Tools: begin updating testing scripts.

test_harness/compile_all_executables.sh

@@ -3,77 +3,36 @@
 # This script does nothing but compile all executables, to be used later in the test. 
 
 # Import modules we will need
-module purge
-module load GNU/4.4.5 MPICH2/1.4.1p1 CUDA/6.0
-module load autoconf/2.69 automake/1.15
 
 ###############
-# MPI Compile #
+# Serial Code #
 ###############
-
-# Compile for MPI 
-cd ..
-./configure --enable-openmp=no --enable-mpi=yes
-make clean && make
-cd test_harness
-
 module purge
-module load GNU/4.8.2 OpenMPI/1.6.5 CUDA/6.0
-module load autoconf/2.69 automake/1.15
-
-#######################
-# MPI_Not_GPU Compile #
-#######################
-
-# Requires an added layer of complexity when dealing with both the mpi_gpu and mpi_not_gpu versions, because they compile to the same name.
-# Need to rename the mpi_not_gpu executable before compiling for mpi_gpu
-
-# Make clean both versions
+module load GNU/6.2
+# Compile for serial (sPuReMD/bin/spuremd) 
 cd ..
-./configure --enable-openmp=no --enable-mpi-gpu=yes
-make clean 
-./configure --enable-openmp=no --enable-mpi-not-gpu=yes
-mv PG-PuReMD/bin/pg-puremd-not-gpu PG-PuReMD/bin/pg-puremd
-make clean 
+./configure --enable-openmp=no --enable-serial=yes
+make
 cd test_harness
 
-# Compile mpi_not_gpu then rename executable
+###############
+# MPI Compile #
+###############
+module purge
+module load GNU/6.2 OpenMPI/2.0.2
+# Compile for MPI (PuReMD/bin/puremd) 
 cd ..
+./configure --enable-openmp=no --enable-mpi-old=yes
 make
-mv PG-PuReMD/bin/pg-puremd PG-PuReMD/bin/pg-puremd-not-gpu
 cd test_harness
 
 ###################
 # MPI-GPU Compile #
 ###################
-
 module purge
-module load GNU/4.8.2 OpenMPI/1.6.5 CUDA/6.0
-module load autoconf/2.69 automake/1.15
-
-# Compile for MPI-GPU
+module load GNU/6.2 OpenMPI/2.0.2 CUDA/9.0
+# Compile for MPI-GPU (PG-PuReMD/bin/pg-puremd) 
 cd ..
 ./configure --enable-openmp=no --enable-mpi-gpu=yes
 make
 cd test_harness
-
-echo "Attempted to compile all executables, check if any errors before this point"
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test_harness/short_jobs.sh

@@ -10,14 +10,35 @@ cd "${PBS_O_WORKDIR}"
 
 # Import modules we will need
 module purge
-module load GNU/4.4.5 MPICH2/1.4.1p1 CUDA/6.0
+module load GNU/6.2 OpenMPI/2.0.2 CUDA/9.0
 
 ############
-# MPI Runs #
+# Serial Runs #
 ############
+../sPuReMD/bin/spuremd ../data/benchmarks/water/water_6540.pdb ../data/benchmarks/water/ffield.water water_6540_control_serial
+
+mv water.6540.log water.6540_serial.log
+mv water.6540.out water.6540_serial.out
+mv water.6540.pot water.6540_serial.pot
+mv water.6540.trj water.6540_serial.trj
+
+../sPuReMD/bin/spuremd ../data/benchmarks/silica/silica_6000.pdb ../data/benchmarks/silica/ffield-bio silica_6000_control_serial
+
+mv silica.6000.log silica.6000_serial.log
+mv silica.6000.out silica.6000_serial.out
+mv silica.6000.pot silica.6000_serial.pot
+mv silica.6000.trj silica.6000_serial.trj
+
+../sPuReMD/bin/spuremd ../data/benchmarks/metal/zno_6912.pdb ../data/benchmarks/metal/ffield.zno zno_6912_control_serial
 
-# Run, after each run we must rename the output files, or another run will overwrite it
+mv zno.6912.log zno.6912_serial.log
+mv zno.6912.out zno.6912_serial.out
+mv zno.6912.pot zno.6912_serial.pot
+mv zno.6912.trj zno.6912_serial.trj
 
+############
+# MPI Runs #
+############
 mpirun -np 2 ../PuReMD/bin/puremd ../data/benchmarks/water/water_6540.pdb ../data/benchmarks/water/ffield.water water_6540_control
 
 mv water.6540.log water.6540_mpi.log
@@ -42,74 +63,23 @@ mv zno.6912.trj zno.6912_mpi.trj
 ################
 # MPI-GPU Runs #
 ################
-
-module purge
-module load GNU/4.8.2 OpenMPI/1.6.5 CUDA/6.0
-
-mpirun -np 2 ../PG-PuReMD/bin/pg-puremd ../data/benchmarks/water/water_6540.pdb ../data/benchmarks/water/ffield.water water_6540_control
+mpirun -np 2 ../PG-PuReMD/bin/pg-puremd ../data/benchmarks/water/water_6540.pdb ../data/benchmarks/water/ffield.water water_6540_control_gpu
 
 mv water.6540.log water.6540_mpi_gpu.log
 mv water.6540.out water.6540_mpi_gpu.out
 mv water.6540.pot water.6540_mpi_gpu.pot
 mv water.6540.trj water.6540_mpi_gpu.trj
 
-mpirun -np 2 ../PG-PuReMD/bin/pg-puremd ../data/benchmarks/silica/silica_6000.pdb ../data/benchmarks/silica/ffield-bio silica_6000_control
+mpirun -np 2 ../PG-PuReMD/bin/pg-puremd ../data/benchmarks/silica/silica_6000.pdb ../data/benchmarks/silica/ffield-bio silica_6000_control_gpu
 
 mv silica.6000.log silica.6000_mpi_gpu.log
 mv silica.6000.out silica.6000_mpi_gpu.out
 mv silica.6000.pot silica.6000_mpi_gpu.pot
 mv silica.6000.trj silica.6000_mpi_gpu.trj
 
-mpirun -np 2 ../PG-PuReMD/bin/pg-puremd ../data/benchmarks/metal/zno_6912.pdb ../data/benchmarks/metal/ffield.zno zno_6912_control
+mpirun -np 2 ../PG-PuReMD/bin/pg-puremd ../data/benchmarks/metal/zno_6912.pdb ../data/benchmarks/metal/ffield.zno zno_6912_control_gpu
 
 mv zno.6912.log zno.6912_mpi_gpu.log
 mv zno.6912.out zno.6912_mpi_gpu.out
 mv zno.6912.pot zno.6912_mpi_gpu.pot
 mv zno.6912.trj zno.6912_mpi_gpu.trj
-
-####################
-# MPI-NOT-GPU Runs #
-####################
-
-mpirun -np 2 ../PG-PuReMD/bin/pg-puremd-not-gpu ../data/benchmarks/water/water_6540.pdb ../data/benchmarks/water/ffield.water water_6540_control
-
-mv water.6540.log water.6540_mpi_not_gpu.log
-mv water.6540.out water.6540_mpi_not_gpu.out
-mv water.6540.pot water.6540_mpi_not_gpu.pot
-mv water.6540.trj water.6540_mpi_not_gpu.trj
-
-mpirun -np 2 ../PG-PuReMD/bin/pg-puremd-not-gpu ../data/benchmarks/silica/silica_6000.pdb ../data/benchmarks/silica/ffield-bio silica_6000_control
-
-mv silica.6000.log silica.6000_mpi_not_gpu.log
-mv silica.6000.out silica.6000_mpi_not_gpu.out
-mv silica.6000.pot silica.6000_mpi_not_gpu.pot
-mv silica.6000.trj silica.6000_mpi_not_gpu.trj
-
-mpirun -np 2 ../PG-PuReMD/bin/pg-puremd-not-gpu ../data/benchmarks/metal/zno_6912.pdb ../data/benchmarks/metal/ffield.zno zno_6912_control
-
-mv zno.6912.log zno.6912_mpi_not_gpu.log
-mv zno.6912.out zno.6912_mpi_not_gpu.out
-mv zno.6912.pot zno.6912_mpi_not_gpu.pot
-mv zno.6912.trj zno.6912_mpi_not_gpu.trj
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test_harness/sim_test_master.sh

@@ -6,7 +6,7 @@
 #
 ###############################################
 
-./compile_all_executables.sh
+#./compile_all_executables.sh
 
 # Will be submitting multiple jobs
 # First, one for all the short jobs
@@ -16,17 +16,17 @@ qsub short_jobs.sh
 qsub med_jobs.sh
 
 # Finally, one for each of the long jobs
-qsub water_long_mpi.sh
-qsub water_long_mpi_gpu.sh
-qsub water_long_mpi_not_gpu.sh
-
-qsub silica_long_mpi.sh
-qsub silica_long_mpi_gpu.sh
-qsub silica_long_mpi_not_gpu.sh
-
-qsub bilayer_long_mpi.sh
-qsub bilayer_long_mpi_gpu.sh
-qsub bilayer_long_mpi_not_gpu.sh
+#qsub water_long_mpi.sh
+#qsub water_long_mpi_gpu.sh
+#qsub water_long_mpi_not_gpu.sh
+#
+#qsub silica_long_mpi.sh
+#qsub silica_long_mpi_gpu.sh
+#qsub silica_long_mpi_not_gpu.sh
+#
+#qsub bilayer_long_mpi.sh
+#qsub bilayer_long_mpi_gpu.sh
+#qsub bilayer_long_mpi_not_gpu.sh
 
 echo "All jobs submitted"