Add GAMESS module

gamess/17.09-r2-libcchem.lua

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+-- The MIT License (MIT)
+--
+-- Copyright (c) 2020 NVIDIA Corporation
+--
+-- Permission is hereby granted, free of charge, to any person obtaining a copy
+-- of this software and associated documentation files (the "Software"), to
+-- deal in the Software without restriction, including without limitation the
+-- rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+-- sell copies of the Software, and to permit persons to whom the Software is
+-- furnished to do so, subject to the following conditions:
+--
+-- The above copyright notice and this permission notice shall be included in
+-- all copies or substantial portions of the Software.
+--
+-- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+-- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+-- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+-- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+-- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+-- FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
+-- IN THE SOFTWARE.
+
+help([==[
+
+Description
+===========
+The General Atomic and Molecular Electronic Structure Systems (GAMESS) program
+simulates molecular quantum chemistry, allowing users to calculate various
+molecular properties and dynamics.
+
+More information
+================
+ - NGC: https://ngc.nvidia.com/catalog/containers/hpc:gamess
+]==])
+
+whatis("Name: gamess")
+whatis("Version: 17.09-r2-libcchem")
+whatis("Description: The General Atomic and Molecular Electronic Structure Systems (GAMESS) program simulates molecular quantum chemistry, allowing users to calculate various molecular properties and dynamics.")
+whatis("URL: https://ngc.nvidia.com/catalog/containers/hpc:gamess")
+
+if not (os.getenv("NGC_SINGULARITY_MODULE") == "none") then
+	local singularity_module = os.getenv("NGC_SINGULARITY_MODULE") or "Singularity"
+	if not (isloaded(singularity_module)) then
+		load(singularity_module)
+	end
+end
+
+conflict(myModuleName())
+
+local image = "nvcr.io_hpc_gamess:17.09-r2-libcchem.sif"
+local uri = "docker://nvcr.io/hpc/gamess:17.09-r2-libcchem"
+local programs = {"rungms"}
+local entrypoint_args = ""
+
+-- This GAMESS installation expects to run in '/workspace' and deliver its
+-- output to '/results'... so we need to bind them into container.
+-- Moreover, it expects things to be as follows:
+-- 	/path/to/your_workspace
+--	    scratch/
+--	    restart/
+--	    your_input.inp
+-- We'd want to point 'scratch' to cluster scratch (if present),
+-- but keep 'workspace' and 'results' in current working directory, so need
+-- to assemble a fancy SINGULARITY_BINDPATH variable.
+local workspace = '.'
+local results   = '.'
+local restart   = pathJoin(workspace, "restart")
+local scratch   = pathJoin(workspace, "scratch")
+if (os.getenv("CLUSTER_SCRATCH")) then
+	scratch = pathJoin(os.getenv("CLUSTER_SCRATCH"), "gamess-ngc")
+end
+append_path("SINGULARITY_BINDPATH", workspace .. ":/workspace", ",")
+append_path("SINGULARITY_BINDPATH", results   .. ":/results",   ",")
+append_path("SINGULARITY_BINDPATH", scratch   .. ":/scratch",   ",")
+
+-- We defined bind points, but we must ensure that they exist on the host.
+-- The catch is that this needs to be done *at run time*, not at module load
+-- time - so we prepare a "pre" command to be executed prior to the main
+-- singularity call.
+-- Note: the way GAMESS is setup in this container, we really need a
+-- "local" workspace/scratch (will only keep one file) and a true /scratch
+-- scratch - so make them both.
+directories = {workspace, results, pathJoin(workspace, "scratch"), scratch, restart}
+preexec_command = "mkdir -p"
+for i,dir in pairs(directories) do
+	preexec_command = preexec_command .. " " .. dir
+end
+
+-- The absolute path to Singularity is needed so it can be invoked on remote
+-- nodes without the corresponding module necessarily being loaded.
+-- Trim off the training newline.
+local singularity = capture("which singularity | head -c -1")
+
+if (os.getenv("NGC_IMAGE_DIR") and mode() == "load") then
+	image = pathJoin(os.getenv("NGC_IMAGE_DIR"), image)
+
+	if not (isFile(image)) then
+		-- The image could not be found in the container directory
+		LmodMessage("file not found: " .. image)
+		LmodMessage("The container image will be pulled upon first use to the Singularity cache")
+		image = uri
+
+		-- Alternatively, this could pull the container image and
+		-- save it in the container directory
+		--subprocess(singularity .. " pull " .. image .. " " .. uri)
+	end
+else
+	-- Look for the image in the Singularity cache, and if not found
+	-- download it when "singularity run" is invoked.
+	image = uri
+end
+
+-- And assemble the preexecution command with actual singularity call.
+-- Note: '--pid' is needed because otherwise Ctrl-C'ing the container
+-- leaves behind lingering mpiexec.hydra processes.
+-- Using 'exec' instead of 'run' to bypass /bin/bash entrypoint that would
+-- othewise expected a "-c 'cd /workspace && rungms $@'" argument.
+local container_launch = singularity .. " exec --nv --pid --pwd /workspace " .. image .. " " .. entrypoint_args
+container_launch = preexec_command .. " && " .. container_launch
+
+-- Programs to setup in the shell
+for i,program in pairs(programs) do
+        set_shell_function(program, container_launch .. " " .. program .. " $@",
+	                            container_launch .. " " .. program .. " $*")
+end