From 3e401146016c561cfa0df1c522a9346241d1574d Mon Sep 17 00:00:00 2001 From: adw62 Date: Tue, 6 Sep 2022 15:39:01 +0100 Subject: [PATCH] ornl crusher/opencl changes --- TIES_MD/TIES.py | 8 ++--- TIES_MD/alch.py | 2 +- TIES_MD/cli.py | 11 +++++-- TIES_MD/doc/source/API.rst | 2 +- TIES_MD/doc/source/binding_free_energies.rst | 11 ++++--- docs/API.html | 2 +- docs/_sources/API.rst.txt | 2 +- docs/_sources/binding_free_energies.rst.txt | 11 ++++--- docs/_static/pygments.css | 34 ++++++++++---------- docs/binding_free_energies.html | 11 ++++--- docs/searchindex.js | 2 +- 11 files changed, 53 insertions(+), 43 deletions(-) diff --git a/TIES_MD/TIES.py b/TIES_MD/TIES.py index 2dccd0f..e6e56b7 100644 --- a/TIES_MD/TIES.py +++ b/TIES_MD/TIES.py @@ -28,7 +28,7 @@ from simtk.openmm import Vec3 from functools import partial -from multiprocess import Pool +from multiprocess.pool import ThreadPool as Pool import numpy as np import os @@ -61,7 +61,7 @@ class TIES(object): ''' def __init__(self, cwd, exp_name='complex', run_type='class', devices=None, rep_id=None, windows_mask=None, - periodic=True, lam=None, platform='CUDA', **kwargs): + periodic=True, platform='CUDA', lam=None, **kwargs): nice_print('TIES') if run_type == 'class' and kwargs == {}: @@ -76,8 +76,8 @@ def __init__(self, cwd, exp_name='complex', run_type='class', devices=None, rep_ ' for molecular dynamics. PLoS computational biology, 13(7), p.e1005659.\n') #check all the config file args we need are present - args_list = ['engine', 'temperature', 'pressure', 'sampling_per_window', 'equili_per_window', 'methods', - 'total_reps', 'split_run', 'elec_edges', 'ster_edges', 'global_lambdas', 'constraint_file', + args_list = ['engine', 'temperature', 'pressure', 'sampling_per_window', 'equili_per_window', + 'methods', 'total_reps', 'split_run', 'elec_edges', 'ster_edges', 'global_lambdas', 'constraint_file', 'constraint_column', 'input_type', 'cell_basis_vec1', 'cell_basis_vec2', 'cell_basis_vec3'] # check we have all required arguments diff --git a/TIES_MD/alch.py b/TIES_MD/alch.py index 13238db..eaad138 100644 --- a/TIES_MD/alch.py +++ b/TIES_MD/alch.py @@ -469,7 +469,7 @@ def build_simulation(self, system, device_id): if self.platform == 'CUDA': properties = {'CudaPrecision': 'mixed', 'CudaDeviceIndex': device_id} elif self.platform == 'OpenCL': - properties = {'OpenCLPrecision': 'mixed', 'OpenCLDeviceIndex': device_id} + properties = {'OpenCLPrecision': 'mixed', 'OpenCLDeviceIndex': device_id, 'OpenCLPlatformIndex': '0'} elif self.platform == 'CPU': properties = {} else: diff --git a/TIES_MD/cli.py b/TIES_MD/cli.py index aab869a..2d7213a 100644 --- a/TIES_MD/cli.py +++ b/TIES_MD/cli.py @@ -31,7 +31,7 @@ TIES_MD Command line input should be used as follows... Usage: -TIES_MD [--devices=LIST] [--run_type=STRING] [--config_file=STRING] [--rep_id=INT] [--windows_mask=LIST] [--exp_name=STR]... +TIES_MD [--platform=STRING] [--devices=LIST] [--run_type=STRING] [--config_file=STRING] [--rep_id=INT] [--windows_mask=LIST] [--exp_name=STR]... """ def main(argv=None): @@ -95,6 +95,13 @@ def main(argv=None): else: devices = None + if args['--platform']: + if not_openmm: + raise ValueError(not_openmm_msg.format('--platform')) + platform = args['--platform'] + else: + platform = 'CUDA' + if args['--rep_id']: if not_openmm: raise ValueError(not_openmm_msg.format('--rep_id')) @@ -107,5 +114,5 @@ def main(argv=None): # removed this as an option there is no need to expose it for now periodic = True - TIES(input_folder, exp_name, run_type, devices, rep_id, mask, periodic, **args_dict) + TIES(input_folder, exp_name, run_type, devices, rep_id, mask, periodic, platform, **args_dict) diff --git a/TIES_MD/doc/source/API.rst b/TIES_MD/doc/source/API.rst index 8b2c913..bffed28 100644 --- a/TIES_MD/doc/source/API.rst +++ b/TIES_MD/doc/source/API.rst @@ -8,7 +8,7 @@ API --- Here we detail all the options in the API and what should be passed. The options that were previously on the command line -can be passed into the TIES class. A minimal evocation would looks like:: +can be passed into the TIES class. A minimal evocation would look like:: from TIES_MD import TIES import os diff --git a/TIES_MD/doc/source/binding_free_energies.rst b/TIES_MD/doc/source/binding_free_energies.rst index 406a619..1586fe4 100644 --- a/TIES_MD/doc/source/binding_free_energies.rst +++ b/TIES_MD/doc/source/binding_free_energies.rst @@ -73,7 +73,7 @@ for how to do this. With ``TIES20`` installed you can use the API as follows to hybrid.prepare_inputs(protein=protein) -This will build all the input needed to run these a BFE for the :math:`{ΔΔ G}` between ligandA and +This will build all the input needed to run a BFE calculation for the :math:`{ΔΔ G}` between ligandA and ligandB. However, in order to run at this point the user must execute their own HPC submission scripts or run via the command line on a cluster. We can however build own submission scripts and or change any of the simulation setting as detailed in the next section. @@ -145,10 +145,11 @@ the ``ties/ties-ligandA-ligandB/(lig/com)`` directory run:: Then modify the analysis.cfg file such the legs option is now to ``legs = lig, com`` (the two legs of our cycle). Note, configured like this the :math:`{ΔΔ G}` is computed as the :math:`{Δ G}` of the ligand simulation minus the :math:`{Δ G}` of the complex simulation, take care this gives you the same :math:`{ΔΔ G}` as you want to compare to in experiment -and it depends on which ligand is ligandA/B in the cycle. running:: +and it depends on which ligand is ligandA/B in the cycle. Running the following command will once again give +a ``results.dat`` file as output:: ties_ana -will once again give a ``results.dat`` file as out put this is the same as in the :ref:`Tutorial` section but it now -contains the :math:`{ΔΔ G}` of each transformation and the associated SEM. The print out on the terminal will detail -the individual :math:`{Δ G}` results for each thermodynamic leg. +``results.dat`` file file will have the same format as in the :ref:`Tutorial` section but it now +contains the :math:`{ΔΔ G}` of each transformation and the associated standard error of the mean (SEM). The print out on +the terminal will detail the individual :math:`{Δ G}` results for each thermodynamic leg. diff --git a/docs/API.html b/docs/API.html index f9b0819..ffceae3 100644 --- a/docs/API.html +++ b/docs/API.html @@ -87,7 +87,7 @@

TIES MD API

API

Here we detail all the options in the API and what should be passed. The options that were previously on the command line -can be passed into the TIES class. A minimal evocation would looks like:

+can be passed into the TIES class. A minimal evocation would look like:

from TIES_MD import TIES
 import os
 md = TIES(cwd=os.path.abspath('./my_ties_sims'))
diff --git a/docs/_sources/API.rst.txt b/docs/_sources/API.rst.txt
index 8b2c913..bffed28 100644
--- a/docs/_sources/API.rst.txt
+++ b/docs/_sources/API.rst.txt
@@ -8,7 +8,7 @@ API
 ---
 
 Here we detail all the options in the API and what should be passed. The options that were previously on the command line
-can be passed into the TIES class. A minimal evocation would looks like::
+can be passed into the TIES class. A minimal evocation would look like::
 
     from TIES_MD import TIES
     import os
diff --git a/docs/_sources/binding_free_energies.rst.txt b/docs/_sources/binding_free_energies.rst.txt
index 406a619..1586fe4 100644
--- a/docs/_sources/binding_free_energies.rst.txt
+++ b/docs/_sources/binding_free_energies.rst.txt
@@ -73,7 +73,7 @@ for how to do this. With ``TIES20`` installed you can use the API as follows to
     hybrid.prepare_inputs(protein=protein)
 
 
-This will build all the input needed to run these a BFE for the :math:`{ΔΔ G}` between ligandA and
+This will build all the input needed to run a BFE calculation for the :math:`{ΔΔ G}` between ligandA and
 ligandB. However, in order to run at this point the user must execute their own HPC submission scripts or run via the
 command line on a cluster. We can however build own submission scripts and or change any of the simulation setting
 as detailed in the next section.
@@ -145,10 +145,11 @@ the ``ties/ties-ligandA-ligandB/(lig/com)`` directory run::
 Then modify the analysis.cfg file such the legs option is now to ``legs = lig, com`` (the two legs of our cycle). Note,
 configured like this the :math:`{ΔΔ G}` is computed as the :math:`{Δ G}` of the ligand simulation minus the :math:`{Δ G}`
 of the complex simulation, take care this gives you the same :math:`{ΔΔ G}` as you want to compare to in experiment
-and it depends on which ligand is ligandA/B in the cycle. running::
+and it depends on which ligand is ligandA/B in the cycle. Running the following command will once again give
+a ``results.dat`` file as output::
 
     ties_ana
 
-will once again give a ``results.dat`` file as out put this is the same as in the :ref:`Tutorial` section but it now
-contains the :math:`{ΔΔ G}` of each transformation and the associated SEM. The print out on the terminal  will detail
-the individual :math:`{Δ G}` results for each thermodynamic leg.
+``results.dat`` file file will have the same format as in the :ref:`Tutorial` section but it now
+contains the :math:`{ΔΔ G}` of each transformation and the associated standard error of the mean (SEM). The print out on
+the terminal  will detail the individual :math:`{Δ G}` results for each thermodynamic leg.
diff --git a/docs/_static/pygments.css b/docs/_static/pygments.css
index 08bec68..582d5c3 100644
--- a/docs/_static/pygments.css
+++ b/docs/_static/pygments.css
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diff --git a/docs/binding_free_energies.html b/docs/binding_free_energies.html
index 02404fc..7791fc9 100644
--- a/docs/binding_free_energies.html
+++ b/docs/binding_free_energies.html
@@ -149,7 +149,7 @@ 
Setup
 hybrid.prepare_inputs(protein=protein)
-

This will build all the input needed to run these a BFE for the \({ΔΔ G}\) between ligandA and +

This will build all the input needed to run a BFE calculation for the \({ΔΔ G}\) between ligandA and ligandB. However, in order to run at this point the user must execute their own HPC submission scripts or run via the command line on a cluster. We can however build own submission scripts and or change any of the simulation setting as detailed in the next section.

@@ -219,13 +219,14 @@

BFE Analysislegs = lig, com (the two legs of our cycle). Note, configured like this the \({ΔΔ G}\) is computed as the \({Δ G}\) of the ligand simulation minus the \({Δ G}\) of the complex simulation, take care this gives you the same \({ΔΔ G}\) as you want to compare to in experiment -and it depends on which ligand is ligandA/B in the cycle. running:

+and it depends on which ligand is ligandA/B in the cycle. Running the following command will once again give +a results.dat file as output:

ties_ana
-

will once again give a results.dat file as out put this is the same as in the Tutorial section but it now -contains the \({ΔΔ G}\) of each transformation and the associated SEM. The print out on the terminal will detail -the individual \({Δ G}\) results for each thermodynamic leg.

+

results.dat file file will have the same format as in the Tutorial section but it now +contains the \({ΔΔ G}\) of each transformation and the associated standard error of the mean (SEM). The print out on +the terminal will detail the individual \({Δ G}\) results for each thermodynamic leg.

diff --git a/docs/searchindex.js b/docs/searchindex.js index f59dca1..d93086f 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["API", "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", "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": ["API.rst", "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.rst", "TIES_MD.eng_scripts.openmm_sub_split.rst", "TIES_MD.openmmtools.rst", "TIES_MD.ties_analysis.rst", 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