passing gromacs tests

imdclient/data/gromacs/md/gromacs_v3_nst1.mdp → imdclient/data/gromacs/md/gmx_serial_test.mdp

@@ -1,15 +1,15 @@
 title                   = PRODUCTION IN NPT
-ld-seed                 = 1
+ld-seed			= 1
 ; Run parameters
 integrator              = md        ; leap-frog integrator
 nsteps                  = 100    ; 1 * 1000 = 1 ps
 dt                      = 0.001     ; 1 fs
 ; Output control
-nstxout                 = 1      ; save coordinates every 1 fs
-nstvout                 = 1      ; save velocities every 1 fs
+nstxout                 = 1      ; save coordinates every 1 ps
+nstvout                 = 1      ; save velocities every 1 ps
 nstfout                 = 1
-nstenergy               = 1      ; save energies every 1 fs
-nstlog                  = 10      ; update log file every 1 ps
+nstenergy               = 1      ; save energies every 1 ps
+nstlog                  = 1      ; update log file every 1 ps
 ; Center of mass (COM) motion
 nstcomm                 = 10        ; remove COM motion every 10 steps
 comm-mode               = Linear    ; remove only COM translation (liquids in PBC) 
@@ -31,7 +31,7 @@ coulombtype             = PME       ; Particle Mesh Ewald for long-range electro
 pme_order               = 4         ; cubic interpolation
 fourierspacing          = 0.12      ; grid spacing for FFT
 ; Temperature coupling is on
-tcoupl                  = Nose-Hoover       ; good for production, after equilibration
+tcoupl                  = Berendsen       ; good for production, after equilibration
 ; we define separate thermostats for the solute and solvent (need to adapt)
 ; see default groups defined by Gromacs for your system or define your own (make_ndx)
 tc-grps                 = Protein  SOL      ; the separate groups for the thermostats

imdclient/data/namd/md/alanin.conf

@@ -0,0 +1,73 @@
+# This is a test namd configuration file
+
+timestep	0.5
+numsteps	10
+structure	alanin.psf
+parameters	alanin.params
+coordinates	alanin.pdb
+exclude		scaled1-4
+1-4scaling	0.4
+outputname 	output[myReplica]
+margin		1.0
+stepspercycle   3
+temperature	0
+
+switching 	on
+switchdist	7.0
+cutoff		8.0
+pairlistdist 	9.0
+
+dcdfile	alanin.dcd
+dcdfreq	1
+# If Box dimensions are defined, the DCD file can contain the box dimensions via the following
+#DCDunitcell    yes
+
+velDCDfile	alanin.vel
+velDCDfreq    1
+
+forceDCDfile	alanin.force
+forceDCDfreq    1
+
+#restartname	alanin.restart
+#restartfreq	10
+
+#langevin	on
+#langevinTemp	300.0
+#langevincol	O
+
+#constraints	on
+
+#fma		on
+
+seed		12345
+
+# IMD parameters
+
+# standard IMD parameters
+# IMDon streaming -- on or off
+IMDon		yes
+# IMDport -- port number to listen on
+IMDport		8888
+# IMDfreq -- frequency to send data
+IMDfreq		1
+# IMDwait -- wait for client to connect before starting simulation
+IMDwait		on
+
+# IMD version -- 2 for VMD and 3 for latest protocol
+IMDversion     3
+# IMD session info settings
+# IMDsendPositions -- sending positions of entire system
+IMDsendPositions        yes
+# IMDsendEnergies -- sending energies and bonded, non-bonded and other contributions
+IMDsendEnergies     yes
+# IMDsendTime -- sending time information (time, dt, step)
+IMDsendTime        yes
+# IMDsendBoxDimensions -- sending box dimensions (lattice vectors a, b, c)
+# If box dimensions are not defined, default unit box is sent
+IMDsendBoxDimensions       yes
+# IMDsendVelocities -- sending velocities of entire system
+IMDsendVelocities       yes
+# IMDsendForces -- sending forces on all atoms
+IMDsendForces      yes
+# IMDwrapPositions -- wrapping positions to box; applicable when IMDsendPositions is yes
+IMDwrapPositions       yes

imdclient/data/namd/md/openmpi-sol.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+# Load the necessary module
+module load openmpi/4.1.5
+
+# Set CPATH environment variable
+export CPATH="/packages/apps/pmix/4.1.3-slurm/include:$CPATH"
+
+# Set LIBRARY_PATH environment variable
+export LIBRARY_PATH="/packages/apps/pmix/4.1.3-slurm/lib:$LIBRARY_PATH"
+
+# Optional: Print the variables to verify they are set
+echo "CPATH is set to: $CPATH"
+echo "LIBRARY_PATH is set to: $LIBRARY_PATH"

imdclient/tests/datafiles.py

@@ -8,7 +8,13 @@
 
 """
 
-__all__ = ["LAMMPS_IN", "LAMMPS_TOPOL", "GROMACS_TRAJ", "GROMACS_MDP"]
+__all__ = [
+    "LAMMPS_IN",
+    "LAMMPS_TOPOL",
+    "GROMACS_TRAJ",
+    "GROMACS_TOPOL",
+    "GROMACS_TPR",
+]
 
 from importlib import resources
 from pathlib import Path
@@ -19,15 +25,15 @@
 LAMMPS_IN = (_data_ref / "lammps" / "md" / "lammps_v3.in").as_posix()
 LAMMPS_TRAJ = (_data_ref / "lammps" / "md" / "lammps_trj.h5md").as_posix()
 GROMACS_TRAJ = (
-    _data_ref / "gromacs" / "md" / "gromacs_v3_nst1.trr"
+    _data_ref / "gromacs" / "md" / "gmx_serial_test.trr"
 ).as_posix()
-GROMACS_TOPOL = (
-    _data_ref / "gromacs" / "md" / "gromacs_struct.gro"
-).as_posix()
-GROMACS_TPR = (_data_ref / "gromacs" / "md" / "gromacs_v3_nst1.tpr").as_posix()
+GROMACS_TOPOL = (_data_ref / "gromacs" / "md" / "struct.gro").as_posix()
+GROMACS_TPR = (_data_ref / "gromacs" / "md" / "gmx_serial_test.tpr").as_posix()
 NAMD_TOPOL = (_data_ref / "namd" / "md" / "alanin.pdb").as_posix()
-NAMD_CONF = (_data_ref / "namd" / "md" / "namd_v3.namd").as_posix()
+NAMD_CONF = (_data_ref / "namd" / "md" / "alanin.namd").as_posix()
 NAMD_TRAJ = (_data_ref / "namd" / "md" / "alanin.dcd").as_posix()
+NAMD_VEL = (_data_ref / "namd" / "md" / "alanin.vel").as_posix()
+NAMD_FORCE = (_data_ref / "namd" / "md" / "alanin.force").as_posix()
 NAMD_PARAMS = (_data_ref / "namd" / "md" / "alanin.params").as_posix()
 NAMD_PSF = (_data_ref / "namd" / "md" / "alanin.psf").as_posix()
 

imdclient/tests/hpc_testing/gromacs/gromacs.md

@@ -0,0 +1,69 @@
+# Manual validation of different compiler options for GROMACS using ASU's SOL
+
+## GPU, MPI, threading
+
+Allocate a GPU node on SOL and clone in https://github.com/hcho38/gromacs.git
+
+After cloning, do:
+```bash
+git checkout imd-v3
+module load cmake-3.21.4-gcc-11.2.0
+module load gcc-10.3.0-gcc-11.2.0
+module load cuda-11.7.0-gcc-11.2.0
+module load openmpi/4.1.5
+
+mkdir -p build_gpu
+cd build_gpu
+
+cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=CUDA -DGMX_MPI=ON
+make -j 4
+make install
+source /your/installation/prefix/here/bin/GMXRC
+```
+
+After GROMACS has been built, change into the directory containing this file.
+
+To test on one node, run this in the shell (assuming there are 4 cores available):
+```bash
+/home/ljwoods2/workspace/gromacs/build_mpi/bin/gmx grompp \
+    -f gmx_gpu_test.mdp \
+    -c struct.gro \
+    -p gmx_gpu_test.top \
+    -imd struct_imd.gro \
+    -o gmx_gpu_test.tpr \
+    -maxwarn 1
+
+/home/ljwoods2/workspace/gromacs/build_mpi/bin/gmx mdrun \
+    -s gmx_gpu_test.tpr \
+    -o gmx_gpu_test.trr \
+    -imdwait \
+    -ntmpi 2 \
+    -ntomp 2
+```
+To test on multiple nodes, run this in the shell (assuming there are 4 nodes and 16 cores available, with 1 GPU on each node):
+
+```bash
+module load openmpi/4.1.5
+
+/home/ljwoods2/workspace/gromacs/build_mpi/bin/mpirun \
+    -np 4 \
+    gmx_mpi mdrun \
+    -s gmx_gpu_test.tpr \
+    -o gmx_gpu_test.trr \
+    -imdwait \
+    -ntomp 4 \
+    -gpu_id 0
+```
+
+And in a different shell (from the same directory), run the following commands:
+
+```bash
+module load mamba
+# Environment containing IMDClient
+source activate imdclient-test
+
+pytest -s ../../test_manual.py \
+    --topol_arg struct.gro \
+    --traj_arg gmx_gpu_test.trr \
+    --first_frame_arg 0
+```

imdclient/tests/hpc_testing/gromacs/run.mdp

@@ -0,0 +1,58 @@
+title                   = PRODUCTION IN NPT
+ld-seed			= 1
+; Run parameters
+integrator              = md        ; leap-frog integrator
+nsteps                  = 1000    ; 1 * 1000 = 1 ps
+dt                      = 0.001     ; 1 fs
+; Output control
+nstxout                 = 10      ; save coordinates every 10 fs
+nstvout                 = 10      ; save velocities every 10 fs
+nstfout                 = 10
+nstenergy               = 10      ; save energies every 10 fs
+nstlog                  = 10      ; update log file every 10 fs
+; Center of mass (COM) motion
+nstcomm                 = 10        ; remove COM motion every 10 steps
+comm-mode               = Linear    ; remove only COM translation (liquids in PBC) 
+; Bond parameters
+continuation            = yes       ; first dynamics run
+constraint_algorithm    = lincs     ; holonomic constraints
+constraints             = all-bonds ; all bonds lengths are constrained
+lincs_iter              = 1         ; accuracy of LINCS
+lincs_order             = 4         ; also related to accuracy
+; Nonbonded settings
+cutoff-scheme           = Verlet    ; Buffered neighbor searching
+ns_type                 = grid      ; search neighboring grid cells
+nstlist                 = 10        ; 10 fs, largely irrelevant with Verlet
+rcoulomb                = 1.0       ; short-range electrostatic cutoff (in nm)
+rvdw                    = 1.0       ; short-range van der Waals cutoff (in nm)
+DispCorr                = EnerPres  ; account for cut-off vdW scheme
+; Electrostatics
+coulombtype             = PME       ; Particle Mesh Ewald for long-range electrostatics
+pme_order               = 4         ; cubic interpolation
+fourierspacing          = 0.12      ; grid spacing for FFT
+; Temperature coupling is on
+tcoupl                  = Nose-Hoover       ; good for production, after equilibration
+; we define separate thermostats for the solute and solvent (need to adapt)
+; see default groups defined by Gromacs for your system or define your own (make_ndx)
+tc-grps                 = Protein  SOL      ; the separate groups for the thermostats
+tau-t                   = 1.0      1.0      ; time constants for thermostats (ps)
+ref-t                   = 300      300      ; reference temperature for thermostats (K)
+; Pressure coupling is off
+pcoupl                  = Parrinello-Rahman ; good for production, after equilibration
+tau-p                   = 2.0               ; time constant for barostat (ps)
+compressibility         = 4.5e-5            ; compressibility (1/bar) set to water at ~300K
+ref-p                   = 1.0               ; reference pressure for barostat (bar)
+; Periodic boundary conditions
+pbc                     = xyz       ; 3-D PBC
+; Velocity generation
+gen_vel                 = no
+IMD-group               = System
+IMD-nst                 = 10
+IMD-version             = 3
+IMD-time                = yes
+IMD-box                 = yes
+IMD-coords              = yes
+IMD-unwrap              = no
+IMD-vels                = yes
+IMD-forces              = yes
+IMD-energies            = yes