------------------------- #
+
+#PBS -N LAMMPS-GPU
+#PBS -j oe
+#PBS -l nodes=1
+#PBS -l ppn=8
+#PBS -l walltime=00:01:00:00
+#PBS -q GSF
+##PBS -m abe
+##PBS -M [email protected]
+#
+## Uncomment the line below and put a desired project name, e.g.:
+## "seminar-default" or "john-project"
+## NOTE: this is required when using organizational accounts.
+## more at https://docs.mat3ra.com/jobs-cli/batch-scripts/directives/.
+## The job will be charged to the corresponding project.
+## When commented out, the default project for user is assumed.
+##PBS -A <PROJECT_NAME_IN_ACCOUNTING_SYSTEM>
+
+# load module
+module load lammps/2024.08.29.2-i-2023.1-cuda-12.4
+
+# go to the job working directory
+cd $PBS_O_WORKDIR
+# `-sf gpu` flag selects number of GPUs automatically. It also appends `/gpu` to
+# all supported pair styles. To set number of GPUs explicitly, use `-pk gpu N`.
+# GPU acceleration can be manually set for a pair style in the input file:
+# - pair_style	lj/cut 2.5
+# + pair_style	lj/cut/gpu 2.5
+# logs are written to log.lammps, it can be specified with `-l output.log`
+mpirun -np $PBS_NP lmp -sf gpu -i in.min

lammps/in.min renamed to lammps/emin/in.min

@@ -25,7 +25,7 @@
 #PBS -l walltime=00:00:10:00
 #PBS -q D
 #PBS -m abe
-#PBS -M [email protected]
+##PBS -M [email protected]
 #
 ## Uncomment the line below and put a desired project name, e.g.:
 ##      "seminar-default", or "john-projectname".
@@ -42,6 +42,7 @@ module load lammps/12Dec2018-i-14.0.3.174-impi-5.0.2.044
 export LAMMPS_EXECUTABLE=lammps
 
 ## Uncomment the lines below module to enable the use of GPU-accelerated version
+## Also, please submit the job to a GPU enabled queue e.g., `#PBS -q GOF`
 # export LAMMPS_EXECUTABLE=lmp
 # module load lammps/2022.01.07-g-11.2.0-ompi-4.1.1-cuda-11.5
 # cp $PBS_NODEFILE .exabyte/$PBS_JOBID