Merge pull request #50 from paulsaxe/main

Switched to new installation scheme

HISTORY.rst

@@ -1,6 +1,11 @@
 =======
 History
 =======
+2024.3.20 -- Switched to new installation scheme
+   * Fully support ~/SEAMM/lammps.ini
+   * Updated to new installer
+   * Support for Conda and Docker installation.
+
 2024.1.18 -- Restructured to support running in containers.
 
 2023.11.7 -- Bugfix: properties that are constant

devtools/conda-envs/test_env.yaml

@@ -2,6 +2,7 @@ name: test
 
 channels:
   - conda-forge
+  - defaults
 
 dependencies:
   # Base depends
@@ -10,7 +11,6 @@ dependencies:
 
   # SEAMM
   - kim-query
-  - pymbar>=4.0
   - seamm
   - seamm-ff-util
   - statsmodels
@@ -29,6 +29,7 @@ dependencies:
 
   # Pip-only installs
   - pip:
+    - pymbar>=4.0
     - seamm-exec
     # Documentation
     - sphinx-copybutton

devtools/docker/Dockerfile

@@ -0,0 +1,8 @@
+FROM molssi/mamba141
+
+COPY ./environment.yml /root/environment.yml
+
+RUN mamba env update -f /root/environment.yml
+
+WORKDIR /home
+ENTRYPOINT ["lmp_serial"]

devtools/docker/environment.yml

@@ -0,0 +1,10 @@
+name: base
+channels:
+  - conda-forge
+dependencies:
+  - python
+    # Executables, etc.
+  - openmpi
+  - lammps
+  - openkim-models
+  - mpi4py

lammps_step/data/configuration.txt

@@ -22,41 +22,6 @@
 
 # html = False
 
-# Information about where/how the executables are installed
-# installation may be 'path', 'conda' or 'modules'. If a module is
-# specified it will be loaded and those executables used.  In this
-# case, any path specified using lammps-path will be ignored.
-
-installation = not installed
-conda-environment =
-modules = 
-gpu-modules =
-
-# The path to the executables. Can be empty or not present, in which
-# case the default PATH is used.  If a path is given, lmp_serial and
-# lmp_mpi from this location will be used. If mpiexec is also present
-# it will be used; otherwise mpiexec from the normal PATH will be
-# used. If mpiexec or lmp_mpi is not found, only the serial version of
-# LAMMPS will be used. Conversely, if lmp_serial is not present,
-# lmp_mpi will always be used, though possible on just one core for
-# smaller calculations.
-#
-# Ignored if a module is used. The default is to use the PATH
-# environment variable.
-
-lammps-path =
-
-# The various LAMMPS executables. You should leave these as their default
-# values unless you have a special need. These values are combined with
-# lammps-path to get the location of the executables.
-#
-# If you are running from a queueing system such as SLURM, if MPI was compiled
-# to know about the batch system, you should be able to use something like
-# 'srun' or 'mpirun' with no further arguments to run parallel tasks. If
-# you are not lucky, and need the parameters, you can add them to the command
-# line like this:
-#
-# mpiexec = mpirun -n {NTASKS} -H {NODELIST} -npernode {NTASKS_PER_NODE}
 #
 # SEAMM picks up the environment variables such as SLURM_NTASKS, strips the
 # prefix from them and replaces any instances in the command line that are

lammps_step/data/lammps.ini

@@ -0,0 +1,87 @@
+# Configuration options for how to run LAMMPS
+
+[docker]
+# The code to use. This may maybe more than just the name of the code, and variables in
+# braces {} will be expanded. For example:
+#   code = mpirun -np {NTASKS} lmp
+# would expand {NTASKS} to the number of tasks and run the command
+#
+# If you are running from a queueing system such as SLURM, if MPI was compiled
+# to know about the batch system, you should be able to use something like
+# 'srun' or 'mpirun' with no further arguments to run parallel tasks. If
+# you are not lucky, and need the parameters, you can add them to the command
+# line like this:
+#
+# code = mpirun -n {NTASKS} -H {NODELIST} -npernode {NTASKS_PER_NODE}
+
+code = mpirun -n {NTASKS} lmp
+
+# The name and location of the Docker container to use, optionally with the version
+
+container = ghcr.io/molssi-seamm/seamm-lammps:{version}
+
+# In addition, you can specify the platform to use. This is useful on e.g. Macs with
+# app silicon (M1, M3...) where the default platform is linux/arm64 but some containers
+# are only available for linux/amd64.
+
+platform = linux/amd64
+
+[local]
+# The type of local installation to use. Options are:
+#     conda: Use a conda environment
+#   modules: Use the modules system
+#     local: Use a local installation
+#    docker: Use a Docker container
+# By default SEAMM installs LAMMPS using conda.
+
+installation = conda
+
+# The command line to use, which should start with the executable followed by any options.
+# Variables in braces {} will be expanded. For example:
+#
+#   code = mpirun -np {NTASKS} lmp
+#
+# would expand {NTASKS} to the number of tasks and run the command.
+# For a 'local' installation, the command line should include the full path to the
+# executable or it should be in the path. 
+#
+# If you are running from a queueing system such as SLURM, if MPI was compiled
+# to know about the batch system, you should be able to use something like
+# 'srun' or 'mpirun' with no further arguments to run parallel tasks. If
+# you are not lucky, and need the parameters, you can add them to the command
+# line like this:
+#
+# code = mpirun -n {NTASKS} -H {NODELIST} -npernode {NTASKS_PER_NODE}
+
+code = mpirun -n {NTASKS} lmp
+
+######################### conda section ############################
+# The full path to the conda executable:
+
+# conda = 
+
+# The Conda environment to use. This is either the name or full path.
+
+# conda-environment = seamm-lammps
+
+######################### modules section ############################
+# The modules to load to run LAMMPS, as a list of strings.
+# For example, to load the modules lammps and openmpi, you would use:
+#   modules = lammps openmpi
+
+# modules = 
+
+######################### local section ############################
+# The full path to the LAMMPS executable should be in the 'code' option.
+
+######################### docker section ############################
+# The name and location of the Docker container to use, optionally with the version.
+# {version} will be expanded to the version of the plug-in.
+
+# container = ghcr.io/molssi-seamm/seamm-lammps:{version}
+
+# In addition, you can specify the platform to use. This is useful on e.g. Macs with
+# app silicon (M1, M3...) where the default platform is linux/arm64 but some containers
+# are only available for linux/amd64.
+
+platform = linux/amd64