From 40c06dc3c6a56f17080836a5c6790a51eaf1c6b9 Mon Sep 17 00:00:00 2001
From: Brandon Clayton <bclayton@usgs.gov>
Date: Thu, 5 Aug 2021 13:20:26 -0600
Subject: [PATCH 1/6] simplify script
---
scripts/docker-entrypoint.sh | 111 +++++++++++++++++++++--------------
1 file changed, 68 insertions(+), 43 deletions(-)
diff --git a/scripts/docker-entrypoint.sh b/scripts/docker-entrypoint.sh
index 3fbe1f8c4..c4a847f80 100644
--- a/scripts/docker-entrypoint.sh
+++ b/scripts/docker-entrypoint.sh
@@ -1,50 +1,75 @@
#!/bin/bash
-# shellcheck disable=SC1090
-
-source "$(dirname "${0}")/docker-config.inc.sh";
-exit_status=${?};
-[ "${exit_status}" -eq 0 ] || exit "${exit_status}";
-
-# Get nshmp program to call
-nshmp_program=$(get_nshmp_program "${PROGRAM}");
-exit_status=${?};
-check_exit_status "${exit_status}";
-
-# Get model path to use
-if [ "${MOUNT_MODEL}" = true ]; then
- nshm_path="model";
-else
- nshm_path=$(get_model_path "${MODEL}" "${NSHM_VERSION}");
+
+##
+# Run nshmp-haz
+##
+main() {
+ # Get name of sites file
+ sites_file=$(ls /app/sites.*);
+
+ # Run nshmp-haz
+ java "${JAVA_OPTS}" \
+ -cp "/app/nshmp-haz.jar" \
+ "gov.usgs.earthquake.nshmp.${CLASS_NAME}" \
+ "${MODEL_PATH}" \
+ "${sites_file}" \
+ ${RETURN_PERIOD:+ "${RETURN_PERIOD}"} \
+ ${IML:+ "${IML}"} \
+ "${CONFIG_FILE}";
+ exit_status=${?};
+ check_exit_status "${exit_status}";
+
+ # Move results to container volume
+ move_to_output_volume;
exit_status=${?};
check_exit_status "${exit_status}";
-fi
-# Check site file and get site file path
-site_file=$(check_sites_file);
-exit_status=${?};
-check_exit_status "${exit_status}";
+ exit ${exit_status};
+}
+
+####
+# Check current exit status.
+#
+# @param $1 exit_status {Integer}
+# Current exit status
+####
+check_exit_status() {
+ local exit_status=${1};
+ [ "${exit_status}" -eq 0 ] || exit "${exit_status}";
+}
+
+####
+# Exit with an error message.
+#
+# @param $1 msg {String}
+# The message for exit
+# @param $2 exit_status {Integer}
+# The exit status
+####
+error_exit() {
+ local msg=${1}; shift;
+ local exit_status=${1}
+ echo "Error: ${msg}" >> /dev/stderr;
+ exit "${exit_status}";
+}
+
+####
+# Move artifacts to mounted volume.
+#
+# @status Integer
+# The status of moving the files.
+####
+move_to_output_volume() {
+ local hazout;
+ hazout=$(jq -r ".output.directory" "${CONFIG_FILE}");
+
+ if [ "${hazout}" == null ]; then
+ hazout="hazout";
+ fi
-# Check config file
-[ -f "${CONFIG_FILE}" ] || echo "{}" > "${CONFIG_FILE}";
-jq empty < "${CONFIG_FILE}";
-exit_status=${?};
-check_exit_status "${exit_status}";
+ mv "${hazout}/*" "${OUTPUT_PATH}/.";
+ return ${?};
+}
# Run nshmp-haz
-java -"Xmx${JAVA_XMX}" \
- -cp "/app/${PROJECT}.jar" \
- "gov.usgs.earthquake.nshmp.${nshmp_program}" \
- "${nshm_path}" \
- "${site_file}" \
- ${RETURN_PERIOD:+ "${RETURN_PERIOD}"} \
- ${IML:+ "${IML}"} \
- "${CONFIG_FILE}";
-exit_status=${?};
-check_exit_status "${exit_status}";
-
-# Move results to container volume
-move_to_output_volume;
-exit_status=${?};
-check_exit_status "${exit_status}";
-
-exit ${exit_status};
+main "$@";
--
GitLab
From 14f640c5e9ac0e233a9ccbfd60a34d06c59fef23 Mon Sep 17 00:00:00 2001
From: Brandon Clayton <bclayton@usgs.gov>
Date: Thu, 5 Aug 2021 13:20:35 -0600
Subject: [PATCH 2/6] remove old scripts
---
scripts/custom.config.sh | 11 --
scripts/docker-config.inc.sh | 28 ---
scripts/docker-functions.inc.sh | 292 --------------------------------
scripts/nshmp-haz.yml | 65 -------
4 files changed, 396 deletions(-)
delete mode 100644 scripts/custom.config.sh
delete mode 100644 scripts/docker-config.inc.sh
delete mode 100644 scripts/docker-functions.inc.sh
delete mode 100644 scripts/nshmp-haz.yml
diff --git a/scripts/custom.config.sh b/scripts/custom.config.sh
deleted file mode 100644
index e0630f304..000000000
--- a/scripts/custom.config.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/bash
-# shellcheck disable=SC2140
-
-export SERVICE_MAP=(
- "/nshmp/ws/conus-2018":"nshmp-haz-conus-2018"
- # "/nshmp/conus-2014":"nshmp-haz-conus-2014"
- # "/nshmp/conus-2014b":"nshmp-haz-conus-2014b"
- # "/nshmp/conus-2008":"nshmp-haz-conus-2008"
- # "/nshmp/hawaii-2020":"nshmp-haz-hi-2020"
- # "/nshmp/alaska-2007":"nshmp-haz-ak-2007"
-);
diff --git a/scripts/docker-config.inc.sh b/scripts/docker-config.inc.sh
deleted file mode 100644
index 3db50451a..000000000
--- a/scripts/docker-config.inc.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/bin/bash
-# shellcheck disable=SC1090
-# shellcheck disable=SC2034
-
-# Prevent configuration from being included multiple times
-[ -z "${CONFIGURATION_COMPLETE}" ] || return;
-source "$(dirname "$0")/docker-functions.inc.sh";
-
-readonly DEBUG="${DEBUG:-false}";
-
-# Turn on debugging if desired. Do this first so each value is echo'd
-if [[ "${DEBUG}" == "true" ]]; then
- set -x;
-fi
-
-readonly CEUS="Central & Eastern US";
-readonly CONFIG_FILE="${CONFIG_FILE:-config.json}";
-readonly CONTEXT_PATH="${CONTEXT_PATH:-/}";
-readonly JAVA_XMX="${JAVA_XMX:-8g}";
-readonly MODEL=$(echo "${MODEL:-CONUS_2008}" | awk \{'print toupper($0)'\});
-readonly NSHM_VERSION="${NSHM_VERSION:-main}";
-readonly PROJECT="${PROJECT:-nshmp-haz}";
-readonly PROGRAM=$(echo "${PROGRAM:-hazard}" | awk \{'print tolower($0)'\});
-readonly WUS="Western US";
-readonly VERSION_2014B="v4.1.1";
-
-# Include guard to prevent accidental re-configuration
-CONFIGURATION_COMPLETE="true";
diff --git a/scripts/docker-functions.inc.sh b/scripts/docker-functions.inc.sh
deleted file mode 100644
index ae711e683..000000000
--- a/scripts/docker-functions.inc.sh
+++ /dev/null
@@ -1,292 +0,0 @@
-#!/bin/bash
-
-####
-# Check current exit status.
-#
-# @param $1 exit_status {Integer}
-# Current exit status
-####
-check_exit_status() {
- local exit_status=${1};
- [ "${exit_status}" -eq 0 ] || exit "${exit_status}";
-}
-
-####
-# Check that the sites file is valid.
-#
-# @return String
-# The site file name
-# @status Integer
-# The exit status
-####
-check_sites_file() {
- local site_file;
- local exit_status;
- site_file=$(ls sites*) || error_exit "Site file does not exist." 1;
-
- # Check if valid JSON or ASCII file
- case ${site_file} in
- *.geojson)
- jq empty < "${site_file}";
- exit_status=${?};
- ;;
- *.csv)
- if [[ "$(file "${site_file}" -b)" != "ASCII text"* ]]; then
- error_exit "Site file [${site_file}] is not valid ASCII" 1;
- fi
- ;;
- *)
- error_exit "Bad site file [${site_file}]." 1;
- ;;
- esac
-
- echo "${site_file}";
- return "${exit_status}";
-}
-
-####
-# Download a repository from Github.
-#
-# @param $1 url {String}
-# The url to download
-# @param $2 branch {String}
-# The branch or tag to checkout
-#
-# @status Integer
-# The status of the curl call
-####
-download_repo() {
- local url=${1};
- local branch=${2};
- local exit_status;
-
- git clone --depth 1 -b "${branch}" "${url}";
- exit_status=${?};
-
- if [ ${exit_status} -ne 0 ]; then
- error_exit "Could not download [${url}]" ${exit_status};
- fi
-
- return ${exit_status};
-}
-
-####
-# Exit with an error message.
-#
-# @param $1 msg {String}
-# The message for exit
-# @param $2 exit_status {Integer}
-# The exit status
-####
-error_exit() {
- local msg=${1};
- local exit_status=${2}
- echo "Error: ${msg}" >> /dev/stderr;
- exit "${exit_status}";
-}
-
-####
-# Returns the model path.
-#
-# @param $1 nshm {String}
-# The NSHM to download.
-# @param $1 nshm_version {String}
-# The version to download from GitHub.
-#
-# @return String
-# The model path
-# @status Integer
-# The result of downloading the repository.
-####
-get_model() {
- local nshm=${1};
- local nshm_version=${2};
- local model;
- local model_path;
- local url;
- local exit_status;
-
- if [ "${nshm_version}" == "null" ]; then
- return 0;
- fi
-
- case ${nshm} in
- "AK_2007")
- model="nshm-ak-2007";
- model_path="${model}";
- url="https://github.com/usgs/${model}.git";
- ;;
- "CEUS_2008")
- model="nshm-cous-2008";
- model_path="${model}/${CEUS}/";
- url="https://github.com/usgs/${model}.git";
- ;;
- "CEUS_2014")
- model="nshm-cous-2014";
- model_path="${model}/${CEUS}/";
- url="https://github.com/usgs/${model}.git";
- ;;
- "CEUS_2014B")
- model="nshm-cous-2014";
- model_path="${model}/${CEUS}/";
- nshm_version="${VERSION_2014B}";
- url="https://github.com/usgs/${model}.git";
- ;;
- "CEUS_2018")
- model="nshm-cous-2018";
- model_path="${model}/${CEUS}/";
- url="https://github.com/usgs/${model}.git";
- ;;
- "CONUS_2008")
- model="nshm-cous-2008";
- model_path="${model}";
- url="https://github.com/usgs/${model}.git";
- ;;
- "CONUS_2014")
- model="nshm-cous-2014";
- model_path="${model}";
- url="https://github.com/usgs/${model}.git";
- ;;
- "CONUS_2014B")
- model="nshm-cous-2014";
- model_path="${model}";
- nshm_version="${VERSION_2014B}";
- url="https://github.com/usgs/${model}.git";
- ;;
- "CONUS_2018")
- model="nshm-cous-2018";
- model_path="${model}";
- url="https://github.com/usgs/${model}.git";
- # model="nshm-conus-2018";
- # url="git@code.usgs.gov:ghsc/nshmp/nshm-conus-2018.git";
- ;;
- # "CONUS_2023")
- # model="nshm-conus-2023";
- # url="git@code.usgs.gov:ghsc/nshmp/nshm-conus-2023.git";
- # ;;
- "HI_2020")
- model="nshm-hi-2020";
- model_path="${model}";
- url="https://github.com/usgs/${model}.git";
- ;;
- "WUS_2008")
- model="nshm-cous-2008";
- model_path="${model}/${WUS}/";
- url="https://github.com/usgs/${model}.git";
- ;;
- "WUS_2014")
- model="nshm-cous-2014";
- model_path="${model}/${WUS}/";
- url="https://github.com/usgs/${model}.git";
- ;;
- "WUS_2014B")
- model="nshm-cous-2014";
- model_path="${model}/${WUS}/";
- nshm_version="${VERSION_2014B}";
- url="https://github.com/usgs/${model}.git";
- ;;
- "WUS_2018")
- model="nshm-cous-2018";
- model_path="${model}/${WUS}/";
- url="https://github.com/usgs/${model}.git";
- ;;
-
- *)
- error_exit "Model [${nshm}] not supported" 1;
- ;;
- esac
-
- download_repo "${url}" "${nshm_version}";
- rm -rf "${model:?}/.git";
- exit_status=${?};
-
- echo "${model_path}";
- return ${exit_status}
-}
-
-####
-# Returns the path to the model.
-#
-# @param $1 nshm {String}
-# The NSHM to download.
-# @param $1 nshm_version {String}
-# The version to download from GitHub.
-#
-# @return String
-# The path to the model
-# @status Integer
-# Status of get_model call
-####
-get_model_path() {
- local nshm=${1};
- local nshm_version=${2};
- local nshmp_model_path;
- local exit_status;
- nshmp_model_path=$(get_model "${nshm}" "${nshm_version}");
- exit_status=${?};
-
- echo "${nshmp_model_path}";
- return ${exit_status};
-}
-
-####
-# Returns to nshmp-haz Java class to call.
-#
-# @param $1 program {String}
-# The program to run
-#
-# @return String
-# The program to call in nshmp-haz
-####
-get_nshmp_program() {
- local program=${1};
- local nshmp_program;
-
- case ${program} in
- "deagg")
- nshmp_program="DeaggCalc";
- ;;
- "deagg-epsilon")
- nshmp_program="DeaggEpsilon";
- ;;
- "deagg-iml")
- nshmp_program="DeaggIml";
- ;;
- "hazard-2018")
- nshmp_program="Hazard2018";
- ;;
- "hazard")
- nshmp_program="HazardCalc";
- ;;
- "rate")
- nshmp_program="RateCalc";
- ;;
- *)
- error_exit "Program [${program}] not supported" 1;
- ;;
- esac
-
- echo "${nshmp_program}";
-}
-
-####
-# Move artifacts to mounted volume.
-#
-# @param $1 config_file {String}
-# The config file
-#
-# @status Integer
-# The status of moving the files.
-####
-move_to_output_volume() {
- local config_file;
- local hazout;
- hazout=$(jq -r ".output.directory" "${config_file}");
-
- if [ "${hazout}" == null ]; then
- hazout="hazout";
- fi
-
- mv ${hazout}/* output/.;
- return ${?};
-}
diff --git a/scripts/nshmp-haz.yml b/scripts/nshmp-haz.yml
deleted file mode 100644
index b1164d857..000000000
--- a/scripts/nshmp-haz.yml
+++ /dev/null
@@ -1,65 +0,0 @@
-version: "3.7"
-
-# General deployment config
-x-app: &app
- image: ${REGISTRY}/nshmp-haz-ws:${CI_COMMIT_REF_SLUG}
- deploy:
- restart_policy:
- condition: any
- delay: 5s
- max_attempts: 3
- window: 120s
- replicas: 1
- update_config:
- order: start-first
- parallelism: 1
- ports:
- - 8080
-
-services:
- # Deploy nshmp-haz with CONUS-2018
- nshmp-haz-conus-2018:
- <<: *app
- environment:
- MODEL: CONUS-2018
- CONTEXT_PATH: /nshmp/ws/conus-2018
-
- # # Deploy nshmp-haz with CONUS-2014
- # nshmp-haz-conus-2014:
- # <<: *app
- # environment:
- # RUN_HAZARD: 'false'
- # MODEL: CONUS-2014
- # CONTEXT_PATH: nshmp/conus-2014
-
- # # Deploy nshmp-haz with CONUS-2014B
- # nshmp-haz-conus-2014b:
- # <<: *app
- # environment:
- # RUN_HAZARD: 'false'
- # MODEL: CONUS-2014B
- # CONTEXT_PATH: nshmp/conus-2014b
-
- # # Deploy nshmp-haz with CONUS-2008
- # nshmp-haz-conus-2008:
- # <<: *app
- # environment:
- # RUN_HAZARD: 'false'
- # MODEL: CONUS-2008
- # CONTEXT_PATH: nshmp/conus-2008
-
- # # Deploy nshmp-haz with HI-2020
- # nshmp-haz-hi-2020:
- # <<: *app
- # environment:
- # RUN_HAZARD: 'false'
- # MODEL: HI-2020
- # CONTEXT_PATH: nshmp/hawaii-2020
-
- # # Deploy nshmp-haz with AK-2007
- # nshmp-haz-ak-2007:
- # <<: *app
- # environment:
- # RUN_HAZARD: 'false'
- # MODEL: AK-2007
- # CONTEXT_PATH: nshmp/alaska-2007
--
GitLab
From 9a52a7bef728d46b10145ec667ce8e2cbcba4890 Mon Sep 17 00:00:00 2001
From: Brandon Clayton <bclayton@usgs.gov>
Date: Thu, 5 Aug 2021 13:21:24 -0600
Subject: [PATCH 3/6] simplify
---
Dockerfile | 76 +++++++++++++++++++++++++-----------------------------
1 file changed, 35 insertions(+), 41 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index e0a43e378..f9d895193 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,48 +1,48 @@
####
-# Run hazard jar file.
+# Run nshmp-haz
+#
+# Pull Docker Image:
+# - Production (stable): docker pull usgs/nshmp-haz:production-latest
+# - Staging (latest, main branch of repo): docker pull usgs/nshmp-haz:staging-latest
+# - Development (developer forks): docker pull usgs/nshmp-haz:development-latest
+#
+# Run Docker Image:
+# Parameters:
+# - CLASS_NAME: The nshmp-haz class name to run (e.g. HazardCalc)
+# - IML: The intensity measure level, used in certain programs
+# - JAVA_OPTS: Any JVM options (e.g. -Xmx8g)
+# - RETURN_PERIOD: The return period, used in certian programs
+#
+# Volumes:
+# - Model: /app/model
+# - Output: /app/output
#
-# Running Hazard:
-# docker pull code.chs.usgs.gov:5001/ghsc/nshmp/images/nshmp-haz;
# docker run \
-# -e PROGRAM=<deagg | deagg-epsilon | deagg-iml | hazard | hazard-2018 | rate> \
-# -e MODEL=<WUS_20[08|14|18] | CEUS_20[08|14|18] | COUS_20[08|14|18] | AK_2007 | HI_2020> \
-# -v /absolute/path/to/sites/file:/app/sites.<geojson | csv> \
-# -v /absolute/path/to/config/file:/app/config.json \
-# -v /absolute/path/to/output:/app/output \
-# code.chs.usgs.gov:5001/ghsc/nshmp/images/nshmp-haz;
+# --env CLASS_NAME="nshmp-haz class name" \
+# --volume "/path/to/model:/app/model" \
+# --volume "/path/to/output:/app/output" \
+# usgs/nshmp-haz:production-latest
#
# Build locally:
-# docker build
-# --build-arg gitlab_token=<git-api-token>
+# docker build \
+# --build-arg GITLAB_TOKEN=<git-api-token> \
# -t nshmp-haz .
####
ARG BUILD_IMAGE=usgs/java:11
ARG FROM_IMAGE=usgs/java:11
-ARG project=nshmp-haz
-ARG builder_workdir=/app/${project}
-ARG libs_dir=${builder_workdir}/build/libs
-
####
# Builder image: Build jar file.
####
FROM ${BUILD_IMAGE} as builder
-ARG builder_workdir
-ARG libs_dir
-
# TODO
# Remove once nshmp-lib is public
-ARG git_username
-ARG git_password
ARG GITLAB_TOKEN=null
ARG CI_JOB_TOKEN=null
-ENV GIT_NSHMP_USERNAME ${git_username}
-ENV GIT_NSHMP_PASSWORD ${git_password}
-
-WORKDIR ${builder_workdir}
+WORKDIR /app
COPY . .
@@ -55,30 +55,24 @@ FROM ${FROM_IMAGE}
LABEL maintainer="Peter Powers <pmpowers@usgs.gov>, Brandon Clayton <bclayton@usgs.gov>"
-ARG builder_workdir
-ARG libs_dir
-ARG project
-ARG ws_file
-
-ENV CONFIG_FILE ""
-ENV DEBUG false
+# nshmp-haz inputs
+ENV CLASS_NAME "HazardCalc"
ENV IML ""
-ENV JAVA_XMX "8g"
-ENV MODEL ""
-ENV MOUNT_MODEL false
-ENV NSHM_VERSION main
-ENV PROGRAM hazard
-ENV PROJECT ${project}
ENV RETURN_PERIOD ""
-VOLUME [ "/app/output" ]
+ENV CONFIG_FILE "/app/config.json"
+ENV JAVA_OPTS "-Xmx8g"
+ENV MODEL_PATH "/app/model"
+ENV OUTPUT_PATH "/app/output"
+
+VOLUME [ "${MODEL_PATH}", "${OUTPUT_PATH}" ]
WORKDIR /app
-COPY --from=builder ${libs_dir}/* ./
+COPY --from=builder /app/build/libs/nshmp-haz.jar .
COPY scripts scripts
-RUN yum install -y jq
+RUN yum install -y jq \
+ && echo "{}" > "${CONFIG_FILE}"
-EXPOSE 8080
ENTRYPOINT [ "bash", "scripts/docker-entrypoint.sh" ]
--
GitLab
From 60782db53b954fac762ea70e14e57914173c6f7b Mon Sep 17 00:00:00 2001
From: Brandon Clayton <bclayton@usgs.gov>
Date: Thu, 5 Aug 2021 14:31:45 -0600
Subject: [PATCH 4/6] update docker section
---
docs/pages/Building-&-Running.md | 173 ++++++++++++++++++++++++-------
1 file changed, 138 insertions(+), 35 deletions(-)
diff --git a/docs/pages/Building-&-Running.md b/docs/pages/Building-&-Running.md
index 8b36c7087..25622afad 100644
--- a/docs/pages/Building-&-Running.md
+++ b/docs/pages/Building-&-Running.md
@@ -72,10 +72,28 @@ files. Disaggregations also have some independent
## Run with [Docker](https://docs.docker.com/install/)
-To ensure you are have the latest *nshmp-haz* update, always first pull the image from Docker:
+nshmp-haz is available as a [public image](https://hub.docker.com/repository/docker/usgs/nshmp-haz)
+with tags:
+
+* `development-latest`: Developer forks
+* `staging-latest`: Latest updates associated with the
+[main](https://code.usgs.gov/ghsc/nshmp/nshmp-haz/-/tree/main) branch
+* `production-latest`: Latest stable release associated with the
+[production](https://code.usgs.gov/ghsc/nshmp/nshmp-haz/-/tree/production) branch
+
+To ensure you have the latest *nshmp-haz* update associated with a specific tag,
+always first pull the image from Docker:
+
+```bash
+docker pull usgs/nshmp-haz:<tag>
+```
+
+> Replace `<tag>` with one of the above tags.
+
+Example:
```bash
-docker pull usgs/nshmp-haz
+docker pull usgs/nshmp-haz:production-latest
```
### Docker Memory on Mac
@@ -84,7 +102,7 @@ By default, Docker Desktop for Mac is set to use 2 GB runtime memory. To run *ns
memory available to Docker must be [increased](https://docs.docker.com/docker-for-mac/#advanced)
to a minimum of 4 GB.
-### Run in Docker
+### Run nshmp-haz in Docker
The *nshmp-haz* application may be run as a Docker container which mitigates the need to install
Git, Java, or other dependencies besides Docker. A public image is available on
@@ -93,63 +111,148 @@ which can be run with:
```bash
docker run \
- -e PROGRAM=<disagg | hazard | rate> \
- -e MODEL=<CONUS_2018 | HAWAII_2021> \
- -e RETURN_PERIOD=<RETURN_PERIOD> \
- -v /absolute/path/to/sites/file:/app/sites.<geojson | csv> \
- -v /absolute/path/to/config/file:/app/config.json \
- -v /absolute/path/to/output:/app/output \
- usgs/nshmp-haz
-
-# Example
-docker run \
- -e PROGRAM=hazard \
- -e MODEL=CONUS_2018 \
- -v $(pwd)/sites.geojson:/app/sites.geojson \
- -v $(pwd)/config.json:/app/config.json \
- -v $(pwd)/hazout:/app/output \
+ --env CLASS_NAME=<DeaggCalc | DeaggIml | HazardCalc | RateCalc> \
+ --env IML=<NUMBER> \
+ --env RETURN_PERIOD=<NUMBER> \
+ --volume /absolute/path/to/sites/file:/app/sites.<geojson | csv> \
+ --volume /absolute/path/to/config/file:/app/config.json \
+ --volume /absolute/path/to/output:/app/output \
usgs/nshmp-haz
```
Where:
-* `PROGRAM` is the nshmp-haz program to run:
- * disagg = `DisaggCalc`
- * hazard = `HazardCalc`
- * rate = `RateCalc`
-
-* `MODEL` is the [USGS model (NSHM)](./USGS-Models.md) to run:
- * `CONUS_2018`: [Conterminous U.S. 2018](https://code.usgs.gov/ghsc/nshmp/nshm-conus)
- * `HAWAII_2021`: [Hawaii 2021](https://code.usgs.gov/ghsc/nshmp/nshm-hawaii)
-
+* `CLASS_NAME` is the nshmp-haz class to run:
+ * [DeaggCalc](../../src/main/java/gov/usgs/earthquake/nshmp/DeaggCalc.java)
+ * [DeaggIml](../../src/main/java/gov/usgs/earthquake/nshmp/DeaggIml.java)
+ * [HazardCalc](../../src/main/java/gov/usgs/earthquake/nshmp/HazardCalc.java)
+ * [RateCalc](../../src/main/java/gov/usgs/earthquake/nshmp/RateCalc.java)
* `RETURN_PERIOD`, in years, is only required when running a disaggregation
-
+* `IML`: intensity measure level, only required when running `DeaggIml`
* Other arguments (local files mapped to files within the Docker container with `:/app/...`):
+ * (required) The absolute path to a [USGS model (NSHM)](./USGS-Models.md)
+ * Example: `$(pwd)/nshm-hawaii:/app/model`
* (required) The absolute path to a GeoJSON or CSV [site(s)](./Site-Specification.md) file
* CSV example: `$(pwd)/my-csv-sites.csv:/app/sites.csv`
* GeoJSON example: `$(pwd)/my-geojson-sites.geojson:/app/sites.geojson`
- * (optional) The absolute path to a [configuration](./Calculation-Configuration.md) file
- * Example: `$(pwd)/my-custom-config.json:/app/config.json`
* (required) The absolute path to an output directory
* Example: `$(pwd)/my-hazard-output:/app/output`
+ * (optional) The absolute path to a [configuration](./Calculation-Configuration.md) file
+ * Example: `$(pwd)/my-custom-config.json:/app/config.json`
+
+### Docker Examples
+
+#### [`DeaggCalc`](../../src/main/java/gov/usgs/earthquake/nshmp/DeaggCalc.java) Example
+
+The following example runs the `DeaggCalc` program in nshmp-haz with the
+[nshm-hawaii](https://code.usgs.gov/ghsc/nshmp/nshms/nshm-hawaii.git) model and the
+assumption a GeoJSON [site](./Site-Specification.md) file exists named `sites.geojson`.
+
+```bash
+# Download Hawaii NSHM
+git clone https://code.usgs.gov/ghsc/nshmp/nshms/nshm-hawaii.git
+
+# Pull image
+docker pull usgs/nshmp-haz:production-latest
+
+# Run nshmp-haz DeaggCalc
+docker run \
+ --env CLASS_NAME="DeaggCalc" \
+ --env RETURN_PERIOD=475 \
+ --volume "$(pwd)/nshm-hawaii:/app/model" \
+ --volume "$(pwd)/sites.geojson" \
+ --volume "$(pwd)/hawaii-disagg-output:/app/output" \
+ usgs/nshmp-haz:production-latest
+```
+
+#### [`DeaggIml`](../../src/main/java/gov/usgs/earthquake/nshmp/DeaggIml.java) Example
+
+The following example runs the `DeaggIml` program in nshmp-haz with the
+[nshm-hawaii](https://code.usgs.gov/ghsc/nshmp/nshms/nshm-hawaii.git) model and the
+assumption a GeoJSON [site](./Site-Specification.md) file exists named `sites.geojson`.
+
+```bash
+# Download Hawaii NSHM
+git clone https://code.usgs.gov/ghsc/nshmp/nshms/nshm-hawaii.git
+
+# Pull image
+docker pull usgs/nshmp-haz:production-latest
+
+# Run nshmp-haz DeaggIml
+docker run \
+ --env CLASS_NAME="DeaggCalc" \
+ --env IML=1 \
+ --volume "$(pwd)/nshm-hawaii:/app/model" \
+ --volume "$(pwd)/sites.geojson" \
+ --volume "$(pwd)/hawaii-disagg-iml-output:/app/output" \
+ usgs/nshmp-haz:production-latest
+```
+
+#### [`HazardCalc`](../../src/main/java/gov/usgs/earthquake/nshmp/HazardCalc.java) Example
+
+The following example runs the `HazardCalc` program in nshmp-haz with the
+[nshm-hawaii](https://code.usgs.gov/ghsc/nshmp/nshms/nshm-hawaii.git) model and the
+assumption a GeoJSON [site](./Site-Specification.md) file exists named `sites.geojson`.
+
+```bash
+# Download Hawaii NSHM
+git clone https://code.usgs.gov/ghsc/nshmp/nshms/nshm-hawaii.git
+
+# Pull image
+docker pull usgs/nshmp-haz:production-latest
+
+# Run nshmp-haz HazardCalc
+docker run \
+ --env CLASS_NAME="HazardCalc" \
+ --volume "$(pwd)/nshm-hawaii:/app/model" \
+ --volume "$(pwd)/sites.geojson" \
+ --volume "$(pwd)/hawaii-hazard-output:/app/output" \
+ usgs/nshmp-haz:production-latest
+```
+
+#### [`RateCalc`](../../src/main/java/gov/usgs/earthquake/nshmp/RateCalc.java) Example
+
+The following example runs the `RateCalc` program in nshmp-haz with the
+[nshm-hawaii](https://code.usgs.gov/ghsc/nshmp/nshms/nshm-hawaii.git) model and the
+assumption a GeoJSON [site](./Site-Specification.md) file exists named `sites.geojson`.
+
+```bash
+# Download Hawaii NSHM
+git clone https://code.usgs.gov/ghsc/nshmp/nshms/nshm-hawaii.git
+
+# Pull image
+docker pull usgs/nshmp-haz:production-latest
+
+# Run nshmp-haz RateCalc
+docker run \
+ --env CLASS_NAME="RateCalc" \
+ --volume "$(pwd)/nshm-hawaii:/app/model" \
+ --volume "$(pwd)/sites.geojson" \
+ --volume "$(pwd)/hawaii-rate-output:/app/output" \
+ usgs/nshmp-haz:production-latest
+```
### Run Customization
-When running *nshmp-haz* with Docker the initial (Xms) and maximum (Xmx) JVM memory sizes can
+When running *nshmp-haz* with Docker the maximum JVM memory size can
be set with the environment flag (-e, -env):
```bash
docker run \
- -e JAVA_XMS=<JAVA_XMS> \
- -e JAVA_XMX=<JAVA_XMX> \
+ --env JAVA_MEMORY=<MEMORY> \
+ ...
+ usgs/nshmp-haz
+
+# Example
+docker run \
+ --env JAVA_MEMORY="12g" \
...
usgs/nshmp-haz
```
Where:
-* `JAVA_XMS` is the intial memory for the JVM (default: system)
-* `JAVA_XMX` is the maximum memory for the JVM (default: 8g)
+* `JAVA_MEMORY` is the maximum memory for the JVM (default: 8g)
---
--
GitLab
From 4ec1cbd9b67ca51cf74538e425ffb17d44d0ce5e Mon Sep 17 00:00:00 2001
From: Brandon Clayton <bclayton@usgs.gov>
Date: Thu, 5 Aug 2021 14:31:58 -0600
Subject: [PATCH 5/6] update parameter
---
Dockerfile | 2 +-
scripts/docker-entrypoint.sh | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index f9d895193..32d8e203c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -61,7 +61,7 @@ ENV IML ""
ENV RETURN_PERIOD ""
ENV CONFIG_FILE "/app/config.json"
-ENV JAVA_OPTS "-Xmx8g"
+ENV JAVA_MEMORY "8g"
ENV MODEL_PATH "/app/model"
ENV OUTPUT_PATH "/app/output"
diff --git a/scripts/docker-entrypoint.sh b/scripts/docker-entrypoint.sh
index c4a847f80..ad3f2b852 100644
--- a/scripts/docker-entrypoint.sh
+++ b/scripts/docker-entrypoint.sh
@@ -8,7 +8,7 @@ main() {
sites_file=$(ls /app/sites.*);
# Run nshmp-haz
- java "${JAVA_OPTS}" \
+ java "-Xmx${JAVA_MEMORY}" \
-cp "/app/nshmp-haz.jar" \
"gov.usgs.earthquake.nshmp.${CLASS_NAME}" \
"${MODEL_PATH}" \
@@ -67,7 +67,7 @@ move_to_output_volume() {
hazout="hazout";
fi
- mv "${hazout}/*" "${OUTPUT_PATH}/.";
+ mv "${hazout}"/* "${OUTPUT_PATH}"/.;
return ${?};
}
--
GitLab
From e9bbcdf00277998d1dc26d1a6372332983688ac5 Mon Sep 17 00:00:00 2001
From: Brandon Clayton <bclayton@usgs.gov>
Date: Thu, 5 Aug 2021 14:38:41 -0600
Subject: [PATCH 6/6] cleanup
---
Dockerfile | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index 32d8e203c..934d0ee14 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -24,9 +24,7 @@
# usgs/nshmp-haz:production-latest
#
# Build locally:
-# docker build \
-# --build-arg GITLAB_TOKEN=<git-api-token> \
-# -t nshmp-haz .
+# docker build -t nshmp-haz .
####
ARG BUILD_IMAGE=usgs/java:11
--
GitLab