Reworking of test harness and small fix

Test harness has been rewritten to get rid of unnecessary compiles. Also small issue resulting from two active jobs writing into same file has been resolved.

test_harness/README

 ######################################################################################################################################################
 #
-# To run test, open up sim_test_master.sh. This script qsubs all parts of the test. Decide which tests you want to run, comment out the rest. 
-# Be aware that running sim_test_master in its entirety requests 56 hours of compute time on Laconia. For quicker checks,
-# it might be better to only qsub short_jobs.sh. This usually gets in the queue almost immediately.
+# To run test, open up sim_test_master.sh. This script compiles all executables and qsubs all parts of the test. 
+# Decide which tests you want to run, comment out the rest. Unless you don't want to recompile, make sure not to comment out ./compile_all_executables.
+# Be aware that running sim_test_master in its entirety requests 32 hours of compute time on Laconia.
 #
 # To begin test:
 #

test_harness/water_327000_control → test_harness/bilayer_340800_mpi_control

-simulation_name	        water.327000    ! output files will carry this name + their specific ext.
+simulation_name	        bilayer.340800_mpi    ! output files will carry this name + their specific ext.
 ensemble_type	 	1	! 0: NVE  1: Berendsen NVT  2: Nose-Hoover NVT(under testing)  3: semi-isotropic NPT  4: isotropic NPT  5: anisotropic NPT (under development)
 nsteps			100    ! number of simulation steps
 dt			0.10 	! time step in fs
-proc_by_dim             1 5 2   ! distribution of processors by dimensions
+proc_by_dim             2 2 2   ! distribution of processors by dimensions
 geo_format 		0 	! 0: custom  1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
 
 tabulate_long_range	0	! number of sampling points for cubic spline interpolation, 0 no interpolation

test_harness/bilayer_340800_mpi_gpu_control

+simulation_name	        bilayer.340800_mpi_gpu    ! output files will carry this name + their specific ext.
+ensemble_type	 	1	! 0: NVE  1: Berendsen NVT  2: Nose-Hoover NVT(under testing)  3: semi-isotropic NPT  4: isotropic NPT  5: anisotropic NPT (under development)
+nsteps			100    ! number of simulation steps
+dt			0.10 	! time step in fs
+proc_by_dim             2 2 2   ! distribution of processors by dimensions
+geo_format 		0 	! 0: custom  1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
+
+tabulate_long_range	0	! number of sampling points for cubic spline interpolation, 0 no interpolation
+energy_update_freq 	10
+remove_CoM_vel	        500	! remove the transrot vel of CoM every 'this many' steps
+reposition_atoms	1	! 1:center of mass to center of box
+
+reneighbor              1
+vlist_buffer            0
+nbrhood_cutoff		4.5 	! bond cutoff in A
+hbond_cutoff		7.5	! hbond cutoff in A
+thb_cutoff		0.001	! cutoff value for three body interactions
+
+qeq_freq                1       ! frequency to update charges with QEq
+q_err			1e-6	! norm of the relative residual in QEq solve
+
+temp_init	        0.01	! initial temperature of the system
+temp_final 	        300.0	! final temperature of the system
+t_mass		        500.0   ! 0.16666 for nhNVT ! 500.0 for bNVT, iNPT, sNPT ! in fs, thermal inertia
+t_rate                  5.0                  ! in K
+t_freq                  1.0                     ! in ps
+t_mode			2	! 2: constant slope
+
+pressure 		0.000101325 0.000101325 0.000101325	! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
+p_mass		        10000.00     10000.00     10000.00  	! in fs, pressure inertia parameter
+
+write_freq		0	! write trajectory after so many steps
+traj_method		1	! 0: simple parallel I/O, 1: MPI I/O
+traj_title		micelle	! (no white spaces)
+atom_info		1	! 0: no atom info, 1: print basic atom info in the trajectory file
+atom_forces		0	! 0: basic atom format, 1: print force on each atom in the trajectory file
+atom_velocities		1	! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
+bond_info		1	! 0: do not print bonds, 1: print bonds in the trajectory file
+angle_info		1	! 0: do not print angles, 1: print angles in the trajectory file 
+
+restart_format          1    ! 0: restarts in ASCII  1: restarts in binary
+restart_freq		10000    ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
+
+bond_graph_cutoff	0.3  ! bond strength cutoff for bond graphs

test_harness/bilayer_long_mpi.sh

 #!/bin/bash -login
 
-#PBS -l nodes=5:ppn=2:gpus=2
-#PBS -l mem=600gb
-#PBS -l walltime=8:00:00
-#PBS -l feature=gpgpu:intel16
+#PBS -l nodes=1:ppn=8
+#PBS -l mem=120gb
+#PBS -l walltime=4:00:00
+#PBS -l feature=intel16
 
-#cd ${PBS_O_WORKDIR}
-cd /mnt/home/korteme1/PuReMD_new/test_harness
+cd "${PBS_O_WORKDIR}"
+#cd /mnt/home/korteme1/PuReMD_new/test_harness
 
 # 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
+module load GNU/4.4.5 MPICH2/1.4.1p1
 
 ############
 # MPI Runs #
 ############
 
-# Compile for MPI 
-cd ..
-./configure --enable-openmp=no --enable-mpi=yes
-make clean && make
-cd test_harness
-
 # Run, after each run we must rename the output files, or another run will overwrite it
 
-mpirun -np 10 ../PuReMD/bin/puremd ../data/benchmarks/bilayer/bilayer_340800.geo ../data/benchmarks/bilayer/ffield-bio bilayer_340800_control
-
-mv bilayer.340800.log bilayer.340800_mpi.log
-mv bilayer.340800.out bilayer.340800_mpi.out
-mv bilayer.340800.pot bilayer.340800_mpi.pot
-mv bilayer.340800.trj bilayer.340800_mpi.trj
-
+mpirun -np 8 ../PuReMD/bin/puremd ../data/benchmarks/bilayer/bilayer_340800.geo ../data/benchmarks/bilayer/ffield-bio bilayer_340800_mpi_control
 
 
 

test_harness/bilayer_long_mpi_gpu.sh

 #!/bin/bash -login
 
-#PBS -l nodes=5:ppn=2:gpus=2
-#PBS -l mem=600gb
-#PBS -l walltime=8:00:00
+#PBS -l nodes=1:ppn=8:gpus=8
+#PBS -l mem=120gb
+#PBS -l walltime=4:00:00
 #PBS -l feature=gpgpu:intel16
 
-#cd ${PBS_O_WORKDIR}
-cd /mnt/home/korteme1/PuReMD_new/test_harness
+cd "${PBS_O_WORKDIR}"
+#cd /mnt/home/korteme1/PuReMD_new/test_harness
 
 ################
 # MPI-GPU Runs #
@@ -14,41 +14,7 @@ cd /mnt/home/korteme1/PuReMD_new/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
-
-
-
-# Compile for MPI-GPU
-cd ..
-./configure --enable-openmp=no --enable-mpi-gpu=yes
-make clean && make
-cd test_harness
-
-
-mpirun -np 10 ../PG-PuReMD/bin/pg-puremd ../data/benchmarks/bilayer/bilayer_340800.geo ../data/benchmarks/bilayer/ffield-bio bilayer_340800_control
-
-mv bilayer.340800.log bilayer.340800_mpi_gpu.log
-mv bilayer.340800.out bilayer.340800_mpi_gpu.out
-mv bilayer.340800.pot bilayer.340800_mpi_gpu.pot
-mv bilayer.340800.trj bilayer.340800_mpi_gpu.trj
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
 
+mpirun -np 8 ../PG-PuReMD/bin/pg-puremd ../data/benchmarks/bilayer/bilayer_340800.geo ../data/benchmarks/bilayer/ffield-bio bilayer_340800_mpi_gpu_control
 
 

test_harness/compile_all_executables.sh

+#!/bin/bash -login
+
+# 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 #
+###############
+
+# Compile for MPI 
+cd ..
+./configure --enable-openmp=no --enable-mpi=yes
+make clean && make
+#make
+cd test_harness
+
+# Run, after each run we must rename the output files, or another run will overwrite it
+
+###################
+# 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
+cd ..
+./configure --enable-openmp=no --enable-mpi-gpu=yes
+make clean && make
+#make
+cd test_harness
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

test_harness/med_jobs.sh

@@ -5,24 +5,17 @@
 #PBS -l walltime=4:00:00
 #PBS -l feature=gpgpu:intel16
 
-#cd ${PBS_O_WORKDIR}
-cd /mnt/home/korteme1/PuReMD_new/test_harness
+cd "${PBS_O_WORKDIR}"
+#cd /mnt/home/korteme1/PuReMD_new/test_harness
 
 # 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 Runs #
 ############
 
-# Compile for MPI 
-cd ..
-./configure --enable-openmp=no --enable-mpi=yes
-make clean && make
-cd test_harness
-
 # Run, after each run we must rename the output files, or another run will overwrite it
 mpirun -np 2 ../PuReMD/bin/puremd ../data/benchmarks/water/water_78480.geo ../data/benchmarks/water/ffield.water water_78480_control
 
@@ -65,13 +58,6 @@ mv petn.trj petn_mpi.trj
 
 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
-cd ..
-./configure --enable-openmp=no --enable-mpi-gpu=yes
-make clean && make
-cd test_harness
 
 mpirun -np 2 ../PG-PuReMD/bin/pg-puremd ../data/benchmarks/water/water_78480.geo ../data/benchmarks/water/ffield.water water_78480_control
 

test_harness/med_jobs.sh.e34223289

-mkdir: cannot create directory `conftest.dir': File exists
-/usr/bin/install: cannot create regular file `/mnt/home/korteme1/PuReMD_new/conftest.dir/conftest.one': File exists
-cat: write error: Stale file handle
-rm: cannot remove `conftest.dir': Is a directory
-cat: conftest.err: No such file or directory
-sed: can't read conftest.c: No such file or directory
-sed: can't read conftest.c: No such file or directory
-grep: conftest.err: No such file or directory
-cat: conftest.er1: No such file or directory
-mv: cannot stat `conftest.er1': No such file or directory
-sed: can't read conftest.c: No such file or directory
-sed: can't read conftest.c: No such file or directory
-cat: conftest.err: No such file or directory
-sed: couldn't close stdout: Stale file handle
-sed: can't read libtoolT: No such file or directory
-cp: cannot create regular file `libtoolT': File exists
-mv: cannot stat `libtoolT.tmp': No such file or directory
-cp: cannot stat `libtoolT.tmp': No such file or directory
-sed: can't read libtoolT: No such file or directory
-config.status: WARNING: Unable to substitute extended shell functions in libtool
-mkdir: cannot create directory `conftest.dir': File exists
-cat: conftest.er1: No such file or directory
-configure: error: in `/mnt/home/korteme1/PuReMD_new/PuReMD':
-configure: error: C compiler cannot create executables
-See `config.log' for more details
-configure: error: ./configure failed for PuReMD
-src/io_tools.c: In function ‘Print_Linear_System’:
-src/io_tools.c:936: warning: unused variable ‘H’
-src/io_tools.c:935: warning: unused variable ‘aj’
-src/io_tools.c:933: warning: unused variable ‘j’
-src/io_tools.c: In function ‘Print_GCell_Exchange_Bounds’:
-src/io_tools.c:678: warning: ‘nbr’ is used uninitialized in this function
-src/box.c: In function ‘Setup_Environment’:
-src/box.c:275: warning: unused variable ‘temp’
-src/box.c: In function ‘Scale_Box’:
-src/box.c:312: warning: ‘mu’ may be used uninitialized in this function
-Warning: changed valency_val to valency_boc for X
-Warning: changed valency_val to valency_boc for X
-mv: cannot stat `water.78480.trj': No such file or directory
-mv: cannot stat `silica.72000.trj': No such file or directory
-p1@count atoms:
-p1: bigN = 56800
-p1: n = 28348
-p1: N = 28348
-
-p0@count atoms:
-p0: bigN = 56800
-p0: n = 28452
-p0: N = 28452
-
-mv: cannot stat `bilayer.56800.trj': No such file or directory
-p1@count atoms:
-p1: bigN = 19733
-p1: n = 9887
-p1: N = 9887
-
-p0@count atoms:
-p0: bigN = 19733
-p0: n = 9846
-p0: N = 9846
-
-mv: cannot stat `dna.trj': No such file or directory
-p1@count atoms:
-p1: bigN = 48256
-p1: n = 24180
-p1: N = 24180
-
-p0@count atoms:
-p0: bigN = 48256
-p0: n = 24076
-p0: N = 24076
-
-[mpiexec@lac-028] HYD_pmcd_pmiserv_send_signal (./pm/pmiserv/pmiserv_cb.c:184): assert (!closed) failed
-[mpiexec@lac-028] ui_cmd_cb (./pm/pmiserv/pmiserv_pmci.c:74): unable to send SIGUSR1 downstream
-[mpiexec@lac-028] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status
-[mpiexec@lac-028] HYDT_bscu_wait_for_completion (./tools/bootstrap/utils/bscu_wait.c:55): error waiting for event
-[mpiexec@lac-028] HYDT_bsci_wait_for_completion (./tools/bootstrap/src/bsci_wait.c:23): launcher returned error waiting for completion
-[mpiexec@lac-028] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:191): launcher returned error waiting for completion
-[mpiexec@lac-028] main (./ui/mpich/mpiexec.c:405): process manager error waiting for completion

test_harness/med_jobs.sh.o34223289

-checking for a BSD-compatible install... ./install-sh -c
-checking whether build environment is sane... yes
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-configure: creating ./config.status
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-=== configuring in PuReMD (/mnt/home/korteme1/PuReMD_new/PuReMD)
-configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local'  '--enable-openmp=no' '--enable-mpi=yes' 'CC=/usr/bin/gcc' 'CPPFLAGS=-I/opt/software/cudatoolkit/6.0/include' --cache-file=/dev/null --srcdir=.
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-Making clean in PuReMD
-make[1]: Entering directory `/mnt/home/korteme1/PuReMD_new/PuReMD'
-test -z "bin/puremd" || rm -f bin/puremd
-rm -f *.o
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-Making all in PuReMD
-make[1]: Entering directory `/mnt/home/korteme1/PuReMD_new/PuReMD'
-  CC       src/bin_puremd-allocate.o
-  CC       src/bin_puremd-basic_comm.o
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-  CC       src/bin_puremd-grid.o
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test_harness/med_jobs.sh.o34223879

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-=== configuring in PG-PuReMD (/mnt/home/korteme1/PuReMD_new/PG-PuReMD)
-configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local'  '--enable-openmp=no' '--enable-mpi-gpu=yes' 'CC=/opt/software/GCC/4.8.2/bin/gcc' 'CPPFLAGS=-I/opt/software/cudatoolkit/6.0/include -I/opt/software/GCC/4.8.2/include' --cache-file=/dev/null --srcdir=.
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-configure: MPI_LDFLAGS=-pthread -L/usr/lib64 -L/opt/software/OpenMPI/1.6.5--GCC-4.8.2/lib -lmpi -lrdmacm -libverbs -lrt -lnsl -lutil -lm -ltorque -lnsl -lutil -lm -lcr -ldl -lm -lnuma -Wl,--export-dynamic -lrt -lnsl -lutil -lm -ldl
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