diff --git a/TIES_MD/doc/source/parallelization.rst b/TIES_MD/doc/source/parallelization.rst index 0484b43..2081d48 100644 --- a/TIES_MD/doc/source/parallelization.rst +++ b/TIES_MD/doc/source/parallelization.rst @@ -28,12 +28,12 @@ and run:: The ``CUDA`` device 0 will then run 6 windows of the first repeat and CUDA device 1 will run 6 windows of the second repeat. Equally ths could be spit into to runs of ``TIES MD`` masked to only see one device:: - ties_md --exp_name=sys_solv --devices=0 --node_id="_alpha" - ties_md --exp_name=sys_solv --devices=1 --node_id="_beta" + ties_md --exp_name=sys_solv --devices=0 --node_id=0 + ties_md --exp_name=sys_solv --devices=1 --node_id=1 To run in this configuration the options ``total_reps=2`` and ``reps_per_exec=1`` are set in TIES.cfg to tell ``TIES MD`` that there are a total of 2 replicas being run and that each execution of ``TIES MD`` should run only one. Also note we have set -``--node_id`` to some different strings for otherwise identical run lines and this ensures these parallel runs write output +``--node_id`` to some different values for otherwise identical run lines and this ensures these parallel runs write output to unique locations. ``--node_id`` only needs to be set when identical replicas of a simulation are run in separate executions of ``TIES MD``. @@ -52,18 +52,18 @@ These commands run submitted to a node with 6 GPUS would run one window on each we could use the resource allocator of the HPC for example `jsrun `_ on Summit ``ORNL`` would allow us to run with 2 replicas of 6 windows as follows:: - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id="_alpha"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id="_alpha"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id="_alpha"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id="_alpha"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id="_alpha"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id="_alpha"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id="_beta"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id="_beta"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id="_beta"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id="_beta"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id="_beta"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id="_beta"& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id=0& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id=0& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id=0& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id=0& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id=0& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id=0& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id=1& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id=1& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id=1& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id=1& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id=1& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id=1& Note here we do not set ``--devices`` as the masking of GPUs is handled by the resource allocator. If a resource allocator is not available an alternative method to run multiple simulations across nodes is to use a message passing interface @@ -71,18 +71,18 @@ is not available an alternative method to run multiple simulations across nodes for all HPC systems, however we provide an example here for reference which would work with `ThetaGPU `_:: - mpirun -host $node1 -np 1 ties_md --devices=0 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id="_alpha"& - mpirun -host $node1 -np 1 ties_md --devices=1 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id="_alpha"& - mpirun -host $node1 -np 1 ties_md --devices=2 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id="_alpha"& - mpirun -host $node1 -np 1 ties_md --devices=3 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id="_alpha"& - mpirun -host $node1 -np 1 ties_md --devices=4 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id="_alpha"& - mpirun -host $node1 -np 1 ties_md --devices=5 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id="_alpha"& - mpirun -host $node2 -np 1 ties_md --devices=0 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id="_beta"& - mpirun -host $node2 -np 1 ties_md --devices=1 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id="_beta"& - mpirun -host $node2 -np 1 ties_md --devices=2 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id="_beta"& - mpirun -host $node2 -np 1 ties_md --devices=3 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id="_beta"& - mpirun -host $node2 -np 1 ties_md --devices=4 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id="_beta"& - mpirun -host $node2 -np 1 ties_md --devices=5 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id="_beta"& + mpirun -host $node1 -np 1 ties_md --devices=0 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id=0& + mpirun -host $node1 -np 1 ties_md --devices=1 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id=0& + mpirun -host $node1 -np 1 ties_md --devices=2 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id=0& + mpirun -host $node1 -np 1 ties_md --devices=3 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id=0& + mpirun -host $node1 -np 1 ties_md --devices=4 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id=0& + mpirun -host $node1 -np 1 ties_md --devices=5 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id=0& + mpirun -host $node2 -np 1 ties_md --devices=0 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id=1& + mpirun -host $node2 -np 1 ties_md --devices=1 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id=1& + mpirun -host $node2 -np 1 ties_md --devices=2 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id=1& + mpirun -host $node2 -np 1 ties_md --devices=3 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id=1& + mpirun -host $node2 -np 1 ties_md --devices=4 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id=1& + mpirun -host $node2 -np 1 ties_md --devices=5 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id=1& TIES-NAMD diff --git a/docs/_sources/parallelization.rst.txt b/docs/_sources/parallelization.rst.txt index 0484b43..2081d48 100644 --- a/docs/_sources/parallelization.rst.txt +++ b/docs/_sources/parallelization.rst.txt @@ -28,12 +28,12 @@ and run:: The ``CUDA`` device 0 will then run 6 windows of the first repeat and CUDA device 1 will run 6 windows of the second repeat. Equally ths could be spit into to runs of ``TIES MD`` masked to only see one device:: - ties_md --exp_name=sys_solv --devices=0 --node_id="_alpha" - ties_md --exp_name=sys_solv --devices=1 --node_id="_beta" + ties_md --exp_name=sys_solv --devices=0 --node_id=0 + ties_md --exp_name=sys_solv --devices=1 --node_id=1 To run in this configuration the options ``total_reps=2`` and ``reps_per_exec=1`` are set in TIES.cfg to tell ``TIES MD`` that there are a total of 2 replicas being run and that each execution of ``TIES MD`` should run only one. Also note we have set -``--node_id`` to some different strings for otherwise identical run lines and this ensures these parallel runs write output +``--node_id`` to some different values for otherwise identical run lines and this ensures these parallel runs write output to unique locations. ``--node_id`` only needs to be set when identical replicas of a simulation are run in separate executions of ``TIES MD``. @@ -52,18 +52,18 @@ These commands run submitted to a node with 6 GPUS would run one window on each we could use the resource allocator of the HPC for example `jsrun `_ on Summit ``ORNL`` would allow us to run with 2 replicas of 6 windows as follows:: - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id="_alpha"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id="_alpha"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id="_alpha"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id="_alpha"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id="_alpha"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id="_alpha"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id="_beta"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id="_beta"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id="_beta"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id="_beta"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id="_beta"& - jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id="_beta"& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id=0& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id=0& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id=0& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id=0& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id=0& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id=0& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id=1& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id=1& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id=1& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id=1& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id=1& + jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id=1& Note here we do not set ``--devices`` as the masking of GPUs is handled by the resource allocator. If a resource allocator is not available an alternative method to run multiple simulations across nodes is to use a message passing interface @@ -71,18 +71,18 @@ is not available an alternative method to run multiple simulations across nodes for all HPC systems, however we provide an example here for reference which would work with `ThetaGPU `_:: - mpirun -host $node1 -np 1 ties_md --devices=0 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id="_alpha"& - mpirun -host $node1 -np 1 ties_md --devices=1 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id="_alpha"& - mpirun -host $node1 -np 1 ties_md --devices=2 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id="_alpha"& - mpirun -host $node1 -np 1 ties_md --devices=3 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id="_alpha"& - mpirun -host $node1 -np 1 ties_md --devices=4 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id="_alpha"& - mpirun -host $node1 -np 1 ties_md --devices=5 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id="_alpha"& - mpirun -host $node2 -np 1 ties_md --devices=0 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id="_beta"& - mpirun -host $node2 -np 1 ties_md --devices=1 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id="_beta"& - mpirun -host $node2 -np 1 ties_md --devices=2 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id="_beta"& - mpirun -host $node2 -np 1 ties_md --devices=3 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id="_beta"& - mpirun -host $node2 -np 1 ties_md --devices=4 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id="_beta"& - mpirun -host $node2 -np 1 ties_md --devices=5 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id="_beta"& + mpirun -host $node1 -np 1 ties_md --devices=0 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id=0& + mpirun -host $node1 -np 1 ties_md --devices=1 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id=0& + mpirun -host $node1 -np 1 ties_md --devices=2 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id=0& + mpirun -host $node1 -np 1 ties_md --devices=3 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id=0& + mpirun -host $node1 -np 1 ties_md --devices=4 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id=0& + mpirun -host $node1 -np 1 ties_md --devices=5 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id=0& + mpirun -host $node2 -np 1 ties_md --devices=0 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id=1& + mpirun -host $node2 -np 1 ties_md --devices=1 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id=1& + mpirun -host $node2 -np 1 ties_md --devices=2 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id=1& + mpirun -host $node2 -np 1 ties_md --devices=3 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id=1& + mpirun -host $node2 -np 1 ties_md --devices=4 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id=1& + mpirun -host $node2 -np 1 ties_md --devices=5 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id=1& TIES-NAMD diff --git a/docs/parallelization.html b/docs/parallelization.html index 5fdfac8..4d31c48 100644 --- a/docs/parallelization.html +++ b/docs/parallelization.html @@ -106,13 +106,13 @@

TIES-OpenMMCUDA device 0 will then run 6 windows of the first repeat and CUDA device 1 will run 6 windows of the second repeat. Equally ths could be spit into to runs of TIES MD masked to only see one device:

-
ties_md --exp_name=sys_solv --devices=0 --node_id="_alpha"
-ties_md --exp_name=sys_solv --devices=1 --node_id="_beta"
+
ties_md --exp_name=sys_solv --devices=0 --node_id=0
+ties_md --exp_name=sys_solv --devices=1 --node_id=1
 

 

 
To run in this configuration the options total_reps=2 and reps_per_exec=1 are set in TIES.cfg to tell TIES MD that
 there are a total of 2 replicas being run and that each execution of TIES MD should run only one. Also note we have set
---node_id to some different strings for otherwise identical run lines and this ensures these parallel runs write output
+--node_id to some different values for otherwise identical run lines and this ensures these parallel runs write output
 to unique locations. --node_id only needs to be set when identical replicas of a simulation are run in separate executions
 of TIES MD.

 
If we need further parallelization over alchemical windows we can use the command line option --windows_mask
@@ -129,18 +129,18 @@ 
TIES-OpenMMjsrun
 on Summit ORNL would allow us to run with 2 replicas of 6 windows as follows:

-
jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id="_alpha"&
-jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id="_alpha"&
-jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id="_alpha"&
-jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id="_alpha"&
-jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id="_alpha"&
-jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id="_alpha"&
-jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id="_beta"&
-jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id="_beta"&
-jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id="_beta"&
-jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id="_beta"&
-jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id="_beta"&
-jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id="_beta"&
+
jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id=0&
+jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id=0&
+jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id=0&
+jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id=0&
+jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id=0&
+jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id=0&
+jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id=1&
+jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id=1&
+jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id=1&
+jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id=1&
+jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id=1&
+jsrun --smpiargs="off" -n 1 -a 1 -c 1 -g 1 -b packed:1 ties_md --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id=1&
 

 

 
Note here we do not set --devices as the masking of GPUs is handled by the resource allocator. If a resource allocator
@@ -148,18 +148,18 @@ 
TIES-OpenMMMPI). The use of MPI can vary from system to system and there is no universal solution to running across many node
 for all HPC systems, however we provide an example here for reference which would work with
 ThetaGPU:

-
mpirun -host $node1 -np 1 ties_md --devices=0 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id="_alpha"&
-mpirun -host $node1 -np 1 ties_md --devices=1 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id="_alpha"&
-mpirun -host $node1 -np 1 ties_md --devices=2 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id="_alpha"&
-mpirun -host $node1 -np 1 ties_md --devices=3 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id="_alpha"&
-mpirun -host $node1 -np 1 ties_md --devices=4 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id="_alpha"&
-mpirun -host $node1 -np 1 ties_md --devices=5 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id="_alpha"&
-mpirun -host $node2 -np 1 ties_md --devices=0 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id="_beta"&
-mpirun -host $node2 -np 1 ties_md --devices=1 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id="_beta"&
-mpirun -host $node2 -np 1 ties_md --devices=2 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id="_beta"&
-mpirun -host $node2 -np 1 ties_md --devices=3 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id="_beta"&
-mpirun -host $node2 -np 1 ties_md --devices=4 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id="_beta"&
-mpirun -host $node2 -np 1 ties_md --devices=5 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id="_beta"&
+
mpirun -host $node1 -np 1 ties_md --devices=0 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id=0&
+mpirun -host $node1 -np 1 ties_md --devices=1 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id=0&
+mpirun -host $node1 -np 1 ties_md --devices=2 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id=0&
+mpirun -host $node1 -np 1 ties_md --devices=3 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id=0&
+mpirun -host $node1 -np 1 ties_md --devices=4 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id=0&
+mpirun -host $node1 -np 1 ties_md --devices=5 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id=0&
+mpirun -host $node2 -np 1 ties_md --devices=0 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=0,1 --node_id=1&
+mpirun -host $node2 -np 1 ties_md --devices=1 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=1,2 --node_id=1&
+mpirun -host $node2 -np 1 ties_md --devices=2 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=2,3 --node_id=1&
+mpirun -host $node2 -np 1 ties_md --devices=3 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=3,4 --node_id=1&
+mpirun -host $node2 -np 1 ties_md --devices=4 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=4,5 --node_id=1&
+mpirun -host $node2 -np 1 ties_md --devices=5 --config_file=$ties_dir/TIES.cfg --exp_name='sys_solv' --windows_mask=5,6 --node_id=1&
 

 

 
diff --git a/docs/searchindex.js b/docs/searchindex.js
index b0ff767..99746d5 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["HPC_submissions", "TIES_MD", "TIES_MD.eng_scripts", "TIES_MD.eng_scripts.cfg_scripts", "TIES_MD.eng_scripts.namd_sub", "TIES_MD.eng_scripts.namd_sub_split", "TIES_MD.eng_scripts.openmm_sub_split", "TIES_MD.openmmtools", "TIES_MD.ties_analysis", "TIES_MD.ties_analysis.engines", "TIES_MD.ties_analysis.methods", "binding_free_energies", "index", "install", "modules", "parallelization", "theory", "tutorial"], "filenames": ["HPC_submissions.rst", "TIES_MD.rst", "TIES_MD.eng_scripts.rst", "TIES_MD.eng_scripts.cfg_scripts.rst", "TIES_MD.eng_scripts.namd_sub.rst", "TIES_MD.eng_scripts.namd_sub_split.rst", "TIES_MD.eng_scripts.openmm_sub_split.rst", "TIES_MD.openmmtools.rst", "TIES_MD.ties_analysis.rst", "TIES_MD.ties_analysis.engines.rst", "TIES_MD.ties_analysis.methods.rst", "binding_free_energies.rst", "index.rst", "install.rst", "modules.rst", "parallelization.rst", "theory.rst", "tutorial.rst"], "titles": ["HPC Submission scripts", "TIES_MD package", "TIES_MD.eng_scripts package", "TIES_MD.eng_scripts.cfg_scripts package", "TIES_MD.eng_scripts.namd_sub package", "TIES_MD.eng_scripts.namd_sub_split package", "TIES_MD.eng_scripts.openmm_sub_split package", "TIES_MD.openmmtools package", "TIES_MD.ties_analysis package", "TIES_MD.ties_analysis.engines package", "TIES_MD.ties_analysis.methods package", "Binding Free Energy Tutorial", "Welcome to the TIES MD documentation.", "Installation", "TIES_MD", "Parallelization", "Theory", "Tutorial"], "terms": {"here": [0, 1, 13, 15, 16, 17], "we": [0, 1, 8, 9, 10, 11, 13, 15, 16, 17], "provid": [0, 1, 13, 15, 16, 17], "some": [0, 1, 11, 13, 15, 16, 17], "exampl": [0, 1, 11, 13, 15, 16, 17], "variou": 0, "system": [0, 1, 7, 11, 12, 13, 15, 16, 17], "i": [0, 1, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17], "an": [0, 1, 7, 9, 12, 13, 15, 16, 17], "larg": 0, "100k": 0, "atom": [0, 1, 11, 16, 17], "run": [0, 1, 8, 9, 12, 13, 15], "supermuc": 0, "ng": 0, "bin": [0, 11, 13], "bash": [0, 11], "sbatch": 0, "job": [0, 1], "name": [0, 1, 7, 9, 11, 13, 17], "ligpair": [0, 11], "o": [0, 11], "x": [0, 1, 11, 13, 16, 17], "j": [0, 11], "out": [0, 1, 11, 17], "e": [0, 1, 7, 9, 11, 16, 17], "err": 0, "d": [0, 1], "node": [0, 1, 15, 17], "130": 0, "task": 0, "per": [0, 1, 17], "48": 0, "requeu": 0, "export": [0, 11, 13], "none": [0, 1, 7, 8, 10, 17], "get": [0, 1, 9, 11, 12], "user": [0, 1, 11, 16, 17], "env": 0, "account": 0, "xxx": 0, "partit": 0, "gener": [0, 8, 9, 12, 15, 16, 17], "time": [0, 1, 9, 10, 11, 17], "10": [0, 11, 13, 17], "00": [0, 9, 13, 17], "modul": [0, 13, 14], "load": [0, 13], "slurm_setup": 0, "2": [0, 9, 11, 13, 15, 16, 17], "14": [0, 1, 17], "gcc8": 0, "impi": 0, "nodes_per_namd": 0, "cpus_per_namd": 0, "480": 0, "echo": 0, "chang": [0, 1, 9, 11, 13, 15, 16, 17], "thi": [0, 1, 7, 9, 10, 11, 12, 13, 15, 16, 17], "line": [0, 1, 11, 12, 15], "point": [0, 1, 9, 10, 11, 17], "your": [0, 13], "project": 0, "ties_dir": [0, 11, 15], "hppf": 0, "work": [0, 1, 13, 15], "pn98ve": 0, "di67rov": 0, "test_ti": 0, "studi": [0, 17], "prot": [0, 9], "ti": [0, 8, 9, 11, 14, 16, 17], "l2": 0, "l1": 0, "com": [0, 11, 13, 17], "stage": [0, 1, 17], "0": [0, 1, 7, 9, 11, 13, 15, 16, 17], "do": [0, 1, 9, 10, 11, 13, 15, 16, 17], "lambda": [0, 7, 9, 10, 11, 14, 16, 17], "05": [0, 16, 17], "1": [0, 1, 7, 9, 11, 13, 15, 16, 17], "4": [0, 11, 13, 15, 16, 17], "5": [0, 11, 15, 16, 17], "6": [0, 11, 13, 15, 16, 17], "7": [0, 11, 13, 16, 17], "8": [0, 11, 13, 16, 17], "9": [0, 11, 13, 16, 17], "95": [0, 16, 17], "cd": [0, 11, 13, 17], "replica": [0, 1, 9, 10, 11, 15, 17], "conf": [0, 1, 17], "srun": [0, 17], "n": [0, 11, 13, 15, 17], "namd2": [0, 1, 17], "tclmain": [0, 17], "sim": [0, 1, 17], "sleep": [0, 17], "done": [0, 11, 17], "wait": [0, 11, 17], "The": [0, 1, 7, 11, 13, 15, 16, 17], "first": [0, 15, 16, 17], "20": [0, 12, 16], "could": [0, 13, 15, 17], "adapt": 0, "smaller": [0, 15], "10k": 0, "follow": [0, 11, 13, 15, 17], "13": [0, 11, 17], "45": 0, "micro": 0, "can": [0, 1, 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9, 10, 11, 15, 16, 17], "file": [1, 8, 9, 10, 11, 15, 16, 17], "properti": 1, "box_typ": [1, 17], "type": [1, 17], "box": [1, 15, 17], "being": [1, 7, 15, 16, 17], "cube": [1, 17], "truncatedoctahedron": [1, 17], "rhombicdodecahedron": [1, 17], "na": [1, 17], "manual": [1, 17], "return": [1, 7, 8, 9, 10, 13, 15], "string": [1, 8, 9, 10, 15, 17], "build_results_dir": 1, "folder": [1, 17], "helper": [1, 9], "build": [1, 8, 9, 11, 12, 13, 17], "output": [1, 9, 10, 13, 15, 17], "param": [1, 8], "elec_edg": [1, 16, 17], "electrostat": [1, 16, 17], "potenti": [1, 9, 10, 17], "begin": [1, 16, 17], "stop": [1, 17], "appear": [1, 9, 16, 17], "when": [1, 11, 15, 16, 17], "molecular": [1, 15, 17], "go": 1, "namd3": [1, 17], "prefix": [1, 13, 17], "expect": [1, 17], "experiment_nam": 1, "get_opt": [1, 8, 11], "print": [1, 8, 11], "option": [1, 7, 8, 9, 11, 15, 16, 17], "global_lambda": [1, 16, 17], "global": [1, 7, 17], "reps_per_exec": [1, 11, 15, 17], "how": [1, 15, 16, 17], "mani": [1, 15, 17], "each": [1, 9, 10, 11, 15, 16, 17], "program": [1, 11, 16, 17], "parallel": [1, 12, 17], "setup": [1, 8, 12, 17], "split_run": 1, "tiesmd": [1, 11], "all": [1, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17], "subset": 1, "bool": [1, 9, 10], "split": 1, "ster_edg": [1, 16, 17], "where": [1, 8, 9, 10, 13, 17], "lennard_jon": [1, 17], "total_rep": [1, 11, 15, 17], "total": [1, 15, 17], "number": [1, 9, 10, 17], "update_cfg": [1, 11], "congig": 1, "after": [1, 17], "api": [1, 11], "made": [1, 17], "write_analysis_cfg": 1, "configur": [1, 11, 13, 15, 17], "analysi": [1, 8, 9, 10, 12], "write_namd_eq": 1, "eq1": [1, 17], "eq2": [1, 17], "equilibr": [1, 17], "write_namd_min": 1, "eq0": [1, 17], "minim": 1, "write_namd_prod": 1, "sim1": [1, 17], "product": [1, 17], "write_namd_script": 1, "need": [1, 11, 13, 15, 16, 17], "write_namd_submiss": 1, "submiss": [1, 11, 12, 17], "hpc": [1, 11, 12, 15, 17], "archer2": 1, "write_openmm_submiss": 1, "get_box_vector": 1, "comput": [1, 10, 11, 13, 17], "vector": 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